Starting phenix.real_space_refine on Tue Feb 20 20:42:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jm7_22389/02_2024/7jm7_22389_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jm7_22389/02_2024/7jm7_22389.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jm7_22389/02_2024/7jm7_22389_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jm7_22389/02_2024/7jm7_22389_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jm7_22389/02_2024/7jm7_22389_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jm7_22389/02_2024/7jm7_22389.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jm7_22389/02_2024/7jm7_22389.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jm7_22389/02_2024/7jm7_22389_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jm7_22389/02_2024/7jm7_22389_trim_updated.pdb" } resolution = 2.82 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= -0.001 sd= 1.144 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: 8 Type Number sf(0) Gaussians P 10 5.49 5 Mg 2 5.21 5 S 90 5.16 5 Cl 6 4.86 5 C 9322 2.51 5 N 2376 2.21 5 O 2736 1.98 5 H 14054 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 107": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 144": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 201": "OE1" <-> "OE2" Residue "B GLU 249": "OE1" <-> "OE2" Residue "B ARG 271": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 95": "OE1" <-> "OE2" Residue "A ASP 100": "OD1" <-> "OD2" Residue "A ARG 113": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 126": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A ARG 271": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 281": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 374": "OE1" <-> "OE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 405": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 498": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 595": "OD1" <-> "OD2" Residue "A PHE 661": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 710": "OD1" <-> "OD2" Residue "A ARG 717": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 731": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 740": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 756": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 761": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 762": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 767": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 773": "OD1" <-> "OD2" Residue "D PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 107": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 144": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 181": "OE1" <-> "OE2" Residue "D PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 201": "OE1" <-> "OE2" Residue "D GLU 249": "OE1" <-> "OE2" Residue "D ARG 271": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 95": "OE1" <-> "OE2" Residue "C ASP 100": "OD1" <-> "OD2" Residue "C ARG 113": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 126": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 198": "OE1" <-> "OE2" Residue "C ARG 271": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 281": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 374": "OE1" <-> "OE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 405": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 459": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 498": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 595": "OD1" <-> "OD2" Residue "C PHE 661": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 710": "OD1" <-> "OD2" Residue "C ARG 717": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 731": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 740": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 756": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 761": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 762": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 767": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 773": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28596 Number of models: 1 Model: "" Number of chains: 16 Chain: "B" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3352 Classifications: {'peptide': 218} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 207} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 10675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 10675 Classifications: {'peptide': 683} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 654} Chain breaks: 3 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3352 Classifications: {'peptide': 218} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 207} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 10675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 10675 Classifications: {'peptide': 683} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 654} Chain breaks: 3 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 80 Unusual residues: {' CL': 3, ' MG': 1, '0J1': 1, 'ATP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 80 Unusual residues: {' CL': 3, ' MG': 1, '0J1': 1, 'ATP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Time building chain proxies: 11.86, per 1000 atoms: 0.41 Number of scatterers: 28596 At special positions: 0 Unit cell: (119.877, 84.4106, 136.901, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Cl 6 17.00 S 90 16.00 P 10 15.00 Mg 2 11.99 O 2736 8.00 N 2376 7.00 C 9322 6.00 H 14054 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 112 " - pdb=" SG CYS B 171 " distance=2.03 Simple disulfide: pdb=" SG CYS B 174 " - pdb=" SG CYS B 255 " distance=2.03 Simple disulfide: pdb=" SG CYS B 199 " - pdb=" SG CYS B 224 " distance=2.03 Simple disulfide: pdb=" SG CYS B 221 " - pdb=" SG CYS B 275 " distance=2.03 Simple disulfide: pdb=" SG CYS A 438 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 112 " - pdb=" SG CYS D 171 " distance=2.03 Simple disulfide: pdb=" SG CYS D 174 " - pdb=" SG CYS D 255 " distance=2.03 Simple disulfide: pdb=" SG CYS D 199 " - pdb=" SG CYS D 224 " distance=2.03 Simple disulfide: pdb=" SG CYS D 221 " - pdb=" SG CYS D 275 " distance=2.03 Simple disulfide: pdb=" SG CYS C 438 " - pdb=" SG CYS C 454 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA H 3 " - " MAN H 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA H 3 " - " MAN H 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG B 502 " - " ASN B 128 " " NAG D 502 " - " ASN D 128 " " NAG F 1 " - " ASN B 184 " " NAG I 1 " - " ASN D 184 " Time building additional restraints: 23.05 Conformation dependent library (CDL) restraints added in 3.5 seconds 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3380 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 74 helices and 8 sheets defined 62.2% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.29 Creating SS restraints... Processing helix chain 'B' and resid 82 through 104 removed outlier: 3.971A pdb=" N GLU B 86 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU B 87 " --> pdb=" O GLU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 130 Proline residue: B 117 - end of helix Processing helix chain 'B' and resid 143 through 147 Processing helix chain 'B' and resid 154 through 169 Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 184 through 202 Processing helix chain 'B' and resid 218 through 246 removed outlier: 5.707A pdb=" N GLU B 226 " --> pdb=" O LYS B 222 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ALA B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 270 Processing helix chain 'B' and resid 282 through 309 Proline residue: B 296 - end of helix Processing helix chain 'A' and resid 105 through 115 Processing helix chain 'A' and resid 122 through 165 Processing helix chain 'A' and resid 173 through 197 Processing helix chain 'A' and resid 199 through 201 No H-bonds generated for 'chain 'A' and resid 199 through 201' Processing helix chain 'A' and resid 206 through 214 Processing helix chain 'A' and resid 224 through 239 Processing helix chain 'A' and resid 248 through 261 removed outlier: 3.937A pdb=" N HIS A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 301 Processing helix chain 'A' and resid 304 through 315 Processing helix chain 'A' and resid 321 through 346 Processing helix chain 'A' and resid 372 through 405 Proline residue: A 376 - end of helix removed outlier: 3.954A pdb=" N MET A 401 " --> pdb=" O TRP A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 434 Processing helix chain 'A' and resid 461 through 466 Processing helix chain 'A' and resid 470 through 478 Processing helix chain 'A' and resid 487 through 504 Processing helix chain 'A' and resid 514 through 535 Processing helix chain 'A' and resid 544 through 559 Processing helix chain 'A' and resid 564 through 574 Processing helix chain 'A' and resid 578 through 597 Proline residue: A 582 - end of helix removed outlier: 3.767A pdb=" N LEU A 587 " --> pdb=" O MET A 584 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR A 589 " --> pdb=" O VAL A 586 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA A 590 " --> pdb=" O LEU A 587 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS A 591 " --> pdb=" O MET A 588 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL A 593 " --> pdb=" O ALA A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 608 Processing helix chain 'A' and resid 620 through 623 removed outlier: 4.030A pdb=" N HIS A 623 " --> pdb=" O VAL A 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 620 through 623' Processing helix chain 'A' and resid 627 through 630 No H-bonds generated for 'chain 'A' and resid 627 through 630' Processing helix chain 'A' and resid 644 through 652 Processing helix chain 'A' and resid 681 through 689 Processing helix chain 'A' and resid 708 through 713 Processing helix chain 'A' and resid 728 through 732 removed outlier: 3.690A pdb=" N GLU A 732 " --> pdb=" O GLN A 728 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 728 through 732' Processing helix chain 'A' and resid 754 through 764 Processing helix chain 'A' and resid 784 through 788 Processing helix chain 'D' and resid 82 through 104 removed outlier: 3.971A pdb=" N GLU D 86 " --> pdb=" O PRO D 82 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU D 87 " --> pdb=" O GLU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 130 Proline residue: D 117 - end of helix Processing helix chain 'D' and resid 143 through 147 Processing helix chain 'D' and resid 154 through 169 Processing helix chain 'D' and resid 171 through 173 No H-bonds generated for 'chain 'D' and resid 171 through 173' Processing helix chain 'D' and resid 184 through 202 Processing helix chain 'D' and resid 218 through 246 removed outlier: 5.706A pdb=" N GLU D 226 " --> pdb=" O LYS D 222 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ALA D 227 " --> pdb=" O ASN D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 270 Processing helix chain 'D' and resid 282 through 309 Proline residue: D 296 - end of helix Processing helix chain 'C' and resid 105 through 115 Processing helix chain 'C' and resid 122 through 165 Processing helix chain 'C' and resid 173 through 197 Processing helix chain 'C' and resid 199 through 201 No H-bonds generated for 'chain 'C' and resid 199 through 201' Processing helix chain 'C' and resid 206 through 214 Processing helix chain 'C' and resid 224 through 239 Processing helix chain 'C' and resid 248 through 261 removed outlier: 3.938A pdb=" N HIS C 252 " --> pdb=" O GLY C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 301 Processing helix chain 'C' and resid 304 through 315 Processing helix chain 'C' and resid 321 through 346 Processing helix chain 'C' and resid 372 through 405 Proline residue: C 376 - end of helix removed outlier: 3.954A pdb=" N MET C 401 " --> pdb=" O TRP C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 434 Processing helix chain 'C' and resid 461 through 466 Processing helix chain 'C' and resid 470 through 478 Processing helix chain 'C' and resid 487 through 504 Processing helix chain 'C' and resid 514 through 535 Processing helix chain 'C' and resid 544 through 559 Processing helix chain 'C' and resid 564 through 574 Processing helix chain 'C' and resid 578 through 597 Proline residue: C 582 - end of helix removed outlier: 3.768A pdb=" N LEU C 587 " --> pdb=" O MET C 584 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR C 589 " --> pdb=" O VAL C 586 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA C 590 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS C 591 " --> pdb=" O MET C 588 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL C 593 " --> pdb=" O ALA C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 608 Processing helix chain 'C' and resid 620 through 623 removed outlier: 4.030A pdb=" N HIS C 623 " --> pdb=" O VAL C 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 620 through 623' Processing helix chain 'C' and resid 627 through 630 No H-bonds generated for 'chain 'C' and resid 627 through 630' Processing helix chain 'C' and resid 644 through 652 Processing helix chain 'C' and resid 681 through 689 Processing helix chain 'C' and resid 708 through 713 Processing helix chain 'C' and resid 728 through 732 removed outlier: 3.690A pdb=" N GLU C 732 " --> pdb=" O GLN C 728 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 728 through 732' Processing helix chain 'C' and resid 754 through 764 Processing helix chain 'C' and resid 784 through 788 Processing sheet with id= A, first strand: chain 'A' and resid 438 through 440 Processing sheet with id= B, first strand: chain 'A' and resid 641 through 643 removed outlier: 3.936A pdb=" N GLU A 642 " --> pdb=" O MET A 735 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 747 through 749 removed outlier: 6.666A pdb=" N VAL A 770 " --> pdb=" O VAL A 748 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 660 through 664 removed outlier: 4.126A pdb=" N GLY A 677 " --> pdb=" O VAL A 663 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 438 through 440 Processing sheet with id= F, first strand: chain 'C' and resid 641 through 643 removed outlier: 3.936A pdb=" N GLU C 642 " --> pdb=" O MET C 735 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 747 through 749 removed outlier: 6.665A pdb=" N VAL C 770 " --> pdb=" O VAL C 748 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 660 through 664 removed outlier: 4.126A pdb=" N GLY C 677 " --> pdb=" O VAL C 663 " (cutoff:3.500A) 804 hydrogen bonds defined for protein. 2190 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: 10.21 Time building geometry restraints manager: 23.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 14034 1.03 - 1.23: 33 1.23 - 1.42: 6099 1.42 - 1.62: 8556 1.62 - 1.82: 142 Bond restraints: 28864 Sorted by residual: bond pdb=" C4 ATP C 901 " pdb=" C5 ATP C 901 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 6.00e+01 bond pdb=" C4 ATP A 901 " pdb=" C5 ATP A 901 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.89e+01 bond pdb=" C5 ATP A 901 " pdb=" C6 ATP A 901 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.79e+01 bond pdb=" C5 ATP C 901 " pdb=" C6 ATP C 901 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.69e+01 bond pdb=" C5 MAN E 4 " pdb=" O5 MAN E 4 " ideal model delta sigma weight residual 1.418 1.518 -0.100 2.00e-02 2.50e+03 2.49e+01 ... (remaining 28859 not shown) Histogram of bond angle deviations from ideal: 74.18 - 89.28: 58 89.28 - 104.38: 239 104.38 - 119.48: 39763 119.48 - 134.58: 11884 134.58 - 149.68: 4 Bond angle restraints: 51948 Sorted by residual: angle pdb=" PB ATP A 901 " pdb=" O3B ATP A 901 " pdb=" PG ATP A 901 " ideal model delta sigma weight residual 139.87 121.31 18.56 1.00e+00 1.00e+00 3.45e+02 angle pdb=" PB ATP C 901 " pdb=" O3B ATP C 901 " pdb=" PG ATP C 901 " ideal model delta sigma weight residual 139.87 121.37 18.50 1.00e+00 1.00e+00 3.42e+02 angle pdb=" PA ATP C 901 " pdb=" O3A ATP C 901 " pdb=" PB ATP C 901 " ideal model delta sigma weight residual 136.83 119.92 16.91 1.00e+00 1.00e+00 2.86e+02 angle pdb=" PA ATP A 901 " pdb=" O3A ATP A 901 " pdb=" PB ATP A 901 " ideal model delta sigma weight residual 136.83 119.93 16.90 1.00e+00 1.00e+00 2.86e+02 angle pdb="HD21 ASN D 128 " pdb=" ND2 ASN D 128 " pdb="HD22 ASN D 128 " ideal model delta sigma weight residual 120.00 74.18 45.82 3.00e+00 1.11e-01 2.33e+02 ... (remaining 51943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.49: 13199 23.49 - 46.97: 600 46.97 - 70.46: 221 70.46 - 93.95: 28 93.95 - 117.43: 14 Dihedral angle restraints: 14062 sinusoidal: 7824 harmonic: 6238 Sorted by residual: dihedral pdb=" CB CYS D 112 " pdb=" SG CYS D 112 " pdb=" SG CYS D 171 " pdb=" CB CYS D 171 " ideal model delta sinusoidal sigma weight residual 93.00 174.76 -81.76 1 1.00e+01 1.00e-02 8.22e+01 dihedral pdb=" CB CYS B 112 " pdb=" SG CYS B 112 " pdb=" SG CYS B 171 " pdb=" CB CYS B 171 " ideal model delta sinusoidal sigma weight residual 93.00 174.72 -81.72 1 1.00e+01 1.00e-02 8.22e+01 dihedral pdb=" CB CYS D 174 " pdb=" SG CYS D 174 " pdb=" SG CYS D 255 " pdb=" CB CYS D 255 " ideal model delta sinusoidal sigma weight residual 93.00 172.23 -79.23 1 1.00e+01 1.00e-02 7.81e+01 ... (remaining 14059 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.996: 2398 0.996 - 1.993: 12 1.993 - 2.989: 0 2.989 - 3.986: 0 3.986 - 4.982: 2 Chirality restraints: 2412 Sorted by residual: chirality pdb=" C1 BMA E 3 " pdb=" O4 NAG E 2 " pdb=" C2 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-02 2.50e+03 7.30e+02 chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-02 2.50e+03 7.27e+02 chirality pdb=" C24 0J1 C 906 " pdb=" C22 0J1 C 906 " pdb=" C26 0J1 C 906 " pdb=" O25 0J1 C 906 " both_signs ideal model delta sigma weight residual False -2.51 2.48 -4.98 2.00e-01 2.50e+01 6.21e+02 ... (remaining 2409 not shown) Planarity restraints: 4190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 271 " -0.229 9.50e-02 1.11e+02 9.07e-02 5.94e+01 pdb=" NE ARG D 271 " 0.068 2.00e-02 2.50e+03 pdb=" CZ ARG D 271 " -0.110 2.00e-02 2.50e+03 pdb=" NH1 ARG D 271 " -0.038 2.00e-02 2.50e+03 pdb=" NH2 ARG D 271 " 0.014 2.00e-02 2.50e+03 pdb="HH11 ARG D 271 " 0.016 2.00e-02 2.50e+03 pdb="HH12 ARG D 271 " 0.052 2.00e-02 2.50e+03 pdb="HH21 ARG D 271 " 0.011 2.00e-02 2.50e+03 pdb="HH22 ARG D 271 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 271 " -0.205 9.50e-02 1.11e+02 8.11e-02 4.79e+01 pdb=" NE ARG B 271 " 0.077 2.00e-02 2.50e+03 pdb=" CZ ARG B 271 " -0.090 2.00e-02 2.50e+03 pdb=" NH1 ARG B 271 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG B 271 " 0.015 2.00e-02 2.50e+03 pdb="HH11 ARG B 271 " -0.021 2.00e-02 2.50e+03 pdb="HH12 ARG B 271 " 0.021 2.00e-02 2.50e+03 pdb="HH21 ARG B 271 " -0.034 2.00e-02 2.50e+03 pdb="HH22 ARG B 271 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 191 " -0.010 2.00e-02 2.50e+03 2.01e-02 6.07e+00 pdb=" CG ASN B 191 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN B 191 " -0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN B 191 " 0.004 2.00e-02 2.50e+03 pdb="HD21 ASN B 191 " -0.012 2.00e-02 2.50e+03 pdb="HD22 ASN B 191 " -0.002 2.00e-02 2.50e+03 ... (remaining 4187 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 1331 2.19 - 2.79: 56864 2.79 - 3.39: 80225 3.39 - 4.00: 103169 4.00 - 4.60: 163181 Nonbonded interactions: 404770 Sorted by model distance: nonbonded pdb=" O ALA C 463 " pdb=" H PHE C 467 " model vdw 1.583 1.850 nonbonded pdb=" O ALA A 463 " pdb=" H PHE A 467 " model vdw 1.583 1.850 nonbonded pdb=" O MET A 368 " pdb=" HH TYR A 579 " model vdw 1.601 1.850 nonbonded pdb=" O MET C 368 " pdb=" HH TYR C 579 " model vdw 1.602 1.850 nonbonded pdb="HH21 ARG C 640 " pdb=" OG SER C 738 " model vdw 1.626 1.850 ... (remaining 404765 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.240 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: 0.000 Extract box with map and model: 20.250 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 88.430 Find NCS groups from input model: 1.060 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: 0.000 Load rotamer database and sin/cos tables:10.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 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 : 0.005 0.100 14810 Z= 0.334 Angle : 0.820 18.562 20124 Z= 0.471 Chirality : 0.188 4.982 2412 Planarity : 0.005 0.121 2474 Dihedral : 15.474 117.433 5754 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.17 % Allowed : 0.39 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 1.63 (0.20), residues: 1774 helix: 2.14 (0.15), residues: 1138 sheet: None (None), residues: 0 loop : -0.92 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 524 HIS 0.004 0.001 HIS A 220 PHE 0.017 0.001 PHE A 273 TYR 0.010 0.001 TYR D 188 ARG 0.094 0.002 ARG D 271 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Evaluate side-chains 266 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 248 time to evaluate : 2.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 199 CYS cc_start: 0.5892 (t) cc_final: 0.5623 (t) REVERT: A 373 HIS cc_start: 0.6697 (m-70) cc_final: 0.6454 (m-70) REVERT: A 595 ASP cc_start: 0.7792 (m-30) cc_final: 0.7541 (m-30) REVERT: A 739 GLU cc_start: 0.7155 (pm20) cc_final: 0.6693 (pm20) REVERT: C 98 ASP cc_start: 0.7878 (m-30) cc_final: 0.7463 (m-30) REVERT: C 373 HIS cc_start: 0.6796 (m-70) cc_final: 0.6595 (m-70) REVERT: C 595 ASP cc_start: 0.7949 (m-30) cc_final: 0.7648 (m-30) REVERT: C 739 GLU cc_start: 0.7214 (pm20) cc_final: 0.6967 (pm20) REVERT: C 773 ASP cc_start: 0.6410 (t0) cc_final: 0.6205 (t0) outliers start: 18 outliers final: 2 residues processed: 256 average time/residue: 1.9762 time to fit residues: 575.1544 Evaluate side-chains 209 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 207 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain D residue 184 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 115 ASN ** D 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 ASN C 101 ASN C 115 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 14810 Z= 0.377 Angle : 0.754 11.310 20124 Z= 0.370 Chirality : 0.125 1.809 2412 Planarity : 0.006 0.074 2474 Dihedral : 12.960 89.506 2588 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.17 % Allowed : 7.24 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 1.13 (0.19), residues: 1774 helix: 1.73 (0.15), residues: 1142 sheet: None (None), residues: 0 loop : -1.11 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 524 HIS 0.006 0.001 HIS C 220 PHE 0.019 0.002 PHE A 392 TYR 0.017 0.002 TYR A 505 ARG 0.010 0.001 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Evaluate side-chains 255 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 237 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 HIS cc_start: 0.6869 (m-70) cc_final: 0.6643 (m-70) REVERT: A 379 ILE cc_start: 0.8057 (mt) cc_final: 0.7833 (mm) REVERT: A 595 ASP cc_start: 0.7943 (m-30) cc_final: 0.7639 (m-30) REVERT: A 678 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8610 (tt) REVERT: A 739 GLU cc_start: 0.7687 (pm20) cc_final: 0.7116 (pm20) REVERT: A 751 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7027 (mp0) REVERT: C 98 ASP cc_start: 0.8067 (m-30) cc_final: 0.7632 (m-30) REVERT: C 373 HIS cc_start: 0.6854 (m-70) cc_final: 0.6632 (m-70) REVERT: C 595 ASP cc_start: 0.8105 (m-30) cc_final: 0.7722 (m-30) REVERT: C 739 GLU cc_start: 0.7635 (pm20) cc_final: 0.7366 (pm20) outliers start: 18 outliers final: 10 residues processed: 248 average time/residue: 2.0869 time to fit residues: 585.4599 Evaluate side-chains 228 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 217 time to evaluate : 2.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain D residue 101 CYS Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 776 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 174 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14810 Z= 0.197 Angle : 0.630 11.221 20124 Z= 0.308 Chirality : 0.120 1.722 2412 Planarity : 0.004 0.039 2474 Dihedral : 11.592 85.225 2586 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.30 % Allowed : 8.93 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 1.46 (0.20), residues: 1774 helix: 1.98 (0.15), residues: 1148 sheet: None (None), residues: 0 loop : -1.01 (0.23), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 524 HIS 0.005 0.001 HIS C 220 PHE 0.011 0.001 PHE D 193 TYR 0.011 0.001 TYR B 116 ARG 0.005 0.000 ARG D 271 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Evaluate side-chains 240 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 220 time to evaluate : 2.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 MET cc_start: 0.8517 (mmm) cc_final: 0.8300 (mmt) REVERT: A 373 HIS cc_start: 0.6838 (m-70) cc_final: 0.6618 (m-70) REVERT: A 379 ILE cc_start: 0.8054 (mt) cc_final: 0.7847 (mm) REVERT: A 678 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8587 (tt) REVERT: A 739 GLU cc_start: 0.7702 (pm20) cc_final: 0.7262 (pm20) REVERT: A 751 GLU cc_start: 0.7363 (mm-30) cc_final: 0.6984 (mp0) REVERT: D 262 MET cc_start: 0.7914 (tpt) cc_final: 0.7568 (tpt) REVERT: C 373 HIS cc_start: 0.6838 (m-70) cc_final: 0.6624 (m-70) REVERT: C 739 GLU cc_start: 0.7643 (pm20) cc_final: 0.7394 (pm20) outliers start: 20 outliers final: 13 residues processed: 229 average time/residue: 2.0936 time to fit residues: 543.6576 Evaluate side-chains 227 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 213 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 101 CYS Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 171 CYS Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 776 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 14810 Z= 0.423 Angle : 0.745 11.470 20124 Z= 0.373 Chirality : 0.124 1.770 2412 Planarity : 0.005 0.046 2474 Dihedral : 11.282 91.669 2586 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.02 % Allowed : 9.91 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.19), residues: 1774 helix: 1.45 (0.15), residues: 1140 sheet: -1.98 (1.32), residues: 10 loop : -1.49 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 319 HIS 0.006 0.001 HIS C 220 PHE 0.023 0.002 PHE A 392 TYR 0.019 0.002 TYR A 505 ARG 0.004 0.001 ARG B 144 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Evaluate side-chains 265 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 234 time to evaluate : 2.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 168 GLU cc_start: 0.7315 (tm-30) cc_final: 0.7027 (tm-30) REVERT: A 238 VAL cc_start: 0.8430 (OUTLIER) cc_final: 0.8202 (t) REVERT: A 373 HIS cc_start: 0.6859 (m-70) cc_final: 0.6630 (m-70) REVERT: A 379 ILE cc_start: 0.8153 (mt) cc_final: 0.7929 (mm) REVERT: A 446 MET cc_start: 0.6891 (mpp) cc_final: 0.6657 (mtm) REVERT: A 678 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8646 (tt) REVERT: A 739 GLU cc_start: 0.7797 (pm20) cc_final: 0.7360 (pm20) REVERT: A 751 GLU cc_start: 0.7421 (mm-30) cc_final: 0.7071 (mp0) REVERT: D 170 ASN cc_start: 0.7970 (t0) cc_final: 0.7668 (t0) REVERT: C 238 VAL cc_start: 0.8449 (OUTLIER) cc_final: 0.8229 (t) REVERT: C 373 HIS cc_start: 0.6906 (m-70) cc_final: 0.6686 (m-70) REVERT: C 379 ILE cc_start: 0.8119 (mt) cc_final: 0.7891 (mm) REVERT: C 595 ASP cc_start: 0.8059 (m-30) cc_final: 0.7711 (m-30) REVERT: C 739 GLU cc_start: 0.7682 (pm20) cc_final: 0.7441 (pm20) outliers start: 31 outliers final: 23 residues processed: 251 average time/residue: 2.3082 time to fit residues: 649.9032 Evaluate side-chains 250 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 224 time to evaluate : 2.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 CYS Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 101 CYS Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 682 SER Chi-restraints excluded: chain C residue 776 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14810 Z= 0.251 Angle : 0.652 11.469 20124 Z= 0.322 Chirality : 0.121 1.738 2412 Planarity : 0.005 0.044 2474 Dihedral : 10.821 88.026 2586 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.69 % Allowed : 11.93 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 0.94 (0.20), residues: 1774 helix: 1.68 (0.15), residues: 1140 sheet: -2.03 (1.32), residues: 10 loop : -1.37 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 524 HIS 0.005 0.001 HIS C 220 PHE 0.013 0.001 PHE A 392 TYR 0.012 0.001 TYR B 116 ARG 0.002 0.000 ARG C 681 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Evaluate side-chains 252 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 226 time to evaluate : 2.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLN cc_start: 0.8610 (mp10) cc_final: 0.8362 (mp10) REVERT: A 238 VAL cc_start: 0.8416 (OUTLIER) cc_final: 0.8194 (t) REVERT: A 373 HIS cc_start: 0.6841 (m-70) cc_final: 0.6621 (m-70) REVERT: A 379 ILE cc_start: 0.8090 (mt) cc_final: 0.7869 (mm) REVERT: A 446 MET cc_start: 0.6826 (OUTLIER) cc_final: 0.6580 (mtm) REVERT: A 607 GLN cc_start: 0.7522 (mt0) cc_final: 0.7239 (mt0) REVERT: A 678 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8593 (tt) REVERT: A 739 GLU cc_start: 0.7712 (pm20) cc_final: 0.7269 (pm20) REVERT: A 751 GLU cc_start: 0.7346 (mm-30) cc_final: 0.6997 (mp0) REVERT: D 148 MET cc_start: 0.6963 (ptt) cc_final: 0.6738 (ptt) REVERT: C 238 VAL cc_start: 0.8429 (OUTLIER) cc_final: 0.8213 (t) REVERT: C 373 HIS cc_start: 0.6893 (m-70) cc_final: 0.6666 (m-70) REVERT: C 379 ILE cc_start: 0.8038 (mt) cc_final: 0.7818 (mm) REVERT: C 739 GLU cc_start: 0.7638 (pm20) cc_final: 0.7409 (pm20) outliers start: 26 outliers final: 16 residues processed: 235 average time/residue: 2.3626 time to fit residues: 621.0947 Evaluate side-chains 245 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 225 time to evaluate : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 CYS Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 101 CYS Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 735 MET Chi-restraints excluded: chain C residue 776 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 172 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 56 optimal weight: 0.0570 chunk 90 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 ASN C 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14810 Z= 0.246 Angle : 0.638 11.608 20124 Z= 0.315 Chirality : 0.121 1.740 2412 Planarity : 0.005 0.043 2474 Dihedral : 10.557 89.600 2586 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.15 % Allowed : 12.39 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 1.11 (0.20), residues: 1774 helix: 1.82 (0.15), residues: 1142 sheet: -2.10 (1.31), residues: 10 loop : -1.34 (0.23), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 524 HIS 0.005 0.001 HIS C 220 PHE 0.013 0.001 PHE A 392 TYR 0.011 0.001 TYR B 116 ARG 0.002 0.000 ARG B 144 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Evaluate side-chains 264 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 231 time to evaluate : 2.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLN cc_start: 0.8623 (mp10) cc_final: 0.8296 (mp10) REVERT: A 373 HIS cc_start: 0.6896 (m-70) cc_final: 0.6677 (m-70) REVERT: A 379 ILE cc_start: 0.8079 (mt) cc_final: 0.7847 (mm) REVERT: A 607 GLN cc_start: 0.7472 (mt0) cc_final: 0.7156 (mt0) REVERT: A 678 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8586 (tt) REVERT: A 739 GLU cc_start: 0.7741 (pm20) cc_final: 0.7315 (pm20) REVERT: A 751 GLU cc_start: 0.7308 (mm-30) cc_final: 0.6948 (mp0) REVERT: D 148 MET cc_start: 0.6996 (ptt) cc_final: 0.6780 (ptt) REVERT: C 238 VAL cc_start: 0.8419 (OUTLIER) cc_final: 0.8201 (t) REVERT: C 373 HIS cc_start: 0.6860 (m-70) cc_final: 0.6628 (m-70) REVERT: C 379 ILE cc_start: 0.8044 (mt) cc_final: 0.7814 (mm) REVERT: C 607 GLN cc_start: 0.7492 (mt0) cc_final: 0.7265 (mt0) REVERT: C 739 GLU cc_start: 0.7675 (pm20) cc_final: 0.7401 (pm20) outliers start: 33 outliers final: 22 residues processed: 247 average time/residue: 2.4166 time to fit residues: 667.3369 Evaluate side-chains 253 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 229 time to evaluate : 2.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 CYS Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 101 CYS Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 223 ASN Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 776 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 144 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 171 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 163 ASN C 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14810 Z= 0.193 Angle : 0.617 11.545 20124 Z= 0.303 Chirality : 0.120 1.739 2412 Planarity : 0.004 0.041 2474 Dihedral : 10.203 84.817 2586 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.69 % Allowed : 13.43 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 1774 helix: 2.02 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -1.19 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 524 HIS 0.004 0.001 HIS C 220 PHE 0.010 0.001 PHE D 193 TYR 0.010 0.001 TYR B 116 ARG 0.002 0.000 ARG C 681 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Evaluate side-chains 259 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 233 time to evaluate : 2.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.7139 (tm-30) cc_final: 0.6916 (tm-30) REVERT: A 208 GLN cc_start: 0.8605 (mp10) cc_final: 0.8278 (mp10) REVERT: A 373 HIS cc_start: 0.6843 (m-70) cc_final: 0.6623 (m-70) REVERT: A 379 ILE cc_start: 0.8072 (mt) cc_final: 0.7834 (mm) REVERT: A 446 MET cc_start: 0.6764 (mpp) cc_final: 0.6501 (ptp) REVERT: A 607 GLN cc_start: 0.7491 (mt0) cc_final: 0.7148 (mt0) REVERT: A 739 GLU cc_start: 0.7712 (pm20) cc_final: 0.7318 (pm20) REVERT: A 751 GLU cc_start: 0.7299 (mm-30) cc_final: 0.6917 (mp0) REVERT: D 148 MET cc_start: 0.6979 (ptt) cc_final: 0.6770 (ptt) REVERT: C 373 HIS cc_start: 0.6870 (m-70) cc_final: 0.6644 (m-70) REVERT: C 379 ILE cc_start: 0.8025 (mt) cc_final: 0.7791 (mm) REVERT: C 607 GLN cc_start: 0.7530 (mt0) cc_final: 0.7299 (mt0) REVERT: C 739 GLU cc_start: 0.7662 (pm20) cc_final: 0.7384 (pm20) outliers start: 26 outliers final: 23 residues processed: 246 average time/residue: 2.3388 time to fit residues: 643.4309 Evaluate side-chains 249 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 226 time to evaluate : 2.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 CYS Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 101 CYS Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 682 SER Chi-restraints excluded: chain C residue 776 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14810 Z= 0.225 Angle : 0.626 11.561 20124 Z= 0.308 Chirality : 0.121 1.744 2412 Planarity : 0.004 0.041 2474 Dihedral : 10.127 84.269 2586 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.83 % Allowed : 13.62 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 1.37 (0.20), residues: 1774 helix: 2.03 (0.15), residues: 1140 sheet: -2.09 (1.34), residues: 10 loop : -1.23 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 524 HIS 0.004 0.001 HIS C 220 PHE 0.012 0.001 PHE A 392 TYR 0.011 0.001 TYR B 116 ARG 0.002 0.000 ARG C 681 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Evaluate side-chains 259 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 231 time to evaluate : 2.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 GLN cc_start: 0.8611 (mp10) cc_final: 0.8290 (mp10) REVERT: A 379 ILE cc_start: 0.8074 (mt) cc_final: 0.7832 (mm) REVERT: A 446 MET cc_start: 0.6744 (OUTLIER) cc_final: 0.6433 (ptp) REVERT: A 607 GLN cc_start: 0.7502 (mt0) cc_final: 0.7124 (mt0) REVERT: A 739 GLU cc_start: 0.7727 (pm20) cc_final: 0.7329 (pm20) REVERT: A 751 GLU cc_start: 0.7286 (mm-30) cc_final: 0.6937 (mp0) REVERT: D 148 MET cc_start: 0.7035 (ptt) cc_final: 0.6830 (ptt) REVERT: C 373 HIS cc_start: 0.6880 (m-70) cc_final: 0.6647 (m-70) REVERT: C 607 GLN cc_start: 0.7513 (mt0) cc_final: 0.7194 (mt0) REVERT: C 739 GLU cc_start: 0.7669 (pm20) cc_final: 0.7390 (pm20) outliers start: 28 outliers final: 24 residues processed: 246 average time/residue: 2.3159 time to fit residues: 637.3442 Evaluate side-chains 251 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 226 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 CYS Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 101 CYS Chi-restraints excluded: chain D residue 144 ARG Chi-restraints excluded: chain D residue 184 ASN Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 682 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 0.9990 chunk 159 optimal weight: 0.5980 chunk 164 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 49 optimal weight: 0.0770 chunk 144 optimal weight: 0.8980 chunk 151 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 HIS C 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14810 Z= 0.167 Angle : 0.607 11.635 20124 Z= 0.296 Chirality : 0.120 1.741 2412 Planarity : 0.004 0.040 2474 Dihedral : 9.742 81.643 2586 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.17 % Allowed : 14.67 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 1.68 (0.20), residues: 1774 helix: 2.24 (0.15), residues: 1136 sheet: None (None), residues: 0 loop : -1.04 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 524 HIS 0.005 0.001 HIS A 373 PHE 0.009 0.001 PHE D 193 TYR 0.009 0.001 TYR B 116 ARG 0.002 0.000 ARG C 681 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Evaluate side-chains 247 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 229 time to evaluate : 2.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.7144 (tm-30) cc_final: 0.6854 (tm-30) REVERT: A 208 GLN cc_start: 0.8589 (mp10) cc_final: 0.8270 (mp10) REVERT: A 379 ILE cc_start: 0.8014 (mt) cc_final: 0.7778 (mm) REVERT: A 446 MET cc_start: 0.6703 (mpp) cc_final: 0.6441 (ptp) REVERT: A 607 GLN cc_start: 0.7447 (mt0) cc_final: 0.7086 (mt0) REVERT: A 739 GLU cc_start: 0.7703 (pm20) cc_final: 0.7296 (pm20) REVERT: A 751 GLU cc_start: 0.7283 (mm-30) cc_final: 0.6910 (mp0) REVERT: C 373 HIS cc_start: 0.6850 (m-70) cc_final: 0.6623 (m-70) REVERT: C 607 GLN cc_start: 0.7481 (mt0) cc_final: 0.7161 (mt0) REVERT: C 739 GLU cc_start: 0.7656 (pm20) cc_final: 0.7390 (pm20) outliers start: 18 outliers final: 17 residues processed: 238 average time/residue: 2.4241 time to fit residues: 655.5774 Evaluate side-chains 243 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 226 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 682 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 177 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 109 optimal weight: 0.0970 chunk 86 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 HIS C 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14810 Z= 0.237 Angle : 0.628 11.568 20124 Z= 0.309 Chirality : 0.121 1.748 2412 Planarity : 0.004 0.041 2474 Dihedral : 9.883 83.747 2584 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.17 % Allowed : 14.60 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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: 1.57 (0.20), residues: 1774 helix: 2.16 (0.15), residues: 1136 sheet: None (None), residues: 0 loop : -1.08 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 524 HIS 0.004 0.001 HIS A 373 PHE 0.013 0.001 PHE A 392 TYR 0.011 0.001 TYR B 116 ARG 0.002 0.000 ARG C 681 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3548 Ramachandran restraints generated. 1774 Oldfield, 0 Emsley, 1774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Residue TYR 217 is missing expected H atoms. Skipping. Residue LEU 352 is missing expected H atoms. Skipping. Evaluate side-chains 250 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 232 time to evaluate : 2.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.7181 (tm-30) cc_final: 0.6904 (tm-30) REVERT: A 208 GLN cc_start: 0.8615 (mp10) cc_final: 0.8293 (mp10) REVERT: A 446 MET cc_start: 0.6737 (mpp) cc_final: 0.6464 (ptp) REVERT: A 739 GLU cc_start: 0.7729 (pm20) cc_final: 0.7306 (pm20) REVERT: A 751 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6941 (mp0) REVERT: C 373 HIS cc_start: 0.6868 (m-70) cc_final: 0.6637 (m-70) REVERT: C 607 GLN cc_start: 0.7503 (mt0) cc_final: 0.7179 (mt0) REVERT: C 739 GLU cc_start: 0.7673 (pm20) cc_final: 0.7383 (pm20) outliers start: 18 outliers final: 17 residues processed: 241 average time/residue: 2.3159 time to fit residues: 624.1088 Evaluate side-chains 245 residues out of total 1556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 228 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 682 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 145 optimal weight: 0.3980 chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 8 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: A 373 HIS C 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.175026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.146622 restraints weight = 42164.368| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 1.92 r_work: 0.3596 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14810 Z= 0.241 Angle : 0.633 11.536 20124 Z= 0.312 Chirality : 0.121 1.749 2412 Planarity : 0.005 0.041 2474 Dihedral : 9.893 84.192 2584 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.37 % Allowed : 14.47 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.20), residues: 1774 helix: 2.10 (0.15), residues: 1136 sheet: -2.04 (1.36), residues: 10 loop : -1.12 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 524 HIS 0.004 0.001 HIS C 220 PHE 0.013 0.001 PHE A 392 TYR 0.013 0.001 TYR C 448 ARG 0.003 0.000 ARG B 144 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10622.75 seconds wall clock time: 187 minutes 26.44 seconds (11246.44 seconds total)