Starting phenix.real_space_refine (version: dev) on Wed Feb 22 14:20:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m99_23720/02_2023/7m99_23720_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m99_23720/02_2023/7m99_23720.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m99_23720/02_2023/7m99_23720.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m99_23720/02_2023/7m99_23720.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m99_23720/02_2023/7m99_23720_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m99_23720/02_2023/7m99_23720_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 82": "OE1" <-> "OE2" Residue "A TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 264": "OD1" <-> "OD2" Residue "A GLU 270": "OE1" <-> "OE2" Residue "B TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 264": "OD1" <-> "OD2" Residue "B GLU 270": "OE1" <-> "OE2" Residue "C TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 264": "OD1" <-> "OD2" Residue "C GLU 270": "OE1" <-> "OE2" Residue "D TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 264": "OD1" <-> "OD2" Residue "D GLU 270": "OE1" <-> "OE2" Residue "E GLU 61": "OE1" <-> "OE2" Residue "E TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 145": "OE1" <-> "OE2" Residue "E PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 264": "OD1" <-> "OD2" Residue "E GLU 270": "OE1" <-> "OE2" Residue "F TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 139": "OE1" <-> "OE2" Residue "F PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 264": "OD1" <-> "OD2" Residue "F GLU 270": "OE1" <-> "OE2" Residue "G ASP 44": "OD1" <-> "OD2" Residue "G TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 139": "OE1" <-> "OE2" Residue "G ASP 147": "OD1" <-> "OD2" Residue "G PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 264": "OD1" <-> "OD2" Residue "G GLU 270": "OE1" <-> "OE2" Residue "H TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 145": "OE1" <-> "OE2" Residue "H PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 264": "OD1" <-> "OD2" Residue "H GLU 270": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 17613 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "B" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "C" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "D" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "E" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "F" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "G" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "H" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "I" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 420 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "J" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 441 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 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, 'AGS': 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, 'AGS': 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, 'AGS': 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, 'AGS': 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, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.33, per 1000 atoms: 0.59 Number of scatterers: 17613 At special positions: 0 Unit cell: (142.31, 133, 119.7, 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 71 16.00 P 63 15.00 Mg 7 11.99 O 3336 8.00 N 3198 7.00 C 10938 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: 7.57 Conformation dependent library (CDL) restraints added in 2.4 seconds 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3856 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 96 helices and 16 sheets defined 54.5% alpha, 5.2% beta 13 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 5.06 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 Processing helix chain 'A' and resid 37 through 52 Processing helix chain 'A' and resid 66 through 76 Processing helix chain 'A' and resid 102 through 113 removed outlier: 3.858A pdb=" N PHE A 106 " --> pdb=" O PRO A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 133 removed outlier: 4.658A pdb=" N ASP A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A 128 " --> pdb=" O ASP A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 163 removed outlier: 3.585A pdb=" N ALA A 155 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG A 158 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP A 159 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP A 163 " --> pdb=" O ILE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 182 removed outlier: 4.120A pdb=" N ALA A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ARG A 182 " --> pdb=" O ALA A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 189 removed outlier: 3.609A pdb=" N ARG A 189 " --> pdb=" O GLN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 214 removed outlier: 3.679A pdb=" N ASN A 206 " --> pdb=" O ASP A 203 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A 212 " --> pdb=" O GLU A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 237 removed outlier: 4.483A pdb=" N ILE A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 258 removed outlier: 3.559A pdb=" N ARG A 258 " --> pdb=" O ARG A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 274 removed outlier: 3.927A pdb=" N GLU A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 28 Processing helix chain 'B' and resid 37 through 52 Processing helix chain 'B' and resid 66 through 76 Processing helix chain 'B' and resid 102 through 112 removed outlier: 3.858A pdb=" N PHE B 106 " --> pdb=" O PRO B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 133 removed outlier: 4.007A pdb=" N ASP B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG B 128 " --> pdb=" O ASP B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 163 removed outlier: 3.585A pdb=" N ALA B 155 " --> pdb=" O GLU B 152 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG B 158 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP B 159 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP B 163 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 182 removed outlier: 4.258A pdb=" N ALA B 178 " --> pdb=" O ASP B 174 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ARG B 182 " --> pdb=" O ALA B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 187 No H-bonds generated for 'chain 'B' and resid 184 through 187' Processing helix chain 'B' and resid 201 through 215 removed outlier: 3.679A pdb=" N ASN B 206 " --> pdb=" O ASP B 203 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU B 212 " --> pdb=" O GLU B 209 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN B 213 " --> pdb=" O MET B 210 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET B 214 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL B 215 " --> pdb=" O GLU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 237 removed outlier: 4.483A pdb=" N ILE B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 258 removed outlier: 3.561A pdb=" N ARG B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 274 removed outlier: 3.928A pdb=" N GLU B 274 " --> pdb=" O GLU B 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 28 Processing helix chain 'C' and resid 37 through 52 Processing helix chain 'C' and resid 66 through 76 Processing helix chain 'C' and resid 102 through 113 removed outlier: 3.856A pdb=" N PHE C 106 " --> pdb=" O PRO C 102 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 113 " --> pdb=" O ILE C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 133 removed outlier: 3.598A pdb=" N ASP C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG C 128 " --> pdb=" O ASP C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 163 removed outlier: 3.584A pdb=" N ALA C 155 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG C 158 " --> pdb=" O ALA C 155 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP C 159 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP C 163 " --> pdb=" O ILE C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 182 removed outlier: 4.041A pdb=" N LYS C 181 " --> pdb=" O ALA C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 189 removed outlier: 3.511A pdb=" N ARG C 189 " --> pdb=" O GLN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 214 removed outlier: 3.678A pdb=" N ASN C 206 " --> pdb=" O ASP C 203 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N MET C 214 " --> pdb=" O TRP C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 237 removed outlier: 4.345A pdb=" N ILE C 232 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 258 removed outlier: 3.560A pdb=" N ARG C 258 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 274 removed outlier: 3.927A pdb=" N GLU C 274 " --> pdb=" O GLU C 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 28 Processing helix chain 'D' and resid 37 through 52 Processing helix chain 'D' and resid 66 through 76 Processing helix chain 'D' and resid 102 through 112 removed outlier: 3.857A pdb=" N PHE D 106 " --> pdb=" O PRO D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 133 Processing helix chain 'D' and resid 151 through 163 removed outlier: 3.584A pdb=" N ALA D 155 " --> pdb=" O GLU D 152 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG D 158 " --> pdb=" O ALA D 155 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP D 159 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP D 163 " --> pdb=" O ILE D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 182 removed outlier: 4.040A pdb=" N LYS D 181 " --> pdb=" O ALA D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 189 removed outlier: 3.510A pdb=" N ARG D 189 " --> pdb=" O GLN D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 214 removed outlier: 3.678A pdb=" N ASN D 206 " --> pdb=" O ASP D 203 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU D 212 " --> pdb=" O GLU D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 237 removed outlier: 4.484A pdb=" N ILE D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 258 removed outlier: 3.560A pdb=" N ARG D 258 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 274 removed outlier: 3.928A pdb=" N GLU D 274 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 28 Processing helix chain 'E' and resid 37 through 52 Processing helix chain 'E' and resid 66 through 76 Processing helix chain 'E' and resid 102 through 112 removed outlier: 3.857A pdb=" N PHE E 106 " --> pdb=" O PRO E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 133 removed outlier: 4.658A pdb=" N ASP E 127 " --> pdb=" O SER E 123 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG E 128 " --> pdb=" O ASP E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 163 removed outlier: 3.585A pdb=" N ALA E 155 " --> pdb=" O GLU E 152 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG E 158 " --> pdb=" O ALA E 155 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP E 159 " --> pdb=" O ASP E 156 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP E 163 " --> pdb=" O ILE E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 182 removed outlier: 4.040A pdb=" N LYS E 181 " --> pdb=" O ALA E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'E' and resid 201 through 214 removed outlier: 3.678A pdb=" N ASN E 206 " --> pdb=" O ASP E 203 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU E 212 " --> pdb=" O GLU E 209 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET E 214 " --> pdb=" O TRP E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 237 removed outlier: 4.488A pdb=" N ILE E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 258 removed outlier: 3.560A pdb=" N ARG E 258 " --> pdb=" O ARG E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 274 removed outlier: 3.928A pdb=" N GLU E 274 " --> pdb=" O GLU E 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 28 Processing helix chain 'F' and resid 37 through 52 Processing helix chain 'F' and resid 66 through 76 Processing helix chain 'F' and resid 102 through 112 removed outlier: 3.857A pdb=" N PHE F 106 " --> pdb=" O PRO F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 133 removed outlier: 3.599A pdb=" N ASP F 127 " --> pdb=" O SER F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 163 removed outlier: 3.584A pdb=" N ALA F 155 " --> pdb=" O GLU F 152 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG F 158 " --> pdb=" O ALA F 155 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP F 159 " --> pdb=" O ASP F 156 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP F 163 " --> pdb=" O ILE F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 182 removed outlier: 4.040A pdb=" N LYS F 181 " --> pdb=" O ALA F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 189 removed outlier: 3.601A pdb=" N ARG F 189 " --> pdb=" O GLN F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 214 removed outlier: 3.679A pdb=" N ASN F 206 " --> pdb=" O ASP F 203 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET F 214 " --> pdb=" O TRP F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 237 removed outlier: 4.487A pdb=" N ILE F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 258 removed outlier: 3.560A pdb=" N ARG F 258 " --> pdb=" O ARG F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 274 removed outlier: 3.927A pdb=" N GLU F 274 " --> pdb=" O GLU F 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 28 Processing helix chain 'G' and resid 37 through 52 removed outlier: 3.817A pdb=" N GLY G 48 " --> pdb=" O ASP G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 76 Processing helix chain 'G' and resid 102 through 112 removed outlier: 3.857A pdb=" N PHE G 106 " --> pdb=" O PRO G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 133 removed outlier: 4.657A pdb=" N ASP G 127 " --> pdb=" O SER G 123 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG G 128 " --> pdb=" O ASP G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 163 removed outlier: 3.585A pdb=" N ALA G 155 " --> pdb=" O GLU G 152 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG G 158 " --> pdb=" O ALA G 155 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP G 159 " --> pdb=" O ASP G 156 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP G 163 " --> pdb=" O ILE G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 182 removed outlier: 4.040A pdb=" N LYS G 181 " --> pdb=" O ALA G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 189 removed outlier: 3.533A pdb=" N ARG G 189 " --> pdb=" O GLN G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 214 removed outlier: 3.679A pdb=" N ASN G 206 " --> pdb=" O ASP G 203 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 237 removed outlier: 4.489A pdb=" N ILE G 232 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 241 through 258 removed outlier: 3.560A pdb=" N ARG G 258 " --> pdb=" O ARG G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 274 removed outlier: 3.928A pdb=" N GLU G 274 " --> pdb=" O GLU G 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 28 Processing helix chain 'H' and resid 37 through 52 Processing helix chain 'H' and resid 66 through 76 Processing helix chain 'H' and resid 102 through 112 removed outlier: 3.857A pdb=" N PHE H 106 " --> pdb=" O PRO H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 133 removed outlier: 4.657A pdb=" N ASP H 127 " --> pdb=" O SER H 123 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG H 128 " --> pdb=" O ASP H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 151 through 163 removed outlier: 3.585A pdb=" N ALA H 155 " --> pdb=" O GLU H 152 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG H 158 " --> pdb=" O ALA H 155 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP H 159 " --> pdb=" O ASP H 156 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP H 163 " --> pdb=" O ILE H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 182 removed outlier: 4.041A pdb=" N LYS H 181 " --> pdb=" O ALA H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 189 removed outlier: 3.527A pdb=" N ARG H 189 " --> pdb=" O GLN H 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 214 removed outlier: 3.679A pdb=" N ASN H 206 " --> pdb=" O ASP H 203 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET H 214 " --> pdb=" O TRP H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 237 removed outlier: 4.482A pdb=" N ILE H 232 " --> pdb=" O GLU H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 258 removed outlier: 3.560A pdb=" N ARG H 258 " --> pdb=" O ARG H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 274 removed outlier: 3.909A pdb=" N GLU H 274 " --> pdb=" O GLU H 270 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 193 through 195 removed outlier: 7.044A pdb=" N ARG A 57 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY A 60 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 91 through 95 removed outlier: 6.527A pdb=" N MET A 140 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ILE A 94 " --> pdb=" O MET A 140 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE A 142 " --> pdb=" O ILE A 94 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 57 through 59 Processing sheet with id= D, first strand: chain 'B' and resid 91 through 95 removed outlier: 6.555A pdb=" N MET B 140 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ILE B 94 " --> pdb=" O MET B 140 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE B 142 " --> pdb=" O ILE B 94 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 193 through 195 removed outlier: 6.403A pdb=" N ARG C 57 " --> pdb=" O LEU C 194 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 91 through 95 removed outlier: 6.545A pdb=" N MET C 140 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ILE C 94 " --> pdb=" O MET C 140 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE C 142 " --> pdb=" O ILE C 94 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'D' and resid 57 through 59 Processing sheet with id= H, first strand: chain 'D' and resid 91 through 95 removed outlier: 6.580A pdb=" N MET D 140 " --> pdb=" O VAL D 92 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ILE D 94 " --> pdb=" O MET D 140 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE D 142 " --> pdb=" O ILE D 94 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'E' and resid 57 through 60 Processing sheet with id= J, first strand: chain 'E' and resid 91 through 95 removed outlier: 6.515A pdb=" N MET E 140 " --> pdb=" O VAL E 92 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ILE E 94 " --> pdb=" O MET E 140 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE E 142 " --> pdb=" O ILE E 94 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'F' and resid 57 through 59 Processing sheet with id= L, first strand: chain 'F' and resid 91 through 95 removed outlier: 6.585A pdb=" N MET F 140 " --> pdb=" O VAL F 92 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ILE F 94 " --> pdb=" O MET F 140 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ILE F 142 " --> pdb=" O ILE F 94 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'G' and resid 57 through 60 Processing sheet with id= N, first strand: chain 'G' and resid 91 through 95 removed outlier: 6.564A pdb=" N MET G 140 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N ILE G 94 " --> pdb=" O MET G 140 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE G 142 " --> pdb=" O ILE G 94 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'H' and resid 57 through 59 Processing sheet with id= P, first strand: chain 'H' and resid 91 through 95 removed outlier: 6.656A pdb=" N MET H 140 " --> pdb=" O VAL H 92 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ILE H 94 " --> pdb=" O MET H 140 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE H 142 " --> pdb=" O ILE H 94 " (cutoff:3.500A) No H-bonds generated for sheet with id= P 662 hydrogen bonds defined for protein. 1542 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 26 hydrogen bonds 52 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 4.60 Time building geometry restraints manager: 8.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.36: 5819 1.36 - 1.54: 11815 1.54 - 1.72: 234 1.72 - 1.90: 96 1.90 - 2.07: 7 Bond restraints: 17971 Sorted by residual: bond pdb=" C4 AGS G 300 " pdb=" C5 AGS G 300 " ideal model delta sigma weight residual 1.386 1.470 -0.084 1.00e-02 1.00e+04 7.03e+01 bond pdb=" C4 AGS H 300 " pdb=" C5 AGS H 300 " ideal model delta sigma weight residual 1.386 1.470 -0.084 1.00e-02 1.00e+04 6.99e+01 bond pdb=" C4 AGS B 300 " pdb=" C5 AGS B 300 " ideal model delta sigma weight residual 1.386 1.469 -0.083 1.00e-02 1.00e+04 6.90e+01 bond pdb=" C4 AGS C 300 " pdb=" C5 AGS C 300 " ideal model delta sigma weight residual 1.386 1.469 -0.083 1.00e-02 1.00e+04 6.90e+01 bond pdb=" C4 AGS D 300 " pdb=" C5 AGS D 300 " ideal model delta sigma weight residual 1.386 1.469 -0.083 1.00e-02 1.00e+04 6.87e+01 ... (remaining 17966 not shown) Histogram of bond angle deviations from ideal: 95.43 - 103.57: 213 103.57 - 111.72: 8879 111.72 - 119.87: 8178 119.87 - 128.01: 6961 128.01 - 136.16: 152 Bond angle restraints: 24383 Sorted by residual: angle pdb=" C5 AGS C 300 " pdb=" C4 AGS C 300 " pdb=" N3 AGS C 300 " ideal model delta sigma weight residual 126.80 118.53 8.27 7.41e-01 1.82e+00 1.25e+02 angle pdb=" C5 AGS E 300 " pdb=" C4 AGS E 300 " pdb=" N3 AGS E 300 " ideal model delta sigma weight residual 126.80 118.61 8.19 7.41e-01 1.82e+00 1.22e+02 angle pdb=" C5 AGS G 300 " pdb=" C4 AGS G 300 " pdb=" N3 AGS G 300 " ideal model delta sigma weight residual 126.80 118.62 8.18 7.41e-01 1.82e+00 1.22e+02 angle pdb=" C5 AGS B 300 " pdb=" C4 AGS B 300 " pdb=" N3 AGS B 300 " ideal model delta sigma weight residual 126.80 118.63 8.17 7.41e-01 1.82e+00 1.22e+02 angle pdb=" C5 AGS D 300 " pdb=" C4 AGS D 300 " pdb=" N3 AGS D 300 " ideal model delta sigma weight residual 126.80 118.69 8.11 7.41e-01 1.82e+00 1.20e+02 ... (remaining 24378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 10569 35.96 - 71.92: 334 71.92 - 107.87: 31 107.87 - 143.83: 5 143.83 - 179.79: 10 Dihedral angle restraints: 10949 sinusoidal: 4989 harmonic: 5960 Sorted by residual: dihedral pdb=" O1B AGS E 300 " pdb=" O3B AGS E 300 " pdb=" PB AGS E 300 " pdb=" PG AGS E 300 " ideal model delta sinusoidal sigma weight residual 68.91 -110.88 179.79 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1B AGS C 300 " pdb=" O3B AGS C 300 " pdb=" PB AGS C 300 " pdb=" PG AGS C 300 " ideal model delta sinusoidal sigma weight residual 68.91 -119.96 -171.13 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" O1A AGS F 300 " pdb=" O3A AGS F 300 " pdb=" PA AGS F 300 " pdb=" PB AGS F 300 " ideal model delta sinusoidal sigma weight residual -67.73 94.94 -162.67 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 10946 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1354 0.078 - 0.156: 1094 0.156 - 0.234: 268 0.234 - 0.312: 28 0.312 - 0.390: 10 Chirality restraints: 2754 Sorted by residual: chirality pdb=" CA PRO F 102 " pdb=" N PRO F 102 " pdb=" C PRO F 102 " pdb=" CB PRO F 102 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CA PRO D 102 " pdb=" N PRO D 102 " pdb=" C PRO D 102 " pdb=" CB PRO D 102 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CA PRO B 102 " pdb=" N PRO B 102 " pdb=" C PRO B 102 " pdb=" CB PRO B 102 " both_signs ideal model delta sigma weight residual False 2.72 2.33 0.39 2.00e-01 2.50e+01 3.79e+00 ... (remaining 2751 not shown) Planarity restraints: 2913 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F 138 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.08e+00 pdb=" C VAL F 138 " -0.043 2.00e-02 2.50e+03 pdb=" O VAL F 138 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU F 139 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS E 56 " 0.012 2.00e-02 2.50e+03 2.45e-02 6.02e+00 pdb=" C CYS E 56 " -0.042 2.00e-02 2.50e+03 pdb=" O CYS E 56 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG E 57 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY E 135 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.91e+00 pdb=" C GLY E 135 " -0.042 2.00e-02 2.50e+03 pdb=" O GLY E 135 " 0.016 2.00e-02 2.50e+03 pdb=" N CYS E 136 " 0.014 2.00e-02 2.50e+03 ... (remaining 2910 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 40 2.44 - 3.05: 10526 3.05 - 3.67: 24890 3.67 - 4.28: 37643 4.28 - 4.90: 62554 Nonbonded interactions: 135653 Sorted by model distance: nonbonded pdb=" NZ LYS B 54 " pdb=" OE1 GLU C 250 " model vdw 1.823 2.520 nonbonded pdb=" OG1 THR H 67 " pdb="MG MG H 301 " model vdw 1.829 2.170 nonbonded pdb=" OG1 THR G 67 " pdb="MG MG G 301 " model vdw 1.874 2.170 nonbonded pdb=" NZ LYS G 103 " pdb=" OP2 DT I 19 " model vdw 1.903 2.520 nonbonded pdb=" S1G AGS G 300 " pdb="MG MG G 301 " model vdw 2.073 2.530 ... (remaining 135648 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 19 through 275) selection = (chain 'C' and resid 19 through 275) selection = (chain 'D' and resid 19 through 275) selection = (chain 'E' and resid 19 through 275) selection = (chain 'F' and resid 19 through 275) selection = (chain 'G' and resid 19 through 275) selection = (chain 'H' and resid 19 through 275) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 63 5.49 5 Mg 7 5.21 5 S 71 5.16 5 C 10938 2.51 5 N 3198 2.21 5 O 3336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 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: 5.330 Check model and map are aligned: 0.290 Process input model: 49.360 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.140 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 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 : 0.014 0.125 17971 Z= 0.884 Angle : 1.527 10.550 24383 Z= 1.224 Chirality : 0.100 0.390 2754 Planarity : 0.006 0.057 2913 Dihedral : 16.604 179.790 7093 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer Outliers : 0.45 % 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: -0.49 (0.17), residues: 2040 helix: -0.32 (0.13), residues: 1176 sheet: -0.04 (0.51), residues: 96 loop : -0.07 (0.21), residues: 768 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 499 time to evaluate : 2.176 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 506 average time/residue: 0.4991 time to fit residues: 326.1480 Evaluate side-chains 247 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 245 time to evaluate : 2.267 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4406 time to fit residues: 4.1801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 159 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 119 optimal weight: 0.9980 chunk 185 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 269 GLN C 37 GLN C 98 GLN C 213 GLN C 269 GLN D 77 HIS ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN E 213 GLN F 98 GLN G 37 GLN H 37 GLN H 206 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 17971 Z= 0.191 Angle : 0.526 8.743 24383 Z= 0.290 Chirality : 0.039 0.136 2754 Planarity : 0.005 0.050 2913 Dihedral : 17.875 177.607 2773 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer Outliers : 2.18 % 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: 0.54 (0.17), residues: 2040 helix: 0.62 (0.14), residues: 1176 sheet: 0.19 (0.53), residues: 96 loop : 0.20 (0.21), residues: 768 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 276 time to evaluate : 2.148 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 20 residues processed: 309 average time/residue: 0.4592 time to fit residues: 189.5782 Evaluate side-chains 241 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 221 time to evaluate : 2.346 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2306 time to fit residues: 10.9102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 0.5980 chunk 57 optimal weight: 0.0050 chunk 154 optimal weight: 5.9990 chunk 126 optimal weight: 0.1980 chunk 51 optimal weight: 0.0980 chunk 185 optimal weight: 2.9990 chunk 200 optimal weight: 10.0000 chunk 165 optimal weight: 0.9990 chunk 184 optimal weight: 0.0070 chunk 63 optimal weight: 0.0970 chunk 148 optimal weight: 0.8980 overall best weight: 0.0810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 269 GLN C 77 HIS C 213 GLN E 81 GLN E 206 ASN ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 17971 Z= 0.126 Angle : 0.434 6.659 24383 Z= 0.240 Chirality : 0.037 0.127 2754 Planarity : 0.004 0.044 2913 Dihedral : 17.780 179.296 2773 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer Outliers : 0.78 % 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: 0.95 (0.18), residues: 2040 helix: 0.87 (0.14), residues: 1184 sheet: 0.59 (0.56), residues: 96 loop : 0.49 (0.22), residues: 760 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 259 time to evaluate : 2.199 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 266 average time/residue: 0.4458 time to fit residues: 158.8219 Evaluate side-chains 230 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 223 time to evaluate : 2.046 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1535 time to fit residues: 4.7463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 186 optimal weight: 0.0970 chunk 197 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 176 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN B 77 HIS B 269 GLN C 77 HIS C 269 GLN E 81 GLN E 98 GLN E 206 ASN E 213 GLN G 37 GLN G 81 GLN H 269 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 17971 Z= 0.273 Angle : 0.557 7.858 24383 Z= 0.295 Chirality : 0.042 0.154 2754 Planarity : 0.005 0.054 2913 Dihedral : 17.952 178.789 2773 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer Outliers : 1.06 % 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: 0.86 (0.18), residues: 2040 helix: 0.98 (0.15), residues: 1176 sheet: 0.01 (0.53), residues: 96 loop : 0.20 (0.22), residues: 768 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 242 time to evaluate : 2.248 Fit side-chains outliers start: 19 outliers final: 11 residues processed: 255 average time/residue: 0.4404 time to fit residues: 151.3519 Evaluate side-chains 227 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 216 time to evaluate : 2.013 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1651 time to fit residues: 6.4453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 136 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 176 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN C 269 GLN D 223 ASN E 206 ASN E 213 GLN F 223 ASN H 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 17971 Z= 0.271 Angle : 0.528 6.546 24383 Z= 0.284 Chirality : 0.041 0.164 2754 Planarity : 0.005 0.054 2913 Dihedral : 17.951 179.527 2773 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer Outliers : 1.17 % 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: 0.71 (0.18), residues: 2040 helix: 0.86 (0.15), residues: 1184 sheet: -0.65 (0.44), residues: 136 loop : 0.27 (0.23), residues: 720 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 228 time to evaluate : 2.163 Fit side-chains outliers start: 21 outliers final: 10 residues processed: 244 average time/residue: 0.4372 time to fit residues: 144.3171 Evaluate side-chains 218 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 208 time to evaluate : 2.207 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1669 time to fit residues: 6.1092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 2.9990 chunk 177 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 197 optimal weight: 4.9990 chunk 163 optimal weight: 0.9990 chunk 91 optimal weight: 0.0020 chunk 16 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN C 77 HIS C 269 GLN D 223 ASN E 206 ASN ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 17971 Z= 0.160 Angle : 0.461 6.858 24383 Z= 0.248 Chirality : 0.039 0.143 2754 Planarity : 0.004 0.038 2913 Dihedral : 17.844 179.350 2773 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 0.61 % 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: 0.91 (0.19), residues: 2040 helix: 1.03 (0.15), residues: 1184 sheet: -0.65 (0.44), residues: 136 loop : 0.37 (0.23), residues: 720 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 221 time to evaluate : 2.509 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 227 average time/residue: 0.4567 time to fit residues: 139.8940 Evaluate side-chains 214 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 207 time to evaluate : 2.216 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1580 time to fit residues: 5.0938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 166 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 196 optimal weight: 8.9990 chunk 123 optimal weight: 2.9990 chunk 119 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN C 269 GLN E 206 ASN E 213 GLN H 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 17971 Z= 0.233 Angle : 0.505 5.362 24383 Z= 0.269 Chirality : 0.040 0.154 2754 Planarity : 0.004 0.041 2913 Dihedral : 17.893 179.700 2773 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 0.67 % 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: 0.83 (0.19), residues: 2040 helix: 1.14 (0.15), residues: 1168 sheet: -0.74 (0.33), residues: 216 loop : 0.16 (0.25), residues: 656 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 216 time to evaluate : 2.124 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 222 average time/residue: 0.4472 time to fit residues: 134.1901 Evaluate side-chains 217 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 208 time to evaluate : 2.200 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1953 time to fit residues: 5.9371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 59 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 125 optimal weight: 9.9990 chunk 133 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 chunk 178 optimal weight: 0.5980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN C 269 GLN E 206 ASN G 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 17971 Z= 0.234 Angle : 0.510 7.137 24383 Z= 0.272 Chirality : 0.040 0.158 2754 Planarity : 0.004 0.041 2913 Dihedral : 17.853 179.374 2773 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 0.67 % 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: 0.78 (0.19), residues: 2040 helix: 1.11 (0.15), residues: 1168 sheet: -0.74 (0.33), residues: 216 loop : 0.10 (0.25), residues: 656 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 217 time to evaluate : 2.066 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 224 average time/residue: 0.4455 time to fit residues: 135.2368 Evaluate side-chains 214 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 209 time to evaluate : 2.201 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1743 time to fit residues: 4.3681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 110 optimal weight: 0.0980 chunk 79 optimal weight: 4.9990 chunk 143 optimal weight: 0.2980 chunk 56 optimal weight: 6.9990 chunk 165 optimal weight: 0.9990 chunk 173 optimal weight: 0.9990 chunk 182 optimal weight: 1.9990 chunk 120 optimal weight: 8.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN C 269 GLN E 206 ASN ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 17971 Z= 0.154 Angle : 0.453 6.691 24383 Z= 0.246 Chirality : 0.038 0.142 2754 Planarity : 0.004 0.037 2913 Dihedral : 17.761 179.744 2773 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer Outliers : 0.45 % 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: 0.94 (0.19), residues: 2040 helix: 1.22 (0.15), residues: 1168 sheet: -0.59 (0.34), residues: 216 loop : 0.17 (0.25), residues: 656 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 224 time to evaluate : 2.095 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 225 average time/residue: 0.4207 time to fit residues: 128.2350 Evaluate side-chains 222 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 217 time to evaluate : 2.036 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1701 time to fit residues: 4.2643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 134 optimal weight: 0.0040 chunk 203 optimal weight: 8.9990 chunk 187 optimal weight: 0.7980 chunk 161 optimal weight: 0.8980 chunk 16 optimal weight: 0.0870 chunk 125 optimal weight: 8.9990 chunk 99 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 overall best weight: 0.4770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN C 213 GLN C 269 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 ASN G 81 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.4649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 17971 Z= 0.141 Angle : 0.454 8.954 24383 Z= 0.244 Chirality : 0.038 0.135 2754 Planarity : 0.004 0.038 2913 Dihedral : 17.698 179.195 2773 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 0.28 % 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: 0.99 (0.19), residues: 2040 helix: 1.26 (0.15), residues: 1168 sheet: -0.50 (0.34), residues: 216 loop : 0.18 (0.25), residues: 656 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 223 time to evaluate : 2.248 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 226 average time/residue: 0.4518 time to fit residues: 138.6856 Evaluate side-chains 217 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 213 time to evaluate : 2.207 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1753 time to fit residues: 4.0985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 149 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 166 optimal weight: 0.0470 chunk 20 optimal weight: 0.4980 chunk 29 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 overall best weight: 2.5084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN C 213 GLN C 269 GLN D 77 HIS ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 ASN F 213 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.178203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.141247 restraints weight = 20602.390| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 1.37 r_work: 0.3522 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.048 17971 Z= 0.373 Angle : 0.615 9.354 24383 Z= 0.323 Chirality : 0.044 0.175 2754 Planarity : 0.005 0.056 2913 Dihedral : 17.928 178.459 2773 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer Outliers : 0.39 % 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: 0.53 (0.18), residues: 2040 helix: 0.96 (0.15), residues: 1168 sheet: -0.82 (0.33), residues: 216 loop : -0.12 (0.24), residues: 656 =============================================================================== Job complete usr+sys time: 3889.40 seconds wall clock time: 71 minutes 9.42 seconds (4269.42 seconds total)