Starting phenix.real_space_refine on Wed Feb 21 22:11:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbo_13297/02_2024/7pbo_13297_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbo_13297/02_2024/7pbo_13297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbo_13297/02_2024/7pbo_13297.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbo_13297/02_2024/7pbo_13297.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbo_13297/02_2024/7pbo_13297_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbo_13297/02_2024/7pbo_13297_neut_trim_updated.pdb" } resolution = 2.9 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 44 5.49 5 Mg 2 5.21 5 S 100 5.16 5 C 10134 2.51 5 N 2757 2.21 5 O 3218 1.98 5 H 15818 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32073 Number of models: 1 Model: "" Number of chains: 16 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: "H" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 760 Classifications: {'peptide': 50} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 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: 13.95, per 1000 atoms: 0.43 Number of scatterers: 32073 At special positions: 0 Unit cell: (125.35, 138.43, 109, 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 44 15.00 Mg 2 11.99 O 3218 8.00 N 2757 7.00 C 10134 6.00 H 15818 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: 29.17 Conformation dependent library (CDL) restraints added in 3.5 seconds 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3624 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 105 helices and 18 sheets defined 50.8% alpha, 10.6% beta 14 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 14.16 Creating SS restraints... Processing helix chain 'A' and resid 32 through 48 removed outlier: 3.629A pdb=" N ILE A 40 " --> pdb=" O ASP A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 76 removed outlier: 3.617A pdb=" N PHE A 70 " --> pdb=" O THR A 66 " (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: 3.510A 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: 4.629A pdb=" N VAL A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A 123 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N SER A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 128 " --> pdb=" O TYR A 124 " (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: 3.793A pdb=" N ARG A 171 " --> pdb=" O PRO A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 196 removed outlier: 3.526A pdb=" N ILE A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 212 removed outlier: 3.566A pdb=" N ARG A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 231 Processing helix chain 'A' and resid 241 through 250 Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 280 through 287 removed outlier: 3.661A pdb=" N ASN A 286 " --> pdb=" O THR A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 297 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 48 Processing helix chain 'B' and resid 65 through 76 removed outlier: 3.545A pdb=" N PHE B 70 " --> pdb=" O THR B 66 " (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: 4.357A pdb=" N VAL B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N SER B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA B 126 " --> pdb=" O VAL B 122 " (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: 3.938A pdb=" N ARG B 171 " --> pdb=" O PRO B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 196 removed outlier: 3.506A pdb=" N ILE B 196 " --> pdb=" O ARG B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 212 removed outlier: 4.143A pdb=" N ARG B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 234 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 removed outlier: 3.605A pdb=" N ASN B 286 " --> pdb=" O THR B 282 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 287 " --> pdb=" O LEU B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 297 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 Processing helix chain 'C' and resid 65 through 76 removed outlier: 3.629A pdb=" N PHE C 70 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 100 removed outlier: 3.756A 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: 4.001A pdb=" N VAL C 122 " --> pdb=" O ALA C 118 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N SER C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 3.762A 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: 3.648A 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 211 removed outlier: 3.546A pdb=" N LEU C 207 " --> pdb=" O PRO C 203 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU C 208 " --> pdb=" O GLU C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 231 Processing helix chain 'C' and resid 243 through 251 Processing helix chain 'C' and resid 260 through 272 Processing helix chain 'C' and resid 280 through 287 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: 3.712A pdb=" N ILE D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 76 removed outlier: 3.597A pdb=" N PHE D 70 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 100 removed outlier: 3.618A 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: 4.459A pdb=" N VAL D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N SER D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA D 126 " --> pdb=" O VAL D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 141 No H-bonds generated for 'chain 'D' and resid 139 through 141' Processing helix chain 'D' and resid 161 through 163 No H-bonds generated for 'chain 'D' and resid 161 through 163' Processing helix chain 'D' and resid 166 through 171 removed outlier: 4.022A pdb=" N ARG D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 196 removed outlier: 4.621A pdb=" N GLU D 188 " --> pdb=" O PRO D 184 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE D 189 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL D 190 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE D 196 " --> pdb=" O ARG D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 212 removed outlier: 3.767A pdb=" N GLU D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG D 212 " --> pdb=" O GLU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 233 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 removed outlier: 3.691A pdb=" N ASN D 286 " --> pdb=" O THR D 282 " (cutoff:3.500A) 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 47 removed outlier: 3.909A pdb=" N ILE E 40 " --> pdb=" O ASP E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 76 removed outlier: 3.629A pdb=" N PHE E 70 " --> pdb=" O THR E 66 " (cutoff:3.500A) 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 100 Processing helix chain 'E' and resid 117 through 128 removed outlier: 3.800A pdb=" N GLU E 121 " --> pdb=" O MET E 117 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER E 125 " --> pdb=" O GLU E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 171 removed outlier: 3.600A pdb=" N ALA E 170 " --> pdb=" O ASN E 166 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG E 171 " --> pdb=" O PRO E 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 166 through 171' Processing helix chain 'E' and resid 183 through 196 Processing helix chain 'E' and resid 203 through 213 Processing helix chain 'E' and resid 217 through 234 removed outlier: 3.728A pdb=" N ILE E 233 " --> pdb=" O ASP E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 251 Processing helix chain 'E' and resid 260 through 273 removed outlier: 3.553A pdb=" N LEU E 266 " --> pdb=" O ASP E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 286 Processing helix chain 'E' and resid 291 through 297 removed outlier: 3.604A pdb=" N ASP E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) 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: 4.007A pdb=" N GLN F 37 " --> pdb=" O LYS F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 76 removed outlier: 3.666A 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: 3.533A pdb=" N VAL F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 3.858A 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: 4.332A pdb=" N VAL F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR F 124 " --> pdb=" O GLU F 120 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N SER F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA F 126 " --> pdb=" O VAL F 122 " (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 166 through 171 removed outlier: 4.009A 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 removed outlier: 3.548A pdb=" N ASP F 229 " --> pdb=" O LYS F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 250 removed outlier: 3.717A pdb=" N GLN F 246 " --> pdb=" O LYS F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 271 removed outlier: 3.688A pdb=" N LYS F 264 " --> pdb=" O TYR F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 287 removed outlier: 3.566A pdb=" N VAL F 285 " --> pdb=" O GLY F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 297 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 202 Processing helix chain 'H' and resid 159 through 169 Processing helix chain 'H' and resid 174 through 183 Processing helix chain 'H' and resid 191 through 202 removed outlier: 3.931A pdb=" N ARG H 200 " --> pdb=" O ARG H 196 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 174 through 177 removed outlier: 3.506A pdb=" N ALA A 157 " --> pdb=" O ILE A 109 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 131 through 136 removed outlier: 3.598A pdb=" N ILE A 136 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A 143 " --> pdb=" O ILE A 136 " (cutoff:3.500A) 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 178 removed outlier: 3.589A pdb=" N GLY B 59 " --> pdb=" O THR B 158 " (cutoff:3.500A) removed outlier: 3.530A 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: 3.557A 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 removed outlier: 3.575A pdb=" N ASP F 110 " --> pdb=" O THR F 83 " (cutoff:3.500A) 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 310 665 hydrogen bonds defined for protein. 1947 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 33 hydrogen bonds 66 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 11.10 Time building geometry restraints manager: 29.23 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: 15818 1.06 - 1.28: 2721 1.28 - 1.50: 6909 1.50 - 1.72: 6775 1.72 - 1.94: 198 Bond restraints: 32421 Sorted by residual: bond pdb=" N THR E 19 " pdb=" H1 THR E 19 " 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 A 19 " pdb=" H1 THR A 19 " 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 C 19 " pdb=" H1 THR C 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 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 2.50e+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 2.49e+01 ... (remaining 32416 not shown) Histogram of bond angle deviations from ideal: 99.27 - 106.75: 777 106.75 - 114.23: 39573 114.23 - 121.70: 12694 121.70 - 129.18: 5567 129.18 - 136.65: 73 Bond angle restraints: 58684 Sorted by residual: angle pdb=" N GLY E 215 " pdb=" CA GLY E 215 " pdb=" C GLY E 215 " ideal model delta sigma weight residual 115.32 120.27 -4.95 1.38e+00 5.25e-01 1.29e+01 angle pdb=" OP1 DT V 4 " pdb=" P DT V 4 " pdb=" OP2 DT V 4 " ideal model delta sigma weight residual 120.00 110.05 9.95 3.00e+00 1.11e-01 1.10e+01 angle pdb=" CA TYR C 124 " pdb=" CB TYR C 124 " pdb=" CG TYR C 124 " ideal model delta sigma weight residual 113.90 119.43 -5.53 1.80e+00 3.09e-01 9.43e+00 angle pdb=" C2' ADP E 600 " pdb=" C3' ADP E 600 " pdb=" C4' ADP E 600 " ideal model delta sigma weight residual 111.00 101.97 9.03 3.00e+00 1.11e-01 9.07e+00 angle pdb=" O3' DT V 3 " pdb=" P DT V 4 " pdb=" OP1 DT V 4 " ideal model delta sigma weight residual 108.00 116.94 -8.94 3.00e+00 1.11e-01 8.88e+00 ... (remaining 58679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.46: 14433 31.46 - 62.92: 557 62.92 - 94.38: 34 94.38 - 125.84: 0 125.84 - 157.30: 6 Dihedral angle restraints: 15030 sinusoidal: 8597 harmonic: 6433 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 97.30 -157.30 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" O2A ADP D 600 " pdb=" O3A ADP D 600 " pdb=" PA ADP D 600 " pdb=" PB ADP D 600 " ideal model delta sinusoidal sigma weight residual -60.00 87.04 -147.04 1 2.00e+01 2.50e-03 4.41e+01 dihedral pdb=" O2A ADP A 600 " pdb=" O3A ADP A 600 " pdb=" PA ADP A 600 " pdb=" PB ADP A 600 " ideal model delta sinusoidal sigma weight residual -60.00 78.45 -138.44 1 2.00e+01 2.50e-03 4.20e+01 ... (remaining 15027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2276 0.073 - 0.146: 269 0.146 - 0.219: 6 0.219 - 0.293: 0 0.293 - 0.366: 1 Chirality restraints: 2552 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 -2.71 -0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" CA PHE D 197 " pdb=" N PHE D 197 " pdb=" C PHE D 197 " pdb=" CB PHE D 197 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.68e-01 chirality pdb=" CA ARG E 214 " pdb=" N ARG E 214 " pdb=" C ARG E 214 " pdb=" CB ARG E 214 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.21e-01 ... (remaining 2549 not shown) Planarity restraints: 4702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 218 " 0.089 9.50e-02 1.11e+02 5.16e-02 4.08e+01 pdb=" NE ARG F 218 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG F 218 " -0.037 2.00e-02 2.50e+03 pdb=" NH1 ARG F 218 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG F 218 " -0.080 2.00e-02 2.50e+03 pdb="HH11 ARG F 218 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG F 218 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG F 218 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG F 218 " 0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 31 " 0.041 2.00e-02 2.50e+03 5.12e-02 3.94e+01 pdb=" CD GLN C 31 " -0.034 2.00e-02 2.50e+03 pdb=" OE1 GLN C 31 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 GLN C 31 " -0.082 2.00e-02 2.50e+03 pdb="HE21 GLN C 31 " -0.002 2.00e-02 2.50e+03 pdb="HE22 GLN C 31 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 48 " -0.028 9.50e-02 1.11e+02 3.64e-02 2.79e+01 pdb=" NE ARG B 48 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG B 48 " -0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG B 48 " -0.062 2.00e-02 2.50e+03 pdb=" NH2 ARG B 48 " 0.024 2.00e-02 2.50e+03 pdb="HH11 ARG B 48 " -0.002 2.00e-02 2.50e+03 pdb="HH12 ARG B 48 " 0.066 2.00e-02 2.50e+03 pdb="HH21 ARG B 48 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 48 " -0.024 2.00e-02 2.50e+03 ... (remaining 4699 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 834 2.14 - 2.76: 58196 2.76 - 3.37: 84258 3.37 - 3.99: 108451 3.99 - 4.60: 174135 Nonbonded interactions: 425874 Sorted by model distance: nonbonded pdb=" HG1 THR F 66 " pdb=" O1B ADP F 600 " model vdw 1.528 1.850 nonbonded pdb=" HH TYR A 273 " pdb=" OD1 ASN A 286 " model vdw 1.552 1.850 nonbonded pdb=" HG1 THR A 311 " pdb=" O GLY A 314 " model vdw 1.556 1.850 nonbonded pdb=" O LEU E 52 " pdb=" HG1 THR E 153 " model vdw 1.573 1.850 nonbonded pdb=" HZ1 LYS F 264 " pdb=" O ILE F 287 " model vdw 1.583 1.850 ... (remaining 425869 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)) } ncs_group { reference = (chain 'G' and (resid 158 through 202 or (resid 203 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD1 or name CD2 or name H or name H \ A or name HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or n \ ame HD21 or name HD22 or name HD23)))) selection = (chain 'H' and resid 158 through 203) } 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: 4.030 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: 0.580 Extract box with map and model: 11.320 Check model and map are aligned: 0.460 Set scattering table: 0.280 Process input model: 111.240 Find NCS groups from input model: 1.510 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: 0.000 Load rotamer database and sin/cos tables:13.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 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 0.040 16603 Z= 0.272 Angle : 0.741 9.946 22607 Z= 0.421 Chirality : 0.045 0.366 2552 Planarity : 0.010 0.133 2808 Dihedral : 14.888 157.300 6403 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 0.12 % Allowed : 1.34 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: -0.74 (0.18), residues: 1950 helix: -1.07 (0.14), residues: 1030 sheet: 0.36 (0.29), residues: 313 loop : 0.58 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.003 HIS F 54 PHE 0.020 0.003 PHE C 25 TYR 0.041 0.006 TYR C 131 ARG 0.048 0.004 ARG H 200 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 515 time to evaluate : 2.681 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: 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 68 MET cc_start: 0.8960 (tpp) cc_final: 0.8637 (tpp) REVERT: A 76 MET cc_start: 0.8264 (mmm) cc_final: 0.8026 (mmt) REVERT: A 144 SER cc_start: 0.8511 (p) cc_final: 0.8021 (t) REVERT: B 185 ASP cc_start: 0.7653 (m-30) cc_final: 0.7384 (m-30) REVERT: B 252 ASP cc_start: 0.7857 (t0) cc_final: 0.7422 (t0) REVERT: B 262 ASP cc_start: 0.8002 (m-30) cc_final: 0.7667 (m-30) REVERT: C 76 MET cc_start: 0.8626 (mmm) cc_final: 0.8366 (mmm) REVERT: C 124 TYR cc_start: 0.8311 (p90) cc_final: 0.8080 (p90) REVERT: C 199 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7572 (mmm) REVERT: C 296 ASP cc_start: 0.7365 (m-30) cc_final: 0.7133 (m-30) REVERT: D 76 MET cc_start: 0.8612 (mmm) cc_final: 0.8406 (mmm) REVERT: D 131 TYR cc_start: 0.8610 (p90) cc_final: 0.8236 (p90) REVERT: D 262 ASP cc_start: 0.7886 (m-30) cc_final: 0.7618 (m-30) REVERT: D 311 THR cc_start: 0.8680 (m) cc_final: 0.8472 (p) REVERT: D 313 THR cc_start: 0.8853 (m) cc_final: 0.8589 (p) REVERT: E 39 LYS cc_start: 0.8245 (mtmt) cc_final: 0.7119 (mtmt) REVERT: E 42 ILE cc_start: 0.8924 (mt) cc_final: 0.8723 (mm) REVERT: E 79 ASN cc_start: 0.7708 (m-40) cc_final: 0.7158 (m110) REVERT: E 99 ASN cc_start: 0.7284 (t0) cc_final: 0.7073 (t0) REVERT: E 110 ASP cc_start: 0.7263 (t0) cc_final: 0.6946 (t0) REVERT: E 252 ASP cc_start: 0.7696 (t0) cc_final: 0.7462 (t0) REVERT: E 289 GLU cc_start: 0.6812 (mm-30) cc_final: 0.6379 (mm-30) REVERT: E 325 MET cc_start: 0.8783 (mmm) cc_final: 0.8472 (mmp) REVERT: F 110 ASP cc_start: 0.7591 (t0) cc_final: 0.6704 (t70) REVERT: F 119 VAL cc_start: 0.7516 (t) cc_final: 0.7159 (t) REVERT: F 253 VAL cc_start: 0.8541 (t) cc_final: 0.8326 (p) REVERT: F 259 ASP cc_start: 0.7045 (t0) cc_final: 0.6716 (t70) outliers start: 2 outliers final: 1 residues processed: 516 average time/residue: 3.3285 time to fit residues: 1866.5101 Evaluate side-chains 402 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 400 time to evaluate : 2.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain F residue 233 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 153 optimal weight: 1.9990 chunk 59 optimal weight: 0.2980 chunk 93 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN C 79 ASN C 166 ASN C 286 ASN D 146 HIS D 166 ASN D 221 ASN E 23 GLN F 255 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16603 Z= 0.250 Angle : 0.661 7.254 22607 Z= 0.348 Chirality : 0.042 0.143 2552 Planarity : 0.006 0.078 2808 Dihedral : 14.477 153.003 2593 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 3.29 % Allowed : 13.77 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 0.45 (0.18), residues: 1950 helix: 0.36 (0.16), residues: 1034 sheet: 0.37 (0.28), residues: 328 loop : 0.51 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS F 255 PHE 0.013 0.001 PHE E 70 TYR 0.025 0.001 TYR C 124 ARG 0.009 0.001 ARG G 200 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 404 time to evaluate : 2.473 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: 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 68 MET cc_start: 0.8880 (tpp) cc_final: 0.8544 (tpp) REVERT: A 76 MET cc_start: 0.8226 (mmm) cc_final: 0.8004 (mmt) REVERT: A 144 SER cc_start: 0.8586 (p) cc_final: 0.8047 (t) REVERT: A 240 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.7194 (m-30) REVERT: A 295 GLU cc_start: 0.7484 (tp30) cc_final: 0.7104 (tp30) REVERT: B 147 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7961 (mt) REVERT: B 185 ASP cc_start: 0.7339 (m-30) cc_final: 0.7061 (m-30) REVERT: B 252 ASP cc_start: 0.7847 (t0) cc_final: 0.7505 (t0) REVERT: C 117 MET cc_start: 0.6139 (tpp) cc_final: 0.5286 (tpp) REVERT: C 121 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6687 (mp0) REVERT: C 124 TYR cc_start: 0.8446 (p90) cc_final: 0.8207 (p90) REVERT: C 182 GLU cc_start: 0.7322 (mm-30) cc_final: 0.7084 (mm-30) REVERT: C 199 MET cc_start: 0.7901 (mmt) cc_final: 0.7680 (mmm) REVERT: D 76 MET cc_start: 0.8563 (mmm) cc_final: 0.8186 (mmt) REVERT: D 122 VAL cc_start: 0.8549 (p) cc_final: 0.8300 (p) REVERT: D 171 ARG cc_start: 0.8601 (mmt90) cc_final: 0.8071 (mpt-90) REVERT: D 179 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6262 (pp20) REVERT: D 182 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6716 (mm-30) REVERT: D 197 PHE cc_start: 0.7680 (OUTLIER) cc_final: 0.5536 (p90) REVERT: D 262 ASP cc_start: 0.7935 (m-30) cc_final: 0.7723 (m-30) REVERT: D 311 THR cc_start: 0.8462 (m) cc_final: 0.8233 (p) REVERT: D 313 THR cc_start: 0.8753 (m) cc_final: 0.8469 (p) REVERT: E 110 ASP cc_start: 0.7376 (t0) cc_final: 0.7037 (t0) REVERT: E 125 SER cc_start: 0.8247 (OUTLIER) cc_final: 0.8034 (t) REVERT: E 289 GLU cc_start: 0.6656 (mm-30) cc_final: 0.6426 (mm-30) REVERT: E 325 MET cc_start: 0.8798 (mmm) cc_final: 0.8538 (mmp) REVERT: F 178 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.8124 (mtm) REVERT: F 204 GLU cc_start: 0.7334 (tp30) cc_final: 0.7122 (tp30) REVERT: F 259 ASP cc_start: 0.6991 (t0) cc_final: 0.6607 (t70) REVERT: G 179 ARG cc_start: 0.7188 (ttt-90) cc_final: 0.6912 (ttt-90) outliers start: 54 outliers final: 19 residues processed: 430 average time/residue: 3.2889 time to fit residues: 1541.2642 Evaluate side-chains 415 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 388 time to evaluate : 2.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 242 LYS Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 179 GLU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 236 ASP Chi-restraints excluded: chain F residue 255 HIS Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain G residue 193 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 178 optimal weight: 0.8980 chunk 192 optimal weight: 0.3980 chunk 158 optimal weight: 0.9990 chunk 176 optimal weight: 0.0980 chunk 60 optimal weight: 0.4980 chunk 143 optimal weight: 0.2980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN C 79 ASN D 99 ASN D 146 HIS D 221 ASN D 286 ASN E 23 GLN F 246 GLN ** F 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16603 Z= 0.182 Angle : 0.592 7.137 22607 Z= 0.302 Chirality : 0.039 0.159 2552 Planarity : 0.005 0.062 2808 Dihedral : 14.307 155.592 2590 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.50 % Allowed : 16.39 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.19), residues: 1950 helix: 0.91 (0.16), residues: 1037 sheet: 0.19 (0.28), residues: 324 loop : 0.67 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.030 0.001 HIS F 255 PHE 0.011 0.001 PHE D 197 TYR 0.019 0.001 TYR C 124 ARG 0.015 0.000 ARG E 310 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 398 time to evaluate : 2.767 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.8894 (tpp) cc_final: 0.8501 (tpp) REVERT: A 76 MET cc_start: 0.8221 (mmm) cc_final: 0.7979 (mmt) REVERT: A 144 SER cc_start: 0.8587 (p) cc_final: 0.8062 (t) REVERT: A 295 GLU cc_start: 0.7549 (tp30) cc_final: 0.7188 (tp30) REVERT: B 147 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7967 (mt) REVERT: B 185 ASP cc_start: 0.7324 (m-30) cc_final: 0.7069 (m-30) REVERT: B 252 ASP cc_start: 0.7800 (t0) cc_final: 0.7492 (t0) REVERT: C 89 GLU cc_start: 0.6969 (mp0) cc_final: 0.6766 (mm-30) REVERT: C 117 MET cc_start: 0.5939 (tpp) cc_final: 0.5276 (tpp) REVERT: C 121 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6602 (mp0) REVERT: C 124 TYR cc_start: 0.8397 (p90) cc_final: 0.8145 (p90) REVERT: C 199 MET cc_start: 0.7823 (mmt) cc_final: 0.7623 (mmm) REVERT: D 76 MET cc_start: 0.8499 (mmm) cc_final: 0.8290 (mmt) REVERT: D 120 GLU cc_start: 0.7253 (tt0) cc_final: 0.6600 (tt0) REVERT: D 131 TYR cc_start: 0.8616 (p90) cc_final: 0.8392 (p90) REVERT: D 171 ARG cc_start: 0.8537 (mmt90) cc_final: 0.8041 (mpt-90) REVERT: D 179 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6280 (pp20) REVERT: D 182 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.6513 (mm-30) REVERT: D 197 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.5680 (p90) REVERT: E 43 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.6695 (mp0) REVERT: E 110 ASP cc_start: 0.7367 (t0) cc_final: 0.7047 (t0) REVERT: E 289 GLU cc_start: 0.6646 (mm-30) cc_final: 0.6443 (mm-30) REVERT: E 325 MET cc_start: 0.8780 (mmm) cc_final: 0.8494 (mmp) REVERT: F 209 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.7879 (tp) REVERT: G 179 ARG cc_start: 0.7207 (ttt-90) cc_final: 0.6915 (ttt-90) outliers start: 41 outliers final: 11 residues processed: 414 average time/residue: 3.2390 time to fit residues: 1463.7878 Evaluate side-chains 397 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 379 time to evaluate : 2.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 148 ASP Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain G residue 193 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 19 optimal weight: 0.0970 chunk 85 optimal weight: 0.9990 chunk 119 optimal weight: 0.1980 chunk 178 optimal weight: 2.9990 chunk 189 optimal weight: 6.9990 chunk 93 optimal weight: 0.5980 chunk 169 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN B 246 GLN C 79 ASN D 99 ASN D 166 ASN D 286 ASN ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN F 246 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16603 Z= 0.196 Angle : 0.581 6.671 22607 Z= 0.293 Chirality : 0.039 0.131 2552 Planarity : 0.005 0.055 2808 Dihedral : 14.246 158.472 2588 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.74 % Allowed : 17.12 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 1.15 (0.19), residues: 1950 helix: 1.14 (0.16), residues: 1039 sheet: 0.26 (0.28), residues: 304 loop : 0.63 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 146 PHE 0.011 0.001 PHE D 197 TYR 0.019 0.001 TYR C 124 ARG 0.010 0.000 ARG D 114 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 384 time to evaluate : 2.509 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: 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 68 MET cc_start: 0.8881 (tpp) cc_final: 0.8507 (tpp) REVERT: A 76 MET cc_start: 0.8229 (mmm) cc_final: 0.8008 (mmt) REVERT: A 144 SER cc_start: 0.8580 (p) cc_final: 0.8078 (t) REVERT: A 240 ASP cc_start: 0.7195 (OUTLIER) cc_final: 0.6842 (m-30) REVERT: A 295 GLU cc_start: 0.7516 (tp30) cc_final: 0.7265 (tp30) REVERT: B 147 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7969 (mt) REVERT: B 185 ASP cc_start: 0.7319 (m-30) cc_final: 0.7078 (m-30) REVERT: B 252 ASP cc_start: 0.7817 (t0) cc_final: 0.7510 (t0) REVERT: C 89 GLU cc_start: 0.7033 (mp0) cc_final: 0.6828 (mm-30) REVERT: C 117 MET cc_start: 0.5935 (tpp) cc_final: 0.5183 (tpp) REVERT: C 121 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6593 (mp0) REVERT: C 124 TYR cc_start: 0.8453 (p90) cc_final: 0.8226 (p90) REVERT: D 171 ARG cc_start: 0.8524 (mmt90) cc_final: 0.8026 (mpt-90) REVERT: D 179 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6334 (pp20) REVERT: D 197 PHE cc_start: 0.7713 (OUTLIER) cc_final: 0.5695 (p90) REVERT: E 110 ASP cc_start: 0.7377 (t0) cc_final: 0.6653 (t0) REVERT: E 289 GLU cc_start: 0.6724 (mm-30) cc_final: 0.6507 (mm-30) REVERT: E 325 MET cc_start: 0.8793 (mmm) cc_final: 0.8502 (mmp) REVERT: F 209 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.7904 (tp) outliers start: 45 outliers final: 21 residues processed: 402 average time/residue: 3.2115 time to fit residues: 1410.1875 Evaluate side-chains 397 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 370 time to evaluate : 2.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 148 ASP Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain D residue 79 ASN Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 236 ASP Chi-restraints excluded: chain F residue 255 HIS Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 197 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 161 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 96 optimal weight: 0.0050 chunk 170 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN C 79 ASN D 99 ASN D 146 HIS D 166 ASN D 286 ASN E 23 GLN F 246 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16603 Z= 0.229 Angle : 0.593 6.778 22607 Z= 0.300 Chirality : 0.040 0.132 2552 Planarity : 0.005 0.061 2808 Dihedral : 14.223 159.127 2588 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.74 % Allowed : 17.49 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 1.12 (0.19), residues: 1950 helix: 1.15 (0.16), residues: 1044 sheet: 0.31 (0.29), residues: 290 loop : 0.51 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 146 PHE 0.014 0.001 PHE D 197 TYR 0.018 0.001 TYR C 124 ARG 0.009 0.001 ARG D 143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 382 time to evaluate : 2.586 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: 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 68 MET cc_start: 0.8858 (tpp) cc_final: 0.8504 (tpp) REVERT: A 76 MET cc_start: 0.8268 (mmm) cc_final: 0.8068 (mmt) REVERT: A 144 SER cc_start: 0.8608 (p) cc_final: 0.8065 (t) REVERT: A 240 ASP cc_start: 0.7286 (OUTLIER) cc_final: 0.6909 (m-30) REVERT: B 147 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8000 (mt) REVERT: B 185 ASP cc_start: 0.7343 (m-30) cc_final: 0.7081 (m-30) REVERT: B 252 ASP cc_start: 0.7854 (t0) cc_final: 0.7520 (t0) REVERT: C 89 GLU cc_start: 0.7015 (mp0) cc_final: 0.6810 (mm-30) REVERT: C 117 MET cc_start: 0.5953 (tpp) cc_final: 0.5242 (tpp) REVERT: C 121 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6638 (mp0) REVERT: D 171 ARG cc_start: 0.8523 (mmt90) cc_final: 0.8047 (mpt-90) REVERT: D 179 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6472 (pp20) REVERT: D 197 PHE cc_start: 0.7793 (OUTLIER) cc_final: 0.5700 (p90) REVERT: E 68 MET cc_start: 0.8512 (tpp) cc_final: 0.8018 (tpt) REVERT: E 110 ASP cc_start: 0.7256 (t0) cc_final: 0.6730 (t0) REVERT: E 289 GLU cc_start: 0.6729 (mm-30) cc_final: 0.6506 (mm-30) REVERT: E 325 MET cc_start: 0.8777 (mmm) cc_final: 0.8540 (mmp) REVERT: F 209 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.7906 (tp) outliers start: 45 outliers final: 20 residues processed: 401 average time/residue: 3.2286 time to fit residues: 1411.7046 Evaluate side-chains 402 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 376 time to evaluate : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 148 ASP Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 179 GLU Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 188 GLU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 236 ASP Chi-restraints excluded: chain F residue 255 HIS Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain F residue 328 ASP Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 197 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 0.9980 chunk 170 optimal weight: 0.6980 chunk 37 optimal weight: 0.0270 chunk 111 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 189 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN C 79 ASN D 286 ASN ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16603 Z= 0.217 Angle : 0.596 7.035 22607 Z= 0.299 Chirality : 0.039 0.129 2552 Planarity : 0.005 0.063 2808 Dihedral : 14.162 159.064 2588 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.38 % Allowed : 19.01 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 1.17 (0.19), residues: 1950 helix: 1.25 (0.16), residues: 1042 sheet: 0.36 (0.29), residues: 297 loop : 0.40 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS D 146 PHE 0.013 0.001 PHE D 197 TYR 0.018 0.001 TYR C 124 ARG 0.011 0.001 ARG F 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 381 time to evaluate : 2.409 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: 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 68 MET cc_start: 0.8841 (tpp) cc_final: 0.8499 (tpp) REVERT: A 76 MET cc_start: 0.8247 (mmm) cc_final: 0.8000 (mmt) REVERT: A 144 SER cc_start: 0.8595 (p) cc_final: 0.8051 (t) REVERT: A 240 ASP cc_start: 0.7261 (OUTLIER) cc_final: 0.6856 (m-30) REVERT: B 185 ASP cc_start: 0.7369 (m-30) cc_final: 0.7122 (m-30) REVERT: B 252 ASP cc_start: 0.7859 (t0) cc_final: 0.7534 (t0) REVERT: C 89 GLU cc_start: 0.7020 (mp0) cc_final: 0.6818 (mm-30) REVERT: C 117 MET cc_start: 0.5922 (tpp) cc_final: 0.4933 (tpp) REVERT: C 121 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6563 (mp0) REVERT: D 171 ARG cc_start: 0.8509 (mmt90) cc_final: 0.8042 (mpt-90) REVERT: D 179 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6593 (pp20) REVERT: D 197 PHE cc_start: 0.7837 (OUTLIER) cc_final: 0.5772 (p90) REVERT: E 68 MET cc_start: 0.8518 (tpp) cc_final: 0.8036 (tpt) REVERT: E 110 ASP cc_start: 0.7227 (t0) cc_final: 0.6690 (t0) REVERT: E 289 GLU cc_start: 0.6751 (mm-30) cc_final: 0.6514 (mm-30) REVERT: E 295 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7587 (tp30) REVERT: E 325 MET cc_start: 0.8787 (mmm) cc_final: 0.8570 (mmp) REVERT: F 209 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.7916 (tp) REVERT: F 259 ASP cc_start: 0.6951 (t0) cc_final: 0.6652 (t70) outliers start: 39 outliers final: 23 residues processed: 402 average time/residue: 3.3017 time to fit residues: 1447.2933 Evaluate side-chains 401 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 373 time to evaluate : 2.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 148 ASP Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 179 GLU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 236 ASP Chi-restraints excluded: chain F residue 255 HIS Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain F residue 328 ASP Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 197 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 159 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 188 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN C 79 ASN D 146 HIS D 286 ASN ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16603 Z= 0.249 Angle : 0.602 8.090 22607 Z= 0.304 Chirality : 0.040 0.156 2552 Planarity : 0.005 0.069 2808 Dihedral : 14.199 159.356 2588 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.62 % Allowed : 19.68 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 1.07 (0.19), residues: 1950 helix: 1.23 (0.16), residues: 1035 sheet: 0.13 (0.28), residues: 301 loop : 0.33 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS D 146 PHE 0.015 0.001 PHE D 197 TYR 0.017 0.001 TYR C 124 ARG 0.009 0.001 ARG D 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 373 time to evaluate : 3.043 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: 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 68 MET cc_start: 0.8847 (tpp) cc_final: 0.8508 (tpp) REVERT: A 76 MET cc_start: 0.8241 (mmm) cc_final: 0.8024 (mmt) REVERT: A 240 ASP cc_start: 0.7333 (OUTLIER) cc_final: 0.6933 (m-30) REVERT: B 185 ASP cc_start: 0.7374 (m-30) cc_final: 0.7148 (m-30) REVERT: B 252 ASP cc_start: 0.7859 (t0) cc_final: 0.7503 (t0) REVERT: C 117 MET cc_start: 0.5844 (tpp) cc_final: 0.5465 (mmm) REVERT: D 63 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8342 (mm) REVERT: D 171 ARG cc_start: 0.8500 (mmt90) cc_final: 0.8038 (mpt-90) REVERT: D 179 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6553 (pp20) REVERT: D 197 PHE cc_start: 0.7847 (OUTLIER) cc_final: 0.5753 (p90) REVERT: E 68 MET cc_start: 0.8535 (tpp) cc_final: 0.8097 (tpt) REVERT: E 110 ASP cc_start: 0.7231 (t0) cc_final: 0.6685 (t0) REVERT: E 289 GLU cc_start: 0.6754 (mm-30) cc_final: 0.6500 (mm-30) REVERT: E 295 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7556 (tp30) REVERT: F 209 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.7829 (tp) REVERT: F 259 ASP cc_start: 0.6971 (t0) cc_final: 0.6693 (t70) outliers start: 43 outliers final: 27 residues processed: 397 average time/residue: 3.3493 time to fit residues: 1446.6175 Evaluate side-chains 402 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 370 time to evaluate : 2.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain C residue 148 ASP Chi-restraints excluded: chain C residue 149 LEU Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 264 LYS Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 129 ASP Chi-restraints excluded: chain E residue 179 GLU Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 236 ASP Chi-restraints excluded: chain F residue 255 HIS Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain F residue 328 ASP Chi-restraints excluded: chain G residue 192 GLU Chi-restraints excluded: chain G residue 193 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 37 optimal weight: 0.0060 chunk 36 optimal weight: 0.5980 chunk 120 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN C 79 ASN D 146 HIS D 286 ASN ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16603 Z= 0.204 Angle : 0.599 7.423 22607 Z= 0.299 Chirality : 0.039 0.127 2552 Planarity : 0.005 0.089 2808 Dihedral : 14.164 159.363 2588 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.32 % Allowed : 20.54 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 1.23 (0.19), residues: 1950 helix: 1.40 (0.17), residues: 1038 sheet: 0.11 (0.28), residues: 301 loop : 0.38 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS D 146 PHE 0.013 0.001 PHE D 197 TYR 0.016 0.001 TYR D 131 ARG 0.011 0.001 ARG D 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 372 time to evaluate : 2.636 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: 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 68 MET cc_start: 0.8824 (tpp) cc_final: 0.8484 (tpp) REVERT: A 76 MET cc_start: 0.8220 (mmm) cc_final: 0.7975 (mmt) REVERT: A 240 ASP cc_start: 0.7314 (OUTLIER) cc_final: 0.6887 (m-30) REVERT: B 185 ASP cc_start: 0.7337 (m-30) cc_final: 0.7110 (m-30) REVERT: B 252 ASP cc_start: 0.7858 (t0) cc_final: 0.7496 (t0) REVERT: C 117 MET cc_start: 0.6123 (tpp) cc_final: 0.5326 (tpp) REVERT: C 121 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6495 (mp0) REVERT: D 147 LEU cc_start: 0.8428 (tp) cc_final: 0.8164 (tm) REVERT: D 171 ARG cc_start: 0.8481 (mmt90) cc_final: 0.8055 (mpt-90) REVERT: D 179 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6609 (pp20) REVERT: D 197 PHE cc_start: 0.7875 (OUTLIER) cc_final: 0.5772 (p90) REVERT: E 68 MET cc_start: 0.8523 (tpp) cc_final: 0.8073 (tpt) REVERT: E 70 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.8104 (t80) REVERT: E 110 ASP cc_start: 0.7222 (t0) cc_final: 0.6681 (t0) REVERT: E 169 ARG cc_start: 0.7694 (ttp-170) cc_final: 0.7430 (mtm-85) REVERT: E 289 GLU cc_start: 0.6734 (mm-30) cc_final: 0.6475 (mm-30) REVERT: E 295 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7501 (tp30) REVERT: F 209 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.7876 (tp) REVERT: F 259 ASP cc_start: 0.6941 (t0) cc_final: 0.6658 (t70) outliers start: 38 outliers final: 22 residues processed: 391 average time/residue: 3.3773 time to fit residues: 1437.7851 Evaluate side-chains 393 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 365 time to evaluate : 2.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 148 ASP Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 236 ASP Chi-restraints excluded: chain F residue 255 HIS Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 299 GLU Chi-restraints excluded: chain F residue 328 ASP Chi-restraints excluded: chain G residue 193 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 105 optimal weight: 0.2980 chunk 76 optimal weight: 0.5980 chunk 138 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 175 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 ASN D 146 HIS D 286 ASN ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16603 Z= 0.265 Angle : 0.620 7.640 22607 Z= 0.312 Chirality : 0.040 0.154 2552 Planarity : 0.005 0.080 2808 Dihedral : 14.198 159.673 2588 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.44 % Allowed : 20.90 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 1950 helix: 1.31 (0.17), residues: 1026 sheet: 0.13 (0.28), residues: 311 loop : 0.27 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS D 146 PHE 0.015 0.001 PHE D 197 TYR 0.019 0.001 TYR C 124 ARG 0.014 0.001 ARG G 196 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 366 time to evaluate : 2.633 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: 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 68 MET cc_start: 0.8838 (tpp) cc_final: 0.8508 (tpp) REVERT: A 76 MET cc_start: 0.8274 (mmm) cc_final: 0.8025 (mmt) REVERT: A 240 ASP cc_start: 0.7312 (OUTLIER) cc_final: 0.6937 (m-30) REVERT: B 185 ASP cc_start: 0.7381 (m-30) cc_final: 0.7165 (m-30) REVERT: B 252 ASP cc_start: 0.7858 (t0) cc_final: 0.7498 (t0) REVERT: C 53 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.7311 (t0) REVERT: C 117 MET cc_start: 0.6107 (tpp) cc_final: 0.5855 (tpp) REVERT: D 63 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8352 (mm) REVERT: D 147 LEU cc_start: 0.8486 (tp) cc_final: 0.8238 (tm) REVERT: D 171 ARG cc_start: 0.8491 (mmt90) cc_final: 0.8043 (mpt-90) REVERT: D 179 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6726 (pp20) REVERT: D 197 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.5808 (p90) REVERT: E 68 MET cc_start: 0.8548 (tpp) cc_final: 0.8129 (tpt) REVERT: E 70 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.8117 (t80) REVERT: E 110 ASP cc_start: 0.7219 (t0) cc_final: 0.6674 (t0) REVERT: E 169 ARG cc_start: 0.7700 (ttp-170) cc_final: 0.7419 (mtm-85) REVERT: E 289 GLU cc_start: 0.6742 (mm-30) cc_final: 0.6484 (mm-30) REVERT: F 209 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.7828 (tp) REVERT: F 259 ASP cc_start: 0.7023 (t0) cc_final: 0.6742 (t70) REVERT: F 320 LYS cc_start: 0.7547 (mtmt) cc_final: 0.7268 (pttp) outliers start: 40 outliers final: 19 residues processed: 388 average time/residue: 3.3767 time to fit residues: 1424.8705 Evaluate side-chains 392 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 366 time to evaluate : 2.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 148 ASP Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 236 ASP Chi-restraints excluded: chain F residue 255 HIS Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 328 ASP Chi-restraints excluded: chain G residue 193 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 0.6980 chunk 186 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 155 optimal weight: 0.0980 chunk 16 optimal weight: 0.7980 chunk 120 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 ASN D 146 HIS D 286 ASN ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 255 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16603 Z= 0.199 Angle : 0.613 7.516 22607 Z= 0.306 Chirality : 0.039 0.142 2552 Planarity : 0.005 0.088 2808 Dihedral : 14.141 159.991 2588 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.89 % Allowed : 21.63 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 1.28 (0.19), residues: 1950 helix: 1.45 (0.17), residues: 1031 sheet: 0.19 (0.28), residues: 313 loop : 0.37 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS D 146 PHE 0.013 0.001 PHE D 197 TYR 0.017 0.001 TYR D 131 ARG 0.012 0.001 ARG F 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3900 Ramachandran restraints generated. 1950 Oldfield, 0 Emsley, 1950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 367 time to evaluate : 2.644 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.8813 (tpp) cc_final: 0.8485 (tpp) REVERT: A 76 MET cc_start: 0.8232 (mmm) cc_final: 0.7989 (mmt) REVERT: A 240 ASP cc_start: 0.7314 (OUTLIER) cc_final: 0.6913 (m-30) REVERT: B 185 ASP cc_start: 0.7355 (m-30) cc_final: 0.7134 (m-30) REVERT: B 252 ASP cc_start: 0.7856 (t0) cc_final: 0.7520 (t0) REVERT: C 117 MET cc_start: 0.6115 (tpp) cc_final: 0.5185 (tmm) REVERT: C 121 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6313 (mp0) REVERT: D 63 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8336 (mm) REVERT: D 171 ARG cc_start: 0.8473 (mmt90) cc_final: 0.8034 (mpt-90) REVERT: D 179 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6738 (pp20) REVERT: D 197 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.5836 (p90) REVERT: E 68 MET cc_start: 0.8530 (tpp) cc_final: 0.8082 (tpt) REVERT: E 70 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.8113 (t80) REVERT: E 110 ASP cc_start: 0.7204 (t0) cc_final: 0.6725 (t0) REVERT: E 169 ARG cc_start: 0.7694 (ttp-170) cc_final: 0.7379 (mtm-85) REVERT: E 289 GLU cc_start: 0.6732 (mm-30) cc_final: 0.6462 (mm-30) REVERT: F 105 ASP cc_start: 0.7317 (m-30) cc_final: 0.7102 (m-30) REVERT: F 209 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.7821 (tp) REVERT: F 259 ASP cc_start: 0.6977 (t0) cc_final: 0.6707 (t70) REVERT: F 320 LYS cc_start: 0.7536 (mtmt) cc_final: 0.7226 (pttp) outliers start: 31 outliers final: 19 residues processed: 385 average time/residue: 3.3623 time to fit residues: 1409.5972 Evaluate side-chains 391 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 365 time to evaluate : 2.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 148 ASP Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 83 THR Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 93 ASP Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 255 HIS Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 328 ASP Chi-restraints excluded: chain G residue 193 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 2.9990 chunk 165 optimal weight: 0.0770 chunk 47 optimal weight: 0.9980 chunk 143 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 159 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 0.0770 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 ASN D 146 HIS D 286 ASN ** E 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 255 HIS F 246 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.119070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.088798 restraints weight = 69094.951| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.30 r_work: 0.2967 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16603 Z= 0.185 Angle : 0.603 7.833 22607 Z= 0.299 Chirality : 0.039 0.148 2552 Planarity : 0.005 0.107 2808 Dihedral : 14.094 161.157 2588 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.89 % Allowed : 22.06 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 1950 helix: 1.53 (0.17), residues: 1034 sheet: 0.21 (0.27), residues: 321 loop : 0.35 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS D 146 PHE 0.012 0.001 PHE D 197 TYR 0.016 0.001 TYR D 131 ARG 0.022 0.001 ARG G 196 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19482.97 seconds wall clock time: 338 minutes 29.26 seconds (20309.26 seconds total)