Starting phenix.real_space_refine on Sat Mar 16 19:59:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plh_13489/03_2024/7plh_13489_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plh_13489/03_2024/7plh_13489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plh_13489/03_2024/7plh_13489.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plh_13489/03_2024/7plh_13489.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plh_13489/03_2024/7plh_13489_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7plh_13489/03_2024/7plh_13489_neut_updated.pdb" } resolution = 3.57 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 65 5.49 5 Mg 7 5.21 5 S 56 5.16 5 C 9594 2.51 5 N 2835 2.21 5 O 2985 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 19": "OE1" <-> "OE2" Residue "A ARG 27": "NH1" <-> "NH2" Residue "A ASP 47": "OD1" <-> "OD2" Residue "A ARG 57": "NH1" <-> "NH2" Residue "A TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 85": "NH1" <-> "NH2" Residue "A TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 147": "OD1" <-> "OD2" Residue "A GLU 152": "OE1" <-> "OE2" Residue "A ASP 163": "OD1" <-> "OD2" Residue "A PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 202": "OE1" <-> "OE2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "A TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 19": "OE1" <-> "OE2" Residue "B ARG 27": "NH1" <-> "NH2" Residue "B ASP 47": "OD1" <-> "OD2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 85": "NH1" <-> "NH2" Residue "B TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 147": "OD1" <-> "OD2" Residue "B GLU 152": "OE1" <-> "OE2" Residue "B ASP 163": "OD1" <-> "OD2" Residue "B PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 202": "OE1" <-> "OE2" Residue "B GLU 212": "OE1" <-> "OE2" Residue "B TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 246": "OE1" <-> "OE2" Residue "B TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 19": "OE1" <-> "OE2" Residue "C ARG 27": "NH1" <-> "NH2" Residue "C ASP 47": "OD1" <-> "OD2" Residue "C ARG 57": "NH1" <-> "NH2" Residue "C TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 85": "NH1" <-> "NH2" Residue "C TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 147": "OD1" <-> "OD2" Residue "C GLU 152": "OE1" <-> "OE2" Residue "C ASP 163": "OD1" <-> "OD2" Residue "C PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 202": "OE1" <-> "OE2" Residue "C GLU 212": "OE1" <-> "OE2" Residue "C TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 246": "OE1" <-> "OE2" Residue "C TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 19": "OE1" <-> "OE2" Residue "D ARG 27": "NH1" <-> "NH2" Residue "D ASP 47": "OD1" <-> "OD2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 85": "NH1" <-> "NH2" Residue "D TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 147": "OD1" <-> "OD2" Residue "D GLU 152": "OE1" <-> "OE2" Residue "D ASP 163": "OD1" <-> "OD2" Residue "D PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 202": "OE1" <-> "OE2" Residue "D GLU 212": "OE1" <-> "OE2" Residue "D TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 246": "OE1" <-> "OE2" Residue "D TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 19": "OE1" <-> "OE2" Residue "E ARG 27": "NH1" <-> "NH2" Residue "E ASP 47": "OD1" <-> "OD2" Residue "E ARG 57": "NH1" <-> "NH2" Residue "E TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 85": "NH1" <-> "NH2" Residue "E TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 147": "OD1" <-> "OD2" Residue "E GLU 152": "OE1" <-> "OE2" Residue "E ASP 163": "OD1" <-> "OD2" Residue "E PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 202": "OE1" <-> "OE2" Residue "E GLU 212": "OE1" <-> "OE2" Residue "E TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 246": "OE1" <-> "OE2" Residue "E TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 19": "OE1" <-> "OE2" Residue "F ARG 27": "NH1" <-> "NH2" Residue "F ASP 47": "OD1" <-> "OD2" Residue "F ARG 57": "NH1" <-> "NH2" Residue "F TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 85": "NH1" <-> "NH2" Residue "F TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 147": "OD1" <-> "OD2" Residue "F GLU 152": "OE1" <-> "OE2" Residue "F ASP 163": "OD1" <-> "OD2" Residue "F PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 202": "OE1" <-> "OE2" Residue "F GLU 212": "OE1" <-> "OE2" Residue "F TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 246": "OE1" <-> "OE2" Residue "F TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 19": "OE1" <-> "OE2" Residue "G ARG 27": "NH1" <-> "NH2" Residue "G ASP 47": "OD1" <-> "OD2" Residue "G ARG 57": "NH1" <-> "NH2" Residue "G TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 85": "NH1" <-> "NH2" Residue "G TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 147": "OD1" <-> "OD2" Residue "G GLU 152": "OE1" <-> "OE2" Residue "G ASP 163": "OD1" <-> "OD2" Residue "G PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 202": "OE1" <-> "OE2" Residue "G GLU 212": "OE1" <-> "OE2" Residue "G TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 246": "OE1" <-> "OE2" Residue "G TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15542 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 2056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2056 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 451 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "I" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 451 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.63, per 1000 atoms: 0.56 Number of scatterers: 15542 At special positions: 0 Unit cell: (128.05, 139.1, 115.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 65 15.00 Mg 7 11.99 O 2985 8.00 N 2835 7.00 C 9594 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.28 Conformation dependent library (CDL) restraints added in 2.6 seconds 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3416 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 84 helices and 7 sheets defined 53.8% alpha, 5.0% beta 16 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 6.40 Creating SS restraints... Processing helix chain 'A' and resid 18 through 29 Processing helix chain 'A' and resid 37 through 51 Processing helix chain 'A' and resid 66 through 76 Processing helix chain 'A' and resid 102 through 112 Processing helix chain 'A' and resid 122 through 135 Processing helix chain 'A' and resid 151 through 164 removed outlier: 4.137A pdb=" N ALA A 155 " --> pdb=" O PRO A 151 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 181 Processing helix chain 'A' and resid 185 through 189 Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 227 through 237 Processing helix chain 'A' and resid 241 through 257 removed outlier: 3.865A pdb=" N GLU A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 273 Processing helix chain 'B' and resid 18 through 29 Processing helix chain 'B' and resid 37 through 51 Processing helix chain 'B' and resid 66 through 76 Processing helix chain 'B' and resid 102 through 112 Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 151 through 164 removed outlier: 4.138A pdb=" N ALA B 155 " --> pdb=" O PRO B 151 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 181 Processing helix chain 'B' and resid 185 through 189 Processing helix chain 'B' and resid 202 through 214 Processing helix chain 'B' and resid 227 through 237 Processing helix chain 'B' and resid 241 through 257 Processing helix chain 'B' and resid 265 through 273 Processing helix chain 'C' and resid 18 through 29 Processing helix chain 'C' and resid 37 through 51 Processing helix chain 'C' and resid 66 through 76 Processing helix chain 'C' and resid 102 through 112 Processing helix chain 'C' and resid 122 through 135 Processing helix chain 'C' and resid 151 through 164 removed outlier: 4.139A pdb=" N ALA C 155 " --> pdb=" O PRO C 151 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP C 156 " --> pdb=" O GLU C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 181 Processing helix chain 'C' and resid 185 through 189 Processing helix chain 'C' and resid 202 through 214 Processing helix chain 'C' and resid 227 through 237 Processing helix chain 'C' and resid 241 through 257 Processing helix chain 'C' and resid 265 through 273 Processing helix chain 'D' and resid 18 through 29 Processing helix chain 'D' and resid 37 through 51 Processing helix chain 'D' and resid 66 through 76 Processing helix chain 'D' and resid 102 through 112 Processing helix chain 'D' and resid 122 through 135 Processing helix chain 'D' and resid 151 through 164 removed outlier: 4.140A pdb=" N ALA D 155 " --> pdb=" O PRO D 151 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP D 156 " --> pdb=" O GLU D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 181 Processing helix chain 'D' and resid 185 through 189 Processing helix chain 'D' and resid 202 through 214 Processing helix chain 'D' and resid 227 through 237 Processing helix chain 'D' and resid 241 through 257 Processing helix chain 'D' and resid 265 through 273 Processing helix chain 'E' and resid 18 through 29 Processing helix chain 'E' and resid 37 through 51 Processing helix chain 'E' and resid 66 through 76 Processing helix chain 'E' and resid 102 through 112 Processing helix chain 'E' and resid 122 through 135 Processing helix chain 'E' and resid 151 through 164 removed outlier: 4.138A pdb=" N ALA E 155 " --> pdb=" O PRO E 151 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ASP E 156 " --> pdb=" O GLU E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 181 Processing helix chain 'E' and resid 185 through 189 Processing helix chain 'E' and resid 202 through 214 Processing helix chain 'E' and resid 227 through 237 Processing helix chain 'E' and resid 241 through 257 Processing helix chain 'E' and resid 265 through 273 Processing helix chain 'F' and resid 18 through 29 Processing helix chain 'F' and resid 37 through 51 Processing helix chain 'F' and resid 66 through 76 Processing helix chain 'F' and resid 102 through 112 Processing helix chain 'F' and resid 122 through 135 Processing helix chain 'F' and resid 151 through 164 removed outlier: 4.138A pdb=" N ALA F 155 " --> pdb=" O PRO F 151 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP F 156 " --> pdb=" O GLU F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 181 Processing helix chain 'F' and resid 185 through 189 Processing helix chain 'F' and resid 202 through 214 Processing helix chain 'F' and resid 227 through 237 Processing helix chain 'F' and resid 241 through 257 Processing helix chain 'F' and resid 265 through 273 Processing helix chain 'G' and resid 18 through 29 Processing helix chain 'G' and resid 37 through 51 Processing helix chain 'G' and resid 66 through 76 Processing helix chain 'G' and resid 102 through 112 Processing helix chain 'G' and resid 122 through 135 Processing helix chain 'G' and resid 151 through 164 removed outlier: 4.137A pdb=" N ALA G 155 " --> pdb=" O PRO G 151 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP G 156 " --> pdb=" O GLU G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 181 Processing helix chain 'G' and resid 185 through 189 Processing helix chain 'G' and resid 202 through 214 Processing helix chain 'G' and resid 227 through 237 Processing helix chain 'G' and resid 241 through 257 Processing helix chain 'G' and resid 265 through 273 Processing sheet with id= A, first strand: chain 'A' and resid 57 through 59 removed outlier: 7.311A pdb=" N VAL A 58 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU A 170 " --> pdb=" O VAL A 58 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 57 through 59 removed outlier: 7.310A pdb=" N VAL B 58 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU B 170 " --> pdb=" O VAL B 58 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 57 through 59 removed outlier: 7.309A pdb=" N VAL C 58 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU C 170 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 57 through 59 removed outlier: 7.310A pdb=" N VAL D 58 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU D 170 " --> pdb=" O VAL D 58 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 57 through 59 removed outlier: 7.311A pdb=" N VAL E 58 " --> pdb=" O VAL E 168 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU E 170 " --> pdb=" O VAL E 58 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 57 through 59 removed outlier: 7.311A pdb=" N VAL F 58 " --> pdb=" O VAL F 168 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU F 170 " --> pdb=" O VAL F 58 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 57 through 59 removed outlier: 7.311A pdb=" N VAL G 58 " --> pdb=" O VAL G 168 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU G 170 " --> pdb=" O VAL G 58 " (cutoff:3.500A) 685 hydrogen bonds defined for protein. 1950 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 4.57 Time building geometry restraints manager: 6.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2492 1.30 - 1.42: 3898 1.42 - 1.55: 9226 1.55 - 1.68: 160 1.68 - 1.80: 91 Bond restraints: 15867 Sorted by residual: bond pdb=" O3A ANP A 301 " pdb=" PB ANP A 301 " ideal model delta sigma weight residual 1.700 1.542 0.158 2.00e-02 2.50e+03 6.22e+01 bond pdb=" O3A ANP F 301 " pdb=" PB ANP F 301 " ideal model delta sigma weight residual 1.700 1.542 0.158 2.00e-02 2.50e+03 6.22e+01 bond pdb=" O3A ANP G 301 " pdb=" PB ANP G 301 " ideal model delta sigma weight residual 1.700 1.543 0.157 2.00e-02 2.50e+03 6.20e+01 bond pdb=" O3A ANP E 301 " pdb=" PB ANP E 301 " ideal model delta sigma weight residual 1.700 1.543 0.157 2.00e-02 2.50e+03 6.20e+01 bond pdb=" O3A ANP D 301 " pdb=" PB ANP D 301 " ideal model delta sigma weight residual 1.700 1.543 0.157 2.00e-02 2.50e+03 6.18e+01 ... (remaining 15862 not shown) Histogram of bond angle deviations from ideal: 96.51 - 104.00: 432 104.00 - 111.49: 6991 111.49 - 118.98: 6520 118.98 - 126.46: 7314 126.46 - 133.95: 340 Bond angle restraints: 21597 Sorted by residual: angle pdb=" O3' DA H 13 " pdb=" C3' DA H 13 " pdb=" C2' DA H 13 " ideal model delta sigma weight residual 111.50 96.51 14.99 1.50e+00 4.44e-01 9.99e+01 angle pdb=" N LEU E 244 " pdb=" CA LEU E 244 " pdb=" C LEU E 244 " ideal model delta sigma weight residual 111.14 100.41 10.73 1.08e+00 8.57e-01 9.87e+01 angle pdb=" N PHE F 204 " pdb=" CA PHE F 204 " pdb=" C PHE F 204 " ideal model delta sigma weight residual 111.36 101.95 9.41 1.09e+00 8.42e-01 7.46e+01 angle pdb=" N PHE B 204 " pdb=" CA PHE B 204 " pdb=" C PHE B 204 " ideal model delta sigma weight residual 111.36 101.96 9.40 1.09e+00 8.42e-01 7.43e+01 angle pdb=" N LEU B 244 " pdb=" CA LEU B 244 " pdb=" C LEU B 244 " ideal model delta sigma weight residual 111.69 101.09 10.60 1.23e+00 6.61e-01 7.43e+01 ... (remaining 21592 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.16: 8455 24.16 - 48.33: 919 48.33 - 72.49: 383 72.49 - 96.66: 72 96.66 - 120.82: 7 Dihedral angle restraints: 9836 sinusoidal: 4558 harmonic: 5278 Sorted by residual: dihedral pdb=" C ARG C 76 " pdb=" N ARG C 76 " pdb=" CA ARG C 76 " pdb=" CB ARG C 76 " ideal model delta harmonic sigma weight residual -122.60 -109.39 -13.21 0 2.50e+00 1.60e-01 2.79e+01 dihedral pdb=" C ARG F 76 " pdb=" N ARG F 76 " pdb=" CA ARG F 76 " pdb=" CB ARG F 76 " ideal model delta harmonic sigma weight residual -122.60 -109.42 -13.18 0 2.50e+00 1.60e-01 2.78e+01 dihedral pdb=" C ARG G 76 " pdb=" N ARG G 76 " pdb=" CA ARG G 76 " pdb=" CB ARG G 76 " ideal model delta harmonic sigma weight residual -122.60 -109.43 -13.17 0 2.50e+00 1.60e-01 2.78e+01 ... (remaining 9833 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1919 0.103 - 0.205: 357 0.205 - 0.308: 120 0.308 - 0.410: 19 0.410 - 0.513: 15 Chirality restraints: 2430 Sorted by residual: chirality pdb=" CA ARG F 76 " pdb=" N ARG F 76 " pdb=" C ARG F 76 " pdb=" CB ARG F 76 " both_signs ideal model delta sigma weight residual False 2.51 3.02 -0.51 2.00e-01 2.50e+01 6.58e+00 chirality pdb=" CA ARG D 76 " pdb=" N ARG D 76 " pdb=" C ARG D 76 " pdb=" CB ARG D 76 " both_signs ideal model delta sigma weight residual False 2.51 3.02 -0.51 2.00e-01 2.50e+01 6.55e+00 chirality pdb=" CA ARG B 76 " pdb=" N ARG B 76 " pdb=" C ARG B 76 " pdb=" CB ARG B 76 " both_signs ideal model delta sigma weight residual False 2.51 3.02 -0.51 2.00e-01 2.50e+01 6.51e+00 ... (remaining 2427 not shown) Planarity restraints: 2577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 241 " 0.027 2.00e-02 2.50e+03 5.38e-02 2.89e+01 pdb=" C ILE A 241 " -0.093 2.00e-02 2.50e+03 pdb=" O ILE A 241 " 0.035 2.00e-02 2.50e+03 pdb=" N GLY A 242 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 242 " -0.026 2.00e-02 2.50e+03 5.14e-02 2.64e+01 pdb=" C GLY C 242 " 0.089 2.00e-02 2.50e+03 pdb=" O GLY C 242 " -0.034 2.00e-02 2.50e+03 pdb=" N ARG C 243 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 242 " 0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C GLY F 242 " -0.060 2.00e-02 2.50e+03 pdb=" O GLY F 242 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG F 243 " 0.020 2.00e-02 2.50e+03 ... (remaining 2574 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 121 2.50 - 3.10: 11537 3.10 - 3.70: 24473 3.70 - 4.30: 34833 4.30 - 4.90: 55989 Nonbonded interactions: 126953 Sorted by model distance: nonbonded pdb=" O1B ANP A 301 " pdb="MG MG A 302 " model vdw 1.901 2.170 nonbonded pdb=" O1B ANP B 301 " pdb="MG MG B 302 " model vdw 1.901 2.170 nonbonded pdb=" O1B ANP D 301 " pdb="MG MG D 302 " model vdw 1.901 2.170 nonbonded pdb=" O1B ANP F 301 " pdb="MG MG F 302 " model vdw 1.901 2.170 nonbonded pdb=" O1B ANP G 301 " pdb="MG MG G 302 " model vdw 1.902 2.170 ... (remaining 126948 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 17 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 276 or resid 301 through 302)) selection = (chain 'B' and (resid 17 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 276 or resid 301 through 302)) selection = (chain 'C' and (resid 17 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 276 or resid 301 through 302)) selection = (chain 'D' and (resid 17 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 276 or resid 301 through 302)) selection = (chain 'E' and (resid 17 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 276 or resid 301 through 302)) selection = chain 'F' selection = (chain 'G' and (resid 17 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 276 or resid 301 through 302)) } ncs_group { reference = chain 'H' selection = chain 'I' } 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: 2.990 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: 0.020 Extract box with map and model: 9.810 Check model and map are aligned: 0.230 Set scattering table: 0.160 Process input model: 47.190 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.120 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 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 : 0.011 0.158 15867 Z= 0.691 Angle : 1.667 24.221 21597 Z= 1.103 Chirality : 0.101 0.513 2430 Planarity : 0.006 0.054 2577 Dihedral : 22.702 120.821 6420 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 8.98 % Allowed : 12.10 % Favored : 78.92 % Cbeta Deviations : 0.82 % Peptide Plane: Cis-proline : 0.00 % 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: -2.29 (0.18), residues: 1806 helix: -0.98 (0.14), residues: 1078 sheet: -1.95 (0.49), residues: 119 loop : -2.19 (0.22), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP G 45 HIS 0.004 0.002 HIS F 43 PHE 0.017 0.002 PHE B 196 TYR 0.012 0.002 TYR D 275 ARG 0.025 0.001 ARG A 57 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 611 time to evaluate : 1.891 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: A 206 ASN cc_start: 0.8134 (m-40) cc_final: 0.7846 (m-40) REVERT: A 234 THR cc_start: 0.9384 (m) cc_final: 0.9021 (p) REVERT: B 209 GLU cc_start: 0.7632 (tp30) cc_final: 0.6917 (tp30) REVERT: C 32 SER cc_start: 0.8442 (t) cc_final: 0.8231 (t) REVERT: C 260 LEU cc_start: 0.6918 (mp) cc_final: 0.6376 (tp) REVERT: D 250 GLU cc_start: 0.8359 (tp30) cc_final: 0.8106 (tp30) REVERT: E 153 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8517 (t) REVERT: E 206 ASN cc_start: 0.8150 (m-40) cc_final: 0.7746 (t0) REVERT: F 163 ASP cc_start: 0.7160 (m-30) cc_final: 0.6428 (m-30) REVERT: G 63 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.5679 (mtm180) REVERT: G 234 THR cc_start: 0.8845 (m) cc_final: 0.8432 (p) REVERT: G 241 ILE cc_start: 0.8907 (mm) cc_final: 0.8696 (mp) outliers start: 135 outliers final: 17 residues processed: 697 average time/residue: 0.3815 time to fit residues: 350.4980 Evaluate side-chains 340 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 321 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 276 LYS Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 276 LYS Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 263 ILE Chi-restraints excluded: chain F residue 276 LYS Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain G residue 276 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 chunk 78 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 168 optimal weight: 0.9980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN A 43 HIS B 37 GLN B 43 HIS B 77 HIS B 185 GLN B 213 GLN C 185 GLN D 43 HIS D 185 GLN E 43 HIS E 185 GLN F 43 HIS F 77 HIS F 185 GLN G 43 HIS G 97 HIS G 206 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15867 Z= 0.262 Angle : 0.677 10.301 21597 Z= 0.349 Chirality : 0.043 0.145 2430 Planarity : 0.005 0.038 2577 Dihedral : 20.157 119.807 2822 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 4.79 % Allowed : 20.88 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.62 (0.19), residues: 1806 helix: 0.56 (0.15), residues: 1092 sheet: -1.49 (0.53), residues: 105 loop : -1.95 (0.23), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 211 HIS 0.004 0.001 HIS E 97 PHE 0.010 0.001 PHE D 196 TYR 0.015 0.002 TYR E 73 ARG 0.008 0.001 ARG B 57 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 356 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 LEU cc_start: 0.7443 (mt) cc_final: 0.7045 (mt) REVERT: A 230 LEU cc_start: 0.9139 (tp) cc_final: 0.8880 (tt) REVERT: B 37 GLN cc_start: 0.7713 (tp-100) cc_final: 0.7302 (tm-30) REVERT: C 229 MET cc_start: 0.7663 (mmm) cc_final: 0.7003 (mmt) REVERT: D 81 GLN cc_start: 0.6511 (mp10) cc_final: 0.6262 (mt0) REVERT: F 262 LYS cc_start: 0.6444 (ptpt) cc_final: 0.5007 (tptp) REVERT: G 210 MET cc_start: 0.7799 (tpp) cc_final: 0.7459 (tpp) REVERT: G 241 ILE cc_start: 0.9036 (mm) cc_final: 0.8752 (mp) REVERT: G 256 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8827 (mm) outliers start: 72 outliers final: 44 residues processed: 410 average time/residue: 0.3103 time to fit residues: 178.0565 Evaluate side-chains 325 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 280 time to evaluate : 1.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 276 LYS Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 213 GLN Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 276 LYS Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 211 TRP Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain F residue 263 ILE Chi-restraints excluded: chain F residue 276 LYS Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain G residue 276 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 140 optimal weight: 0.0870 chunk 115 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 169 optimal weight: 0.0010 chunk 182 optimal weight: 20.0000 chunk 150 optimal weight: 20.0000 chunk 167 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 135 optimal weight: 0.9990 overall best weight: 3.6170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 213 GLN B 43 HIS B 98 GLN B 206 ASN D 98 GLN ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 HIS E 185 GLN F 43 HIS F 77 HIS G 185 GLN G 213 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.5050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15867 Z= 0.293 Angle : 0.647 10.425 21597 Z= 0.332 Chirality : 0.042 0.150 2430 Planarity : 0.004 0.035 2577 Dihedral : 18.594 118.163 2808 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 5.39 % Allowed : 21.81 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.36 (0.20), residues: 1806 helix: 0.72 (0.16), residues: 1099 sheet: -1.49 (0.49), residues: 105 loop : -1.74 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 211 HIS 0.004 0.001 HIS E 97 PHE 0.011 0.001 PHE D 196 TYR 0.017 0.002 TYR E 112 ARG 0.007 0.001 ARG E 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 312 time to evaluate : 1.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 GLN cc_start: 0.7676 (tp-100) cc_final: 0.7312 (tm-30) REVERT: B 196 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.7995 (m-80) REVERT: C 229 MET cc_start: 0.7621 (mmm) cc_final: 0.7140 (mmt) REVERT: D 81 GLN cc_start: 0.6769 (mp10) cc_final: 0.6500 (mt0) REVERT: D 85 ARG cc_start: 0.7307 (mmm160) cc_final: 0.6780 (mtt180) REVERT: D 273 LYS cc_start: 0.7301 (ptmt) cc_final: 0.7046 (pttp) REVERT: E 27 ARG cc_start: 0.8004 (ttp80) cc_final: 0.7531 (ttp80) REVERT: E 63 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8128 (mpt180) REVERT: F 262 LYS cc_start: 0.6356 (ptpt) cc_final: 0.4815 (tptp) REVERT: G 196 PHE cc_start: 0.8499 (OUTLIER) cc_final: 0.8144 (m-10) REVERT: G 241 ILE cc_start: 0.9088 (mm) cc_final: 0.8846 (mp) REVERT: G 256 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8879 (mm) outliers start: 81 outliers final: 45 residues processed: 369 average time/residue: 0.3002 time to fit residues: 158.6694 Evaluate side-chains 309 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 260 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 124 ASP Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 185 GLN Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain F residue 263 ILE Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 185 GLN Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain G residue 256 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 5.9990 chunk 127 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 169 optimal weight: 0.5980 chunk 179 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 160 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN B 98 GLN ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.5485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15867 Z= 0.216 Angle : 0.594 10.566 21597 Z= 0.304 Chirality : 0.040 0.129 2430 Planarity : 0.004 0.039 2577 Dihedral : 17.877 114.397 2789 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 4.72 % Allowed : 24.47 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.15 (0.20), residues: 1806 helix: 0.94 (0.16), residues: 1099 sheet: -2.07 (0.37), residues: 175 loop : -1.47 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 211 HIS 0.004 0.001 HIS E 97 PHE 0.019 0.001 PHE C 204 TYR 0.010 0.001 TYR E 112 ARG 0.006 0.001 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 290 time to evaluate : 2.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 GLN cc_start: 0.7656 (tp-100) cc_final: 0.7300 (tm-30) REVERT: C 229 MET cc_start: 0.7609 (mmm) cc_final: 0.7225 (mmt) REVERT: D 33 ILE cc_start: 0.7610 (mm) cc_final: 0.7280 (tp) REVERT: D 81 GLN cc_start: 0.6896 (mp10) cc_final: 0.6616 (mt0) REVERT: D 85 ARG cc_start: 0.7348 (mmm160) cc_final: 0.6909 (mmt90) REVERT: D 273 LYS cc_start: 0.7351 (ptmt) cc_final: 0.7142 (pttp) REVERT: E 27 ARG cc_start: 0.8063 (ttp80) cc_final: 0.7733 (ttp80) REVERT: E 63 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.8093 (mpt180) REVERT: E 210 MET cc_start: 0.7983 (tpp) cc_final: 0.7726 (ttm) REVERT: E 229 MET cc_start: 0.7328 (mmp) cc_final: 0.7004 (mmm) REVERT: F 262 LYS cc_start: 0.6347 (ptpt) cc_final: 0.4856 (tptp) REVERT: G 196 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.7884 (m-10) REVERT: G 241 ILE cc_start: 0.9091 (mm) cc_final: 0.8827 (mp) REVERT: G 256 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8872 (mm) outliers start: 71 outliers final: 45 residues processed: 344 average time/residue: 0.2967 time to fit residues: 146.5584 Evaluate side-chains 310 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 262 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 125 PHE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain G residue 269 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 10.0000 chunk 102 optimal weight: 20.0000 chunk 2 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 153 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 161 optimal weight: 10.0000 chunk 45 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN C 77 HIS D 77 HIS D 206 ASN D 269 GLN E 43 HIS F 77 HIS G 213 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.5936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15867 Z= 0.242 Angle : 0.588 10.633 21597 Z= 0.301 Chirality : 0.040 0.131 2430 Planarity : 0.004 0.038 2577 Dihedral : 17.428 110.544 2787 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 5.25 % Allowed : 24.34 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.03 (0.20), residues: 1806 helix: 1.03 (0.16), residues: 1099 sheet: -2.12 (0.35), residues: 175 loop : -1.37 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 20 HIS 0.004 0.001 HIS E 97 PHE 0.016 0.001 PHE E 204 TYR 0.011 0.001 TYR E 112 ARG 0.005 0.001 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 287 time to evaluate : 1.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 GLN cc_start: 0.6960 (mt0) cc_final: 0.6685 (mt0) REVERT: C 229 MET cc_start: 0.7569 (mmm) cc_final: 0.7235 (mmt) REVERT: D 81 GLN cc_start: 0.7059 (mp10) cc_final: 0.6729 (mt0) REVERT: D 85 ARG cc_start: 0.7379 (mmm160) cc_final: 0.7018 (mmt90) REVERT: E 63 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8208 (mpt180) REVERT: G 196 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.7961 (m-10) REVERT: G 241 ILE cc_start: 0.9111 (mm) cc_final: 0.8834 (mp) REVERT: G 256 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8879 (mm) outliers start: 79 outliers final: 57 residues processed: 344 average time/residue: 0.2974 time to fit residues: 148.0976 Evaluate side-chains 325 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 265 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 125 PHE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 131 GLU Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain G residue 269 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 105 optimal weight: 0.0050 chunk 44 optimal weight: 9.9990 chunk 179 optimal weight: 10.0000 chunk 149 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 94 optimal weight: 8.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN D 77 HIS D 206 ASN E 43 HIS F 77 HIS G 213 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.6139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15867 Z= 0.168 Angle : 0.551 10.849 21597 Z= 0.285 Chirality : 0.039 0.131 2430 Planarity : 0.004 0.041 2577 Dihedral : 17.187 103.474 2785 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.12 % Allowed : 25.80 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.19 (0.20), residues: 1806 helix: 1.21 (0.16), residues: 1099 sheet: -2.04 (0.35), residues: 175 loop : -1.30 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 20 HIS 0.004 0.001 HIS E 97 PHE 0.025 0.001 PHE C 204 TYR 0.009 0.001 TYR E 112 ARG 0.011 0.000 ARG E 85 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 289 time to evaluate : 1.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 GLN cc_start: 0.7013 (mt0) cc_final: 0.6767 (mt0) REVERT: C 210 MET cc_start: 0.7681 (ttt) cc_final: 0.7261 (ttm) REVERT: C 229 MET cc_start: 0.7521 (mmm) cc_final: 0.7248 (mmt) REVERT: D 81 GLN cc_start: 0.7069 (mp10) cc_final: 0.6753 (mt0) REVERT: D 85 ARG cc_start: 0.7412 (mmm160) cc_final: 0.7082 (mmt90) REVERT: D 232 ILE cc_start: 0.8325 (tt) cc_final: 0.8078 (tp) REVERT: E 27 ARG cc_start: 0.8082 (ttp80) cc_final: 0.7738 (ttp80) REVERT: E 63 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8046 (mpt180) REVERT: E 229 MET cc_start: 0.7232 (mmp) cc_final: 0.7011 (mmm) REVERT: G 241 ILE cc_start: 0.9090 (mm) cc_final: 0.8832 (mp) REVERT: G 256 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8858 (mm) outliers start: 62 outliers final: 51 residues processed: 329 average time/residue: 0.2866 time to fit residues: 135.1949 Evaluate side-chains 316 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 263 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 125 PHE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain G residue 269 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 102 optimal weight: 20.0000 chunk 131 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 151 optimal weight: 0.0050 chunk 100 optimal weight: 9.9990 chunk 179 optimal weight: 9.9990 chunk 112 optimal weight: 0.2980 chunk 109 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 overall best weight: 2.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 ASN D 77 HIS D 206 ASN E 43 HIS F 77 HIS F 98 GLN G 213 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.6310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15867 Z= 0.218 Angle : 0.572 10.505 21597 Z= 0.295 Chirality : 0.040 0.145 2430 Planarity : 0.004 0.044 2577 Dihedral : 17.106 101.907 2785 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.39 % Allowed : 25.66 % Favored : 69.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.18 (0.20), residues: 1806 helix: 1.22 (0.16), residues: 1099 sheet: -2.10 (0.34), residues: 175 loop : -1.31 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 20 HIS 0.004 0.001 HIS E 97 PHE 0.017 0.001 PHE E 204 TYR 0.011 0.001 TYR F 275 ARG 0.006 0.000 ARG C 254 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 274 time to evaluate : 1.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 229 MET cc_start: 0.7514 (mmm) cc_final: 0.7257 (mmt) REVERT: D 81 GLN cc_start: 0.7167 (mp10) cc_final: 0.6836 (mt0) REVERT: D 85 ARG cc_start: 0.7490 (mmm160) cc_final: 0.7141 (mmt90) REVERT: D 98 GLN cc_start: 0.8245 (tp40) cc_final: 0.8039 (tp40) REVERT: E 63 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8047 (mpt180) REVERT: E 229 MET cc_start: 0.7344 (mmp) cc_final: 0.7059 (mmm) REVERT: G 196 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.7754 (m-10) REVERT: G 241 ILE cc_start: 0.9099 (mm) cc_final: 0.8849 (mp) REVERT: G 256 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8884 (mm) outliers start: 66 outliers final: 54 residues processed: 323 average time/residue: 0.2853 time to fit residues: 133.3651 Evaluate side-chains 320 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 263 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 125 PHE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain G residue 269 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 107 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 16 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN B 206 ASN C 213 GLN D 77 HIS D 206 ASN F 77 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.6478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15867 Z= 0.189 Angle : 0.564 10.677 21597 Z= 0.291 Chirality : 0.039 0.156 2430 Planarity : 0.004 0.033 2577 Dihedral : 16.944 95.978 2785 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.12 % Allowed : 26.13 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.27 (0.20), residues: 1806 helix: 1.31 (0.16), residues: 1092 sheet: -2.16 (0.34), residues: 175 loop : -1.29 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 20 HIS 0.004 0.001 HIS E 97 PHE 0.017 0.001 PHE E 106 TYR 0.009 0.001 TYR A 93 ARG 0.006 0.000 ARG E 85 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 274 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7073 (ptpt) cc_final: 0.6841 (ttmt) REVERT: D 85 ARG cc_start: 0.7545 (mmm160) cc_final: 0.7262 (mmt90) REVERT: D 98 GLN cc_start: 0.8283 (tp40) cc_final: 0.8083 (tp40) REVERT: D 232 ILE cc_start: 0.8373 (tt) cc_final: 0.8111 (tp) REVERT: E 63 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8061 (mpt180) REVERT: G 241 ILE cc_start: 0.9101 (mm) cc_final: 0.8859 (mp) REVERT: G 256 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8883 (mm) outliers start: 62 outliers final: 51 residues processed: 317 average time/residue: 0.2896 time to fit residues: 131.6576 Evaluate side-chains 313 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 260 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 125 PHE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain G residue 269 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 8.9990 chunk 171 optimal weight: 4.9990 chunk 156 optimal weight: 20.0000 chunk 167 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 72 optimal weight: 30.0000 chunk 131 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 150 optimal weight: 30.0000 chunk 158 optimal weight: 2.9990 chunk 166 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 ASN D 77 HIS D 206 ASN F 77 HIS F 97 HIS G 43 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.6720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 15867 Z= 0.378 Angle : 0.666 10.172 21597 Z= 0.342 Chirality : 0.043 0.163 2430 Planarity : 0.004 0.049 2577 Dihedral : 17.061 97.367 2785 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.72 % Allowed : 25.86 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.15 (0.20), residues: 1806 helix: 0.97 (0.16), residues: 1085 sheet: -2.47 (0.32), residues: 175 loop : -1.35 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 211 HIS 0.005 0.001 HIS D 77 PHE 0.014 0.002 PHE E 204 TYR 0.017 0.002 TYR E 115 ARG 0.007 0.001 ARG E 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 262 time to evaluate : 1.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 37 GLN cc_start: 0.7641 (tp-100) cc_final: 0.7308 (tm-30) REVERT: D 85 ARG cc_start: 0.7660 (mmm160) cc_final: 0.7293 (ttt180) REVERT: E 63 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8309 (mpt180) REVERT: E 196 PHE cc_start: 0.8726 (OUTLIER) cc_final: 0.8099 (m-80) REVERT: G 196 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.8095 (m-10) REVERT: G 241 ILE cc_start: 0.9166 (mm) cc_final: 0.8946 (mp) REVERT: G 256 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8947 (mm) outliers start: 71 outliers final: 57 residues processed: 311 average time/residue: 0.2962 time to fit residues: 131.7414 Evaluate side-chains 307 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 246 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 125 PHE Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 131 GLU Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 253 ILE Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain G residue 269 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 185 optimal weight: 10.0000 chunk 170 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN F 77 HIS G 43 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.6847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15867 Z= 0.169 Angle : 0.575 10.789 21597 Z= 0.298 Chirality : 0.039 0.214 2430 Planarity : 0.004 0.037 2577 Dihedral : 16.737 84.873 2785 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.12 % Allowed : 27.39 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.17 (0.20), residues: 1806 helix: 1.23 (0.16), residues: 1085 sheet: -2.33 (0.32), residues: 175 loop : -1.22 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 20 HIS 0.004 0.001 HIS E 97 PHE 0.019 0.001 PHE E 204 TYR 0.008 0.001 TYR A 93 ARG 0.009 0.000 ARG E 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 270 time to evaluate : 1.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 273 LYS cc_start: 0.6638 (tmtt) cc_final: 0.6427 (tmtt) REVERT: D 85 ARG cc_start: 0.7665 (mmm160) cc_final: 0.7400 (ttt180) REVERT: D 232 ILE cc_start: 0.8453 (tt) cc_final: 0.8201 (tp) REVERT: E 63 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.8030 (mpt180) REVERT: G 241 ILE cc_start: 0.9105 (mm) cc_final: 0.8847 (mp) outliers start: 47 outliers final: 41 residues processed: 301 average time/residue: 0.2855 time to fit residues: 124.0293 Evaluate side-chains 296 residues out of total 1589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 254 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 125 PHE Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 269 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 9.9990 chunk 157 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 136 optimal weight: 0.5980 chunk 21 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 147 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN B 206 ASN D 77 HIS D 206 ASN F 77 HIS G 213 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.132919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.105983 restraints weight = 25736.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.108979 restraints weight = 13860.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.110939 restraints weight = 9467.708| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.6906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15867 Z= 0.209 Angle : 0.590 10.658 21597 Z= 0.303 Chirality : 0.040 0.222 2430 Planarity : 0.004 0.042 2577 Dihedral : 16.713 83.719 2785 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.99 % Allowed : 28.06 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.18 (0.20), residues: 1806 helix: 1.23 (0.16), residues: 1085 sheet: -2.32 (0.33), residues: 175 loop : -1.18 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 20 HIS 0.004 0.001 HIS E 97 PHE 0.035 0.001 PHE B 204 TYR 0.009 0.001 TYR A 93 ARG 0.009 0.000 ARG E 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3930.01 seconds wall clock time: 71 minutes 12.11 seconds (4272.11 seconds total)