Starting phenix.real_space_refine on Wed Feb 21 17:12:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbl_13294/02_2024/7pbl_13294_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbl_13294/02_2024/7pbl_13294.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/7pbl_13294/02_2024/7pbl_13294.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbl_13294/02_2024/7pbl_13294.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbl_13294/02_2024/7pbl_13294_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbl_13294/02_2024/7pbl_13294_neut_trim_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= 0.002 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: 7 Type Number sf(0) Gaussians P 45 5.49 5 Mg 3 5.21 5 S 100 5.16 5 C 9900 2.51 5 N 2683 2.21 5 O 3148 1.98 5 H 15439 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 299": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31318 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "B" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "C" Number of atoms: 4895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 4895 Classifications: {'peptide': 309} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 294} Chain breaks: 1 Chain: "D" Number of atoms: 4934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 4934 Classifications: {'peptide': 313} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 298} Chain: "E" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "F" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "G" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 719 Classifications: {'peptide': 48} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "U" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 479 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "V" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 474 Classifications: {'DNA': 15} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 14} Chain: "A" 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: "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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.13, per 1000 atoms: 0.48 Number of scatterers: 31318 At special positions: 0 Unit cell: (124.26, 138.43, 107.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 100 16.00 P 45 15.00 Mg 3 11.99 O 3148 8.00 N 2683 7.00 C 9900 6.00 H 15439 1.00 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: 24.70 Conformation dependent library (CDL) restraints added in 3.4 seconds 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3526 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 102 helices and 18 sheets defined 50.4% alpha, 11.0% beta 12 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 19.64 Creating SS restraints... Processing helix chain 'A' and resid 32 through 48 removed outlier: 3.607A pdb=" N GLN A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 76 removed outlier: 3.654A pdb=" N PHE A 70 " --> pdb=" O THR A 66 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 73 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 87 No H-bonds generated for 'chain 'A' and resid 85 through 87' Processing helix chain 'A' and resid 91 through 100 removed outlier: 3.610A pdb=" N ASP A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 117 through 129 removed outlier: 4.318A pdb=" N VAL A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A 123 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N SER A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 166 through 171 removed outlier: 3.943A pdb=" N ARG A 171 " --> pdb=" O PRO A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 196 removed outlier: 3.765A pdb=" N GLU A 188 " --> pdb=" O PRO A 184 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 212 removed outlier: 3.576A pdb=" N ARG A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 Processing helix chain 'A' and resid 241 through 251 removed outlier: 3.614A pdb=" N ASP A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 273 Processing helix chain 'A' and resid 280 through 287 removed outlier: 3.514A pdb=" N VAL A 285 " --> pdb=" O GLY A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 297 removed outlier: 3.615A pdb=" N GLU A 295 " --> pdb=" O ARG A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 319 through 325 Processing helix chain 'B' and resid 32 through 47 removed outlier: 3.552A pdb=" N ILE B 40 " --> pdb=" O ASP B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 76 removed outlier: 3.782A pdb=" N PHE B 70 " --> pdb=" O THR B 66 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 97 Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 117 through 129 removed outlier: 3.566A pdb=" N GLU B 121 " --> pdb=" O MET B 117 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N SER B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA B 126 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU B 128 " --> pdb=" O TYR B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 166 through 171 removed outlier: 3.847A pdb=" N ARG B 171 " --> pdb=" O PRO B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 196 Processing helix chain 'B' and resid 203 through 212 removed outlier: 3.775A pdb=" N ARG B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 Processing helix chain 'B' and resid 241 through 251 Processing helix chain 'B' and resid 260 through 272 Processing helix chain 'B' and resid 280 through 287 Processing helix chain 'B' and resid 291 through 297 removed outlier: 3.506A pdb=" N ASP B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 304 Processing helix chain 'B' and resid 319 through 325 Processing helix chain 'C' and resid 32 through 47 removed outlier: 3.553A pdb=" N ILE C 40 " --> pdb=" O ASP C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 76 removed outlier: 3.659A pdb=" N PHE C 70 " --> pdb=" O THR C 66 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 100 removed outlier: 3.819A pdb=" N ASP C 100 " --> pdb=" O ALA C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 114 No H-bonds generated for 'chain 'C' and resid 112 through 114' Processing helix chain 'C' and resid 117 through 129 removed outlier: 4.004A pdb=" N VAL C 122 " --> pdb=" O ALA C 118 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU C 128 " --> pdb=" O TYR C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 163 No H-bonds generated for 'chain 'C' and resid 161 through 163' Processing helix chain 'C' and resid 166 through 171 removed outlier: 3.726A pdb=" N ARG C 171 " --> pdb=" O PRO C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 196 Processing helix chain 'C' and resid 203 through 210 removed outlier: 3.586A pdb=" N LEU C 207 " --> pdb=" O PRO C 203 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU C 208 " --> pdb=" O GLU C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 234 Processing helix chain 'C' and resid 241 through 251 removed outlier: 3.697A pdb=" N ASP C 245 " --> pdb=" O ASP C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 272 Processing helix chain 'C' and resid 280 through 286 Processing helix chain 'C' and resid 291 through 297 Processing helix chain 'C' and resid 299 through 304 Processing helix chain 'C' and resid 319 through 325 Processing helix chain 'D' and resid 32 through 46 removed outlier: 3.738A pdb=" N ILE D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 76 removed outlier: 3.511A pdb=" N ALA D 69 " --> pdb=" O LYS D 65 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE D 70 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 87 No H-bonds generated for 'chain 'D' and resid 85 through 87' Processing helix chain 'D' and resid 91 through 100 removed outlier: 3.774A pdb=" N ASP D 100 " --> pdb=" O ALA D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 114 No H-bonds generated for 'chain 'D' and resid 112 through 114' Processing helix chain 'D' and resid 117 through 129 removed outlier: 3.667A pdb=" N GLU D 121 " --> pdb=" O MET D 117 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N VAL D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 171 removed outlier: 3.588A pdb=" N ARG D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 195 removed outlier: 4.093A pdb=" N GLU D 188 " --> pdb=" O PRO D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 212 removed outlier: 3.676A pdb=" N ARG D 212 " --> pdb=" O GLU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 231 removed outlier: 3.558A pdb=" N TYR D 230 " --> pdb=" O ARG D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 250 Processing helix chain 'D' and resid 260 through 273 Processing helix chain 'D' and resid 280 through 287 Processing helix chain 'D' and resid 291 through 296 Processing helix chain 'D' and resid 299 through 304 Processing helix chain 'D' and resid 319 through 325 Processing helix chain 'E' and resid 32 through 48 removed outlier: 3.736A pdb=" N ILE E 40 " --> pdb=" O ASP E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 76 Processing helix chain 'E' and resid 85 through 87 No H-bonds generated for 'chain 'E' and resid 85 through 87' Processing helix chain 'E' and resid 91 through 99 Processing helix chain 'E' and resid 117 through 128 removed outlier: 3.869A pdb=" N GLU E 121 " --> pdb=" O MET E 117 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU E 123 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER E 125 " --> pdb=" O GLU E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 171 removed outlier: 3.715A pdb=" N ARG E 171 " --> pdb=" O PRO E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 196 removed outlier: 3.830A pdb=" N ILE E 196 " --> pdb=" O ARG E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 212 removed outlier: 3.527A pdb=" N LEU E 207 " --> pdb=" O PRO E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 234 removed outlier: 3.819A pdb=" N ILE E 233 " --> pdb=" O ASP E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 250 Processing helix chain 'E' and resid 260 through 273 Processing helix chain 'E' and resid 280 through 286 Processing helix chain 'E' and resid 291 through 297 Processing helix chain 'E' and resid 299 through 304 Processing helix chain 'E' and resid 319 through 325 Processing helix chain 'F' and resid 32 through 47 removed outlier: 3.545A pdb=" N GLN F 37 " --> pdb=" O LYS F 33 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE F 40 " --> pdb=" O ASP F 36 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU F 47 " --> pdb=" O GLU F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 76 removed outlier: 3.574A pdb=" N PHE F 70 " --> pdb=" O THR F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 87 No H-bonds generated for 'chain 'F' and resid 85 through 87' Processing helix chain 'F' and resid 91 through 100 removed outlier: 3.603A pdb=" N ASP F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 114 No H-bonds generated for 'chain 'F' and resid 112 through 114' Processing helix chain 'F' and resid 117 through 129 removed outlier: 4.627A pdb=" N VAL F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR F 124 " --> pdb=" O GLU F 120 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA F 126 " --> pdb=" O VAL F 122 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU F 128 " --> pdb=" O TYR F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 141 No H-bonds generated for 'chain 'F' and resid 139 through 141' Processing helix chain 'F' and resid 161 through 163 No H-bonds generated for 'chain 'F' and resid 161 through 163' Processing helix chain 'F' and resid 166 through 171 removed outlier: 3.819A pdb=" N ARG F 171 " --> pdb=" O PRO F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 196 Processing helix chain 'F' and resid 203 through 211 Processing helix chain 'F' and resid 217 through 233 Processing helix chain 'F' and resid 241 through 250 Processing helix chain 'F' and resid 260 through 272 Processing helix chain 'F' and resid 280 through 287 Processing helix chain 'F' and resid 291 through 296 Processing helix chain 'F' and resid 299 through 304 Processing helix chain 'F' and resid 319 through 325 Processing helix chain 'G' and resid 157 through 169 Processing helix chain 'G' and resid 174 through 182 Processing helix chain 'G' and resid 191 through 201 Processing sheet with id= A, first strand: chain 'A' and resid 174 through 177 removed outlier: 3.550A pdb=" N ALA A 157 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP A 110 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 131 through 137 Processing sheet with id= C, first strand: chain 'A' and resid 308 through 311 Processing sheet with id= D, first strand: chain 'B' and resid 174 through 177 removed outlier: 3.607A pdb=" N ALA B 157 " --> pdb=" O ILE B 109 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 131 through 136 Processing sheet with id= F, first strand: chain 'B' and resid 308 through 311 Processing sheet with id= G, first strand: chain 'C' and resid 174 through 177 removed outlier: 3.533A pdb=" N ALA C 157 " --> pdb=" O ILE C 109 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 131 through 136 Processing sheet with id= I, first strand: chain 'C' and resid 308 through 311 Processing sheet with id= J, first strand: chain 'D' and resid 174 through 177 Processing sheet with id= K, first strand: chain 'D' and resid 131 through 136 Processing sheet with id= L, first strand: chain 'D' and resid 308 through 311 Processing sheet with id= M, first strand: chain 'E' and resid 174 through 177 Processing sheet with id= N, first strand: chain 'E' and resid 131 through 136 Processing sheet with id= O, first strand: chain 'E' and resid 308 through 311 Processing sheet with id= P, first strand: chain 'F' and resid 174 through 177 Processing sheet with id= Q, first strand: chain 'F' and resid 131 through 136 Processing sheet with id= R, first strand: chain 'F' and resid 308 through 311 645 hydrogen bonds defined for protein. 1884 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 12.20 Time building geometry restraints manager: 25.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 15439 1.06 - 1.28: 2655 1.28 - 1.50: 6776 1.50 - 1.73: 6592 1.73 - 1.95: 197 Bond restraints: 31659 Sorted by residual: bond pdb=" N THR E 19 " pdb=" H1 THR E 19 " ideal model delta sigma weight residual 0.960 0.859 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" N THR C 19 " pdb=" H1 THR C 19 " ideal model delta sigma weight residual 0.960 0.859 0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" N SER G 156 " pdb=" H1 SER G 156 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N THR D 19 " pdb=" H1 THR D 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" N THR F 19 " pdb=" H1 THR F 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 ... (remaining 31654 not shown) Histogram of bond angle deviations from ideal: 99.13 - 106.59: 736 106.59 - 114.04: 38386 114.04 - 121.50: 12358 121.50 - 128.95: 5744 128.95 - 136.41: 83 Bond angle restraints: 57307 Sorted by residual: angle pdb=" OP1 DT V 4 " pdb=" P DT V 4 " pdb=" OP2 DT V 4 " ideal model delta sigma weight residual 120.00 109.84 10.16 3.00e+00 1.11e-01 1.15e+01 angle pdb=" N LEU D 251 " pdb=" CA LEU D 251 " pdb=" C LEU D 251 " ideal model delta sigma weight residual 110.50 106.07 4.43 1.41e+00 5.03e-01 9.89e+00 angle pdb=" C1' ADP D 600 " pdb=" C2' ADP D 600 " pdb=" C3' ADP D 600 " ideal model delta sigma weight residual 111.00 101.71 9.29 3.00e+00 1.11e-01 9.59e+00 angle pdb=" N PHE B 197 " pdb=" CA PHE B 197 " pdb=" C PHE B 197 " ideal model delta sigma weight residual 110.35 106.13 4.22 1.38e+00 5.25e-01 9.34e+00 angle pdb=" CA TYR C 124 " pdb=" CB TYR C 124 " pdb=" CG TYR C 124 " ideal model delta sigma weight residual 113.90 119.08 -5.18 1.80e+00 3.09e-01 8.28e+00 ... (remaining 57302 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.95: 14102 31.95 - 63.90: 548 63.90 - 95.84: 25 95.84 - 127.79: 2 127.79 - 159.74: 4 Dihedral angle restraints: 14681 sinusoidal: 8412 harmonic: 6269 Sorted by residual: dihedral pdb=" O2A ADP F 600 " pdb=" O3A ADP F 600 " pdb=" PA ADP F 600 " pdb=" PB ADP F 600 " ideal model delta sinusoidal sigma weight residual -60.00 99.74 -159.74 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" O2A ADP E 600 " pdb=" O3A ADP E 600 " pdb=" PA ADP E 600 " pdb=" PB ADP E 600 " ideal model delta sinusoidal sigma weight residual -60.00 81.44 -141.44 1 2.00e+01 2.50e-03 4.28e+01 dihedral pdb=" C5' ADP D 600 " pdb=" O5' ADP D 600 " pdb=" PA ADP D 600 " pdb=" O2A ADP D 600 " ideal model delta sinusoidal sigma weight residual -60.00 36.91 -96.91 1 2.00e+01 2.50e-03 2.69e+01 ... (remaining 14678 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2224 0.072 - 0.144: 266 0.144 - 0.215: 3 0.215 - 0.287: 0 0.287 - 0.359: 1 Chirality restraints: 2494 Sorted by residual: chirality pdb=" P DT V 4 " pdb=" OP1 DT V 4 " pdb=" OP2 DT V 4 " pdb=" O5' DT V 4 " both_signs ideal model delta sigma weight residual True 2.35 -2.70 -0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CA ARG B 114 " pdb=" N ARG B 114 " pdb=" C ARG B 114 " pdb=" CB ARG B 114 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.17e-01 chirality pdb=" CA TYR C 124 " pdb=" N TYR C 124 " pdb=" C TYR C 124 " pdb=" CB TYR C 124 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.79e-01 ... (remaining 2491 not shown) Planarity restraints: 4586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 192 " 0.143 9.50e-02 1.11e+02 6.44e-02 4.44e+01 pdb=" NE ARG A 192 " 0.004 2.00e-02 2.50e+03 pdb=" CZ ARG A 192 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 192 " 0.045 2.00e-02 2.50e+03 pdb=" NH2 ARG A 192 " -0.077 2.00e-02 2.50e+03 pdb="HH11 ARG A 192 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG A 192 " -0.051 2.00e-02 2.50e+03 pdb="HH21 ARG A 192 " -0.003 2.00e-02 2.50e+03 pdb="HH22 ARG A 192 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 232 " -0.044 2.00e-02 2.50e+03 5.42e-02 4.40e+01 pdb=" CD GLN D 232 " 0.040 2.00e-02 2.50e+03 pdb=" OE1 GLN D 232 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 GLN D 232 " 0.085 2.00e-02 2.50e+03 pdb="HE21 GLN D 232 " 0.003 2.00e-02 2.50e+03 pdb="HE22 GLN D 232 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 31 " 0.043 2.00e-02 2.50e+03 5.29e-02 4.20e+01 pdb=" CD GLN C 31 " -0.037 2.00e-02 2.50e+03 pdb=" OE1 GLN C 31 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 GLN C 31 " -0.083 2.00e-02 2.50e+03 pdb="HE21 GLN C 31 " -0.003 2.00e-02 2.50e+03 pdb="HE22 GLN C 31 " 0.081 2.00e-02 2.50e+03 ... (remaining 4583 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 582 2.11 - 2.73: 53092 2.73 - 3.35: 84015 3.35 - 3.98: 106600 3.98 - 4.60: 172534 Nonbonded interactions: 416823 Sorted by model distance: nonbonded pdb=" OE1 GLU D 121 " pdb=" HH TYR D 124 " model vdw 1.487 1.850 nonbonded pdb=" HG1 THR A 311 " pdb=" O GLY A 314 " model vdw 1.518 1.850 nonbonded pdb=" HZ1 LYS F 81 " pdb=" O ASP F 100 " model vdw 1.543 1.850 nonbonded pdb=" HZ3 LYS E 90 " pdb=" OD1 ASP E 93 " model vdw 1.562 1.850 nonbonded pdb=" O ALA F 138 " pdb=" HG1 THR F 141 " model vdw 1.569 1.850 ... (remaining 416818 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'B' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'C' and resid 19 through 330) selection = (chain 'D' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'E' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'F' and (resid 19 through 136 or resid 141 through 330)) } 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: 2.440 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: 0.470 Extract box with map and model: 10.110 Check model and map are aligned: 0.500 Set scattering table: 0.310 Process input model: 114.290 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 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 : 0.004 0.034 16220 Z= 0.245 Angle : 0.696 10.160 22091 Z= 0.396 Chirality : 0.044 0.359 2494 Planarity : 0.010 0.132 2739 Dihedral : 14.609 159.741 6269 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.06 % Allowed : 1.25 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.65 (0.18), residues: 1902 helix: -0.88 (0.14), residues: 1009 sheet: 0.16 (0.28), residues: 322 loop : 0.57 (0.27), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.003 HIS F 54 PHE 0.018 0.003 PHE F 25 TYR 0.036 0.005 TYR E 131 ARG 0.033 0.003 ARG F 312 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 426 time to evaluate : 2.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8067 (mt-10) REVERT: A 256 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8307 (mm-30) REVERT: B 49 ASP cc_start: 0.7646 (t0) cc_final: 0.7397 (t0) REVERT: C 124 TYR cc_start: 0.8404 (p90) cc_final: 0.8159 (p90) REVERT: D 245 ASP cc_start: 0.7716 (m-30) cc_final: 0.7298 (m-30) REVERT: D 250 MET cc_start: 0.8836 (ttp) cc_final: 0.8600 (ttp) REVERT: D 290 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7492 (mm-30) REVERT: D 305 LYS cc_start: 0.8482 (mmmt) cc_final: 0.8256 (mtpp) REVERT: D 309 MET cc_start: 0.8673 (mtp) cc_final: 0.8460 (mtm) REVERT: E 135 MET cc_start: 0.1184 (mtm) cc_final: 0.0910 (mtm) REVERT: E 291 ARG cc_start: 0.8214 (ptm-80) cc_final: 0.7851 (ptm160) REVERT: F 125 SER cc_start: 0.9078 (m) cc_final: 0.8856 (p) REVERT: F 222 ARG cc_start: 0.8522 (ttp-110) cc_final: 0.8302 (ttm-80) REVERT: F 236 ASP cc_start: 0.7209 (m-30) cc_final: 0.6635 (p0) outliers start: 1 outliers final: 1 residues processed: 427 average time/residue: 0.8192 time to fit residues: 478.1848 Evaluate side-chains 276 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 275 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 286 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 161 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 ASN C 82 GLN D 82 GLN E 31 GLN F 286 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16220 Z= 0.266 Angle : 0.617 6.545 22091 Z= 0.329 Chirality : 0.042 0.146 2494 Planarity : 0.005 0.049 2739 Dihedral : 14.524 158.722 2545 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.37 % Allowed : 6.80 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 0.59 (0.19), residues: 1902 helix: 0.49 (0.16), residues: 1010 sheet: 0.35 (0.29), residues: 320 loop : 0.60 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 113 PHE 0.007 0.001 PHE B 108 TYR 0.027 0.001 TYR C 124 ARG 0.005 0.001 ARG G 196 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 287 time to evaluate : 2.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8168 (mm-30) REVERT: A 309 MET cc_start: 0.7734 (ttm) cc_final: 0.7435 (ttp) REVERT: B 49 ASP cc_start: 0.7790 (t0) cc_final: 0.7587 (t0) REVERT: C 81 LYS cc_start: 0.8096 (mptt) cc_final: 0.7570 (mttt) REVERT: C 124 TYR cc_start: 0.8587 (p90) cc_final: 0.8384 (p90) REVERT: D 245 ASP cc_start: 0.7816 (m-30) cc_final: 0.7382 (m-30) REVERT: E 135 MET cc_start: 0.1351 (mtm) cc_final: 0.0902 (mtm) REVERT: E 252 ASP cc_start: 0.8402 (t0) cc_final: 0.8082 (t0) REVERT: F 117 MET cc_start: 0.7360 (tpp) cc_final: 0.6272 (tpp) REVERT: F 125 SER cc_start: 0.9149 (m) cc_final: 0.8907 (p) REVERT: F 222 ARG cc_start: 0.8256 (ttp-110) cc_final: 0.8035 (ttm-80) REVERT: F 236 ASP cc_start: 0.7384 (m-30) cc_final: 0.6800 (p0) REVERT: G 179 ARG cc_start: 0.7751 (ttt-90) cc_final: 0.7527 (ttt-90) outliers start: 22 outliers final: 16 residues processed: 298 average time/residue: 0.7988 time to fit residues: 334.1939 Evaluate side-chains 278 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 262 time to evaluate : 2.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain D residue 292 GLU Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain F residue 160 ARG Chi-restraints excluded: chain G residue 180 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 96 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 144 optimal weight: 2.9990 chunk 118 optimal weight: 0.0970 chunk 47 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 chunk 187 optimal weight: 0.7980 chunk 154 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN D 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16220 Z= 0.195 Angle : 0.552 6.023 22091 Z= 0.288 Chirality : 0.040 0.142 2494 Planarity : 0.004 0.039 2739 Dihedral : 14.435 158.805 2545 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.00 % Allowed : 8.17 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.19), residues: 1902 helix: 0.97 (0.17), residues: 1010 sheet: 0.47 (0.29), residues: 328 loop : 0.51 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 146 PHE 0.012 0.001 PHE E 152 TYR 0.019 0.001 TYR C 124 ARG 0.007 0.000 ARG F 267 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 272 time to evaluate : 2.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8123 (mm-30) REVERT: A 309 MET cc_start: 0.7729 (ttm) cc_final: 0.7437 (ttp) REVERT: B 49 ASP cc_start: 0.7816 (t0) cc_final: 0.7615 (t0) REVERT: C 81 LYS cc_start: 0.8088 (mptt) cc_final: 0.7574 (mttt) REVERT: C 272 MET cc_start: 0.7905 (mtp) cc_final: 0.7646 (mtp) REVERT: D 245 ASP cc_start: 0.7822 (m-30) cc_final: 0.7383 (m-30) REVERT: E 111 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7624 (mt-10) REVERT: E 114 ARG cc_start: 0.7725 (mmp80) cc_final: 0.7447 (mmp80) REVERT: E 135 MET cc_start: 0.1192 (mtm) cc_final: 0.0843 (mtm) REVERT: E 252 ASP cc_start: 0.8430 (t0) cc_final: 0.8128 (t0) REVERT: F 125 SER cc_start: 0.9112 (m) cc_final: 0.8891 (p) REVERT: F 236 ASP cc_start: 0.7476 (m-30) cc_final: 0.6942 (p0) outliers start: 16 outliers final: 12 residues processed: 282 average time/residue: 0.7686 time to fit residues: 300.9407 Evaluate side-chains 270 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 258 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain F residue 160 ARG Chi-restraints excluded: chain G residue 180 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 171 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 174 optimal weight: 0.9990 chunk 184 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16220 Z= 0.243 Angle : 0.551 5.987 22091 Z= 0.288 Chirality : 0.040 0.145 2494 Planarity : 0.004 0.041 2739 Dihedral : 14.416 160.953 2545 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.37 % Allowed : 8.30 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.19), residues: 1902 helix: 1.15 (0.17), residues: 1008 sheet: 0.44 (0.29), residues: 322 loop : 0.39 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 146 PHE 0.006 0.001 PHE B 307 TYR 0.018 0.001 TYR C 124 ARG 0.007 0.000 ARG F 267 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 266 time to evaluate : 2.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 144 SER cc_start: 0.8524 (p) cc_final: 0.7821 (t) REVERT: B 178 MET cc_start: 0.9231 (mmt) cc_final: 0.8974 (mmt) REVERT: B 188 GLU cc_start: 0.7051 (mp0) cc_final: 0.6750 (mp0) REVERT: C 81 LYS cc_start: 0.8148 (mptt) cc_final: 0.7650 (mttt) REVERT: D 21 ARG cc_start: 0.7414 (ttp80) cc_final: 0.7154 (ttp80) REVERT: D 121 GLU cc_start: 0.7898 (mp0) cc_final: 0.7698 (mp0) REVERT: E 111 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7638 (mt-10) REVERT: E 135 MET cc_start: 0.1218 (mtm) cc_final: 0.0851 (mtm) REVERT: E 252 ASP cc_start: 0.8473 (t0) cc_final: 0.8196 (t0) REVERT: F 125 SER cc_start: 0.9137 (m) cc_final: 0.8931 (p) REVERT: F 236 ASP cc_start: 0.7533 (m-30) cc_final: 0.6930 (p0) REVERT: F 273 TYR cc_start: 0.7208 (m-80) cc_final: 0.6781 (m-80) outliers start: 22 outliers final: 20 residues processed: 279 average time/residue: 0.7768 time to fit residues: 303.5152 Evaluate side-chains 276 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 256 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 124 TYR Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 160 ARG Chi-restraints excluded: chain G residue 180 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 153 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 76 optimal weight: 0.0050 chunk 157 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16220 Z= 0.207 Angle : 0.537 7.532 22091 Z= 0.278 Chirality : 0.039 0.141 2494 Planarity : 0.004 0.044 2739 Dihedral : 14.354 161.585 2545 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.43 % Allowed : 9.23 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.19), residues: 1902 helix: 1.27 (0.17), residues: 1009 sheet: 0.41 (0.29), residues: 324 loop : 0.41 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 146 PHE 0.005 0.001 PHE B 307 TYR 0.016 0.001 TYR D 124 ARG 0.006 0.000 ARG F 267 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 262 time to evaluate : 2.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 144 SER cc_start: 0.8529 (p) cc_final: 0.7920 (t) REVERT: B 178 MET cc_start: 0.9223 (mmt) cc_final: 0.8976 (mmt) REVERT: B 188 GLU cc_start: 0.7039 (mp0) cc_final: 0.6737 (mp0) REVERT: C 81 LYS cc_start: 0.8158 (mptt) cc_final: 0.7668 (mttt) REVERT: D 121 GLU cc_start: 0.7872 (mp0) cc_final: 0.7667 (mp0) REVERT: D 160 ARG cc_start: 0.7362 (ttm110) cc_final: 0.7030 (mtm-85) REVERT: E 111 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7592 (mt-10) REVERT: E 114 ARG cc_start: 0.7917 (mmp80) cc_final: 0.7548 (mmp80) REVERT: E 135 MET cc_start: 0.1234 (mtm) cc_final: 0.0918 (mtm) REVERT: E 252 ASP cc_start: 0.8481 (t0) cc_final: 0.8202 (t0) REVERT: F 236 ASP cc_start: 0.7556 (m-30) cc_final: 0.6934 (p0) REVERT: F 267 ARG cc_start: 0.7915 (ttp-110) cc_final: 0.7696 (ttm110) REVERT: F 273 TYR cc_start: 0.7340 (m-80) cc_final: 0.6935 (m-80) outliers start: 23 outliers final: 21 residues processed: 274 average time/residue: 0.7453 time to fit residues: 287.0113 Evaluate side-chains 272 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 251 time to evaluate : 2.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 199 MET Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 160 ARG Chi-restraints excluded: chain G residue 180 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 62 optimal weight: 0.9980 chunk 166 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 184 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 54 HIS D 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16220 Z= 0.248 Angle : 0.544 7.776 22091 Z= 0.282 Chirality : 0.040 0.139 2494 Planarity : 0.004 0.047 2739 Dihedral : 14.343 163.265 2545 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.81 % Allowed : 9.11 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.19), residues: 1902 helix: 1.33 (0.17), residues: 1009 sheet: 0.34 (0.29), residues: 322 loop : 0.33 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 146 PHE 0.016 0.001 PHE E 58 TYR 0.017 0.001 TYR C 124 ARG 0.006 0.000 ARG D 114 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 257 time to evaluate : 2.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 178 MET cc_start: 0.9218 (mmt) cc_final: 0.8978 (mmt) REVERT: B 188 GLU cc_start: 0.7103 (mp0) cc_final: 0.6833 (mp0) REVERT: C 81 LYS cc_start: 0.8229 (mptt) cc_final: 0.7751 (mttt) REVERT: C 272 MET cc_start: 0.7853 (mtp) cc_final: 0.7624 (mtp) REVERT: D 121 GLU cc_start: 0.7905 (mp0) cc_final: 0.7674 (mp0) REVERT: E 111 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7631 (mt-10) REVERT: E 114 ARG cc_start: 0.7876 (mmp80) cc_final: 0.7522 (mmp80) REVERT: E 252 ASP cc_start: 0.8492 (t0) cc_final: 0.8170 (t0) REVERT: F 163 MET cc_start: 0.8473 (tpp) cc_final: 0.8202 (mmm) REVERT: F 236 ASP cc_start: 0.7620 (m-30) cc_final: 0.6915 (p0) REVERT: F 273 TYR cc_start: 0.7392 (m-80) cc_final: 0.6973 (m-80) REVERT: G 179 ARG cc_start: 0.7744 (ttt-90) cc_final: 0.7541 (ttt-90) outliers start: 29 outliers final: 25 residues processed: 272 average time/residue: 0.7557 time to fit residues: 288.6085 Evaluate side-chains 280 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 255 time to evaluate : 2.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 199 MET Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 160 ARG Chi-restraints excluded: chain F residue 262 ASP Chi-restraints excluded: chain F residue 308 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 178 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 155 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN D 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16220 Z= 0.215 Angle : 0.531 7.789 22091 Z= 0.274 Chirality : 0.039 0.130 2494 Planarity : 0.004 0.046 2739 Dihedral : 14.289 163.316 2545 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.87 % Allowed : 9.61 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.19), residues: 1902 helix: 1.44 (0.17), residues: 1006 sheet: 0.30 (0.29), residues: 316 loop : 0.33 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 146 PHE 0.005 0.001 PHE F 108 TYR 0.016 0.001 TYR C 124 ARG 0.005 0.000 ARG F 267 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 261 time to evaluate : 2.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 178 MET cc_start: 0.9205 (mmt) cc_final: 0.8966 (mmt) REVERT: B 188 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6856 (mp0) REVERT: B 290 GLU cc_start: 0.6753 (tm-30) cc_final: 0.6083 (mt-10) REVERT: C 81 LYS cc_start: 0.8145 (mptt) cc_final: 0.7721 (mttt) REVERT: C 272 MET cc_start: 0.7854 (mtp) cc_final: 0.7638 (mtp) REVERT: D 121 GLU cc_start: 0.7946 (mp0) cc_final: 0.7693 (mp0) REVERT: E 111 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7605 (mt-10) REVERT: E 114 ARG cc_start: 0.7876 (mmp80) cc_final: 0.7521 (mmp80) REVERT: E 252 ASP cc_start: 0.8521 (t0) cc_final: 0.8201 (t0) REVERT: F 236 ASP cc_start: 0.7666 (m-30) cc_final: 0.6919 (p0) REVERT: F 273 TYR cc_start: 0.7304 (m-80) cc_final: 0.7035 (m-80) REVERT: F 305 LYS cc_start: 0.8827 (mmmt) cc_final: 0.8591 (mtpp) outliers start: 30 outliers final: 25 residues processed: 277 average time/residue: 0.7706 time to fit residues: 298.7041 Evaluate side-chains 283 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 257 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 160 ARG Chi-restraints excluded: chain F residue 262 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 113 optimal weight: 1.9990 chunk 73 optimal weight: 0.3980 chunk 109 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 117 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN D 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16220 Z= 0.203 Angle : 0.527 8.009 22091 Z= 0.271 Chirality : 0.039 0.130 2494 Planarity : 0.004 0.047 2739 Dihedral : 14.240 162.876 2545 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.56 % Allowed : 10.17 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.19), residues: 1902 helix: 1.52 (0.17), residues: 1006 sheet: 0.28 (0.29), residues: 307 loop : 0.33 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 146 PHE 0.005 0.001 PHE E 58 TYR 0.016 0.001 TYR C 124 ARG 0.008 0.000 ARG F 267 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 260 time to evaluate : 2.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 178 MET cc_start: 0.9217 (mmt) cc_final: 0.8971 (mmt) REVERT: B 188 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6852 (mp0) REVERT: B 292 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6812 (pm20) REVERT: C 81 LYS cc_start: 0.8147 (mptt) cc_final: 0.7719 (mttt) REVERT: D 121 GLU cc_start: 0.7949 (mp0) cc_final: 0.7686 (mp0) REVERT: E 111 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7593 (mt-10) REVERT: E 114 ARG cc_start: 0.7867 (mmp80) cc_final: 0.7508 (mmp80) REVERT: E 252 ASP cc_start: 0.8523 (t0) cc_final: 0.8202 (t0) REVERT: F 236 ASP cc_start: 0.7678 (m-30) cc_final: 0.6909 (p0) REVERT: F 273 TYR cc_start: 0.7335 (m-80) cc_final: 0.7069 (m-80) outliers start: 25 outliers final: 22 residues processed: 273 average time/residue: 0.7928 time to fit residues: 302.9091 Evaluate side-chains 281 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 257 time to evaluate : 2.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 199 MET Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain F residue 160 ARG Chi-restraints excluded: chain F residue 262 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 167 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 162 optimal weight: 0.5980 chunk 170 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN D 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16220 Z= 0.202 Angle : 0.524 8.139 22091 Z= 0.269 Chirality : 0.039 0.130 2494 Planarity : 0.004 0.047 2739 Dihedral : 14.206 162.969 2545 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.62 % Allowed : 10.48 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.19), residues: 1902 helix: 1.60 (0.17), residues: 1006 sheet: 0.28 (0.29), residues: 307 loop : 0.34 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 146 PHE 0.006 0.001 PHE C 25 TYR 0.015 0.001 TYR C 124 ARG 0.007 0.000 ARG F 267 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 262 time to evaluate : 2.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 178 MET cc_start: 0.9216 (mmt) cc_final: 0.8975 (mmt) REVERT: B 188 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6855 (mp0) REVERT: C 81 LYS cc_start: 0.8174 (mptt) cc_final: 0.7749 (mttt) REVERT: D 121 GLU cc_start: 0.7952 (mp0) cc_final: 0.7695 (mp0) REVERT: E 111 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7593 (mt-10) REVERT: E 114 ARG cc_start: 0.7872 (mmp80) cc_final: 0.7509 (mmp80) REVERT: E 252 ASP cc_start: 0.8525 (t0) cc_final: 0.8209 (t0) REVERT: F 236 ASP cc_start: 0.7737 (m-30) cc_final: 0.6951 (p0) REVERT: F 273 TYR cc_start: 0.7339 (m-80) cc_final: 0.7083 (m-80) outliers start: 26 outliers final: 23 residues processed: 275 average time/residue: 0.7361 time to fit residues: 282.2153 Evaluate side-chains 277 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 253 time to evaluate : 2.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 199 MET Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 262 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 112 optimal weight: 0.9980 chunk 181 optimal weight: 6.9990 chunk 110 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN D 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16220 Z= 0.237 Angle : 0.535 8.363 22091 Z= 0.275 Chirality : 0.040 0.132 2494 Planarity : 0.005 0.060 2739 Dihedral : 14.241 164.170 2545 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.50 % Allowed : 10.48 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.20), residues: 1902 helix: 1.56 (0.17), residues: 1006 sheet: 0.28 (0.29), residues: 307 loop : 0.25 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 146 PHE 0.006 0.001 PHE F 108 TYR 0.017 0.001 TYR C 124 ARG 0.008 0.000 ARG F 267 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 256 time to evaluate : 2.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 144 SER cc_start: 0.8539 (p) cc_final: 0.7896 (t) REVERT: B 178 MET cc_start: 0.9218 (mmt) cc_final: 0.8980 (mmt) REVERT: B 188 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6895 (mp0) REVERT: C 81 LYS cc_start: 0.8176 (mptt) cc_final: 0.7758 (mttt) REVERT: D 121 GLU cc_start: 0.7973 (mp0) cc_final: 0.7700 (mp0) REVERT: E 111 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7612 (mt-10) REVERT: E 114 ARG cc_start: 0.7868 (mmp80) cc_final: 0.7504 (mmp80) REVERT: E 252 ASP cc_start: 0.8530 (t0) cc_final: 0.8213 (t0) REVERT: E 290 GLU cc_start: 0.7581 (mp0) cc_final: 0.7085 (mt-10) REVERT: F 236 ASP cc_start: 0.7793 (m-30) cc_final: 0.6971 (p0) outliers start: 24 outliers final: 23 residues processed: 270 average time/residue: 0.7494 time to fit residues: 284.0551 Evaluate side-chains 278 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 254 time to evaluate : 2.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 194 SER Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 286 ASN Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 93 ASP Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 199 MET Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 262 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 120 optimal weight: 0.3980 chunk 161 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 42 optimal weight: 0.1980 chunk 151 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 155 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN D 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.116331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.082164 restraints weight = 73004.706| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.52 r_work: 0.2803 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16220 Z= 0.172 Angle : 0.519 8.356 22091 Z= 0.264 Chirality : 0.039 0.127 2494 Planarity : 0.004 0.056 2739 Dihedral : 14.165 162.713 2545 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.31 % Allowed : 10.92 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.20), residues: 1902 helix: 1.67 (0.17), residues: 1008 sheet: 0.28 (0.29), residues: 307 loop : 0.36 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 146 PHE 0.009 0.001 PHE F 197 TYR 0.015 0.001 TYR D 124 ARG 0.010 0.000 ARG F 267 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8044.10 seconds wall clock time: 142 minutes 32.10 seconds (8552.10 seconds total)