Starting phenix.real_space_refine on Thu Feb 22 14:57:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkp_34856/02_2024/8hkp_34856_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkp_34856/02_2024/8hkp_34856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkp_34856/02_2024/8hkp_34856.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkp_34856/02_2024/8hkp_34856.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkp_34856/02_2024/8hkp_34856_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hkp_34856/02_2024/8hkp_34856_trim_updated.pdb" } resolution = 3.6 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= 0.005 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: 5 Type Number sf(0) Gaussians S 156 5.16 5 C 11364 2.51 5 N 2712 2.21 5 O 3024 1.98 5 H 16842 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 48": "OD1" <-> "OD2" Residue "B PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 210": "OE1" <-> "OE2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 271": "OE1" <-> "OE2" Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 210": "OE1" <-> "OE2" Residue "C GLU 230": "OE1" <-> "OE2" Residue "C PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 271": "OE1" <-> "OE2" Residue "D PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 210": "OE1" <-> "OE2" Residue "D GLU 230": "OE1" <-> "OE2" Residue "D PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 12": "OE1" <-> "OE2" Residue "E ASP 48": "OD1" <-> "OD2" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 210": "OE1" <-> "OE2" Residue "E GLU 230": "OE1" <-> "OE2" Residue "E PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 271": "OE1" <-> "OE2" Residue "F PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 210": "OE1" <-> "OE2" Residue "F PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 24": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 34": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 47": "OD1" <-> "OD2" Residue "G ASP 48": "OD1" <-> "OD2" Residue "G PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 69": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 77": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 246": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 24": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 34": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 48": "OD1" <-> "OD2" Residue "H PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 69": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 77": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 246": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 24": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 34": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 48": "OD1" <-> "OD2" Residue "I PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 69": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 77": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 246": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 24": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 34": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ASP 48": "OD1" <-> "OD2" Residue "J PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 69": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 77": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 246": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 24": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 34": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 48": "OD1" <-> "OD2" Residue "K PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 69": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 77": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 246": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 24": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 34": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 48": "OD1" <-> "OD2" Residue "L PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 69": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 77": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 246": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 34098 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 2914 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "B" Number of atoms: 2914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 2914 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "C" Number of atoms: 2914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 2914 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "D" Number of atoms: 2914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 2914 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "E" Number of atoms: 2914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 2914 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "F" Number of atoms: 2914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 2914 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "G" Number of atoms: 2700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2700 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 160} Chain breaks: 1 Chain: "H" Number of atoms: 2700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2700 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 160} Chain breaks: 1 Chain: "I" Number of atoms: 2700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2700 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 160} Chain breaks: 1 Chain: "J" Number of atoms: 2700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2700 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 160} Chain breaks: 1 Chain: "K" Number of atoms: 2700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2700 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 160} Chain breaks: 1 Chain: "L" Number of atoms: 2700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2700 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 160} Chain breaks: 1 Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'AV0': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'AV0': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'AV0': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'AV0': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'AV0': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'AV0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.69, per 1000 atoms: 0.46 Number of scatterers: 34098 At special positions: 0 Unit cell: (116.048, 104.579, 148.434, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 156 16.00 O 3024 8.00 N 2712 7.00 C 11364 6.00 H 16842 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 236 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS D 55 " - pdb=" SG CYS D 242 " distance=2.03 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 236 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 231 " distance=2.03 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 242 " distance=2.03 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 236 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 231 " distance=2.03 Simple disulfide: pdb=" SG CYS F 55 " - pdb=" SG CYS F 242 " distance=2.03 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 236 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 231 " distance=2.03 Simple disulfide: pdb=" SG CYS G 55 " - pdb=" SG CYS G 242 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 236 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 231 " distance=2.03 Simple disulfide: pdb=" SG CYS H 55 " - pdb=" SG CYS H 242 " distance=2.03 Simple disulfide: pdb=" SG CYS H 62 " - pdb=" SG CYS H 236 " distance=2.03 Simple disulfide: pdb=" SG CYS H 66 " - pdb=" SG CYS H 231 " distance=2.03 Simple disulfide: pdb=" SG CYS I 55 " - pdb=" SG CYS I 242 " distance=2.03 Simple disulfide: pdb=" SG CYS I 62 " - pdb=" SG CYS I 236 " distance=2.03 Simple disulfide: pdb=" SG CYS I 66 " - pdb=" SG CYS I 231 " distance=2.03 Simple disulfide: pdb=" SG CYS J 55 " - pdb=" SG CYS J 242 " distance=2.03 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 236 " distance=2.03 Simple disulfide: pdb=" SG CYS J 66 " - pdb=" SG CYS J 231 " distance=2.03 Simple disulfide: pdb=" SG CYS K 55 " - pdb=" SG CYS K 242 " distance=2.03 Simple disulfide: pdb=" SG CYS K 62 " - pdb=" SG CYS K 236 " distance=2.03 Simple disulfide: pdb=" SG CYS K 66 " - pdb=" SG CYS K 231 " distance=2.03 Simple disulfide: pdb=" SG CYS L 55 " - pdb=" SG CYS L 242 " distance=2.03 Simple disulfide: pdb=" SG CYS L 62 " - pdb=" SG CYS L 236 " distance=2.03 Simple disulfide: pdb=" SG CYS L 66 " - pdb=" SG CYS L 231 " distance=2.04 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: 24.42 Conformation dependent library (CDL) restraints added in 3.4 seconds 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3936 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 80 helices and 12 sheets defined 62.4% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.98 Creating SS restraints... Processing helix chain 'A' and resid 5 through 14 Processing helix chain 'A' and resid 21 through 32 Processing helix chain 'A' and resid 35 through 40 removed outlier: 3.758A pdb=" N ILE A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 70 Processing helix chain 'A' and resid 75 through 91 Proline residue: A 89 - end of helix Processing helix chain 'A' and resid 93 through 100 removed outlier: 4.131A pdb=" N VAL A 98 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N HIS A 99 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN A 100 " --> pdb=" O TYR A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 220 Processing helix chain 'A' and resid 251 through 273 Processing helix chain 'B' and resid 5 through 14 Processing helix chain 'B' and resid 21 through 32 Processing helix chain 'B' and resid 35 through 41 removed outlier: 3.597A pdb=" N ILE B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 70 Processing helix chain 'B' and resid 75 through 100 Proline residue: B 89 - end of helix removed outlier: 4.314A pdb=" N PHE B 93 " --> pdb=" O PRO B 89 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ILE B 94 " --> pdb=" O SER B 90 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL B 98 " --> pdb=" O ILE B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 220 Processing helix chain 'B' and resid 249 through 273 removed outlier: 4.023A pdb=" N PHE B 253 " --> pdb=" O GLU B 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 13 Processing helix chain 'C' and resid 21 through 32 Processing helix chain 'C' and resid 35 through 41 removed outlier: 3.618A pdb=" N ILE C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 70 Processing helix chain 'C' and resid 75 through 100 Proline residue: C 89 - end of helix removed outlier: 4.598A pdb=" N PHE C 93 " --> pdb=" O PRO C 89 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ILE C 94 " --> pdb=" O SER C 90 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL C 98 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N HIS C 99 " --> pdb=" O THR C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 220 Processing helix chain 'C' and resid 249 through 274 removed outlier: 4.030A pdb=" N PHE C 253 " --> pdb=" O GLU C 249 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N HIS C 274 " --> pdb=" O ALA C 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 14 Processing helix chain 'D' and resid 21 through 33 Processing helix chain 'D' and resid 35 through 41 removed outlier: 3.689A pdb=" N ILE D 40 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 70 Processing helix chain 'D' and resid 75 through 98 Proline residue: D 89 - end of helix removed outlier: 4.386A pdb=" N PHE D 93 " --> pdb=" O PRO D 89 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ILE D 94 " --> pdb=" O SER D 90 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL D 98 " --> pdb=" O ILE D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 220 Processing helix chain 'D' and resid 249 through 273 removed outlier: 4.036A pdb=" N PHE D 253 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 14 Processing helix chain 'E' and resid 21 through 32 Processing helix chain 'E' and resid 35 through 41 removed outlier: 3.561A pdb=" N ILE E 40 " --> pdb=" O LEU E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 70 Processing helix chain 'E' and resid 75 through 100 Proline residue: E 89 - end of helix removed outlier: 4.363A pdb=" N PHE E 93 " --> pdb=" O PRO E 89 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ILE E 94 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR E 95 " --> pdb=" O LEU E 91 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL E 98 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N HIS E 99 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN E 100 " --> pdb=" O TYR E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 220 Processing helix chain 'E' and resid 251 through 273 Processing helix chain 'F' and resid 5 through 14 Processing helix chain 'F' and resid 21 through 32 Processing helix chain 'F' and resid 35 through 41 removed outlier: 3.610A pdb=" N ILE F 40 " --> pdb=" O LEU F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 70 Processing helix chain 'F' and resid 75 through 100 Proline residue: F 89 - end of helix removed outlier: 4.426A pdb=" N PHE F 93 " --> pdb=" O PRO F 89 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ILE F 94 " --> pdb=" O SER F 90 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N THR F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR F 96 " --> pdb=" O CYS F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 220 Processing helix chain 'F' and resid 251 through 273 Processing helix chain 'G' and resid 22 through 40 Processing helix chain 'G' and resid 62 through 70 Processing helix chain 'G' and resid 75 through 86 Processing helix chain 'G' and resid 88 through 98 Processing helix chain 'G' and resid 196 through 220 Processing helix chain 'G' and resid 247 through 275 Processing helix chain 'H' and resid 22 through 40 Processing helix chain 'H' and resid 63 through 70 Processing helix chain 'H' and resid 75 through 86 Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 196 through 220 Processing helix chain 'H' and resid 247 through 275 Processing helix chain 'I' and resid 22 through 45 removed outlier: 4.564A pdb=" N GLU I 43 " --> pdb=" O ALA I 39 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N THR I 44 " --> pdb=" O ILE I 40 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL I 45 " --> pdb=" O VAL I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 70 Processing helix chain 'I' and resid 75 through 86 Processing helix chain 'I' and resid 88 through 98 Processing helix chain 'I' and resid 195 through 220 Processing helix chain 'I' and resid 247 through 275 Processing helix chain 'J' and resid 22 through 40 Processing helix chain 'J' and resid 62 through 70 Processing helix chain 'J' and resid 75 through 86 Processing helix chain 'J' and resid 88 through 98 Processing helix chain 'J' and resid 196 through 220 Processing helix chain 'J' and resid 249 through 275 Processing helix chain 'K' and resid 22 through 40 Processing helix chain 'K' and resid 62 through 70 Processing helix chain 'K' and resid 75 through 86 Processing helix chain 'K' and resid 88 through 98 Processing helix chain 'K' and resid 196 through 220 Processing helix chain 'K' and resid 247 through 275 Processing helix chain 'L' and resid 22 through 40 Processing helix chain 'L' and resid 42 through 45 No H-bonds generated for 'chain 'L' and resid 42 through 45' Processing helix chain 'L' and resid 62 through 70 Processing helix chain 'L' and resid 75 through 86 Processing helix chain 'L' and resid 88 through 98 Processing helix chain 'L' and resid 196 through 220 Processing helix chain 'L' and resid 247 through 275 Processing sheet with id= A, first strand: chain 'A' and resid 228 through 231 Processing sheet with id= B, first strand: chain 'B' and resid 228 through 231 Processing sheet with id= C, first strand: chain 'C' and resid 228 through 231 Processing sheet with id= D, first strand: chain 'D' and resid 228 through 231 Processing sheet with id= E, first strand: chain 'E' and resid 228 through 231 Processing sheet with id= F, first strand: chain 'F' and resid 229 through 231 Processing sheet with id= G, first strand: chain 'G' and resid 229 through 231 Processing sheet with id= H, first strand: chain 'H' and resid 228 through 231 Processing sheet with id= I, first strand: chain 'I' and resid 229 through 231 Processing sheet with id= J, first strand: chain 'J' and resid 229 through 231 Processing sheet with id= K, first strand: chain 'K' and resid 228 through 231 Processing sheet with id= L, first strand: chain 'L' and resid 229 through 231 974 hydrogen bonds defined for protein. 2871 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: 11.11 Time building geometry restraints manager: 25.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 16806 1.03 - 1.23: 100 1.23 - 1.43: 7388 1.43 - 1.62: 10014 1.62 - 1.82: 222 Bond restraints: 34530 Sorted by residual: bond pdb=" CBK AV0 D 401 " pdb=" CBQ AV0 D 401 " ideal model delta sigma weight residual 1.525 1.655 -0.130 2.00e-02 2.50e+03 4.24e+01 bond pdb=" CBK AV0 F 401 " pdb=" CBQ AV0 F 401 " ideal model delta sigma weight residual 1.525 1.654 -0.129 2.00e-02 2.50e+03 4.19e+01 bond pdb=" CBK AV0 B 401 " pdb=" CBQ AV0 B 401 " ideal model delta sigma weight residual 1.525 1.654 -0.129 2.00e-02 2.50e+03 4.18e+01 bond pdb=" CBK AV0 E 401 " pdb=" CBQ AV0 E 401 " ideal model delta sigma weight residual 1.525 1.654 -0.129 2.00e-02 2.50e+03 4.17e+01 bond pdb=" CBK AV0 A 401 " pdb=" CBQ AV0 A 401 " ideal model delta sigma weight residual 1.525 1.654 -0.129 2.00e-02 2.50e+03 4.14e+01 ... (remaining 34525 not shown) Histogram of bond angle deviations from ideal: 99.20 - 106.16: 331 106.16 - 113.13: 39400 113.13 - 120.09: 11306 120.09 - 127.06: 10844 127.06 - 134.03: 159 Bond angle restraints: 62040 Sorted by residual: angle pdb=" N ILE F 237 " pdb=" CA ILE F 237 " pdb=" C ILE F 237 " ideal model delta sigma weight residual 106.55 111.71 -5.16 1.45e+00 4.76e-01 1.27e+01 angle pdb=" N ILE G 195 " pdb=" CA ILE G 195 " pdb=" C ILE G 195 " ideal model delta sigma weight residual 111.62 108.87 2.75 7.90e-01 1.60e+00 1.21e+01 angle pdb=" N ILE J 195 " pdb=" CA ILE J 195 " pdb=" C ILE J 195 " ideal model delta sigma weight residual 111.62 108.88 2.74 7.90e-01 1.60e+00 1.20e+01 angle pdb=" N ILE L 195 " pdb=" CA ILE L 195 " pdb=" C ILE L 195 " ideal model delta sigma weight residual 111.62 108.90 2.72 7.90e-01 1.60e+00 1.18e+01 angle pdb=" N ILE H 195 " pdb=" CA ILE H 195 " pdb=" C ILE H 195 " ideal model delta sigma weight residual 111.62 108.93 2.69 7.90e-01 1.60e+00 1.16e+01 ... (remaining 62035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 16271 35.96 - 71.92: 497 71.92 - 107.88: 81 107.88 - 143.85: 83 143.85 - 179.81: 12 Dihedral angle restraints: 16944 sinusoidal: 9294 harmonic: 7650 Sorted by residual: dihedral pdb=" CCH AV0 C 401 " pdb=" CCQ AV0 C 401 " pdb=" OCB AV0 C 401 " pdb=" CCS AV0 C 401 " ideal model delta sinusoidal sigma weight residual 127.39 -52.80 -179.81 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CCH AV0 F 401 " pdb=" CCQ AV0 F 401 " pdb=" OCB AV0 F 401 " pdb=" CCS AV0 F 401 " ideal model delta sinusoidal sigma weight residual 127.39 -52.85 -179.76 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CCH AV0 B 401 " pdb=" CCQ AV0 B 401 " pdb=" OCB AV0 B 401 " pdb=" CCS AV0 B 401 " ideal model delta sinusoidal sigma weight residual 127.39 -52.25 179.64 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 16941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1850 0.039 - 0.077: 763 0.077 - 0.116: 197 0.116 - 0.154: 28 0.154 - 0.193: 12 Chirality restraints: 2850 Sorted by residual: chirality pdb=" CCV AV0 B 401 " pdb=" CCR AV0 B 401 " pdb=" CCT AV0 B 401 " pdb=" OAU AV0 B 401 " both_signs ideal model delta sigma weight residual False -2.30 -2.49 0.19 2.00e-01 2.50e+01 9.32e-01 chirality pdb=" CCV AV0 E 401 " pdb=" CCR AV0 E 401 " pdb=" CCT AV0 E 401 " pdb=" OAU AV0 E 401 " both_signs ideal model delta sigma weight residual False -2.30 -2.49 0.19 2.00e-01 2.50e+01 9.19e-01 chirality pdb=" CCV AV0 F 401 " pdb=" CCR AV0 F 401 " pdb=" CCT AV0 F 401 " pdb=" OAU AV0 F 401 " both_signs ideal model delta sigma weight residual False -2.30 -2.49 0.19 2.00e-01 2.50e+01 9.15e-01 ... (remaining 2847 not shown) Planarity restraints: 4896 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG H 246 " 0.037 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO H 247 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO H 247 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO H 247 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG K 246 " -0.037 5.00e-02 4.00e+02 5.60e-02 5.02e+00 pdb=" N PRO K 247 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO K 247 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO K 247 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG L 246 " -0.036 5.00e-02 4.00e+02 5.53e-02 4.89e+00 pdb=" N PRO L 247 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO L 247 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO L 247 " -0.031 5.00e-02 4.00e+02 ... (remaining 4893 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 2863 2.23 - 2.82: 72477 2.82 - 3.42: 78737 3.42 - 4.01: 107583 4.01 - 4.60: 169860 Nonbonded interactions: 431520 Sorted by model distance: nonbonded pdb="HH11 ARG A 77 " pdb=" OE2 GLU B 249 " model vdw 1.639 1.850 nonbonded pdb="HH11 ARG B 77 " pdb=" OE2 GLU C 249 " model vdw 1.686 1.850 nonbonded pdb=" O ILE L 73 " pdb=" HH TYR L 221 " model vdw 1.692 1.850 nonbonded pdb=" O ILE G 73 " pdb=" HH TYR G 221 " model vdw 1.692 1.850 nonbonded pdb="HH11 ARG E 77 " pdb=" OE2 GLU F 249 " model vdw 1.698 1.850 ... (remaining 431515 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 19 and (name N or name CA or name C or name O or name CB \ or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 20 through \ 100 or resid 196 through 276)) selection = (chain 'B' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 20 through \ 100 or resid 196 through 276)) selection = (chain 'C' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 20 through \ 100 or resid 196 through 276)) selection = (chain 'D' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 20 through \ 100 or resid 196 through 276)) selection = (chain 'E' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 20 through \ 100 or resid 196 through 276)) selection = (chain 'F' and ((resid 19 and (name N or name CA or name C or name O or name CB \ or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 20 through \ 100 or resid 196 through 276)) selection = (chain 'G' and (resid 19 through 100 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB or name OG or name HA or name HB2 or name HB3 or name H \ G )) or resid 197 through 276)) selection = (chain 'H' and (resid 19 through 100 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB or name OG or name HA or name HB2 or name HB3 or name H \ G )) or resid 197 through 276)) selection = (chain 'I' and (resid 19 through 100 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB or name OG or name HA or name HB2 or name HB3 or name H \ G )) or resid 197 through 276)) selection = (chain 'J' and (resid 19 through 100 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB or name OG or name HA or name HB2 or name HB3 or name H \ G )) or resid 197 through 276)) selection = (chain 'K' and (resid 19 through 100 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB or name OG or name HA or name HB2 or name HB3 or name H \ G )) or resid 197 through 276)) selection = (chain 'L' and (resid 19 through 100 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB or name OG or name HA or name HB2 or name HB3 or name H \ G )) or resid 197 through 276)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.630 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: 0.560 Extract box with map and model: 17.820 Check model and map are aligned: 0.510 Set scattering table: 0.350 Process input model: 103.270 Find NCS groups from input model: 1.950 Set up NCS constraints: 0.110 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 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 0.130 17688 Z= 0.617 Angle : 0.683 6.958 24060 Z= 0.353 Chirality : 0.044 0.193 2850 Planarity : 0.004 0.056 2904 Dihedral : 23.505 179.808 6828 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % 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: -2.19 (0.16), residues: 2040 helix: -0.53 (0.13), residues: 1326 sheet: -2.17 (0.43), residues: 120 loop : -3.25 (0.21), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 79 HIS 0.006 0.001 HIS J 75 PHE 0.021 0.001 PHE J 33 TYR 0.009 0.001 TYR J 218 ARG 0.003 0.000 ARG D 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 2.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 100 GLN cc_start: 0.7964 (tp-100) cc_final: 0.7750 (mm-40) REVERT: C 100 GLN cc_start: 0.7638 (tp40) cc_final: 0.7160 (tm-30) REVERT: I 278 ARG cc_start: 0.5862 (mtp85) cc_final: 0.5141 (ptm160) REVERT: K 69 ARG cc_start: 0.7627 (tpt170) cc_final: 0.7414 (tpp80) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.7615 time to fit residues: 272.5136 Evaluate side-chains 207 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 2.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 185 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 GLN ** J 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17688 Z= 0.196 Angle : 0.646 10.292 24060 Z= 0.298 Chirality : 0.042 0.177 2850 Planarity : 0.004 0.049 2904 Dihedral : 21.423 174.699 3048 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.80 % Allowed : 4.99 % Favored : 94.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.19), residues: 2040 helix: 1.60 (0.14), residues: 1326 sheet: -1.67 (0.45), residues: 120 loop : -2.72 (0.23), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 79 HIS 0.005 0.001 HIS I 75 PHE 0.017 0.001 PHE J 33 TYR 0.009 0.001 TYR G 218 ARG 0.003 0.000 ARG H 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 210 time to evaluate : 3.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 52 MET cc_start: 0.8848 (mmt) cc_final: 0.8392 (mmt) outliers start: 15 outliers final: 12 residues processed: 215 average time/residue: 0.6478 time to fit residues: 209.2989 Evaluate side-chains 209 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 197 time to evaluate : 2.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 224 SER Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 224 SER Chi-restraints excluded: chain H residue 273 ASN Chi-restraints excluded: chain I residue 224 SER Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 224 SER Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain K residue 224 SER Chi-restraints excluded: chain K residue 273 ASN Chi-restraints excluded: chain L residue 224 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 1.9990 chunk 57 optimal weight: 0.3980 chunk 154 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 185 optimal weight: 0.5980 chunk 200 optimal weight: 0.5980 chunk 165 optimal weight: 7.9990 chunk 184 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 148 optimal weight: 0.0670 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 ASN ** B 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 ASN ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 ASN ** E 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 ASN ** F 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 17688 Z= 0.135 Angle : 0.582 10.567 24060 Z= 0.265 Chirality : 0.042 0.319 2850 Planarity : 0.003 0.048 2904 Dihedral : 17.367 166.766 3048 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.21 % Allowed : 6.37 % Favored : 93.42 % 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: 1.38 (0.20), residues: 2040 helix: 2.59 (0.15), residues: 1308 sheet: -1.44 (0.46), residues: 120 loop : -2.53 (0.22), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP I 277 HIS 0.003 0.001 HIS J 75 PHE 0.018 0.001 PHE J 33 TYR 0.015 0.001 TYR A 218 ARG 0.013 0.000 ARG I 278 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 211 time to evaluate : 2.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 37 ILE cc_start: 0.9204 (mt) cc_final: 0.8981 (mm) REVERT: I 52 MET cc_start: 0.8858 (mmt) cc_final: 0.8583 (mmt) REVERT: I 278 ARG cc_start: 0.6407 (mtp85) cc_final: 0.5687 (ptt-90) REVERT: L 52 MET cc_start: 0.8814 (mmt) cc_final: 0.8537 (mmt) outliers start: 4 outliers final: 1 residues processed: 212 average time/residue: 0.6227 time to fit residues: 203.2206 Evaluate side-chains 207 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 206 time to evaluate : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 37 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 186 optimal weight: 0.7980 chunk 197 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 176 optimal weight: 0.0040 chunk 53 optimal weight: 5.9990 overall best weight: 2.3598 ------------------------------------------------------------------------------- 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: 0.8622 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17688 Z= 0.236 Angle : 0.574 6.424 24060 Z= 0.282 Chirality : 0.042 0.303 2850 Planarity : 0.004 0.044 2904 Dihedral : 16.126 167.177 3048 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.16 % Allowed : 7.75 % Favored : 92.09 % 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: 1.54 (0.19), residues: 2040 helix: 2.54 (0.14), residues: 1326 sheet: -1.06 (0.47), residues: 120 loop : -2.25 (0.23), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 277 HIS 0.005 0.001 HIS H 75 PHE 0.017 0.001 PHE J 33 TYR 0.012 0.001 TYR C 218 ARG 0.003 0.000 ARG I 278 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 230 time to evaluate : 3.055 Fit side-chains REVERT: H 37 ILE cc_start: 0.9209 (mt) cc_final: 0.8997 (mm) REVERT: I 52 MET cc_start: 0.8979 (mmt) cc_final: 0.8720 (mmt) REVERT: L 52 MET cc_start: 0.8975 (mmt) cc_final: 0.8660 (mmt) outliers start: 3 outliers final: 2 residues processed: 232 average time/residue: 0.6133 time to fit residues: 217.2831 Evaluate side-chains 218 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 216 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain K residue 220 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 9.9990 chunk 111 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 chunk 136 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 75 HIS K 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 17688 Z= 0.231 Angle : 0.557 4.861 24060 Z= 0.278 Chirality : 0.042 0.233 2850 Planarity : 0.004 0.060 2904 Dihedral : 15.486 168.505 3048 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.53 % Allowed : 8.12 % Favored : 91.35 % 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: 1.76 (0.19), residues: 2040 helix: 2.66 (0.14), residues: 1326 sheet: -0.65 (0.49), residues: 120 loop : -2.11 (0.23), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 79 HIS 0.006 0.001 HIS I 75 PHE 0.020 0.001 PHE J 33 TYR 0.010 0.001 TYR A 218 ARG 0.006 0.000 ARG I 278 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 235 time to evaluate : 2.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 33 PHE cc_start: 0.8396 (t80) cc_final: 0.8194 (t80) REVERT: I 52 MET cc_start: 0.9046 (mmt) cc_final: 0.8785 (mmt) REVERT: I 278 ARG cc_start: 0.7037 (mtp85) cc_final: 0.5656 (tpt90) REVERT: L 52 MET cc_start: 0.9057 (mmt) cc_final: 0.8740 (mmt) outliers start: 10 outliers final: 7 residues processed: 240 average time/residue: 0.6393 time to fit residues: 235.4259 Evaluate side-chains 229 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 222 time to evaluate : 2.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 273 ASN Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain H residue 273 ASN Chi-restraints excluded: chain I residue 273 ASN Chi-restraints excluded: chain J residue 273 ASN Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 273 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 163 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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: 0.8722 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17688 Z= 0.335 Angle : 0.619 5.585 24060 Z= 0.313 Chirality : 0.043 0.233 2850 Planarity : 0.004 0.051 2904 Dihedral : 15.577 173.551 3048 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.64 % Allowed : 8.70 % Favored : 90.66 % 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: 1.67 (0.19), residues: 2040 helix: 2.54 (0.14), residues: 1326 sheet: -0.46 (0.48), residues: 120 loop : -2.05 (0.23), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 79 HIS 0.007 0.001 HIS J 75 PHE 0.012 0.001 PHE I 33 TYR 0.014 0.002 TYR D 218 ARG 0.003 0.000 ARG L 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 233 time to evaluate : 2.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 68 ASP cc_start: 0.8815 (t70) cc_final: 0.8547 (t0) REVERT: I 52 MET cc_start: 0.9066 (mmt) cc_final: 0.8830 (mmt) REVERT: I 278 ARG cc_start: 0.7136 (mtp85) cc_final: 0.5724 (tpt90) REVERT: J 68 ASP cc_start: 0.8732 (t70) cc_final: 0.8517 (t0) REVERT: K 68 ASP cc_start: 0.8681 (t70) cc_final: 0.8468 (t0) REVERT: L 52 MET cc_start: 0.9083 (mmt) cc_final: 0.8802 (mmt) outliers start: 12 outliers final: 10 residues processed: 240 average time/residue: 0.5947 time to fit residues: 218.1479 Evaluate side-chains 239 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 229 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 273 ASN Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain H residue 273 ASN Chi-restraints excluded: chain I residue 273 ASN Chi-restraints excluded: chain J residue 273 ASN Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 273 ASN Chi-restraints excluded: chain L residue 269 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 144 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 196 optimal weight: 9.9990 chunk 123 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17688 Z= 0.208 Angle : 0.529 4.841 24060 Z= 0.267 Chirality : 0.040 0.204 2850 Planarity : 0.004 0.046 2904 Dihedral : 15.419 176.143 3048 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.64 % Allowed : 9.13 % Favored : 90.23 % 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: 2.06 (0.19), residues: 2040 helix: 2.86 (0.14), residues: 1326 sheet: -0.33 (0.49), residues: 120 loop : -1.96 (0.23), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP I 79 HIS 0.006 0.001 HIS J 75 PHE 0.009 0.001 PHE I 33 TYR 0.010 0.001 TYR J 218 ARG 0.003 0.000 ARG I 278 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 227 time to evaluate : 3.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 52 MET cc_start: 0.9070 (mmm) cc_final: 0.8859 (mmt) REVERT: G 68 ASP cc_start: 0.8784 (t70) cc_final: 0.8494 (t0) REVERT: H 253 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.8144 (m-80) REVERT: I 52 MET cc_start: 0.9074 (mmt) cc_final: 0.8805 (mmt) REVERT: I 253 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.7812 (m-80) REVERT: I 278 ARG cc_start: 0.7178 (mtp85) cc_final: 0.5753 (tpt90) REVERT: J 52 MET cc_start: 0.9075 (mmm) cc_final: 0.8866 (mmt) REVERT: J 68 ASP cc_start: 0.8696 (t70) cc_final: 0.8454 (t0) REVERT: L 52 MET cc_start: 0.9075 (mmt) cc_final: 0.8767 (mmt) REVERT: L 253 PHE cc_start: 0.8810 (OUTLIER) cc_final: 0.7815 (m-80) outliers start: 12 outliers final: 9 residues processed: 233 average time/residue: 0.6466 time to fit residues: 228.7137 Evaluate side-chains 235 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 223 time to evaluate : 2.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain G residue 273 ASN Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain H residue 253 PHE Chi-restraints excluded: chain H residue 273 ASN Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain I residue 273 ASN Chi-restraints excluded: chain J residue 273 ASN Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 273 ASN Chi-restraints excluded: chain L residue 253 PHE Chi-restraints excluded: chain L residue 269 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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: 0.8710 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17688 Z= 0.257 Angle : 0.550 4.913 24060 Z= 0.277 Chirality : 0.041 0.197 2850 Planarity : 0.004 0.047 2904 Dihedral : 15.328 178.420 3048 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.58 % Allowed : 9.55 % Favored : 89.86 % 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: 2.11 (0.19), residues: 2040 helix: 2.88 (0.14), residues: 1326 sheet: -0.32 (0.49), residues: 120 loop : -1.90 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 79 HIS 0.005 0.001 HIS J 75 PHE 0.011 0.001 PHE I 33 TYR 0.015 0.001 TYR E 218 ARG 0.003 0.000 ARG I 278 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 230 time to evaluate : 2.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 52 MET cc_start: 0.9080 (mmm) cc_final: 0.8864 (mmt) REVERT: G 68 ASP cc_start: 0.8815 (t70) cc_final: 0.8527 (t0) REVERT: H 253 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.8227 (m-80) REVERT: I 52 MET cc_start: 0.9089 (mmt) cc_final: 0.8835 (mmt) REVERT: I 253 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.7865 (m-80) REVERT: I 278 ARG cc_start: 0.7252 (mtp85) cc_final: 0.5803 (tpt90) REVERT: J 68 ASP cc_start: 0.8734 (t70) cc_final: 0.8520 (t0) REVERT: L 52 MET cc_start: 0.9087 (mmt) cc_final: 0.8789 (mmt) REVERT: L 253 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.7871 (m-80) outliers start: 11 outliers final: 8 residues processed: 236 average time/residue: 0.6051 time to fit residues: 218.2469 Evaluate side-chains 241 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 230 time to evaluate : 2.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 239 GLU Chi-restraints excluded: chain G residue 273 ASN Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain H residue 253 PHE Chi-restraints excluded: chain H residue 273 ASN Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain I residue 273 ASN Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 273 ASN Chi-restraints excluded: chain L residue 253 PHE Chi-restraints excluded: chain L residue 269 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 79 optimal weight: 0.3980 chunk 143 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 182 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17688 Z= 0.236 Angle : 0.534 4.891 24060 Z= 0.271 Chirality : 0.040 0.184 2850 Planarity : 0.004 0.049 2904 Dihedral : 15.349 179.902 3048 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.64 % Allowed : 9.55 % Favored : 89.81 % 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: 2.24 (0.19), residues: 2040 helix: 2.98 (0.14), residues: 1326 sheet: -0.27 (0.49), residues: 120 loop : -1.84 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 79 HIS 0.006 0.001 HIS J 75 PHE 0.014 0.001 PHE I 205 TYR 0.013 0.001 TYR C 218 ARG 0.002 0.000 ARG K 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 230 time to evaluate : 2.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.8692 (mmt) cc_final: 0.8436 (mmp) REVERT: G 68 ASP cc_start: 0.8818 (t70) cc_final: 0.8527 (t0) REVERT: H 253 PHE cc_start: 0.8747 (OUTLIER) cc_final: 0.8223 (m-80) REVERT: I 52 MET cc_start: 0.9095 (mmt) cc_final: 0.8849 (mmt) REVERT: I 253 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.7899 (m-80) REVERT: I 278 ARG cc_start: 0.7172 (mtp85) cc_final: 0.5793 (tpt90) REVERT: J 68 ASP cc_start: 0.8736 (t70) cc_final: 0.8524 (t0) REVERT: L 37 ILE cc_start: 0.9270 (mt) cc_final: 0.9050 (mm) REVERT: L 52 MET cc_start: 0.9101 (mmt) cc_final: 0.8814 (mmt) REVERT: L 253 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.7886 (m-80) outliers start: 12 outliers final: 8 residues processed: 235 average time/residue: 0.6249 time to fit residues: 224.0270 Evaluate side-chains 237 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 226 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 273 ASN Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain H residue 253 PHE Chi-restraints excluded: chain H residue 273 ASN Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain I residue 273 ASN Chi-restraints excluded: chain J residue 273 ASN Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 273 ASN Chi-restraints excluded: chain L residue 253 PHE Chi-restraints excluded: chain L residue 269 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 203 optimal weight: 6.9990 chunk 187 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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: 0.8698 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17688 Z= 0.198 Angle : 0.514 4.848 24060 Z= 0.262 Chirality : 0.040 0.162 2850 Planarity : 0.004 0.047 2904 Dihedral : 15.251 179.609 3048 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.53 % Allowed : 10.14 % Favored : 89.33 % 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: 2.40 (0.19), residues: 2040 helix: 3.11 (0.14), residues: 1326 sheet: -0.26 (0.49), residues: 120 loop : -1.77 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP L 277 HIS 0.005 0.001 HIS J 75 PHE 0.018 0.001 PHE G 205 TYR 0.011 0.001 TYR A 218 ARG 0.002 0.000 ARG I 278 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 219 time to evaluate : 2.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.8694 (mmt) cc_final: 0.8399 (mmp) REVERT: G 68 ASP cc_start: 0.8806 (t70) cc_final: 0.8518 (t0) REVERT: H 253 PHE cc_start: 0.8736 (OUTLIER) cc_final: 0.8231 (m-80) REVERT: I 52 MET cc_start: 0.9091 (mmt) cc_final: 0.8847 (mmt) REVERT: I 253 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.7892 (m-80) REVERT: I 278 ARG cc_start: 0.7191 (mtp85) cc_final: 0.5791 (tpt90) REVERT: J 68 ASP cc_start: 0.8718 (t70) cc_final: 0.8479 (t0) REVERT: L 52 MET cc_start: 0.9105 (mmt) cc_final: 0.8767 (mmt) REVERT: L 253 PHE cc_start: 0.8848 (OUTLIER) cc_final: 0.7893 (m-80) outliers start: 10 outliers final: 5 residues processed: 223 average time/residue: 0.6184 time to fit residues: 210.9422 Evaluate side-chains 225 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 217 time to evaluate : 2.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 220 LEU Chi-restraints excluded: chain H residue 253 PHE Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain I residue 273 ASN Chi-restraints excluded: chain J residue 273 ASN Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain L residue 253 PHE Chi-restraints excluded: chain L residue 269 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 162 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.119136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.095827 restraints weight = 63596.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.098893 restraints weight = 31920.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.100732 restraints weight = 21441.603| |-----------------------------------------------------------------------------| r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17688 Z= 0.232 Angle : 0.527 4.874 24060 Z= 0.268 Chirality : 0.040 0.161 2850 Planarity : 0.004 0.048 2904 Dihedral : 15.219 179.952 3048 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.58 % Allowed : 10.24 % Favored : 89.17 % 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: 2.40 (0.19), residues: 2040 helix: 3.10 (0.14), residues: 1326 sheet: -0.23 (0.49), residues: 120 loop : -1.76 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 277 HIS 0.005 0.001 HIS J 75 PHE 0.011 0.001 PHE G 205 TYR 0.014 0.001 TYR E 218 ARG 0.003 0.000 ARG I 278 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5853.25 seconds wall clock time: 104 minutes 53.59 seconds (6293.59 seconds total)