Starting phenix.real_space_refine on Sun Mar 17 11:42:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m99_23720/03_2024/7m99_23720_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m99_23720/03_2024/7m99_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_23720/03_2024/7m99_23720.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m99_23720/03_2024/7m99_23720.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m99_23720/03_2024/7m99_23720_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m99_23720/03_2024/7m99_23720_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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. 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 9.80, per 1000 atoms: 0.56 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: 7.02 Conformation dependent library (CDL) restraints added in 3.0 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: 7.00 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: 4.19 Time building geometry restraints manager: 7.63 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: 10685 35.96 - 71.92: 379 71.92 - 107.87: 31 107.87 - 143.83: 5 143.83 - 179.79: 10 Dihedral angle restraints: 11110 sinusoidal: 5150 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 11107 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 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.340 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 50.510 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.090 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 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 : 17.058 179.790 7254 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 % Allowed : 3.07 % Favored : 96.48 % 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: -0.49 (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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP G 45 HIS 0.001 0.000 HIS F 77 PHE 0.007 0.001 PHE F 125 TYR 0.007 0.000 TYR C 75 ARG 0.003 0.000 ARG A 116 *********************** 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 : 2.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 GLN cc_start: 0.7162 (mt0) cc_final: 0.6953 (mt0) REVERT: B 66 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7314 (mtmt) REVERT: C 129 THR cc_start: 0.8179 (m) cc_final: 0.7972 (m) REVERT: C 188 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7248 (mm-30) REVERT: D 129 THR cc_start: 0.7824 (m) cc_final: 0.7623 (m) REVERT: D 188 GLU cc_start: 0.7320 (mm-30) cc_final: 0.7073 (mm-30) REVERT: D 223 ASN cc_start: 0.6312 (t0) cc_final: 0.5523 (t0) REVERT: D 246 GLU cc_start: 0.6564 (mt-10) cc_final: 0.6337 (mt-10) REVERT: E 33 ILE cc_start: 0.7764 (mt) cc_final: 0.7557 (mp) REVERT: E 140 MET cc_start: 0.8659 (ttm) cc_final: 0.8234 (ttm) REVERT: E 188 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7227 (mm-30) REVERT: E 275 TYR cc_start: 0.8061 (m-80) cc_final: 0.7572 (m-80) REVERT: F 66 LYS cc_start: 0.6625 (OUTLIER) cc_final: 0.5818 (ttpt) REVERT: F 112 TYR cc_start: 0.8542 (t80) cc_final: 0.8053 (t80) REVERT: F 188 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7421 (mm-30) REVERT: G 140 MET cc_start: 0.8814 (ttm) cc_final: 0.8531 (ttm) REVERT: G 188 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7500 (mm-30) REVERT: G 229 MET cc_start: 0.7094 (mtm) cc_final: 0.6865 (mtp) outliers start: 8 outliers final: 2 residues processed: 506 average time/residue: 0.4980 time to fit residues: 327.5420 Evaluate side-chains 254 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 250 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain F residue 66 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.9990 chunk 154 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 159 optimal weight: 0.9990 chunk 61 optimal weight: 0.0470 chunk 97 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 185 optimal weight: 0.8980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 GLN C 98 GLN C 213 GLN C 269 GLN D 77 HIS 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.2691 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= 0.183 Angle : 0.523 8.892 24383 Z= 0.286 Chirality : 0.039 0.139 2754 Planarity : 0.005 0.050 2913 Dihedral : 18.654 177.569 2948 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.34 % Allowed : 8.98 % Favored : 88.67 % 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: 0.63 (0.17), residues: 2040 helix: 0.67 (0.14), residues: 1168 sheet: 0.24 (0.53), residues: 96 loop : 0.28 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 211 HIS 0.005 0.001 HIS C 77 PHE 0.017 0.001 PHE B 125 TYR 0.017 0.001 TYR D 73 ARG 0.004 0.001 ARG G 76 *********************** 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 325 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 283 time to evaluate : 2.235 Fit side-chains REVERT: A 29 LYS cc_start: 0.7562 (ttpp) cc_final: 0.7268 (ttpp) REVERT: A 184 GLU cc_start: 0.7877 (tt0) cc_final: 0.7438 (pt0) REVERT: A 240 TYR cc_start: 0.7492 (m-10) cc_final: 0.7124 (m-10) REVERT: B 261 LYS cc_start: 0.6604 (mttm) cc_final: 0.6047 (mmmt) REVERT: C 37 GLN cc_start: 0.7161 (tp-100) cc_final: 0.6918 (tp-100) REVERT: C 76 ARG cc_start: 0.6829 (OUTLIER) cc_final: 0.6280 (ttp-170) REVERT: C 188 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7265 (mm-30) REVERT: C 214 MET cc_start: 0.6984 (mtp) cc_final: 0.6620 (mtt) REVERT: C 227 LYS cc_start: 0.6239 (tttm) cc_final: 0.5966 (tttm) REVERT: D 75 TYR cc_start: 0.7324 (m-80) cc_final: 0.7058 (m-80) REVERT: D 188 GLU cc_start: 0.7418 (mm-30) cc_final: 0.7139 (mm-30) REVERT: D 246 GLU cc_start: 0.6698 (mt-10) cc_final: 0.6383 (mt-10) REVERT: E 181 LYS cc_start: 0.7875 (mttt) cc_final: 0.7637 (mtpp) REVERT: E 188 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7471 (mm-30) REVERT: E 222 SER cc_start: 0.7462 (m) cc_final: 0.7085 (m) REVERT: F 66 LYS cc_start: 0.7114 (OUTLIER) cc_final: 0.6415 (ttpt) REVERT: F 188 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7440 (mm-30) REVERT: G 81 GLN cc_start: 0.5615 (mt0) cc_final: 0.5328 (mt0) REVERT: G 124 ASP cc_start: 0.8189 (m-30) cc_final: 0.7926 (m-30) REVERT: G 140 MET cc_start: 0.8586 (ttm) cc_final: 0.8076 (ttm) REVERT: G 188 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7595 (mm-30) REVERT: G 246 GLU cc_start: 0.6518 (mt-10) cc_final: 0.6220 (mt-10) REVERT: G 256 LEU cc_start: 0.8497 (mt) cc_final: 0.8239 (mp) REVERT: H 140 MET cc_start: 0.8486 (ttm) cc_final: 0.7702 (ttm) REVERT: H 148 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7644 (ptt180) outliers start: 42 outliers final: 20 residues processed: 319 average time/residue: 0.4465 time to fit residues: 190.7310 Evaluate side-chains 262 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 239 time to evaluate : 2.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain F residue 66 LYS Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 225 LYS Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 148 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 185 optimal weight: 2.9990 chunk 200 optimal weight: 8.9990 chunk 165 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 63 optimal weight: 0.0970 chunk 148 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 213 GLN C 269 GLN E 206 ASN ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17971 Z= 0.221 Angle : 0.501 6.238 24383 Z= 0.271 Chirality : 0.040 0.145 2754 Planarity : 0.005 0.046 2913 Dihedral : 18.444 177.277 2938 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.84 % Allowed : 11.16 % Favored : 87.00 % 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: 0.81 (0.18), residues: 2040 helix: 0.87 (0.15), residues: 1184 sheet: 0.09 (0.53), residues: 96 loop : 0.29 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 45 HIS 0.005 0.001 HIS F 97 PHE 0.015 0.002 PHE D 125 TYR 0.011 0.001 TYR H 93 ARG 0.005 0.000 ARG D 258 *********************** 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 294 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 261 time to evaluate : 2.067 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7498 (ttpp) cc_final: 0.7259 (ttpp) REVERT: A 184 GLU cc_start: 0.7998 (tt0) cc_final: 0.7567 (pt0) REVERT: B 129 THR cc_start: 0.8526 (m) cc_final: 0.8320 (m) REVERT: B 261 LYS cc_start: 0.6712 (mttm) cc_final: 0.6172 (mmmt) REVERT: C 76 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.6846 (ttp-170) REVERT: C 188 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7480 (mm-30) REVERT: D 75 TYR cc_start: 0.7633 (m-80) cc_final: 0.7263 (m-80) REVERT: D 188 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7128 (mm-30) REVERT: E 181 LYS cc_start: 0.7969 (mttt) cc_final: 0.7715 (mtpp) REVERT: E 188 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7408 (mm-30) REVERT: G 81 GLN cc_start: 0.5625 (mt0) cc_final: 0.5400 (mt0) REVERT: G 124 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.8046 (m-30) REVERT: G 131 GLU cc_start: 0.7496 (tt0) cc_final: 0.7245 (mt-10) REVERT: G 140 MET cc_start: 0.8652 (ttm) cc_final: 0.8120 (ttm) REVERT: G 188 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7489 (mm-30) REVERT: G 256 LEU cc_start: 0.8479 (mt) cc_final: 0.8240 (mp) REVERT: H 140 MET cc_start: 0.8588 (ttm) cc_final: 0.7985 (ttm) REVERT: H 182 ARG cc_start: 0.7805 (mtm180) cc_final: 0.7604 (mtm180) outliers start: 33 outliers final: 25 residues processed: 287 average time/residue: 0.4356 time to fit residues: 168.5421 Evaluate side-chains 266 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 239 time to evaluate : 2.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 206 ASN Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 124 ASP Chi-restraints excluded: chain H residue 196 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 0.8980 chunk 139 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 124 optimal weight: 8.9990 chunk 186 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 97 optimal weight: 0.1980 chunk 176 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 269 GLN D 213 GLN E 81 GLN E 206 ASN E 213 GLN G 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17971 Z= 0.213 Angle : 0.485 4.858 24383 Z= 0.262 Chirality : 0.040 0.148 2754 Planarity : 0.004 0.041 2913 Dihedral : 18.308 177.862 2934 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.46 % Allowed : 12.33 % Favored : 85.21 % 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: 0.88 (0.18), residues: 2040 helix: 0.96 (0.15), residues: 1184 sheet: 0.09 (0.54), residues: 96 loop : 0.24 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 45 HIS 0.005 0.001 HIS F 97 PHE 0.013 0.002 PHE F 125 TYR 0.011 0.001 TYR H 93 ARG 0.008 0.001 ARG B 249 *********************** 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 288 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 244 time to evaluate : 2.167 Fit side-chains REVERT: A 29 LYS cc_start: 0.7410 (ttpp) cc_final: 0.7196 (ttpp) REVERT: A 76 ARG cc_start: 0.7191 (ttm170) cc_final: 0.6964 (ttm170) REVERT: A 170 LEU cc_start: 0.8429 (mt) cc_final: 0.8221 (mp) REVERT: A 184 GLU cc_start: 0.8093 (tt0) cc_final: 0.7782 (pt0) REVERT: B 229 MET cc_start: 0.6295 (mtt) cc_final: 0.5973 (mtt) REVERT: B 261 LYS cc_start: 0.6730 (mttm) cc_final: 0.6241 (mmmt) REVERT: C 76 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.6797 (ttp-170) REVERT: C 188 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7476 (mm-30) REVERT: D 75 TYR cc_start: 0.7811 (m-80) cc_final: 0.7459 (m-80) REVERT: D 188 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7164 (mm-30) REVERT: E 181 LYS cc_start: 0.8033 (mttt) cc_final: 0.7783 (mtpp) REVERT: E 188 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7299 (mm-30) REVERT: G 81 GLN cc_start: 0.5487 (mt0) cc_final: 0.5275 (mt0) REVERT: G 124 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.8149 (m-30) REVERT: G 140 MET cc_start: 0.8622 (ttm) cc_final: 0.8306 (ttm) REVERT: G 188 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7493 (mm-30) REVERT: G 200 SER cc_start: 0.8110 (t) cc_final: 0.7896 (t) REVERT: G 203 ASP cc_start: 0.7583 (m-30) cc_final: 0.7295 (m-30) REVERT: G 256 LEU cc_start: 0.8475 (mt) cc_final: 0.8231 (mp) REVERT: G 275 TYR cc_start: 0.7859 (m-80) cc_final: 0.7523 (m-80) REVERT: H 140 MET cc_start: 0.8689 (ttm) cc_final: 0.8080 (ttm) REVERT: H 182 ARG cc_start: 0.7849 (mtm180) cc_final: 0.7630 (mtm180) outliers start: 44 outliers final: 28 residues processed: 277 average time/residue: 0.4344 time to fit residues: 161.8296 Evaluate side-chains 255 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 225 time to evaluate : 2.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 225 LYS Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 196 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 146 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 168 optimal weight: 9.9990 chunk 136 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 176 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 213 GLN E 206 ASN H 37 GLN H 269 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17971 Z= 0.323 Angle : 0.567 8.012 24383 Z= 0.302 Chirality : 0.043 0.185 2754 Planarity : 0.005 0.058 2913 Dihedral : 18.365 177.707 2934 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.12 % Allowed : 13.28 % Favored : 84.60 % 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: 0.63 (0.18), residues: 2040 helix: 0.85 (0.15), residues: 1184 sheet: -0.76 (0.44), residues: 136 loop : 0.14 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 45 HIS 0.007 0.001 HIS F 97 PHE 0.020 0.002 PHE F 125 TYR 0.010 0.002 TYR H 93 ARG 0.005 0.001 ARG B 148 *********************** 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 271 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 233 time to evaluate : 2.211 Fit side-chains REVERT: A 170 LEU cc_start: 0.8460 (mt) cc_final: 0.8244 (mp) REVERT: A 184 GLU cc_start: 0.8101 (tt0) cc_final: 0.7847 (pt0) REVERT: B 217 LYS cc_start: 0.7164 (mmtt) cc_final: 0.6896 (mmtp) REVERT: B 261 LYS cc_start: 0.6846 (mttm) cc_final: 0.6578 (mmmt) REVERT: C 75 TYR cc_start: 0.7845 (m-80) cc_final: 0.7618 (m-80) REVERT: C 85 ARG cc_start: 0.5853 (OUTLIER) cc_final: 0.5053 (mmt180) REVERT: C 188 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7688 (mm-30) REVERT: D 76 ARG cc_start: 0.7417 (mtp180) cc_final: 0.7198 (mtp180) REVERT: D 188 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7379 (mm-30) REVERT: E 181 LYS cc_start: 0.8080 (mttt) cc_final: 0.7819 (mtpp) REVERT: F 196 PHE cc_start: 0.8989 (OUTLIER) cc_final: 0.8095 (t80) REVERT: F 260 LEU cc_start: 0.7611 (mp) cc_final: 0.7298 (mp) REVERT: G 124 ASP cc_start: 0.8400 (m-30) cc_final: 0.8171 (m-30) REVERT: G 203 ASP cc_start: 0.7511 (m-30) cc_final: 0.7186 (m-30) REVERT: G 254 ARG cc_start: 0.7984 (ttm170) cc_final: 0.7714 (mtt180) REVERT: G 256 LEU cc_start: 0.8468 (mt) cc_final: 0.8217 (mp) REVERT: H 140 MET cc_start: 0.8749 (ttm) cc_final: 0.8122 (ttm) REVERT: H 182 ARG cc_start: 0.7950 (mtm180) cc_final: 0.7665 (mtm180) outliers start: 38 outliers final: 32 residues processed: 264 average time/residue: 0.4275 time to fit residues: 152.0129 Evaluate side-chains 248 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 214 time to evaluate : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 206 ASN Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain F residue 196 PHE Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 196 PHE 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: 0.7980 chunk 38 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 197 optimal weight: 3.9990 chunk 163 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 chunk 65 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 185 GLN E 206 ASN ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.4166 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 : 0.453 5.640 24383 Z= 0.247 Chirality : 0.038 0.147 2754 Planarity : 0.004 0.040 2913 Dihedral : 18.157 179.460 2934 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.95 % Allowed : 13.62 % Favored : 84.43 % 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: 1.01 (0.15), residues: 1184 sheet: -0.11 (0.55), residues: 96 loop : 0.07 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 45 HIS 0.003 0.001 HIS A 43 PHE 0.015 0.001 PHE E 125 TYR 0.010 0.001 TYR H 93 ARG 0.005 0.000 ARG A 76 *********************** 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 266 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 231 time to evaluate : 2.471 Fit side-chains REVERT: A 184 GLU cc_start: 0.8011 (tt0) cc_final: 0.7761 (pt0) REVERT: B 217 LYS cc_start: 0.7164 (mmtt) cc_final: 0.6836 (mmtp) REVERT: B 261 LYS cc_start: 0.6837 (mttm) cc_final: 0.6582 (mmmt) REVERT: C 188 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7657 (mm-30) REVERT: D 185 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8313 (mt0) REVERT: D 188 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7395 (mm-30) REVERT: D 229 MET cc_start: 0.7360 (mtt) cc_final: 0.7127 (mtt) REVERT: E 181 LYS cc_start: 0.8068 (mttt) cc_final: 0.7822 (mtpp) REVERT: E 188 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7329 (mm-30) REVERT: F 196 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.8129 (t80) REVERT: F 229 MET cc_start: 0.8223 (mtt) cc_final: 0.7923 (mtt) REVERT: G 124 ASP cc_start: 0.8322 (m-30) cc_final: 0.8093 (m-30) REVERT: G 140 MET cc_start: 0.8650 (ttm) cc_final: 0.8357 (ttm) REVERT: G 203 ASP cc_start: 0.7464 (m-30) cc_final: 0.7187 (m-30) REVERT: G 254 ARG cc_start: 0.7947 (ttm170) cc_final: 0.7685 (mtt180) REVERT: G 256 LEU cc_start: 0.8441 (mt) cc_final: 0.8182 (mp) REVERT: H 140 MET cc_start: 0.8720 (ttm) cc_final: 0.8071 (ttm) outliers start: 35 outliers final: 27 residues processed: 255 average time/residue: 0.4264 time to fit residues: 147.7827 Evaluate side-chains 249 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 220 time to evaluate : 2.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 185 GLN Chi-restraints excluded: chain D residue 206 ASN Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain F residue 196 PHE Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 196 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 112 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 196 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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: 0.6995 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17971 Z= 0.198 Angle : 0.471 5.523 24383 Z= 0.254 Chirality : 0.039 0.150 2754 Planarity : 0.004 0.039 2913 Dihedral : 18.144 179.041 2934 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.29 % Allowed : 13.28 % Favored : 84.43 % 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: 0.85 (0.19), residues: 2040 helix: 1.05 (0.15), residues: 1184 sheet: -0.78 (0.44), residues: 136 loop : 0.23 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 45 HIS 0.004 0.001 HIS F 97 PHE 0.014 0.001 PHE E 125 TYR 0.011 0.001 TYR H 93 ARG 0.005 0.000 ARG D 258 *********************** 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 264 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 223 time to evaluate : 2.196 Fit side-chains REVERT: A 184 GLU cc_start: 0.8025 (tt0) cc_final: 0.7770 (pt0) REVERT: B 217 LYS cc_start: 0.7101 (mmtt) cc_final: 0.6789 (mmtp) REVERT: B 261 LYS cc_start: 0.6858 (mttm) cc_final: 0.6606 (mmmt) REVERT: C 188 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7640 (mm-30) REVERT: D 188 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7385 (mm-30) REVERT: E 181 LYS cc_start: 0.8071 (mttt) cc_final: 0.7828 (mtpp) REVERT: E 188 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7416 (mm-30) REVERT: F 196 PHE cc_start: 0.8954 (OUTLIER) cc_final: 0.8098 (t80) REVERT: G 124 ASP cc_start: 0.8362 (m-30) cc_final: 0.8123 (m-30) REVERT: G 140 MET cc_start: 0.8686 (ttm) cc_final: 0.8326 (ttm) REVERT: G 203 ASP cc_start: 0.7457 (m-30) cc_final: 0.7188 (m-30) REVERT: G 227 LYS cc_start: 0.7346 (ttpt) cc_final: 0.7059 (mmtm) REVERT: G 256 LEU cc_start: 0.8439 (mt) cc_final: 0.8203 (mp) REVERT: H 140 MET cc_start: 0.8733 (ttm) cc_final: 0.8081 (ttm) outliers start: 41 outliers final: 33 residues processed: 252 average time/residue: 0.4069 time to fit residues: 139.1530 Evaluate side-chains 250 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 216 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 206 ASN Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain F residue 196 PHE Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 225 LYS Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 196 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 59 optimal weight: 0.0470 chunk 38 optimal weight: 0.9990 chunk 125 optimal weight: 9.9990 chunk 133 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 overall best weight: 2.0086 ------------------------------------------------------------------------------- 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 98 GLN E 206 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.4513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17971 Z= 0.309 Angle : 0.564 6.382 24383 Z= 0.300 Chirality : 0.043 0.177 2754 Planarity : 0.005 0.053 2913 Dihedral : 18.358 178.750 2934 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.62 % Allowed : 13.17 % Favored : 84.21 % 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: 0.58 (0.18), residues: 2040 helix: 0.89 (0.15), residues: 1184 sheet: -1.17 (0.42), residues: 136 loop : 0.07 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 211 HIS 0.005 0.001 HIS F 97 PHE 0.019 0.002 PHE G 125 TYR 0.012 0.002 TYR H 93 ARG 0.006 0.001 ARG D 85 *********************** 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 269 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 222 time to evaluate : 2.198 Fit side-chains REVERT: A 196 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7866 (t80) REVERT: B 179 VAL cc_start: 0.8648 (t) cc_final: 0.8326 (t) REVERT: B 196 PHE cc_start: 0.9173 (OUTLIER) cc_final: 0.8348 (m-80) REVERT: B 217 LYS cc_start: 0.7025 (mmtt) cc_final: 0.6704 (mmtp) REVERT: C 85 ARG cc_start: 0.6005 (OUTLIER) cc_final: 0.4919 (mmt180) REVERT: C 203 ASP cc_start: 0.7573 (t0) cc_final: 0.7110 (t0) REVERT: D 170 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8426 (mt) REVERT: D 188 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7411 (mm-30) REVERT: D 213 GLN cc_start: 0.7024 (OUTLIER) cc_final: 0.6732 (mt0) REVERT: E 181 LYS cc_start: 0.8107 (mttt) cc_final: 0.7842 (mtpp) REVERT: F 196 PHE cc_start: 0.9025 (OUTLIER) cc_final: 0.8060 (t80) REVERT: F 260 LEU cc_start: 0.7557 (mp) cc_final: 0.7297 (mp) REVERT: G 124 ASP cc_start: 0.8409 (m-30) cc_final: 0.8193 (m-30) REVERT: G 140 MET cc_start: 0.8738 (ttm) cc_final: 0.8391 (ttm) REVERT: G 203 ASP cc_start: 0.7569 (m-30) cc_final: 0.7322 (m-30) REVERT: G 227 LYS cc_start: 0.7397 (ttpt) cc_final: 0.7086 (mmtm) REVERT: G 256 LEU cc_start: 0.8434 (mt) cc_final: 0.8195 (mp) REVERT: H 140 MET cc_start: 0.8673 (ttm) cc_final: 0.8025 (ttm) REVERT: H 148 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.6595 (ptp-170) REVERT: H 182 ARG cc_start: 0.7970 (mtm180) cc_final: 0.7716 (mtm-85) REVERT: H 246 GLU cc_start: 0.7006 (mt-10) cc_final: 0.6453 (mt-10) outliers start: 47 outliers final: 33 residues processed: 257 average time/residue: 0.4149 time to fit residues: 145.5070 Evaluate side-chains 256 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 216 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 206 ASN Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain E residue 127 ASP Chi-restraints excluded: chain F residue 196 PHE Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain G residue 174 ASP Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 194 LEU Chi-restraints excluded: chain H residue 196 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 0.0670 chunk 171 optimal weight: 0.0770 chunk 183 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 143 optimal weight: 0.2980 chunk 56 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 173 optimal weight: 7.9990 chunk 182 optimal weight: 0.7980 chunk 120 optimal weight: 0.6980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 206 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.4552 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= 0.139 Angle : 0.448 6.959 24383 Z= 0.243 Chirality : 0.038 0.137 2754 Planarity : 0.004 0.039 2913 Dihedral : 18.129 179.387 2934 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.51 % Allowed : 14.90 % Favored : 83.59 % 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 (0.19), residues: 2040 helix: 1.10 (0.15), residues: 1184 sheet: -0.61 (0.34), residues: 216 loop : 0.23 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 45 HIS 0.004 0.000 HIS B 43 PHE 0.013 0.001 PHE E 125 TYR 0.010 0.001 TYR F 75 ARG 0.006 0.000 ARG D 258 *********************** 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 263 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 236 time to evaluate : 2.184 Fit side-chains REVERT: B 179 VAL cc_start: 0.8438 (t) cc_final: 0.8107 (t) REVERT: B 217 LYS cc_start: 0.7169 (mmtt) cc_final: 0.6904 (mmtp) REVERT: B 261 LYS cc_start: 0.6002 (mmmt) cc_final: 0.5688 (mttm) REVERT: D 188 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7329 (mm-30) REVERT: D 213 GLN cc_start: 0.6974 (OUTLIER) cc_final: 0.6653 (mt0) REVERT: E 74 ARG cc_start: 0.7604 (ttp80) cc_final: 0.7401 (ttp-170) REVERT: E 181 LYS cc_start: 0.8052 (mttt) cc_final: 0.7811 (mtpp) REVERT: F 196 PHE cc_start: 0.8853 (OUTLIER) cc_final: 0.8049 (t80) REVERT: F 210 MET cc_start: 0.7794 (mtp) cc_final: 0.7579 (mtm) REVERT: F 260 LEU cc_start: 0.7524 (mp) cc_final: 0.7267 (mp) REVERT: G 124 ASP cc_start: 0.8232 (m-30) cc_final: 0.8014 (m-30) REVERT: G 140 MET cc_start: 0.8595 (ttm) cc_final: 0.8238 (ttm) REVERT: G 227 LYS cc_start: 0.7397 (ttpt) cc_final: 0.7085 (mmtm) REVERT: G 256 LEU cc_start: 0.8391 (mt) cc_final: 0.8136 (mp) REVERT: H 140 MET cc_start: 0.8642 (ttm) cc_final: 0.8140 (ttm) REVERT: H 148 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.6452 (ptp-170) outliers start: 27 outliers final: 23 residues processed: 253 average time/residue: 0.4044 time to fit residues: 139.4680 Evaluate side-chains 250 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 224 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 206 ASN Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain F residue 196 PHE Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 196 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 7.9990 chunk 118 optimal weight: 0.2980 chunk 91 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 203 optimal weight: 8.9990 chunk 187 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 125 optimal weight: 8.9990 chunk 99 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 H 269 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17971 Z= 0.170 Angle : 0.468 7.015 24383 Z= 0.251 Chirality : 0.039 0.142 2754 Planarity : 0.004 0.039 2913 Dihedral : 18.113 179.390 2934 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.40 % Allowed : 15.01 % Favored : 83.59 % 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: 1.15 (0.15), residues: 1184 sheet: -0.61 (0.34), residues: 216 loop : 0.23 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 45 HIS 0.002 0.001 HIS F 97 PHE 0.013 0.001 PHE E 125 TYR 0.010 0.001 TYR H 93 ARG 0.005 0.000 ARG D 258 ********************** 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 248 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 223 time to evaluate : 1.978 Fit side-chains REVERT: B 76 ARG cc_start: 0.7560 (mtp180) cc_final: 0.7358 (mtm110) REVERT: B 196 PHE cc_start: 0.9132 (OUTLIER) cc_final: 0.8313 (m-80) REVERT: B 217 LYS cc_start: 0.7238 (mmtt) cc_final: 0.6932 (mmtp) REVERT: B 261 LYS cc_start: 0.6160 (mmmt) cc_final: 0.5723 (mttm) REVERT: D 188 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7416 (mm-30) REVERT: D 213 GLN cc_start: 0.7017 (OUTLIER) cc_final: 0.6710 (mt0) REVERT: E 74 ARG cc_start: 0.7652 (ttp80) cc_final: 0.7410 (ttp-170) REVERT: F 210 MET cc_start: 0.7798 (mtp) cc_final: 0.7581 (mtm) REVERT: F 260 LEU cc_start: 0.7520 (mp) cc_final: 0.7268 (mp) REVERT: G 124 ASP cc_start: 0.8273 (m-30) cc_final: 0.8063 (m-30) REVERT: G 140 MET cc_start: 0.8709 (ttm) cc_final: 0.8323 (ttm) REVERT: G 227 LYS cc_start: 0.7422 (ttpt) cc_final: 0.7103 (mmtm) REVERT: G 256 LEU cc_start: 0.8400 (mt) cc_final: 0.8152 (mp) REVERT: H 140 MET cc_start: 0.8645 (ttm) cc_final: 0.8162 (ttm) REVERT: H 148 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.6503 (ptp-170) REVERT: H 182 ARG cc_start: 0.7855 (mtm180) cc_final: 0.7638 (mtm180) REVERT: H 246 GLU cc_start: 0.7025 (mt-10) cc_final: 0.6441 (mt-10) outliers start: 25 outliers final: 20 residues processed: 238 average time/residue: 0.4124 time to fit residues: 133.9981 Evaluate side-chains 238 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 215 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 206 ASN Chi-restraints excluded: chain D residue 213 GLN Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 148 ARG Chi-restraints excluded: chain H residue 196 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 149 optimal weight: 0.0270 chunk 23 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 162 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 overall best weight: 2.0044 ------------------------------------------------------------------------------- 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 77 HIS E 206 ASN ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.181014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.141588 restraints weight = 20620.669| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.59 r_work: 0.3532 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17971 Z= 0.311 Angle : 0.573 7.312 24383 Z= 0.303 Chirality : 0.043 0.171 2754 Planarity : 0.005 0.048 2913 Dihedral : 18.321 178.803 2934 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.43 % Favored : 96.52 % Rotamer: Outliers : 1.84 % Allowed : 14.62 % Favored : 83.54 % 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: 0.58 (0.19), residues: 2040 helix: 0.95 (0.15), residues: 1184 sheet: -0.84 (0.33), residues: 216 loop : 0.01 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 211 HIS 0.005 0.001 HIS F 97 PHE 0.020 0.002 PHE G 125 TYR 0.012 0.002 TYR H 93 ARG 0.006 0.001 ARG B 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4203.77 seconds wall clock time: 76 minutes 4.82 seconds (4564.82 seconds total)