Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 03:27:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qet_13940/04_2023/7qet_13940_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qet_13940/04_2023/7qet_13940.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qet_13940/04_2023/7qet_13940.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qet_13940/04_2023/7qet_13940.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qet_13940/04_2023/7qet_13940_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qet_13940/04_2023/7qet_13940_updated.pdb" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 168 5.16 5 C 12720 2.51 5 N 2952 2.21 5 O 3365 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "B PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 147": "OE1" <-> "OE2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 209": "OE1" <-> "OE2" Residue "C PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 147": "OE1" <-> "OE2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 209": "OE1" <-> "OE2" Residue "D PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 147": "OE1" <-> "OE2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 209": "OE1" <-> "OE2" Residue "E PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 147": "OE1" <-> "OE2" Residue "E GLU 187": "OE1" <-> "OE2" Residue "E PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 209": "OE1" <-> "OE2" Residue "F PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 147": "OE1" <-> "OE2" Residue "F GLU 187": "OE1" <-> "OE2" Residue "F PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 209": "OE1" <-> "OE2" Residue "G PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 147": "OE1" <-> "OE2" Residue "G GLU 187": "OE1" <-> "OE2" Residue "G PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 209": "OE1" <-> "OE2" Residue "H PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 147": "OE1" <-> "OE2" Residue "H GLU 187": "OE1" <-> "OE2" Residue "H PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 209": "OE1" <-> "OE2" Residue "I PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 147": "OE1" <-> "OE2" Residue "I GLU 187": "OE1" <-> "OE2" Residue "I PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 209": "OE1" <-> "OE2" Residue "J PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 147": "OE1" <-> "OE2" Residue "J GLU 187": "OE1" <-> "OE2" Residue "J PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 209": "OE1" <-> "OE2" Residue "K PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 147": "OE1" <-> "OE2" Residue "K GLU 187": "OE1" <-> "OE2" Residue "K PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 209": "OE1" <-> "OE2" Residue "L PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 147": "OE1" <-> "OE2" Residue "L GLU 187": "OE1" <-> "OE2" Residue "L PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 209": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 19205 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1527 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Chain: "B" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1527 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Chain: "C" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1527 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Chain: "D" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1527 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Chain: "E" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1527 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Chain: "F" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1527 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Chain: "G" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1527 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Chain: "H" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1527 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Chain: "I" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1527 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Chain: "J" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1527 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Chain: "K" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1527 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Chain: "L" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1527 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "F" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "I" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "K" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "L" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "E" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "F" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "G" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "I" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "J" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "L" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Time building chain proxies: 10.35, per 1000 atoms: 0.54 Number of scatterers: 19205 At special positions: 0 Unit cell: (99.45, 109.65, 155.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 168 16.00 O 3365 8.00 N 2952 7.00 C 12720 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 180 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 174 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 169 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 180 " distance=2.04 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 174 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 169 " distance=2.03 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 180 " distance=2.03 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 174 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 169 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS E 180 " distance=2.04 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 174 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 169 " distance=2.03 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 180 " distance=2.03 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 174 " distance=2.03 Simple disulfide: pdb=" SG CYS F 64 " - pdb=" SG CYS F 169 " distance=2.03 Simple disulfide: pdb=" SG CYS G 53 " - pdb=" SG CYS G 180 " distance=2.03 Simple disulfide: pdb=" SG CYS G 60 " - pdb=" SG CYS G 174 " distance=2.03 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 169 " distance=2.03 Simple disulfide: pdb=" SG CYS H 53 " - pdb=" SG CYS H 180 " distance=2.04 Simple disulfide: pdb=" SG CYS H 60 " - pdb=" SG CYS H 174 " distance=2.03 Simple disulfide: pdb=" SG CYS H 64 " - pdb=" SG CYS H 169 " distance=2.03 Simple disulfide: pdb=" SG CYS I 53 " - pdb=" SG CYS I 180 " distance=2.03 Simple disulfide: pdb=" SG CYS I 60 " - pdb=" SG CYS I 174 " distance=2.03 Simple disulfide: pdb=" SG CYS I 64 " - pdb=" SG CYS I 169 " distance=2.03 Simple disulfide: pdb=" SG CYS J 53 " - pdb=" SG CYS J 180 " distance=2.04 Simple disulfide: pdb=" SG CYS J 60 " - pdb=" SG CYS J 174 " distance=2.03 Simple disulfide: pdb=" SG CYS J 64 " - pdb=" SG CYS J 169 " distance=2.03 Simple disulfide: pdb=" SG CYS K 53 " - pdb=" SG CYS K 180 " distance=2.04 Simple disulfide: pdb=" SG CYS K 60 " - pdb=" SG CYS K 174 " distance=2.03 Simple disulfide: pdb=" SG CYS K 64 " - pdb=" SG CYS K 169 " distance=2.03 Simple disulfide: pdb=" SG CYS L 53 " - pdb=" SG CYS L 180 " distance=2.04 Simple disulfide: pdb=" SG CYS L 60 " - pdb=" SG CYS L 174 " distance=2.03 Simple disulfide: pdb=" SG CYS L 64 " - pdb=" SG CYS L 169 " 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: 7.91 Conformation dependent library (CDL) restraints added in 2.5 seconds 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4296 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 84 helices and 12 sheets defined 69.7% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 5 through 14 Processing helix chain 'A' and resid 19 through 38 removed outlier: 3.689A pdb=" N ILE A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 42 No H-bonds generated for 'chain 'A' and resid 40 through 42' Processing helix chain 'A' and resid 60 through 68 Processing helix chain 'A' and resid 73 through 101 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 130 through 158 Processing helix chain 'A' and resid 185 through 215 Processing helix chain 'B' and resid 5 through 14 Processing helix chain 'B' and resid 19 through 38 removed outlier: 3.688A pdb=" N ILE B 23 " --> pdb=" O SER B 19 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU B 25 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N THR B 26 " --> pdb=" O LYS B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 42 No H-bonds generated for 'chain 'B' and resid 40 through 42' Processing helix chain 'B' and resid 60 through 68 Processing helix chain 'B' and resid 73 through 101 Proline residue: B 87 - end of helix Processing helix chain 'B' and resid 130 through 158 Processing helix chain 'B' and resid 185 through 215 Processing helix chain 'C' and resid 5 through 14 Processing helix chain 'C' and resid 19 through 38 removed outlier: 3.689A pdb=" N ILE C 23 " --> pdb=" O SER C 19 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU C 25 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N THR C 26 " --> pdb=" O LYS C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 42 No H-bonds generated for 'chain 'C' and resid 40 through 42' Processing helix chain 'C' and resid 60 through 68 Processing helix chain 'C' and resid 73 through 101 Proline residue: C 87 - end of helix Processing helix chain 'C' and resid 130 through 158 Processing helix chain 'C' and resid 185 through 215 Processing helix chain 'D' and resid 5 through 14 Processing helix chain 'D' and resid 19 through 38 removed outlier: 3.689A pdb=" N ILE D 23 " --> pdb=" O SER D 19 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU D 25 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR D 26 " --> pdb=" O LYS D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 42 No H-bonds generated for 'chain 'D' and resid 40 through 42' Processing helix chain 'D' and resid 60 through 68 Processing helix chain 'D' and resid 73 through 101 Proline residue: D 87 - end of helix Processing helix chain 'D' and resid 130 through 158 Processing helix chain 'D' and resid 185 through 215 Processing helix chain 'E' and resid 5 through 14 Processing helix chain 'E' and resid 19 through 38 removed outlier: 3.689A pdb=" N ILE E 23 " --> pdb=" O SER E 19 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU E 25 " --> pdb=" O GLY E 21 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR E 26 " --> pdb=" O LYS E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 42 No H-bonds generated for 'chain 'E' and resid 40 through 42' Processing helix chain 'E' and resid 60 through 68 Processing helix chain 'E' and resid 73 through 101 Proline residue: E 87 - end of helix Processing helix chain 'E' and resid 130 through 158 Processing helix chain 'E' and resid 185 through 215 Processing helix chain 'F' and resid 5 through 14 Processing helix chain 'F' and resid 19 through 38 removed outlier: 3.689A pdb=" N ILE F 23 " --> pdb=" O SER F 19 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU F 25 " --> pdb=" O GLY F 21 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR F 26 " --> pdb=" O LYS F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 42 No H-bonds generated for 'chain 'F' and resid 40 through 42' Processing helix chain 'F' and resid 60 through 68 Processing helix chain 'F' and resid 73 through 101 Proline residue: F 87 - end of helix Processing helix chain 'F' and resid 130 through 158 Processing helix chain 'F' and resid 185 through 215 Processing helix chain 'G' and resid 5 through 14 Processing helix chain 'G' and resid 19 through 38 removed outlier: 3.688A pdb=" N ILE G 23 " --> pdb=" O SER G 19 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU G 25 " --> pdb=" O GLY G 21 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR G 26 " --> pdb=" O LYS G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 42 No H-bonds generated for 'chain 'G' and resid 40 through 42' Processing helix chain 'G' and resid 60 through 68 Processing helix chain 'G' and resid 73 through 101 Proline residue: G 87 - end of helix Processing helix chain 'G' and resid 130 through 158 Processing helix chain 'G' and resid 185 through 215 Processing helix chain 'H' and resid 5 through 14 Processing helix chain 'H' and resid 19 through 38 removed outlier: 3.688A pdb=" N ILE H 23 " --> pdb=" O SER H 19 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU H 25 " --> pdb=" O GLY H 21 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR H 26 " --> pdb=" O LYS H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 42 No H-bonds generated for 'chain 'H' and resid 40 through 42' Processing helix chain 'H' and resid 60 through 68 Processing helix chain 'H' and resid 73 through 101 Proline residue: H 87 - end of helix Processing helix chain 'H' and resid 130 through 158 Processing helix chain 'H' and resid 185 through 215 Processing helix chain 'I' and resid 5 through 14 Processing helix chain 'I' and resid 19 through 38 removed outlier: 3.689A pdb=" N ILE I 23 " --> pdb=" O SER I 19 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU I 25 " --> pdb=" O GLY I 21 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR I 26 " --> pdb=" O LYS I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 42 No H-bonds generated for 'chain 'I' and resid 40 through 42' Processing helix chain 'I' and resid 60 through 68 Processing helix chain 'I' and resid 73 through 101 Proline residue: I 87 - end of helix Processing helix chain 'I' and resid 130 through 158 Processing helix chain 'I' and resid 185 through 215 Processing helix chain 'J' and resid 5 through 14 Processing helix chain 'J' and resid 19 through 38 removed outlier: 3.689A pdb=" N ILE J 23 " --> pdb=" O SER J 19 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU J 25 " --> pdb=" O GLY J 21 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR J 26 " --> pdb=" O LYS J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 42 No H-bonds generated for 'chain 'J' and resid 40 through 42' Processing helix chain 'J' and resid 60 through 68 Processing helix chain 'J' and resid 73 through 101 Proline residue: J 87 - end of helix Processing helix chain 'J' and resid 130 through 158 Processing helix chain 'J' and resid 185 through 215 Processing helix chain 'K' and resid 5 through 14 Processing helix chain 'K' and resid 19 through 38 removed outlier: 3.690A pdb=" N ILE K 23 " --> pdb=" O SER K 19 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU K 25 " --> pdb=" O GLY K 21 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N THR K 26 " --> pdb=" O LYS K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 42 No H-bonds generated for 'chain 'K' and resid 40 through 42' Processing helix chain 'K' and resid 60 through 68 Processing helix chain 'K' and resid 73 through 101 Proline residue: K 87 - end of helix Processing helix chain 'K' and resid 130 through 158 Processing helix chain 'K' and resid 185 through 215 Processing helix chain 'L' and resid 5 through 14 Processing helix chain 'L' and resid 19 through 38 removed outlier: 3.689A pdb=" N ILE L 23 " --> pdb=" O SER L 19 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU L 25 " --> pdb=" O GLY L 21 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR L 26 " --> pdb=" O LYS L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 42 No H-bonds generated for 'chain 'L' and resid 40 through 42' Processing helix chain 'L' and resid 60 through 68 Processing helix chain 'L' and resid 73 through 101 Proline residue: L 87 - end of helix Processing helix chain 'L' and resid 130 through 158 Processing helix chain 'L' and resid 185 through 215 Processing sheet with id= A, first strand: chain 'A' and resid 166 through 169 Processing sheet with id= B, first strand: chain 'B' and resid 166 through 169 Processing sheet with id= C, first strand: chain 'C' and resid 166 through 169 Processing sheet with id= D, first strand: chain 'D' and resid 166 through 169 Processing sheet with id= E, first strand: chain 'E' and resid 166 through 169 Processing sheet with id= F, first strand: chain 'F' and resid 166 through 169 Processing sheet with id= G, first strand: chain 'G' and resid 166 through 169 Processing sheet with id= H, first strand: chain 'H' and resid 166 through 169 Processing sheet with id= I, first strand: chain 'I' and resid 166 through 169 Processing sheet with id= J, first strand: chain 'J' and resid 166 through 169 Processing sheet with id= K, first strand: chain 'K' and resid 166 through 169 Processing sheet with id= L, first strand: chain 'L' and resid 166 through 169 1224 hydrogen bonds defined for protein. 3636 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.45 Time building geometry restraints manager: 8.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5424 1.34 - 1.46: 4495 1.46 - 1.58: 9197 1.58 - 1.69: 0 1.69 - 1.81: 240 Bond restraints: 19356 Sorted by residual: bond pdb=" C1 LMT H 303 " pdb=" C2 LMT H 303 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" C1 LMT L 301 " pdb=" C2 LMT L 301 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.10e+00 bond pdb=" C1 LMT A 303 " pdb=" C2 LMT A 303 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.09e+00 bond pdb=" C1 LMT I 303 " pdb=" C2 LMT I 303 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.08e+00 bond pdb=" C1 LMT E 303 " pdb=" C2 LMT E 303 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.06e+00 ... (remaining 19351 not shown) Histogram of bond angle deviations from ideal: 100.19 - 106.96: 480 106.96 - 113.72: 11181 113.72 - 120.49: 7586 120.49 - 127.25: 6565 127.25 - 134.02: 276 Bond angle restraints: 26088 Sorted by residual: angle pdb=" C6 LMT E 303 " pdb=" C7 LMT E 303 " pdb=" C8 LMT E 303 " ideal model delta sigma weight residual 117.26 109.37 7.89 3.00e+00 1.11e-01 6.91e+00 angle pdb=" C6 LMT H 303 " pdb=" C7 LMT H 303 " pdb=" C8 LMT H 303 " ideal model delta sigma weight residual 117.26 109.38 7.88 3.00e+00 1.11e-01 6.90e+00 angle pdb=" C6 LMT A 303 " pdb=" C7 LMT A 303 " pdb=" C8 LMT A 303 " ideal model delta sigma weight residual 117.26 109.40 7.86 3.00e+00 1.11e-01 6.86e+00 angle pdb=" C6 LMT I 303 " pdb=" C7 LMT I 303 " pdb=" C8 LMT I 303 " ideal model delta sigma weight residual 117.26 109.41 7.85 3.00e+00 1.11e-01 6.85e+00 angle pdb=" C6 LMT C 305 " pdb=" C7 LMT C 305 " pdb=" C8 LMT C 305 " ideal model delta sigma weight residual 117.26 109.41 7.85 3.00e+00 1.11e-01 6.85e+00 ... (remaining 26083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 10251 16.01 - 32.02: 717 32.02 - 48.03: 228 48.03 - 64.04: 48 64.04 - 80.05: 24 Dihedral angle restraints: 11268 sinusoidal: 4632 harmonic: 6636 Sorted by residual: dihedral pdb=" CB GLU I 209 " pdb=" CG GLU I 209 " pdb=" CD GLU I 209 " pdb=" OE1 GLU I 209 " ideal model delta sinusoidal sigma weight residual 0.00 -80.05 80.05 1 3.00e+01 1.11e-03 8.82e+00 dihedral pdb=" CB GLU L 209 " pdb=" CG GLU L 209 " pdb=" CD GLU L 209 " pdb=" OE1 GLU L 209 " ideal model delta sinusoidal sigma weight residual 0.00 -80.04 80.04 1 3.00e+01 1.11e-03 8.82e+00 dihedral pdb=" CB GLU D 209 " pdb=" CG GLU D 209 " pdb=" CD GLU D 209 " pdb=" OE1 GLU D 209 " ideal model delta sinusoidal sigma weight residual 0.00 -80.03 80.03 1 3.00e+01 1.11e-03 8.82e+00 ... (remaining 11265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1450 0.025 - 0.049: 969 0.049 - 0.074: 328 0.074 - 0.098: 122 0.098 - 0.123: 71 Chirality restraints: 2940 Sorted by residual: chirality pdb=" CA PRO K 185 " pdb=" N PRO K 185 " pdb=" C PRO K 185 " pdb=" CB PRO K 185 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.79e-01 chirality pdb=" CA PRO L 185 " pdb=" N PRO L 185 " pdb=" C PRO L 185 " pdb=" CB PRO L 185 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.76e-01 chirality pdb=" CA PRO A 185 " pdb=" N PRO A 185 " pdb=" C PRO A 185 " pdb=" CB PRO A 185 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.75e-01 ... (remaining 2937 not shown) Planarity restraints: 3084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I 65 " 0.011 2.00e-02 2.50e+03 6.14e-03 7.54e-01 pdb=" CG TYR I 65 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR I 65 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR I 65 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR I 65 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR I 65 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR I 65 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR I 65 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 65 " 0.011 2.00e-02 2.50e+03 6.02e-03 7.25e-01 pdb=" CG TYR B 65 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR B 65 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR B 65 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 65 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 65 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 65 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 65 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 65 " -0.011 2.00e-02 2.50e+03 6.00e-03 7.20e-01 pdb=" CG TYR G 65 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR G 65 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR G 65 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR G 65 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR G 65 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR G 65 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR G 65 " -0.003 2.00e-02 2.50e+03 ... (remaining 3081 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 396 2.69 - 3.24: 18710 3.24 - 3.80: 30392 3.80 - 4.35: 40502 4.35 - 4.90: 65905 Nonbonded interactions: 155905 Sorted by model distance: nonbonded pdb=" O ILE H 71 " pdb=" OH TYR H 158 " model vdw 2.140 2.440 nonbonded pdb=" O ILE I 71 " pdb=" OH TYR I 158 " model vdw 2.140 2.440 nonbonded pdb=" O ILE J 71 " pdb=" OH TYR J 158 " model vdw 2.140 2.440 nonbonded pdb=" O ILE G 71 " pdb=" OH TYR G 158 " model vdw 2.140 2.440 nonbonded pdb=" O ILE D 71 " pdb=" OH TYR D 158 " model vdw 2.140 2.440 ... (remaining 155900 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 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'B' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'C' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'D' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'E' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'F' and (resid 4 through 217 or (resid 301 and (name C2 or name C3 or nam \ e C4 or name C5 or name C6 or name C7 or name C8 )) or resid 303 through 304)) selection = (chain 'G' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'H' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'I' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'J' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'K' and (resid 4 through 217 or resid 301 or resid 303 through 304)) selection = (chain 'L' and (resid 4 through 217 or (resid 301 and (name C2 or name C3 or nam \ e C4 or name C5 or name C6 or name C7 or name C8 )) or resid 303 through 304)) } 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: 0.010 Normalize map: mean=0, sd=1: 5.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 18.480 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 47.840 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.980 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.050 19356 Z= 0.378 Angle : 0.877 7.887 26088 Z= 0.366 Chirality : 0.039 0.123 2940 Planarity : 0.003 0.021 3084 Dihedral : 13.419 80.046 6864 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.17), residues: 2208 helix: 1.53 (0.12), residues: 1524 sheet: 2.44 (0.43), residues: 132 loop : -0.86 (0.27), residues: 552 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 302 time to evaluate : 2.044 Fit side-chains outliers start: 48 outliers final: 13 residues processed: 335 average time/residue: 1.2117 time to fit residues: 461.2406 Evaluate side-chains 269 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 256 time to evaluate : 2.166 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 0.3443 time to fit residues: 3.3804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.7980 chunk 163 optimal weight: 7.9990 chunk 90 optimal weight: 20.0000 chunk 55 optimal weight: 8.9990 chunk 110 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 169 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 126 optimal weight: 0.3980 chunk 196 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.8767 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 19356 Z= 0.176 Angle : 0.530 5.707 26088 Z= 0.290 Chirality : 0.039 0.148 2940 Planarity : 0.003 0.019 3084 Dihedral : 9.153 58.087 2796 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.13 (0.17), residues: 2208 helix: 3.02 (0.12), residues: 1524 sheet: 2.54 (0.40), residues: 132 loop : -0.97 (0.25), residues: 552 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 289 time to evaluate : 2.200 Fit side-chains outliers start: 41 outliers final: 26 residues processed: 314 average time/residue: 1.1158 time to fit residues: 402.5634 Evaluate side-chains 276 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 250 time to evaluate : 2.200 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 14 residues processed: 12 average time/residue: 1.7091 time to fit residues: 25.2677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 196 optimal weight: 2.9990 chunk 212 optimal weight: 0.8980 chunk 175 optimal weight: 2.9990 chunk 194 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 157 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 GLN E 57 GLN G 57 GLN J 57 GLN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 19356 Z= 0.249 Angle : 0.541 6.487 26088 Z= 0.295 Chirality : 0.041 0.176 2940 Planarity : 0.003 0.017 3084 Dihedral : 8.708 57.728 2796 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer Outliers : 3.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.26 (0.17), residues: 2208 helix: 3.18 (0.12), residues: 1524 sheet: 2.50 (0.42), residues: 132 loop : -1.11 (0.25), residues: 552 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 266 time to evaluate : 2.101 Fit side-chains outliers start: 69 outliers final: 33 residues processed: 315 average time/residue: 1.1379 time to fit residues: 410.2225 Evaluate side-chains 294 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 261 time to evaluate : 2.118 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 23 residues processed: 10 average time/residue: 1.7452 time to fit residues: 21.8108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 0.2980 chunk 147 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 197 optimal weight: 0.9990 chunk 208 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 186 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 19356 Z= 0.182 Angle : 0.516 7.752 26088 Z= 0.274 Chirality : 0.040 0.170 2940 Planarity : 0.003 0.017 3084 Dihedral : 8.025 55.895 2796 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer Outliers : 2.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.49 (0.17), residues: 2208 helix: 3.31 (0.12), residues: 1536 sheet: 2.73 (0.42), residues: 132 loop : -1.04 (0.25), residues: 540 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 266 time to evaluate : 2.194 Fit side-chains outliers start: 60 outliers final: 36 residues processed: 312 average time/residue: 1.1614 time to fit residues: 413.9384 Evaluate side-chains 296 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 260 time to evaluate : 2.172 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 25 residues processed: 11 average time/residue: 1.6344 time to fit residues: 22.5898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 178 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 106 optimal weight: 0.8980 chunk 187 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 19356 Z= 0.204 Angle : 0.525 9.649 26088 Z= 0.278 Chirality : 0.040 0.175 2940 Planarity : 0.003 0.026 3084 Dihedral : 7.789 54.038 2796 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer Outliers : 2.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.44 (0.17), residues: 2208 helix: 3.38 (0.12), residues: 1536 sheet: 1.39 (0.39), residues: 204 loop : -1.44 (0.25), residues: 468 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 266 time to evaluate : 2.298 Fit side-chains outliers start: 56 outliers final: 41 residues processed: 301 average time/residue: 1.1763 time to fit residues: 403.6634 Evaluate side-chains 300 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 259 time to evaluate : 2.051 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 25 residues processed: 16 average time/residue: 1.2484 time to fit residues: 25.2011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 2.9990 chunk 188 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 208 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 109 optimal weight: 7.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 19356 Z= 0.223 Angle : 0.534 8.371 26088 Z= 0.283 Chirality : 0.041 0.177 2940 Planarity : 0.003 0.031 3084 Dihedral : 7.844 57.763 2796 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer Outliers : 3.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.47 (0.17), residues: 2208 helix: 3.41 (0.12), residues: 1536 sheet: 1.37 (0.39), residues: 204 loop : -1.43 (0.25), residues: 468 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 268 time to evaluate : 2.210 Fit side-chains outliers start: 61 outliers final: 41 residues processed: 302 average time/residue: 1.2177 time to fit residues: 418.6934 Evaluate side-chains 299 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 258 time to evaluate : 2.189 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 24 residues processed: 17 average time/residue: 1.2177 time to fit residues: 26.2804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 208 optimal weight: 0.4980 chunk 130 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 19356 Z= 0.225 Angle : 0.533 7.912 26088 Z= 0.282 Chirality : 0.041 0.176 2940 Planarity : 0.003 0.037 3084 Dihedral : 7.847 59.868 2796 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer Outliers : 2.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.47 (0.17), residues: 2208 helix: 3.41 (0.12), residues: 1536 sheet: 1.35 (0.39), residues: 204 loop : -1.41 (0.25), residues: 468 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 260 time to evaluate : 2.203 Fit side-chains outliers start: 54 outliers final: 43 residues processed: 291 average time/residue: 1.2270 time to fit residues: 405.5306 Evaluate side-chains 300 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 257 time to evaluate : 2.220 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 24 residues processed: 19 average time/residue: 1.0691 time to fit residues: 26.6794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 163 optimal weight: 8.9990 chunk 189 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 19356 Z= 0.228 Angle : 0.538 7.372 26088 Z= 0.284 Chirality : 0.041 0.177 2940 Planarity : 0.003 0.036 3084 Dihedral : 7.706 57.646 2796 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.49 (0.17), residues: 2208 helix: 3.43 (0.12), residues: 1548 sheet: 1.35 (0.39), residues: 204 loop : -1.54 (0.25), residues: 456 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 256 time to evaluate : 2.240 Fit side-chains outliers start: 45 outliers final: 34 residues processed: 287 average time/residue: 1.2338 time to fit residues: 401.9307 Evaluate side-chains 284 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 250 time to evaluate : 2.259 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 24 residues processed: 10 average time/residue: 1.3332 time to fit residues: 17.8440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 0.0770 chunk 181 optimal weight: 0.3980 chunk 194 optimal weight: 0.6980 chunk 116 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 183 optimal weight: 0.5980 chunk 193 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 19356 Z= 0.158 Angle : 0.500 7.278 26088 Z= 0.263 Chirality : 0.039 0.169 2940 Planarity : 0.003 0.044 3084 Dihedral : 6.993 56.937 2796 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.67 (0.17), residues: 2208 helix: 3.58 (0.12), residues: 1548 sheet: 1.45 (0.38), residues: 204 loop : -1.60 (0.24), residues: 456 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 259 time to evaluate : 2.363 Fit side-chains outliers start: 38 outliers final: 30 residues processed: 286 average time/residue: 1.2265 time to fit residues: 400.5625 Evaluate side-chains 281 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 251 time to evaluate : 2.123 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 24 residues processed: 6 average time/residue: 0.7928 time to fit residues: 8.6142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 198 optimal weight: 9.9990 chunk 171 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 19356 Z= 0.266 Angle : 0.555 7.051 26088 Z= 0.294 Chirality : 0.042 0.180 2940 Planarity : 0.003 0.046 3084 Dihedral : 7.305 56.492 2796 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.46 (0.17), residues: 2208 helix: 3.39 (0.12), residues: 1548 sheet: 1.41 (0.39), residues: 204 loop : -1.52 (0.25), residues: 456 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 251 time to evaluate : 2.135 Fit side-chains outliers start: 36 outliers final: 35 residues processed: 276 average time/residue: 1.2888 time to fit residues: 402.6498 Evaluate side-chains 285 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 250 time to evaluate : 2.244 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 24 residues processed: 11 average time/residue: 1.1524 time to fit residues: 17.4439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 171 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 176 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 150 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.137354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.082636 restraints weight = 26032.563| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.83 r_work: 0.2910 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 19356 Z= 0.218 Angle : 0.531 6.949 26088 Z= 0.281 Chirality : 0.040 0.175 2940 Planarity : 0.003 0.048 3084 Dihedral : 7.074 58.148 2796 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.47 (0.17), residues: 2208 helix: 3.41 (0.12), residues: 1548 sheet: 1.37 (0.39), residues: 204 loop : -1.57 (0.24), residues: 456 =============================================================================== Job complete usr+sys time: 7534.02 seconds wall clock time: 134 minutes 33.75 seconds (8073.75 seconds total)