Starting phenix.real_space_refine on Fri Feb 6 21:16:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qba_13885/02_2026/7qba_13885.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qba_13885/02_2026/7qba_13885.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qba_13885/02_2026/7qba_13885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qba_13885/02_2026/7qba_13885.map" model { file = "/net/cci-nas-00/data/ceres_data/7qba_13885/02_2026/7qba_13885.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qba_13885/02_2026/7qba_13885.cif" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.081 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9481 atoms to isotropic. 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 Ca 2 9.91 5 P 6 5.49 5 Mg 2 5.21 5 S 99 5.16 5 C 13351 2.51 5 N 3644 2.21 5 O 3882 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20986 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3149 Classifications: {'peptide': 403} Link IDs: {'PTRANS': 16, 'TRANS': 386} Chain: "B" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2295 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 12, 'TRANS': 285} Chain: "C" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2295 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 12, 'TRANS': 285} Chain: "D" Number of atoms: 2073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2073 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 8, 'TRANS': 266} Chain: "E" Number of atoms: 1966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1966 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain breaks: 2 Chain: "H" Number of atoms: 4575 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 581, 4567 Classifications: {'peptide': 581} Link IDs: {'CIS': 2, 'PCIS': 4, 'PTRANS': 25, 'TRANS': 549} Conformer: "B" Number of residues, atoms: 581, 4567 Classifications: {'peptide': 581} Link IDs: {'CIS': 2, 'PCIS': 4, 'PTRANS': 25, 'TRANS': 549} bond proxies already assigned to first conformer: 4669 Chain: "I" Number of atoms: 4567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4567 Classifications: {'peptide': 581} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 25, 'TRANS': 550} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 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, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.42, per 1000 atoms: 0.26 Number of scatterers: 20986 At special positions: 0 Unit cell: (169.65, 162.69, 139.2, 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) Ca 2 19.99 S 99 16.00 P 6 15.00 Mg 2 11.99 O 3882 8.00 N 3644 7.00 C 13351 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.40 Conformation dependent library (CDL) restraints added in 1.1 seconds 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4892 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 35 sheets defined 32.2% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.626A pdb=" N ARG A 158 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 383 Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 392 through 403 Processing helix chain 'B' and resid 41 through 49 Processing helix chain 'B' and resid 69 through 75 removed outlier: 3.769A pdb=" N GLN B 75 " --> pdb=" O GLN B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 103 Processing helix chain 'B' and resid 107 through 116 Processing helix chain 'B' and resid 130 through 143 Processing helix chain 'B' and resid 160 through 177 Processing helix chain 'B' and resid 190 through 195 removed outlier: 4.464A pdb=" N HIS B 194 " --> pdb=" O GLY B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 219 Processing helix chain 'B' and resid 234 through 242 removed outlier: 4.014A pdb=" N ASP B 242 " --> pdb=" O GLN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 274 removed outlier: 5.102A pdb=" N ARG B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLN B 270 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU B 274 " --> pdb=" O GLN B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 299 Processing helix chain 'C' and resid 41 through 51 Processing helix chain 'C' and resid 69 through 75 removed outlier: 4.133A pdb=" N ARG C 73 " --> pdb=" O ASP C 69 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN C 75 " --> pdb=" O GLN C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 103 Processing helix chain 'C' and resid 105 through 117 removed outlier: 3.962A pdb=" N VAL C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASP C 110 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU C 111 " --> pdb=" O THR C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'C' and resid 160 through 177 Processing helix chain 'C' and resid 212 through 220 removed outlier: 3.609A pdb=" N ALA C 219 " --> pdb=" O LEU C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 242 removed outlier: 3.988A pdb=" N ASP C 242 " --> pdb=" O GLN C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 265 No H-bonds generated for 'chain 'C' and resid 263 through 265' Processing helix chain 'C' and resid 266 through 272 removed outlier: 4.034A pdb=" N GLN C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 298 Processing helix chain 'D' and resid 3 through 18 Processing helix chain 'D' and resid 19 through 37 removed outlier: 3.531A pdb=" N ALA D 36 " --> pdb=" O ALA D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 75 removed outlier: 3.763A pdb=" N ALA D 59 " --> pdb=" O ILE D 55 " (cutoff:3.500A) Proline residue: D 67 - end of helix Processing helix chain 'D' and resid 78 through 85 Processing helix chain 'D' and resid 86 through 93 removed outlier: 3.655A pdb=" N THR D 92 " --> pdb=" O MET D 88 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 131 Processing helix chain 'D' and resid 135 through 168 Processing helix chain 'D' and resid 170 through 201 removed outlier: 3.544A pdb=" N VAL D 186 " --> pdb=" O TRP D 182 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE D 189 " --> pdb=" O PHE D 185 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASP D 190 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU D 193 " --> pdb=" O PHE D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 213 removed outlier: 3.582A pdb=" N LEU D 212 " --> pdb=" O LEU D 208 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU D 213 " --> pdb=" O LEU D 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 208 through 213' Processing helix chain 'D' and resid 216 through 228 removed outlier: 3.652A pdb=" N GLY D 228 " --> pdb=" O ILE D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 244 removed outlier: 3.505A pdb=" N ASP D 244 " --> pdb=" O SER D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 273 removed outlier: 3.526A pdb=" N ARG D 273 " --> pdb=" O ALA D 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 18 Processing helix chain 'E' and resid 19 through 38 removed outlier: 4.086A pdb=" N LEU E 26 " --> pdb=" O LEU E 22 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU E 27 " --> pdb=" O ALA E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 44 removed outlier: 3.848A pdb=" N GLY E 44 " --> pdb=" O ALA E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 72 removed outlier: 3.600A pdb=" N SER E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE E 64 " --> pdb=" O SER E 60 " (cutoff:3.500A) Proline residue: E 67 - end of helix Processing helix chain 'E' and resid 75 through 84 removed outlier: 4.330A pdb=" N VAL E 79 " --> pdb=" O TYR E 75 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLU E 81 " --> pdb=" O ALA E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 93 removed outlier: 4.487A pdb=" N LEU E 89 " --> pdb=" O GLY E 85 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR E 93 " --> pdb=" O LEU E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 131 removed outlier: 3.647A pdb=" N ILE E 100 " --> pdb=" O GLY E 96 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU E 101 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 166 Processing helix chain 'E' and resid 170 through 187 removed outlier: 3.803A pdb=" N GLY E 176 " --> pdb=" O SER E 172 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL E 181 " --> pdb=" O LEU E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 200 Processing helix chain 'E' and resid 205 through 207 No H-bonds generated for 'chain 'E' and resid 205 through 207' Processing helix chain 'E' and resid 208 through 215 removed outlier: 3.544A pdb=" N LEU E 212 " --> pdb=" O LEU E 208 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU E 215 " --> pdb=" O TRP E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 225 Processing helix chain 'E' and resid 248 through 273 removed outlier: 4.108A pdb=" N LEU E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG E 273 " --> pdb=" O ALA E 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 118 Processing helix chain 'H' and resid 119 through 123 removed outlier: 3.850A pdb=" N LYS H 122 " --> pdb=" O ASP H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 264 through 269 removed outlier: 3.861A pdb=" N MET H 267 " --> pdb=" O LEU H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 290 Processing helix chain 'H' and resid 354 through 361 Processing helix chain 'H' and resid 365 through 368 Processing helix chain 'H' and resid 406 through 415 Processing helix chain 'H' and resid 514 through 516 No H-bonds generated for 'chain 'H' and resid 514 through 516' Processing helix chain 'H' and resid 517 through 527 Processing helix chain 'I' and resid 77 through 80 Processing helix chain 'I' and resid 110 through 118 Processing helix chain 'I' and resid 119 through 121 No H-bonds generated for 'chain 'I' and resid 119 through 121' Processing helix chain 'I' and resid 264 through 269 Processing helix chain 'I' and resid 280 through 290 Processing helix chain 'I' and resid 354 through 360 Processing helix chain 'I' and resid 365 through 368 Processing helix chain 'I' and resid 405 through 414 Processing helix chain 'I' and resid 514 through 516 No H-bonds generated for 'chain 'I' and resid 514 through 516' Processing helix chain 'I' and resid 517 through 527 Processing helix chain 'I' and resid 625 through 629 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 47 removed outlier: 6.844A pdb=" N MET A 62 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N GLU A 91 " --> pdb=" O MET A 62 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU A 64 " --> pdb=" O GLU A 91 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N VAL A 88 " --> pdb=" O GLN A 119 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N SER A 121 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N VAL A 90 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA A 170 " --> pdb=" O HIS A 193 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N GLU A 195 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL A 172 " --> pdb=" O GLU A 195 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ILE A 217 " --> pdb=" O ASN A 192 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU A 194 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 53 removed outlier: 6.581A pdb=" N TYR A 52 " --> pdb=" O GLN A 73 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU A 95 " --> pdb=" O ARG A 126 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N MET A 125 " --> pdb=" O ASP A 148 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL A 177 " --> pdb=" O GLU A 200 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 56 through 58 Processing sheet with id=AA4, first strand: chain 'A' and resid 107 through 111 removed outlier: 6.571A pdb=" N SER A 107 " --> pdb=" O GLY A 131 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N PHE A 133 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL A 109 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ASP A 135 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ILE A 111 " --> pdb=" O ASP A 135 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLY A 161 " --> pdb=" O PHE A 130 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL A 132 " --> pdb=" O GLY A 161 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ILE A 184 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N MET A 209 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE A 186 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL A 206 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N MET A 231 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TYR A 208 " --> pdb=" O MET A 231 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N SER A 233 " --> pdb=" O TYR A 208 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE A 256 " --> pdb=" O GLN A 232 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ARG A 234 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR A 313 " --> pdb=" O ILE A 290 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 265 through 267 removed outlier: 6.143A pdb=" N VAL A 266 " --> pdb=" O GLU A 304 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 17 through 26 removed outlier: 6.095A pdb=" N VAL B 18 " --> pdb=" O ARG B 12 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ARG B 12 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N HIS B 20 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N SER B 10 " --> pdb=" O HIS B 20 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU B 22 " --> pdb=" O GLY B 8 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY B 8 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 4 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN B 7 " --> pdb=" O GLN B 59 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN B 59 " --> pdb=" O GLN B 7 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL B 9 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLU B 57 " --> pdb=" O VAL B 9 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 77 through 79 removed outlier: 3.856A pdb=" N LEU B 79 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU B 152 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU B 32 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 224 through 226 Processing sheet with id=AA9, first strand: chain 'B' and resid 246 through 248 removed outlier: 3.980A pdb=" N SER B 246 " --> pdb=" O VAL B 258 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 4 through 5 Processing sheet with id=AB2, first strand: chain 'C' and resid 9 through 13 removed outlier: 6.562A pdb=" N VAL C 9 " --> pdb=" O HIS C 20 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N HIS C 20 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLN C 11 " --> pdb=" O VAL C 18 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 76 through 79 removed outlier: 6.615A pdb=" N GLY C 77 " --> pdb=" O LEU C 151 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N VAL C 31 " --> pdb=" O ARG C 197 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ALA C 199 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLY C 33 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N LEU C 201 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N PHE C 35 " --> pdb=" O LEU C 201 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 247 through 250 removed outlier: 3.502A pdb=" N ARG C 248 " --> pdb=" O GLU C 256 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE C 255 " --> pdb=" O ALA C 227 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA C 227 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL C 257 " --> pdb=" O ILE C 225 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 92 through 96 removed outlier: 7.069A pdb=" N GLU H 92 " --> pdb=" O GLY H 86 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLY H 86 " --> pdb=" O GLU H 92 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 132 through 136 removed outlier: 11.347A pdb=" N HIS H 132 " --> pdb=" O LYS H 143 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N LYS H 143 " --> pdb=" O HIS H 132 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N SER H 134 " --> pdb=" O ASP H 141 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ARG H 159 " --> pdb=" O CYS H 165 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N CYS H 165 " --> pdb=" O ARG H 159 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 175 through 182 removed outlier: 7.371A pdb=" N ALA H 176 " --> pdb=" O GLU H 196 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ASN H 194 " --> pdb=" O HIS H 178 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU H 180 " --> pdb=" O PHE H 192 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE H 192 " --> pdb=" O LEU H 180 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LEU H 182 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N TYR H 190 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA H 195 " --> pdb=" O MET H 218 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N MET H 218 " --> pdb=" O ALA H 195 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N PHE H 197 " --> pdb=" O TYR H 216 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N TYR H 216 " --> pdb=" O PHE H 197 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE H 199 " --> pdb=" O TYR H 216 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 175 through 182 removed outlier: 7.371A pdb=" N ALA H 176 " --> pdb=" O GLU H 196 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ASN H 194 " --> pdb=" O HIS H 178 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU H 180 " --> pdb=" O PHE H 192 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE H 192 " --> pdb=" O LEU H 180 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LEU H 182 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N TYR H 190 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA H 195 " --> pdb=" O MET H 218 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N MET H 218 " --> pdb=" O ALA H 195 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N PHE H 197 " --> pdb=" O TYR H 216 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N TYR H 216 " --> pdb=" O PHE H 197 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR H 217 " --> pdb=" O VAL H 235 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ASP H 223 " --> pdb=" O MET H 229 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N MET H 229 " --> pdb=" O ASP H 223 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA H 230 " --> pdb=" O PRO H 301 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N LEU H 303 " --> pdb=" O ALA H 230 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLN H 232 " --> pdb=" O LEU H 303 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N THR H 300 " --> pdb=" O LEU H 295 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LEU H 295 " --> pdb=" O THR H 300 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 239 through 244 removed outlier: 6.562A pdb=" N THR H 254 " --> pdb=" O ASP H 240 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N THR H 242 " --> pdb=" O ALA H 252 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ALA H 252 " --> pdb=" O THR H 242 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ALA H 244 " --> pdb=" O PHE H 250 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N PHE H 250 " --> pdb=" O ALA H 244 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 328 through 330 removed outlier: 6.739A pdb=" N MET H 349 " --> pdb=" O VAL H 371 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 380 through 385 removed outlier: 4.569A pdb=" N HIS H 382 " --> pdb=" O THR H 394 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN H 423 " --> pdb=" O LYS H 403 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ASN H 405 " --> pdb=" O ILE H 421 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE H 421 " --> pdb=" O ASN H 405 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 431 through 436 removed outlier: 4.369A pdb=" N HIS H 433 " --> pdb=" O LEU H 452 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLU H 469 " --> pdb=" O PRO H 488 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ASP H 471 " --> pdb=" O ASP H 486 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASP H 486 " --> pdb=" O ASP H 471 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU H 473 " --> pdb=" O VAL H 484 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS H 482 " --> pdb=" O ASP H 475 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 536 through 540 removed outlier: 3.672A pdb=" N MET H 551 " --> pdb=" O ALA H 554 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 536 through 540 removed outlier: 6.633A pdb=" N VAL H 544 " --> pdb=" O THR H 569 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N THR H 571 " --> pdb=" O VAL H 544 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL H 546 " --> pdb=" O THR H 571 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N THR H 573 " --> pdb=" O VAL H 546 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N MET H 548 " --> pdb=" O THR H 573 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 562 through 563 removed outlier: 4.129A pdb=" N VAL H 592 " --> pdb=" O VAL H 587 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 92 through 96 removed outlier: 6.907A pdb=" N GLU I 92 " --> pdb=" O GLY I 86 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLY I 86 " --> pdb=" O GLU I 92 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 132 through 136 removed outlier: 5.020A pdb=" N TYR I 144 " --> pdb=" O SER I 134 " (cutoff:3.500A) removed outlier: 9.681A pdb=" N THR I 136 " --> pdb=" O GLY I 142 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N GLY I 142 " --> pdb=" O THR I 136 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS I 167 " --> pdb=" O ARG I 157 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ARG I 159 " --> pdb=" O CYS I 165 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N CYS I 165 " --> pdb=" O ARG I 159 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 175 through 182 removed outlier: 8.243A pdb=" N ILE I 177 " --> pdb=" O GLU I 196 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLU I 196 " --> pdb=" O ILE I 177 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY I 179 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA I 195 " --> pdb=" O MET I 218 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N MET I 218 " --> pdb=" O ALA I 195 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N PHE I 197 " --> pdb=" O TYR I 216 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TYR I 216 " --> pdb=" O PHE I 197 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE I 199 " --> pdb=" O TYR I 216 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 175 through 182 removed outlier: 8.243A pdb=" N ILE I 177 " --> pdb=" O GLU I 196 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLU I 196 " --> pdb=" O ILE I 177 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY I 179 " --> pdb=" O ASN I 194 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA I 195 " --> pdb=" O MET I 218 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N MET I 218 " --> pdb=" O ALA I 195 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N PHE I 197 " --> pdb=" O TYR I 216 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TYR I 216 " --> pdb=" O PHE I 197 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR I 217 " --> pdb=" O VAL I 235 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL I 235 " --> pdb=" O THR I 217 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ASP I 223 " --> pdb=" O MET I 229 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N MET I 229 " --> pdb=" O ASP I 223 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 239 through 244 removed outlier: 3.875A pdb=" N ASN I 241 " --> pdb=" O THR I 254 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N TRP I 274 " --> pdb=" O CYS I 255 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 336 through 339 removed outlier: 3.593A pdb=" N ALA I 339 " --> pdb=" O SER I 348 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N MET I 349 " --> pdb=" O VAL I 371 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 380 through 384 removed outlier: 4.736A pdb=" N HIS I 382 " --> pdb=" O THR I 394 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 431 through 436 removed outlier: 5.360A pdb=" N LEU I 452 " --> pdb=" O GLY I 432 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LEU I 434 " --> pdb=" O VAL I 450 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL I 450 " --> pdb=" O LEU I 434 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ASP I 475 " --> pdb=" O LEU I 483 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LEU I 483 " --> pdb=" O ASP I 475 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 536 through 540 removed outlier: 3.610A pdb=" N MET I 551 " --> pdb=" O ALA I 554 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 536 through 540 Processing sheet with id=AD8, first strand: chain 'I' and resid 559 through 563 removed outlier: 6.320A pdb=" N PHE I 560 " --> pdb=" O MET I 634 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N GLU I 636 " --> pdb=" O PHE I 560 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL I 562 " --> pdb=" O GLU I 636 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL I 592 " --> pdb=" O VAL I 587 " (cutoff:3.500A) 860 hydrogen bonds defined for protein. 2399 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.69 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 3502 1.28 - 1.42: 5400 1.42 - 1.55: 12347 1.55 - 1.68: 19 1.68 - 1.81: 170 Bond restraints: 21438 Sorted by residual: bond pdb=" C LEU D 196 " pdb=" O LEU D 196 " ideal model delta sigma weight residual 1.236 1.151 0.086 1.15e-02 7.56e+03 5.55e+01 bond pdb=" CA SER H 456 " pdb=" CB SER H 456 " ideal model delta sigma weight residual 1.534 1.439 0.095 1.45e-02 4.76e+03 4.28e+01 bond pdb=" CA SER C 130 " pdb=" CB SER C 130 " ideal model delta sigma weight residual 1.530 1.448 0.082 1.49e-02 4.50e+03 3.04e+01 bond pdb=" CG PRO I 380 " pdb=" CD PRO I 380 " ideal model delta sigma weight residual 1.503 1.317 0.186 3.40e-02 8.65e+02 2.99e+01 bond pdb=" C LEU D 197 " pdb=" O LEU D 197 " ideal model delta sigma weight residual 1.236 1.294 -0.057 1.15e-02 7.56e+03 2.48e+01 ... (remaining 21433 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.50: 28826 4.50 - 8.99: 243 8.99 - 13.49: 20 13.49 - 17.99: 2 17.99 - 22.48: 2 Bond angle restraints: 29093 Sorted by residual: angle pdb=" PB ATP B 402 " pdb=" O3B ATP B 402 " pdb=" PG ATP B 402 " ideal model delta sigma weight residual 139.87 117.39 22.48 1.00e+00 1.00e+00 5.05e+02 angle pdb=" PB ATP C 402 " pdb=" O3B ATP C 402 " pdb=" PG ATP C 402 " ideal model delta sigma weight residual 139.87 122.38 17.49 1.00e+00 1.00e+00 3.06e+02 angle pdb=" PA ATP B 402 " pdb=" O3A ATP B 402 " pdb=" PB ATP B 402 " ideal model delta sigma weight residual 136.83 121.93 14.90 1.00e+00 1.00e+00 2.22e+02 angle pdb=" N PRO A 411 " pdb=" CA PRO A 411 " pdb=" C PRO A 411 " ideal model delta sigma weight residual 110.80 90.30 20.50 1.51e+00 4.39e-01 1.84e+02 angle pdb=" PA ATP C 402 " pdb=" O3A ATP C 402 " pdb=" PB ATP C 402 " ideal model delta sigma weight residual 136.83 123.42 13.41 1.00e+00 1.00e+00 1.80e+02 ... (remaining 29088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 11506 17.94 - 35.88: 996 35.88 - 53.81: 187 53.81 - 71.75: 35 71.75 - 89.69: 23 Dihedral angle restraints: 12747 sinusoidal: 5089 harmonic: 7658 Sorted by residual: dihedral pdb=" C ASP C 160 " pdb=" N ASP C 160 " pdb=" CA ASP C 160 " pdb=" CB ASP C 160 " ideal model delta harmonic sigma weight residual -122.60 -106.43 -16.17 0 2.50e+00 1.60e-01 4.18e+01 dihedral pdb=" C TYR B 13 " pdb=" N TYR B 13 " pdb=" CA TYR B 13 " pdb=" CB TYR B 13 " ideal model delta harmonic sigma weight residual -122.60 -137.43 14.83 0 2.50e+00 1.60e-01 3.52e+01 dihedral pdb=" C THR D 54 " pdb=" N THR D 54 " pdb=" CA THR D 54 " pdb=" CB THR D 54 " ideal model delta harmonic sigma weight residual -122.00 -134.87 12.87 0 2.50e+00 1.60e-01 2.65e+01 ... (remaining 12744 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2887 0.092 - 0.185: 296 0.185 - 0.277: 45 0.277 - 0.369: 17 0.369 - 0.462: 8 Chirality restraints: 3253 Sorted by residual: chirality pdb=" CA TRP A 358 " pdb=" N TRP A 358 " pdb=" C TRP A 358 " pdb=" CB TRP A 358 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.33e+00 chirality pdb=" CA PRO E 52 " pdb=" N PRO E 52 " pdb=" C PRO E 52 " pdb=" CB PRO E 52 " both_signs ideal model delta sigma weight residual False 2.72 2.30 0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" CA TYR B 13 " pdb=" N TYR B 13 " pdb=" C TYR B 13 " pdb=" CB TYR B 13 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.02e+00 ... (remaining 3250 not shown) Planarity restraints: 3755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 197 " -0.039 2.00e-02 2.50e+03 7.77e-02 6.03e+01 pdb=" C LEU D 197 " 0.134 2.00e-02 2.50e+03 pdb=" O LEU D 197 " -0.049 2.00e-02 2.50e+03 pdb=" N VAL D 198 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 196 " 0.033 2.00e-02 2.50e+03 6.88e-02 4.73e+01 pdb=" C LEU D 196 " -0.119 2.00e-02 2.50e+03 pdb=" O LEU D 196 " 0.045 2.00e-02 2.50e+03 pdb=" N LEU D 197 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 50 " -0.032 2.00e-02 2.50e+03 6.47e-02 4.19e+01 pdb=" C SER E 50 " 0.112 2.00e-02 2.50e+03 pdb=" O SER E 50 " -0.043 2.00e-02 2.50e+03 pdb=" N ILE E 51 " -0.037 2.00e-02 2.50e+03 ... (remaining 3752 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.07: 5 2.07 - 2.78: 4343 2.78 - 3.49: 29888 3.49 - 4.19: 51055 4.19 - 4.90: 90848 Nonbonded interactions: 176139 Sorted by model distance: nonbonded pdb=" O GLN E 45 " pdb=" CD1 LEU E 46 " model vdw 1.363 3.460 nonbonded pdb=" OD2 ASP H 273 " pdb="CA CA H 701 " model vdw 1.515 2.510 nonbonded pdb=" C GLN E 45 " pdb=" CD1 LEU E 46 " model vdw 1.940 3.690 nonbonded pdb=" OE2 GLU H 259 " pdb="CA CA H 701 " model vdw 1.962 2.510 nonbonded pdb="MG MG B 401 " pdb=" O2B ATP B 402 " model vdw 2.057 2.170 ... (remaining 176134 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and (resid 2 through 137 or resid 139 through 229 or resid 245 throug \ h 275)) selection = chain 'E' } ncs_group { reference = (chain 'H' and (resid 58 through 136 or resid 138 through 601 or resid 603 throu \ gh 701)) selection = (chain 'I' and (resid 58 through 136 or resid 138 through 601 or resid 603 throu \ gh 701)) } 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=0.28 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.190 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 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 : 0.006 0.186 21438 Z= 0.353 Angle : 1.074 22.483 29093 Z= 0.684 Chirality : 0.065 0.462 3253 Planarity : 0.007 0.132 3755 Dihedral : 14.321 89.692 7855 Min Nonbonded Distance : 1.363 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.57 % Favored : 94.06 % Rotamer: Outliers : 0.72 % Allowed : 1.70 % Favored : 97.58 % Cbeta Deviations : 0.74 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.16), residues: 2678 helix: 0.38 (0.19), residues: 755 sheet: -0.94 (0.22), residues: 583 loop : -1.96 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 459 TYR 0.045 0.002 TYR H 256 PHE 0.044 0.002 PHE H 385 TRP 0.064 0.003 TRP H 74 HIS 0.013 0.002 HIS H 494 Details of bonding type rmsd covalent geometry : bond 0.00593 (21438) covalent geometry : angle 1.07357 (29093) hydrogen bonds : bond 0.17494 ( 835) hydrogen bonds : angle 7.75268 ( 2399) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 760 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 THR cc_start: 0.8493 (p) cc_final: 0.8102 (p) REVERT: A 126 ARG cc_start: 0.7299 (ttp-170) cc_final: 0.7073 (ttp80) REVERT: A 150 ASP cc_start: 0.7703 (m-30) cc_final: 0.7278 (m-30) REVERT: A 219 ASN cc_start: 0.8729 (m-40) cc_final: 0.8016 (m-40) REVERT: B 16 MET cc_start: 0.6712 (ttt) cc_final: 0.6503 (mmt) REVERT: B 111 GLU cc_start: 0.6311 (mt-10) cc_final: 0.6077 (tt0) REVERT: B 115 GLN cc_start: 0.8040 (tt0) cc_final: 0.7099 (mt0) REVERT: C 127 LYS cc_start: 0.8687 (tttt) cc_final: 0.8409 (tptm) REVERT: C 214 GLN cc_start: 0.7980 (mp10) cc_final: 0.7779 (mp10) REVERT: C 216 ARG cc_start: 0.7685 (mtp85) cc_final: 0.7371 (ttm-80) REVERT: D 211 TRP cc_start: 0.7838 (OUTLIER) cc_final: 0.7082 (m100) REVERT: H 144 TYR cc_start: 0.8449 (m-80) cc_final: 0.7989 (m-80) REVERT: H 234 ILE cc_start: 0.8734 (mt) cc_final: 0.8508 (mt) REVERT: H 267 MET cc_start: 0.8465 (mtt) cc_final: 0.8220 (mtt) REVERT: H 298 SER cc_start: 0.8893 (t) cc_final: 0.8459 (m) REVERT: H 307 LYS cc_start: 0.7331 (mttm) cc_final: 0.6838 (mtmt) REVERT: H 308 LYS cc_start: 0.7473 (tppt) cc_final: 0.6530 (ttmm) REVERT: H 419 ASN cc_start: 0.7045 (m-40) cc_final: 0.6834 (m-40) REVERT: H 512 ARG cc_start: 0.8262 (mmm160) cc_final: 0.7939 (tpp80) REVERT: H 526 LYS cc_start: 0.8403 (mmtt) cc_final: 0.8032 (mmmt) REVERT: H 551 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7825 (ttt) REVERT: H 567 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7883 (mt-10) REVERT: I 68 ASP cc_start: 0.7457 (m-30) cc_final: 0.7252 (m-30) REVERT: I 119 ASP cc_start: 0.8200 (p0) cc_final: 0.7884 (p0) REVERT: I 257 ASN cc_start: 0.8901 (t0) cc_final: 0.8377 (t0) REVERT: I 272 ARG cc_start: 0.7385 (mtp85) cc_final: 0.6957 (mtt180) REVERT: I 300 THR cc_start: 0.9050 (m) cc_final: 0.8741 (p) REVERT: I 354 LYS cc_start: 0.7523 (mttt) cc_final: 0.7316 (mttm) REVERT: I 440 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8330 (mm-30) REVERT: I 498 MET cc_start: 0.8246 (mtt) cc_final: 0.8044 (mtt) REVERT: I 564 GLN cc_start: 0.8648 (tt0) cc_final: 0.8390 (tt0) REVERT: I 601 THR cc_start: 0.9410 (m) cc_final: 0.9011 (m) outliers start: 16 outliers final: 3 residues processed: 767 average time/residue: 0.1462 time to fit residues: 174.3230 Evaluate side-chains 651 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 646 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain H residue 551 MET Chi-restraints excluded: chain H residue 557 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 ASN B 108 GLN B 196 ASN C 23 ASN C 82 ASN C 115 GLN C 196 ASN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN ** H 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 ASN ** I 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.146182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.118114 restraints weight = 30443.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.121479 restraints weight = 14391.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.123601 restraints weight = 8328.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.125058 restraints weight = 5583.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.125943 restraints weight = 4214.282| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21438 Z= 0.183 Angle : 0.714 13.036 29093 Z= 0.364 Chirality : 0.048 0.209 3253 Planarity : 0.005 0.080 3755 Dihedral : 7.144 71.309 2983 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.34 % Favored : 94.54 % Rotamer: Outliers : 2.64 % Allowed : 12.82 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.16), residues: 2678 helix: 0.53 (0.18), residues: 792 sheet: -0.78 (0.22), residues: 537 loop : -1.75 (0.16), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 100 TYR 0.022 0.002 TYR B 13 PHE 0.045 0.002 PHE H 385 TRP 0.033 0.002 TRP A 98 HIS 0.006 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00425 (21438) covalent geometry : angle 0.71388 (29093) hydrogen bonds : bond 0.04355 ( 835) hydrogen bonds : angle 5.92458 ( 2399) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 648 time to evaluate : 0.798 Fit side-chains revert: symmetry clash REVERT: A 157 ASP cc_start: 0.8228 (t0) cc_final: 0.7804 (t0) REVERT: A 174 HIS cc_start: 0.8292 (m90) cc_final: 0.8017 (m90) REVERT: A 219 ASN cc_start: 0.8945 (m-40) cc_final: 0.8518 (m-40) REVERT: A 241 ASN cc_start: 0.8510 (m-40) cc_final: 0.8213 (m-40) REVERT: A 244 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7608 (mt-10) REVERT: A 403 ARG cc_start: 0.6886 (ptp-170) cc_final: 0.6589 (mtm110) REVERT: B 16 MET cc_start: 0.6753 (ttt) cc_final: 0.6236 (mmt) REVERT: B 73 ARG cc_start: 0.8899 (mtm180) cc_final: 0.8550 (mtm-85) REVERT: B 125 ARG cc_start: 0.6640 (OUTLIER) cc_final: 0.5664 (mtt-85) REVERT: B 295 MET cc_start: 0.7727 (tpp) cc_final: 0.7278 (tpp) REVERT: C 11 GLN cc_start: 0.7837 (tp40) cc_final: 0.7525 (tp40) REVERT: C 127 LYS cc_start: 0.8687 (tttt) cc_final: 0.8304 (tptm) REVERT: C 216 ARG cc_start: 0.7660 (mtp85) cc_final: 0.7358 (ttm-80) REVERT: D 211 TRP cc_start: 0.7699 (OUTLIER) cc_final: 0.6836 (m100) REVERT: E 272 ARG cc_start: 0.7444 (mtm180) cc_final: 0.6755 (mtt180) REVERT: H 61 HIS cc_start: 0.7314 (m-70) cc_final: 0.6870 (m-70) REVERT: H 144 TYR cc_start: 0.8655 (m-80) cc_final: 0.8171 (m-80) REVERT: H 308 LYS cc_start: 0.7626 (tppt) cc_final: 0.6517 (ttmm) REVERT: H 443 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7524 (mt-10) REVERT: H 512 ARG cc_start: 0.8525 (mmm160) cc_final: 0.8008 (tpp80) REVERT: H 526 LYS cc_start: 0.8160 (mmtt) cc_final: 0.7767 (mmmt) REVERT: H 551 MET cc_start: 0.8687 (ttt) cc_final: 0.8395 (ttp) REVERT: H 567 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7955 (mt-10) REVERT: H 593 SER cc_start: 0.9048 (t) cc_final: 0.8813 (m) REVERT: H 621 PHE cc_start: 0.8372 (t80) cc_final: 0.8048 (t80) REVERT: H 629 MET cc_start: 0.7813 (mtp) cc_final: 0.7519 (mtp) REVERT: I 68 ASP cc_start: 0.7508 (m-30) cc_final: 0.7261 (m-30) REVERT: I 300 THR cc_start: 0.9052 (m) cc_final: 0.8732 (p) REVERT: I 422 LYS cc_start: 0.8629 (mtpp) cc_final: 0.8404 (mttt) REVERT: I 440 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8493 (mm-30) REVERT: I 523 MET cc_start: 0.7981 (ttm) cc_final: 0.7742 (ttm) REVERT: I 561 THR cc_start: 0.9023 (OUTLIER) cc_final: 0.8498 (t) outliers start: 59 outliers final: 41 residues processed: 661 average time/residue: 0.1330 time to fit residues: 139.9254 Evaluate side-chains 648 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 604 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 108 GLN Chi-restraints excluded: chain B residue 125 ARG Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 133 ILE Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 258 SER Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 313 SER Chi-restraints excluded: chain H residue 557 VAL Chi-restraints excluded: chain H residue 581 VAL Chi-restraints excluded: chain H residue 595 GLU Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 148 ASN Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 220 ASN Chi-restraints excluded: chain I residue 316 THR Chi-restraints excluded: chain I residue 393 THR Chi-restraints excluded: chain I residue 428 HIS Chi-restraints excluded: chain I residue 439 CYS Chi-restraints excluded: chain I residue 561 THR Chi-restraints excluded: chain I residue 563 LYS Chi-restraints excluded: chain I residue 572 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 21 optimal weight: 0.9990 chunk 161 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 221 optimal weight: 6.9990 chunk 237 optimal weight: 6.9990 chunk 32 optimal weight: 0.5980 chunk 60 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN B 135 GLN C 82 ASN D 225 ASN ** H 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 132 HIS I 148 ASN ** I 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.146526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.117409 restraints weight = 35196.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.121016 restraints weight = 16172.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.123292 restraints weight = 9130.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.124772 restraints weight = 6061.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.125713 restraints weight = 4524.746| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21438 Z= 0.147 Angle : 0.648 13.091 29093 Z= 0.331 Chirality : 0.045 0.176 3253 Planarity : 0.005 0.048 3755 Dihedral : 6.857 75.989 2979 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.97 % Favored : 94.96 % Rotamer: Outliers : 3.18 % Allowed : 16.14 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.16), residues: 2678 helix: 0.65 (0.18), residues: 809 sheet: -0.88 (0.22), residues: 575 loop : -1.63 (0.16), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 100 TYR 0.021 0.002 TYR B 78 PHE 0.038 0.002 PHE H 385 TRP 0.025 0.001 TRP A 98 HIS 0.004 0.001 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00339 (21438) covalent geometry : angle 0.64811 (29093) hydrogen bonds : bond 0.03682 ( 835) hydrogen bonds : angle 5.47143 ( 2399) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 597 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8427 (tt) REVERT: A 141 GLN cc_start: 0.7808 (mt0) cc_final: 0.7553 (mt0) REVERT: A 174 HIS cc_start: 0.8136 (m90) cc_final: 0.7888 (m90) REVERT: A 219 ASN cc_start: 0.8933 (m-40) cc_final: 0.8507 (m-40) REVERT: A 241 ASN cc_start: 0.8594 (m-40) cc_final: 0.8238 (m-40) REVERT: A 244 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7594 (mt-10) REVERT: B 16 MET cc_start: 0.6776 (ttt) cc_final: 0.6224 (mmt) REVERT: B 73 ARG cc_start: 0.8907 (mtm180) cc_final: 0.8504 (mtm-85) REVERT: B 125 ARG cc_start: 0.6713 (OUTLIER) cc_final: 0.5755 (mtt-85) REVERT: C 11 GLN cc_start: 0.7766 (tp40) cc_final: 0.7519 (tp40) REVERT: C 50 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8766 (mm) REVERT: C 78 TYR cc_start: 0.8687 (t80) cc_final: 0.8370 (t80) REVERT: C 127 LYS cc_start: 0.8693 (tttt) cc_final: 0.8330 (tptm) REVERT: C 211 SER cc_start: 0.7943 (p) cc_final: 0.7464 (p) REVERT: C 216 ARG cc_start: 0.7630 (mtp85) cc_final: 0.7388 (ttm-80) REVERT: D 211 TRP cc_start: 0.7691 (OUTLIER) cc_final: 0.7017 (m100) REVERT: E 21 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7474 (tp) REVERT: E 45 GLN cc_start: 0.7046 (OUTLIER) cc_final: 0.6831 (tm-30) REVERT: E 272 ARG cc_start: 0.7463 (mtm180) cc_final: 0.6825 (mtt180) REVERT: H 144 TYR cc_start: 0.8572 (m-80) cc_final: 0.8152 (m-80) REVERT: H 259 GLU cc_start: 0.8476 (mp0) cc_final: 0.7552 (mp0) REVERT: H 308 LYS cc_start: 0.7655 (tppt) cc_final: 0.6541 (ttmm) REVERT: H 443 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7458 (mt-10) REVERT: H 492 GLU cc_start: 0.8125 (tt0) cc_final: 0.7439 (tp30) REVERT: H 512 ARG cc_start: 0.8531 (mmm160) cc_final: 0.7928 (tpp80) REVERT: H 551 MET cc_start: 0.8652 (ttt) cc_final: 0.8433 (ttp) REVERT: H 567 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7987 (mt-10) REVERT: H 629 MET cc_start: 0.7833 (mtp) cc_final: 0.7547 (mtp) REVERT: I 68 ASP cc_start: 0.7566 (m-30) cc_final: 0.7276 (m-30) REVERT: I 95 ARG cc_start: 0.7995 (mtp-110) cc_final: 0.7706 (mtp-110) REVERT: I 300 THR cc_start: 0.9018 (m) cc_final: 0.8675 (p) REVERT: I 422 LYS cc_start: 0.8556 (mtpp) cc_final: 0.8324 (mttt) REVERT: I 440 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8499 (mm-30) REVERT: I 532 ASP cc_start: 0.8680 (OUTLIER) cc_final: 0.8132 (m-30) REVERT: I 558 GLN cc_start: 0.7907 (mt0) cc_final: 0.7699 (mt0) REVERT: I 561 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8545 (t) outliers start: 71 outliers final: 52 residues processed: 623 average time/residue: 0.1337 time to fit residues: 133.7235 Evaluate side-chains 634 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 574 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 108 GLN Chi-restraints excluded: chain B residue 125 ARG Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain D residue 2 ASN Chi-restraints excluded: chain D residue 20 TRP Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 45 GLN Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 258 SER Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 426 ASP Chi-restraints excluded: chain H residue 557 VAL Chi-restraints excluded: chain H residue 581 VAL Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 220 ASN Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 316 THR Chi-restraints excluded: chain I residue 393 THR Chi-restraints excluded: chain I residue 402 VAL Chi-restraints excluded: chain I residue 428 HIS Chi-restraints excluded: chain I residue 439 CYS Chi-restraints excluded: chain I residue 511 ASP Chi-restraints excluded: chain I residue 532 ASP Chi-restraints excluded: chain I residue 561 THR Chi-restraints excluded: chain I residue 563 LYS Chi-restraints excluded: chain I residue 572 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 167 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 251 optimal weight: 5.9990 chunk 245 optimal weight: 0.0570 chunk 8 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 190 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 chunk 241 optimal weight: 2.9990 chunk 253 optimal weight: 5.9990 overall best weight: 1.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS B 108 GLN C 82 ASN C 165 GLN ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 ASN ** I 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.146072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.116975 restraints weight = 35287.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.120527 restraints weight = 16153.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.122818 restraints weight = 9158.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.124274 restraints weight = 6054.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.125353 restraints weight = 4512.973| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21438 Z= 0.145 Angle : 0.624 11.407 29093 Z= 0.317 Chirality : 0.045 0.173 3253 Planarity : 0.004 0.044 3755 Dihedral : 6.700 79.885 2979 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.04 % Favored : 94.88 % Rotamer: Outliers : 3.99 % Allowed : 17.84 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.16), residues: 2678 helix: 0.82 (0.18), residues: 802 sheet: -0.86 (0.21), residues: 577 loop : -1.53 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 100 TYR 0.023 0.002 TYR B 78 PHE 0.033 0.002 PHE H 385 TRP 0.024 0.001 TRP A 98 HIS 0.007 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00336 (21438) covalent geometry : angle 0.62365 (29093) hydrogen bonds : bond 0.03424 ( 835) hydrogen bonds : angle 5.25297 ( 2399) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 572 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8450 (tt) REVERT: A 141 GLN cc_start: 0.7764 (mt0) cc_final: 0.7512 (mt0) REVERT: A 174 HIS cc_start: 0.8109 (m90) cc_final: 0.7854 (m90) REVERT: A 219 ASN cc_start: 0.8905 (m-40) cc_final: 0.8482 (m-40) REVERT: A 385 GLN cc_start: 0.8220 (mm-40) cc_final: 0.8015 (mm-40) REVERT: B 16 MET cc_start: 0.6857 (ttt) cc_final: 0.6310 (mmt) REVERT: B 203 LYS cc_start: 0.7334 (ptpt) cc_final: 0.7072 (ptpt) REVERT: C 11 GLN cc_start: 0.7793 (tp40) cc_final: 0.7501 (tp40) REVERT: C 50 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8827 (mm) REVERT: C 127 LYS cc_start: 0.8692 (tttt) cc_final: 0.8322 (tptm) REVERT: C 154 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8553 (mt0) REVERT: C 188 LEU cc_start: 0.8976 (mm) cc_final: 0.8775 (mm) REVERT: C 211 SER cc_start: 0.7928 (p) cc_final: 0.7689 (p) REVERT: C 216 ARG cc_start: 0.7641 (mtp85) cc_final: 0.7358 (mtp-110) REVERT: D 211 TRP cc_start: 0.7728 (OUTLIER) cc_final: 0.7227 (m100) REVERT: E 272 ARG cc_start: 0.7481 (mtm180) cc_final: 0.6884 (mtt180) REVERT: H 144 TYR cc_start: 0.8575 (m-80) cc_final: 0.8202 (m-80) REVERT: H 259 GLU cc_start: 0.8478 (mp0) cc_final: 0.7592 (mp0) REVERT: H 397 ILE cc_start: 0.8693 (mt) cc_final: 0.8420 (mt) REVERT: H 492 GLU cc_start: 0.8116 (tt0) cc_final: 0.7820 (tp30) REVERT: H 512 ARG cc_start: 0.8565 (mmm160) cc_final: 0.7977 (tpp80) REVERT: H 551 MET cc_start: 0.8669 (ttt) cc_final: 0.8440 (ttp) REVERT: H 567 GLU cc_start: 0.8220 (mt-10) cc_final: 0.8019 (mt-10) REVERT: I 68 ASP cc_start: 0.7575 (m-30) cc_final: 0.7278 (m-30) REVERT: I 95 ARG cc_start: 0.8014 (mtp-110) cc_final: 0.7688 (mtp-110) REVERT: I 300 THR cc_start: 0.9173 (m) cc_final: 0.8836 (p) REVERT: I 440 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8512 (mm-30) REVERT: I 492 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8391 (mt-10) REVERT: I 532 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8199 (m-30) REVERT: I 561 THR cc_start: 0.8946 (OUTLIER) cc_final: 0.8563 (t) REVERT: I 627 MET cc_start: 0.7482 (mmp) cc_final: 0.7169 (mmm) outliers start: 89 outliers final: 62 residues processed: 612 average time/residue: 0.1398 time to fit residues: 136.1787 Evaluate side-chains 639 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 571 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 108 GLN Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 154 GLN Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain D residue 20 TRP Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 258 SER Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 426 ASP Chi-restraints excluded: chain H residue 557 VAL Chi-restraints excluded: chain H residue 581 VAL Chi-restraints excluded: chain H residue 595 GLU Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain I residue 148 ASN Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 220 ASN Chi-restraints excluded: chain I residue 316 THR Chi-restraints excluded: chain I residue 393 THR Chi-restraints excluded: chain I residue 398 ASP Chi-restraints excluded: chain I residue 402 VAL Chi-restraints excluded: chain I residue 428 HIS Chi-restraints excluded: chain I residue 439 CYS Chi-restraints excluded: chain I residue 511 ASP Chi-restraints excluded: chain I residue 532 ASP Chi-restraints excluded: chain I residue 561 THR Chi-restraints excluded: chain I residue 563 LYS Chi-restraints excluded: chain I residue 572 ILE Chi-restraints excluded: chain I residue 629 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 33 optimal weight: 0.0770 chunk 201 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 123 optimal weight: 0.9990 chunk 179 optimal weight: 0.9980 chunk 265 optimal weight: 3.9990 chunk 12 optimal weight: 0.2980 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 0.0870 chunk 186 optimal weight: 4.9990 chunk 63 optimal weight: 0.0020 overall best weight: 0.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN C 186 HIS H 419 ASN ** H 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 626 HIS I 148 ASN ** I 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.151300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.121719 restraints weight = 40392.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.125653 restraints weight = 17678.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.128093 restraints weight = 9701.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.129740 restraints weight = 6219.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.130735 restraints weight = 4520.429| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3298 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3298 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 21438 Z= 0.105 Angle : 0.586 10.177 29093 Z= 0.297 Chirality : 0.043 0.164 3253 Planarity : 0.004 0.044 3755 Dihedral : 6.466 88.541 2979 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.67 % Favored : 95.25 % Rotamer: Outliers : 3.54 % Allowed : 19.23 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.16), residues: 2678 helix: 1.00 (0.18), residues: 809 sheet: -0.72 (0.22), residues: 574 loop : -1.45 (0.17), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 500 TYR 0.017 0.001 TYR B 78 PHE 0.029 0.001 PHE H 262 TRP 0.024 0.001 TRP D 141 HIS 0.005 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00233 (21438) covalent geometry : angle 0.58632 (29093) hydrogen bonds : bond 0.03047 ( 835) hydrogen bonds : angle 5.04695 ( 2399) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 570 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8558 (tt) REVERT: A 94 THR cc_start: 0.8447 (m) cc_final: 0.7924 (p) REVERT: A 174 HIS cc_start: 0.7998 (m90) cc_final: 0.7785 (m90) REVERT: A 219 ASN cc_start: 0.8833 (m-40) cc_final: 0.8561 (m-40) REVERT: A 305 LYS cc_start: 0.8658 (mttt) cc_final: 0.8290 (mmtp) REVERT: A 385 GLN cc_start: 0.8221 (mm-40) cc_final: 0.8003 (mm-40) REVERT: B 16 MET cc_start: 0.6794 (ttt) cc_final: 0.6217 (mmt) REVERT: B 30 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7527 (mt-10) REVERT: B 214 GLN cc_start: 0.7589 (mt0) cc_final: 0.7264 (mt0) REVERT: C 11 GLN cc_start: 0.7638 (tp40) cc_final: 0.7287 (tp40) REVERT: C 50 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8803 (mm) REVERT: C 113 LEU cc_start: 0.8180 (mt) cc_final: 0.7953 (mt) REVERT: C 127 LYS cc_start: 0.8612 (tttt) cc_final: 0.8236 (tptm) REVERT: C 188 LEU cc_start: 0.8936 (mm) cc_final: 0.8718 (mm) REVERT: C 211 SER cc_start: 0.8029 (p) cc_final: 0.7685 (p) REVERT: C 216 ARG cc_start: 0.7567 (mtp85) cc_final: 0.7319 (mtp-110) REVERT: D 135 GLU cc_start: 0.7109 (tm-30) cc_final: 0.6694 (tm-30) REVERT: D 211 TRP cc_start: 0.7606 (OUTLIER) cc_final: 0.7195 (m100) REVERT: E 272 ARG cc_start: 0.7433 (mtm180) cc_final: 0.6862 (mtt180) REVERT: H 144 TYR cc_start: 0.8469 (m-80) cc_final: 0.8137 (m-80) REVERT: H 177 ILE cc_start: 0.8665 (mm) cc_final: 0.8390 (tt) REVERT: H 223 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.8238 (m-30) REVERT: H 308 LYS cc_start: 0.7576 (tppt) cc_final: 0.6483 (ttmm) REVERT: H 397 ILE cc_start: 0.8708 (mt) cc_final: 0.8361 (mt) REVERT: H 492 GLU cc_start: 0.7994 (tt0) cc_final: 0.7630 (tp30) REVERT: H 512 ARG cc_start: 0.8439 (mmm160) cc_final: 0.7949 (tpp80) REVERT: H 551 MET cc_start: 0.8574 (ttt) cc_final: 0.8326 (ttp) REVERT: H 567 GLU cc_start: 0.8233 (mt-10) cc_final: 0.8022 (mt-10) REVERT: I 68 ASP cc_start: 0.7565 (m-30) cc_final: 0.7297 (m-30) REVERT: I 94 MET cc_start: 0.8407 (tpt) cc_final: 0.8019 (tpt) REVERT: I 95 ARG cc_start: 0.8050 (mtp-110) cc_final: 0.7737 (mtp-110) REVERT: I 300 THR cc_start: 0.9143 (m) cc_final: 0.8811 (p) REVERT: I 335 LYS cc_start: 0.8894 (ptmm) cc_final: 0.8500 (ptmm) REVERT: I 402 VAL cc_start: 0.8192 (OUTLIER) cc_final: 0.7983 (m) REVERT: I 424 LYS cc_start: 0.6589 (mtpt) cc_final: 0.5462 (mttp) REVERT: I 492 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8351 (mt-10) REVERT: I 511 ASP cc_start: 0.7944 (m-30) cc_final: 0.7487 (t70) REVERT: I 532 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8074 (m-30) outliers start: 79 outliers final: 53 residues processed: 608 average time/residue: 0.1367 time to fit residues: 131.5099 Evaluate side-chains 603 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 544 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 66 CYS Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain D residue 2 ASN Chi-restraints excluded: chain D residue 20 TRP Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain E residue 50 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 223 ASP Chi-restraints excluded: chain H residue 258 SER Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 557 VAL Chi-restraints excluded: chain H residue 581 VAL Chi-restraints excluded: chain H residue 595 GLU Chi-restraints excluded: chain H residue 626 HIS Chi-restraints excluded: chain I residue 148 ASN Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 393 THR Chi-restraints excluded: chain I residue 398 ASP Chi-restraints excluded: chain I residue 402 VAL Chi-restraints excluded: chain I residue 428 HIS Chi-restraints excluded: chain I residue 439 CYS Chi-restraints excluded: chain I residue 532 ASP Chi-restraints excluded: chain I residue 563 LYS Chi-restraints excluded: chain I residue 572 ILE Chi-restraints excluded: chain I residue 629 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 153 optimal weight: 7.9990 chunk 124 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 218 optimal weight: 2.9990 chunk 191 optimal weight: 0.7980 chunk 55 optimal weight: 9.9990 chunk 249 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 151 optimal weight: 2.9990 chunk 126 optimal weight: 0.1980 chunk 157 optimal weight: 7.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 GLN I 148 ASN I 382 HIS ** I 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.142911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.113153 restraints weight = 39195.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.116831 restraints weight = 17506.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.119177 restraints weight = 9788.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.120739 restraints weight = 6393.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.121786 restraints weight = 4730.223| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 21438 Z= 0.199 Angle : 0.653 12.283 29093 Z= 0.333 Chirality : 0.046 0.174 3253 Planarity : 0.004 0.043 3755 Dihedral : 6.610 88.692 2978 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.98 % Favored : 93.95 % Rotamer: Outliers : 4.39 % Allowed : 19.09 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.16), residues: 2678 helix: 0.94 (0.18), residues: 800 sheet: -0.84 (0.22), residues: 582 loop : -1.50 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 100 TYR 0.015 0.002 TYR A 204 PHE 0.031 0.002 PHE H 385 TRP 0.025 0.001 TRP D 141 HIS 0.008 0.001 HIS H 626 Details of bonding type rmsd covalent geometry : bond 0.00460 (21438) covalent geometry : angle 0.65302 (29093) hydrogen bonds : bond 0.03552 ( 835) hydrogen bonds : angle 5.15819 ( 2399) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 573 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8569 (tt) REVERT: A 105 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.7359 (mtm) REVERT: A 138 ARG cc_start: 0.6945 (OUTLIER) cc_final: 0.6127 (ptt90) REVERT: A 174 HIS cc_start: 0.8118 (m90) cc_final: 0.7888 (m90) REVERT: A 219 ASN cc_start: 0.8898 (m-40) cc_final: 0.8631 (m-40) REVERT: B 16 MET cc_start: 0.6770 (ttt) cc_final: 0.6208 (mmt) REVERT: C 11 GLN cc_start: 0.7846 (tp40) cc_final: 0.7541 (tp40) REVERT: C 22 LEU cc_start: 0.8419 (tp) cc_final: 0.8190 (tp) REVERT: C 50 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8811 (mm) REVERT: C 127 LYS cc_start: 0.8624 (tttt) cc_final: 0.8236 (tptm) REVERT: C 135 GLN cc_start: 0.8589 (tp-100) cc_final: 0.8217 (tp-100) REVERT: C 141 GLN cc_start: 0.8166 (tm-30) cc_final: 0.7738 (tm-30) REVERT: C 154 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8629 (mt0) REVERT: C 188 LEU cc_start: 0.8969 (mm) cc_final: 0.8738 (mm) REVERT: C 211 SER cc_start: 0.8057 (p) cc_final: 0.7738 (p) REVERT: C 216 ARG cc_start: 0.7661 (mtp85) cc_final: 0.7373 (mtp-110) REVERT: D 135 GLU cc_start: 0.7235 (tm-30) cc_final: 0.6821 (tm-30) REVERT: D 211 TRP cc_start: 0.7670 (OUTLIER) cc_final: 0.7381 (m100) REVERT: E 272 ARG cc_start: 0.7538 (mtm180) cc_final: 0.6982 (mtt180) REVERT: H 144 TYR cc_start: 0.8620 (m-80) cc_final: 0.8175 (m-80) REVERT: H 335 LYS cc_start: 0.7640 (mtpt) cc_final: 0.7298 (mtmt) REVERT: H 492 GLU cc_start: 0.8108 (tt0) cc_final: 0.7752 (tp30) REVERT: H 512 ARG cc_start: 0.8626 (mmm160) cc_final: 0.8085 (tpp80) REVERT: H 525 LYS cc_start: 0.7903 (mptt) cc_final: 0.7630 (mppt) REVERT: H 551 MET cc_start: 0.8586 (ttt) cc_final: 0.8345 (ttp) REVERT: H 567 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7805 (mt-10) REVERT: H 629 MET cc_start: 0.7856 (mtp) cc_final: 0.7569 (mtp) REVERT: I 68 ASP cc_start: 0.7599 (m-30) cc_final: 0.7325 (m-30) REVERT: I 94 MET cc_start: 0.8473 (tpt) cc_final: 0.8109 (tpt) REVERT: I 300 THR cc_start: 0.9322 (m) cc_final: 0.9025 (p) REVERT: I 335 LYS cc_start: 0.8890 (ptmm) cc_final: 0.8487 (ptmm) REVERT: I 440 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8571 (mm-30) REVERT: I 492 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8466 (mt-10) REVERT: I 511 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7727 (t70) REVERT: I 532 ASP cc_start: 0.8676 (OUTLIER) cc_final: 0.8165 (t0) REVERT: I 595 GLU cc_start: 0.7169 (tm-30) cc_final: 0.6955 (tm-30) outliers start: 98 outliers final: 69 residues processed: 614 average time/residue: 0.1309 time to fit residues: 128.4004 Evaluate side-chains 629 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 552 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 108 GLN Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 154 GLN Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain D residue 20 TRP Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 133 ILE Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 258 SER Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 426 ASP Chi-restraints excluded: chain H residue 557 VAL Chi-restraints excluded: chain H residue 581 VAL Chi-restraints excluded: chain H residue 595 GLU Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 148 ASN Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 198 ILE Chi-restraints excluded: chain I residue 220 ASN Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 393 THR Chi-restraints excluded: chain I residue 398 ASP Chi-restraints excluded: chain I residue 402 VAL Chi-restraints excluded: chain I residue 428 HIS Chi-restraints excluded: chain I residue 439 CYS Chi-restraints excluded: chain I residue 506 THR Chi-restraints excluded: chain I residue 511 ASP Chi-restraints excluded: chain I residue 523 MET Chi-restraints excluded: chain I residue 532 ASP Chi-restraints excluded: chain I residue 563 LYS Chi-restraints excluded: chain I residue 572 ILE Chi-restraints excluded: chain I residue 629 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 157 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 187 optimal weight: 3.9990 chunk 253 optimal weight: 4.9990 chunk 248 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 82 ASN C 154 GLN ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 564 GLN ** H 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 ASN ** I 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.144777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.115249 restraints weight = 41135.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.119095 restraints weight = 18002.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.121510 restraints weight = 9889.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.123087 restraints weight = 6370.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.124056 restraints weight = 4675.119| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21438 Z= 0.152 Angle : 0.631 11.158 29093 Z= 0.318 Chirality : 0.045 0.207 3253 Planarity : 0.004 0.040 3755 Dihedral : 6.532 85.659 2978 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.46 % Favored : 94.47 % Rotamer: Outliers : 4.08 % Allowed : 20.39 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.16), residues: 2678 helix: 0.98 (0.18), residues: 801 sheet: -0.79 (0.21), residues: 589 loop : -1.52 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 403 TYR 0.013 0.002 TYR A 204 PHE 0.030 0.002 PHE H 262 TRP 0.024 0.001 TRP D 141 HIS 0.004 0.001 HIS H 626 Details of bonding type rmsd covalent geometry : bond 0.00353 (21438) covalent geometry : angle 0.63136 (29093) hydrogen bonds : bond 0.03320 ( 835) hydrogen bonds : angle 5.11506 ( 2399) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 545 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8547 (tt) REVERT: A 105 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7325 (mtm) REVERT: A 157 ASP cc_start: 0.8118 (t0) cc_final: 0.7685 (t0) REVERT: A 174 HIS cc_start: 0.8156 (m90) cc_final: 0.7882 (m90) REVERT: A 219 ASN cc_start: 0.8885 (m-40) cc_final: 0.8637 (m-40) REVERT: B 16 MET cc_start: 0.6809 (ttt) cc_final: 0.6200 (mmt) REVERT: B 30 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7734 (mt-10) REVERT: B 214 GLN cc_start: 0.7646 (mt0) cc_final: 0.7354 (mt0) REVERT: C 11 GLN cc_start: 0.7818 (tp40) cc_final: 0.7498 (tp40) REVERT: C 22 LEU cc_start: 0.8430 (tp) cc_final: 0.8211 (tp) REVERT: C 50 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8807 (mm) REVERT: C 90 SER cc_start: 0.8125 (p) cc_final: 0.7440 (t) REVERT: C 100 ARG cc_start: 0.8329 (mtp85) cc_final: 0.7416 (mtm180) REVERT: C 113 LEU cc_start: 0.8228 (mt) cc_final: 0.7967 (mt) REVERT: C 127 LYS cc_start: 0.8609 (tttt) cc_final: 0.8223 (tptm) REVERT: C 135 GLN cc_start: 0.8584 (tp-100) cc_final: 0.8374 (tp40) REVERT: C 188 LEU cc_start: 0.8966 (mm) cc_final: 0.8724 (mm) REVERT: C 211 SER cc_start: 0.7978 (p) cc_final: 0.7524 (p) REVERT: C 216 ARG cc_start: 0.7651 (mtp85) cc_final: 0.7335 (mtp-110) REVERT: C 221 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7505 (tt) REVERT: D 135 GLU cc_start: 0.7195 (tm-30) cc_final: 0.6774 (tm-30) REVERT: D 211 TRP cc_start: 0.7662 (OUTLIER) cc_final: 0.7380 (m100) REVERT: E 158 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8127 (mp) REVERT: E 272 ARG cc_start: 0.7512 (mtm180) cc_final: 0.6924 (mtt180) REVERT: H 144 TYR cc_start: 0.8601 (m-80) cc_final: 0.8140 (m-80) REVERT: H 335 LYS cc_start: 0.7711 (mtpt) cc_final: 0.7231 (mtmt) REVERT: H 375 GLU cc_start: 0.8186 (tt0) cc_final: 0.7754 (tm-30) REVERT: H 454 LYS cc_start: 0.8435 (mmmm) cc_final: 0.8037 (mmmm) REVERT: H 512 ARG cc_start: 0.8615 (mmm160) cc_final: 0.7960 (tpp80) REVERT: H 551 MET cc_start: 0.8549 (ttt) cc_final: 0.8315 (ttp) REVERT: H 567 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7812 (mt-10) REVERT: H 629 MET cc_start: 0.7905 (mtp) cc_final: 0.7617 (mtp) REVERT: I 68 ASP cc_start: 0.7587 (m-30) cc_final: 0.7279 (m-30) REVERT: I 94 MET cc_start: 0.8451 (tpt) cc_final: 0.8143 (tpt) REVERT: I 300 THR cc_start: 0.9336 (m) cc_final: 0.9034 (p) REVERT: I 335 LYS cc_start: 0.8903 (ptmm) cc_final: 0.8510 (ptmm) REVERT: I 422 LYS cc_start: 0.8568 (mttt) cc_final: 0.8181 (mttt) REVERT: I 440 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8469 (mm-30) REVERT: I 492 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8472 (mt-10) REVERT: I 511 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7743 (t70) REVERT: I 532 ASP cc_start: 0.8661 (OUTLIER) cc_final: 0.8103 (m-30) outliers start: 91 outliers final: 67 residues processed: 586 average time/residue: 0.1311 time to fit residues: 123.1796 Evaluate side-chains 616 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 541 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain D residue 20 TRP Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 174 VAL Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 223 ASP Chi-restraints excluded: chain H residue 258 SER Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 393 THR Chi-restraints excluded: chain H residue 426 ASP Chi-restraints excluded: chain H residue 557 VAL Chi-restraints excluded: chain H residue 581 VAL Chi-restraints excluded: chain H residue 595 GLU Chi-restraints excluded: chain I residue 148 ASN Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 220 ASN Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 393 THR Chi-restraints excluded: chain I residue 398 ASP Chi-restraints excluded: chain I residue 402 VAL Chi-restraints excluded: chain I residue 428 HIS Chi-restraints excluded: chain I residue 439 CYS Chi-restraints excluded: chain I residue 477 SER Chi-restraints excluded: chain I residue 511 ASP Chi-restraints excluded: chain I residue 523 MET Chi-restraints excluded: chain I residue 532 ASP Chi-restraints excluded: chain I residue 561 THR Chi-restraints excluded: chain I residue 563 LYS Chi-restraints excluded: chain I residue 572 ILE Chi-restraints excluded: chain I residue 629 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 149 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 83 optimal weight: 0.0870 chunk 53 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 145 optimal weight: 7.9990 chunk 210 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 253 optimal weight: 4.9990 chunk 174 optimal weight: 0.2980 chunk 6 optimal weight: 3.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN C 82 ASN C 141 GLN ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 326 HIS ** I 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.148238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.119699 restraints weight = 32722.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.123181 restraints weight = 15270.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.125430 restraints weight = 8736.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.126728 restraints weight = 5794.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.127760 restraints weight = 4420.412| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3258 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3258 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21438 Z= 0.114 Angle : 0.610 10.351 29093 Z= 0.306 Chirality : 0.044 0.231 3253 Planarity : 0.004 0.041 3755 Dihedral : 6.362 83.369 2978 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.34 % Favored : 94.58 % Rotamer: Outliers : 3.45 % Allowed : 21.47 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.16), residues: 2678 helix: 1.09 (0.19), residues: 800 sheet: -0.69 (0.22), residues: 582 loop : -1.51 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 403 TYR 0.016 0.001 TYR H 216 PHE 0.033 0.002 PHE H 250 TRP 0.025 0.001 TRP D 141 HIS 0.004 0.001 HIS H 626 Details of bonding type rmsd covalent geometry : bond 0.00261 (21438) covalent geometry : angle 0.61006 (29093) hydrogen bonds : bond 0.03085 ( 835) hydrogen bonds : angle 5.02103 ( 2399) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 571 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8545 (tt) REVERT: A 105 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.7325 (mtm) REVERT: A 157 ASP cc_start: 0.8027 (t0) cc_final: 0.7564 (t0) REVERT: A 174 HIS cc_start: 0.8053 (m90) cc_final: 0.7853 (m90) REVERT: A 219 ASN cc_start: 0.8817 (m-40) cc_final: 0.8602 (m-40) REVERT: A 403 ARG cc_start: 0.6711 (mtm110) cc_final: 0.6504 (mtm110) REVERT: B 2 ASN cc_start: 0.7755 (m-40) cc_final: 0.7484 (m110) REVERT: B 16 MET cc_start: 0.6799 (ttt) cc_final: 0.6182 (mmt) REVERT: B 214 GLN cc_start: 0.7618 (mt0) cc_final: 0.7280 (mt0) REVERT: C 11 GLN cc_start: 0.7724 (tp40) cc_final: 0.7435 (tp-100) REVERT: C 22 LEU cc_start: 0.8346 (tp) cc_final: 0.8135 (tp) REVERT: C 50 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8817 (mm) REVERT: C 90 SER cc_start: 0.8094 (p) cc_final: 0.7400 (t) REVERT: C 100 ARG cc_start: 0.8248 (mtp85) cc_final: 0.7389 (mtm180) REVERT: C 127 LYS cc_start: 0.8569 (tttt) cc_final: 0.8199 (tptm) REVERT: C 188 LEU cc_start: 0.8959 (mm) cc_final: 0.8695 (mm) REVERT: C 216 ARG cc_start: 0.7567 (mtp85) cc_final: 0.7286 (mtp-110) REVERT: C 221 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7465 (tt) REVERT: D 135 GLU cc_start: 0.7229 (tm-30) cc_final: 0.6787 (tm-30) REVERT: D 211 TRP cc_start: 0.7616 (OUTLIER) cc_final: 0.7340 (m100) REVERT: E 272 ARG cc_start: 0.7471 (mtm180) cc_final: 0.6930 (mtt180) REVERT: H 144 TYR cc_start: 0.8535 (m-80) cc_final: 0.8090 (m-80) REVERT: H 223 ASP cc_start: 0.8688 (OUTLIER) cc_final: 0.8282 (m-30) REVERT: H 335 LYS cc_start: 0.7620 (mtpt) cc_final: 0.7233 (mtmt) REVERT: H 375 GLU cc_start: 0.8134 (tt0) cc_final: 0.7744 (tm-30) REVERT: H 512 ARG cc_start: 0.8590 (mmm160) cc_final: 0.8077 (tpp80) REVERT: H 551 MET cc_start: 0.8523 (ttt) cc_final: 0.8261 (ttp) REVERT: H 629 MET cc_start: 0.7804 (mtp) cc_final: 0.7540 (mtp) REVERT: I 68 ASP cc_start: 0.7618 (m-30) cc_final: 0.7338 (m-30) REVERT: I 94 MET cc_start: 0.8430 (tpt) cc_final: 0.8098 (tpt) REVERT: I 95 ARG cc_start: 0.8034 (mtp-110) cc_final: 0.7621 (mtp-110) REVERT: I 300 THR cc_start: 0.9311 (m) cc_final: 0.9012 (p) REVERT: I 335 LYS cc_start: 0.8934 (ptmm) cc_final: 0.8546 (ptmm) REVERT: I 422 LYS cc_start: 0.8488 (mttt) cc_final: 0.8083 (mttt) REVERT: I 440 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8412 (mm-30) REVERT: I 492 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8445 (mt-10) REVERT: I 511 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7703 (t70) REVERT: I 532 ASP cc_start: 0.8620 (OUTLIER) cc_final: 0.7900 (m-30) outliers start: 77 outliers final: 61 residues processed: 605 average time/residue: 0.1381 time to fit residues: 133.0086 Evaluate side-chains 618 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 549 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain D residue 20 TRP Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 223 ASP Chi-restraints excluded: chain H residue 258 SER Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 393 THR Chi-restraints excluded: chain H residue 426 ASP Chi-restraints excluded: chain H residue 557 VAL Chi-restraints excluded: chain H residue 581 VAL Chi-restraints excluded: chain H residue 595 GLU Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 169 ILE Chi-restraints excluded: chain I residue 220 ASN Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 393 THR Chi-restraints excluded: chain I residue 398 ASP Chi-restraints excluded: chain I residue 402 VAL Chi-restraints excluded: chain I residue 428 HIS Chi-restraints excluded: chain I residue 439 CYS Chi-restraints excluded: chain I residue 511 ASP Chi-restraints excluded: chain I residue 532 ASP Chi-restraints excluded: chain I residue 561 THR Chi-restraints excluded: chain I residue 563 LYS Chi-restraints excluded: chain I residue 572 ILE Chi-restraints excluded: chain I residue 629 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 240 optimal weight: 0.7980 chunk 12 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 221 optimal weight: 4.9990 chunk 225 optimal weight: 2.9990 chunk 65 optimal weight: 50.0000 chunk 11 optimal weight: 0.8980 chunk 262 optimal weight: 6.9990 chunk 182 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN C 82 ASN ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 326 HIS ** I 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.147644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.118269 restraints weight = 38647.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.122025 restraints weight = 17221.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.124405 restraints weight = 9557.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.125970 restraints weight = 6194.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.126933 restraints weight = 4583.246| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3249 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3249 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21438 Z= 0.129 Angle : 0.617 11.189 29093 Z= 0.308 Chirality : 0.044 0.246 3253 Planarity : 0.004 0.040 3755 Dihedral : 6.344 84.146 2978 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.31 % Favored : 94.62 % Rotamer: Outliers : 3.77 % Allowed : 21.38 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.16), residues: 2678 helix: 1.09 (0.18), residues: 800 sheet: -0.58 (0.22), residues: 574 loop : -1.49 (0.17), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 500 TYR 0.014 0.002 TYR H 216 PHE 0.030 0.002 PHE H 250 TRP 0.026 0.001 TRP D 141 HIS 0.004 0.001 HIS H 626 Details of bonding type rmsd covalent geometry : bond 0.00302 (21438) covalent geometry : angle 0.61733 (29093) hydrogen bonds : bond 0.03128 ( 835) hydrogen bonds : angle 4.95410 ( 2399) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 558 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8514 (tt) REVERT: A 105 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.7298 (mtm) REVERT: A 138 ARG cc_start: 0.7074 (OUTLIER) cc_final: 0.6040 (ptt90) REVERT: A 157 ASP cc_start: 0.8048 (t0) cc_final: 0.7592 (t0) REVERT: A 174 HIS cc_start: 0.8092 (m90) cc_final: 0.7881 (m90) REVERT: A 219 ASN cc_start: 0.8784 (m-40) cc_final: 0.8565 (m-40) REVERT: A 244 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7305 (mt-10) REVERT: A 305 LYS cc_start: 0.8711 (mptt) cc_final: 0.8419 (mttt) REVERT: A 390 MET cc_start: 0.8997 (mpp) cc_final: 0.8753 (mpp) REVERT: B 2 ASN cc_start: 0.7860 (m-40) cc_final: 0.7594 (m110) REVERT: B 16 MET cc_start: 0.6738 (ttt) cc_final: 0.6176 (mmt) REVERT: B 150 LEU cc_start: 0.7506 (tt) cc_final: 0.7294 (tt) REVERT: B 214 GLN cc_start: 0.7617 (mt0) cc_final: 0.7282 (mt0) REVERT: C 11 GLN cc_start: 0.7753 (tp40) cc_final: 0.7446 (tp-100) REVERT: C 22 LEU cc_start: 0.8355 (tp) cc_final: 0.8148 (tp) REVERT: C 50 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8851 (mm) REVERT: C 90 SER cc_start: 0.8086 (p) cc_final: 0.7439 (t) REVERT: C 100 ARG cc_start: 0.8256 (mtp85) cc_final: 0.7722 (mtm-85) REVERT: C 127 LYS cc_start: 0.8562 (tttt) cc_final: 0.8187 (tptm) REVERT: C 188 LEU cc_start: 0.8937 (mm) cc_final: 0.8667 (mm) REVERT: C 216 ARG cc_start: 0.7572 (mtp85) cc_final: 0.7267 (mtp-110) REVERT: C 221 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7471 (tt) REVERT: D 135 GLU cc_start: 0.7267 (tm-30) cc_final: 0.6775 (tm-30) REVERT: D 211 TRP cc_start: 0.7636 (OUTLIER) cc_final: 0.7358 (m100) REVERT: E 158 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8128 (mp) REVERT: E 272 ARG cc_start: 0.7456 (mtm180) cc_final: 0.6937 (mtt180) REVERT: H 144 TYR cc_start: 0.8542 (m-80) cc_final: 0.8077 (m-80) REVERT: H 335 LYS cc_start: 0.7634 (mtpt) cc_final: 0.7243 (mtmt) REVERT: H 375 GLU cc_start: 0.8115 (tt0) cc_final: 0.7729 (tm-30) REVERT: H 512 ARG cc_start: 0.8591 (mmm160) cc_final: 0.8075 (tpp80) REVERT: I 68 ASP cc_start: 0.7590 (m-30) cc_final: 0.7316 (m-30) REVERT: I 94 MET cc_start: 0.8512 (tpt) cc_final: 0.8151 (tpt) REVERT: I 300 THR cc_start: 0.9320 (m) cc_final: 0.9007 (p) REVERT: I 335 LYS cc_start: 0.8941 (ptmm) cc_final: 0.8546 (ptmm) REVERT: I 422 LYS cc_start: 0.8471 (mttt) cc_final: 0.8072 (mttt) REVERT: I 440 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8393 (mm-30) REVERT: I 492 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8484 (mt-10) REVERT: I 511 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7726 (t70) REVERT: I 532 ASP cc_start: 0.8635 (OUTLIER) cc_final: 0.8069 (t0) REVERT: I 634 MET cc_start: 0.8186 (mpp) cc_final: 0.7658 (mmm) outliers start: 84 outliers final: 65 residues processed: 597 average time/residue: 0.1512 time to fit residues: 143.0598 Evaluate side-chains 624 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 550 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 138 ARG Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain D residue 20 TRP Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 258 SER Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 393 THR Chi-restraints excluded: chain H residue 426 ASP Chi-restraints excluded: chain H residue 557 VAL Chi-restraints excluded: chain H residue 581 VAL Chi-restraints excluded: chain H residue 595 GLU Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 169 ILE Chi-restraints excluded: chain I residue 220 ASN Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 303 LEU Chi-restraints excluded: chain I residue 393 THR Chi-restraints excluded: chain I residue 398 ASP Chi-restraints excluded: chain I residue 402 VAL Chi-restraints excluded: chain I residue 428 HIS Chi-restraints excluded: chain I residue 439 CYS Chi-restraints excluded: chain I residue 477 SER Chi-restraints excluded: chain I residue 511 ASP Chi-restraints excluded: chain I residue 523 MET Chi-restraints excluded: chain I residue 532 ASP Chi-restraints excluded: chain I residue 561 THR Chi-restraints excluded: chain I residue 563 LYS Chi-restraints excluded: chain I residue 578 ILE Chi-restraints excluded: chain I residue 629 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 50 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 257 optimal weight: 3.9990 chunk 239 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 213 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 243 optimal weight: 5.9990 chunk 51 optimal weight: 0.0770 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 GLN C 82 ASN ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 GLN I 148 ASN I 211 GLN ** I 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.140331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.110680 restraints weight = 40852.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.114395 restraints weight = 18057.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.116695 restraints weight = 10005.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.118251 restraints weight = 6562.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.119341 restraints weight = 4841.122| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 21438 Z= 0.237 Angle : 0.703 13.632 29093 Z= 0.354 Chirality : 0.047 0.301 3253 Planarity : 0.005 0.045 3755 Dihedral : 6.763 84.427 2978 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.43 % Favored : 93.50 % Rotamer: Outliers : 3.90 % Allowed : 21.65 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.16), residues: 2678 helix: 0.84 (0.18), residues: 799 sheet: -0.70 (0.21), residues: 591 loop : -1.57 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 500 TYR 0.016 0.002 TYR A 204 PHE 0.037 0.002 PHE H 250 TRP 0.026 0.002 TRP D 141 HIS 0.006 0.001 HIS H 201 Details of bonding type rmsd covalent geometry : bond 0.00550 (21438) covalent geometry : angle 0.70350 (29093) hydrogen bonds : bond 0.03770 ( 835) hydrogen bonds : angle 5.21437 ( 2399) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 577 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8482 (tt) REVERT: A 97 GLU cc_start: 0.7360 (mt-10) cc_final: 0.7153 (mt-10) REVERT: A 157 ASP cc_start: 0.8329 (t0) cc_final: 0.7950 (t0) REVERT: A 174 HIS cc_start: 0.8307 (m90) cc_final: 0.7992 (m90) REVERT: A 219 ASN cc_start: 0.8923 (m-40) cc_final: 0.8704 (m-40) REVERT: B 16 MET cc_start: 0.6752 (ttt) cc_final: 0.6349 (mmt) REVERT: B 214 GLN cc_start: 0.7638 (mt0) cc_final: 0.7279 (mt0) REVERT: C 50 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8838 (mm) REVERT: C 74 ARG cc_start: 0.7552 (tpp-160) cc_final: 0.7348 (tpp80) REVERT: C 90 SER cc_start: 0.8088 (p) cc_final: 0.7431 (t) REVERT: C 127 LYS cc_start: 0.8628 (tttt) cc_final: 0.8214 (tptm) REVERT: C 135 GLN cc_start: 0.8579 (tp-100) cc_final: 0.8249 (tp-100) REVERT: C 188 LEU cc_start: 0.8990 (mm) cc_final: 0.8710 (mm) REVERT: C 216 ARG cc_start: 0.7623 (mtp85) cc_final: 0.7325 (mtp-110) REVERT: D 135 GLU cc_start: 0.7374 (tm-30) cc_final: 0.6928 (tm-30) REVERT: D 211 TRP cc_start: 0.7781 (OUTLIER) cc_final: 0.7383 (m100) REVERT: E 158 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8143 (mp) REVERT: H 144 TYR cc_start: 0.8683 (m-80) cc_final: 0.8140 (m-80) REVERT: H 454 LYS cc_start: 0.8595 (tptm) cc_final: 0.8101 (tptm) REVERT: H 501 ARG cc_start: 0.8254 (ttt180) cc_final: 0.7950 (ttt-90) REVERT: H 512 ARG cc_start: 0.8672 (mmm160) cc_final: 0.8115 (tpp80) REVERT: I 94 MET cc_start: 0.8501 (tpt) cc_final: 0.8216 (tpt) REVERT: I 135 MET cc_start: 0.7939 (ptp) cc_final: 0.7224 (ptp) REVERT: I 228 GLU cc_start: 0.7148 (mp0) cc_final: 0.6733 (mp0) REVERT: I 300 THR cc_start: 0.9383 (m) cc_final: 0.9105 (p) REVERT: I 335 LYS cc_start: 0.8914 (ptmm) cc_final: 0.8511 (ptmm) REVERT: I 422 LYS cc_start: 0.8555 (mttt) cc_final: 0.8231 (mttt) REVERT: I 440 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8416 (mm-30) REVERT: I 492 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8553 (mt-10) REVERT: I 532 ASP cc_start: 0.8683 (OUTLIER) cc_final: 0.8295 (m-30) REVERT: I 580 ASP cc_start: 0.6716 (t0) cc_final: 0.6401 (t0) outliers start: 87 outliers final: 67 residues processed: 614 average time/residue: 0.1346 time to fit residues: 129.8545 Evaluate side-chains 632 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 560 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 108 GLN Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 82 ASN Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain D residue 20 TRP Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 64 PHE Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 223 ASP Chi-restraints excluded: chain H residue 258 SER Chi-restraints excluded: chain H residue 371 VAL Chi-restraints excluded: chain H residue 393 THR Chi-restraints excluded: chain H residue 426 ASP Chi-restraints excluded: chain H residue 557 VAL Chi-restraints excluded: chain H residue 581 VAL Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain I residue 148 ASN Chi-restraints excluded: chain I residue 153 SER Chi-restraints excluded: chain I residue 220 ASN Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 393 THR Chi-restraints excluded: chain I residue 398 ASP Chi-restraints excluded: chain I residue 402 VAL Chi-restraints excluded: chain I residue 428 HIS Chi-restraints excluded: chain I residue 439 CYS Chi-restraints excluded: chain I residue 477 SER Chi-restraints excluded: chain I residue 523 MET Chi-restraints excluded: chain I residue 532 ASP Chi-restraints excluded: chain I residue 561 THR Chi-restraints excluded: chain I residue 563 LYS Chi-restraints excluded: chain I residue 578 ILE Chi-restraints excluded: chain I residue 629 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 218 optimal weight: 0.9990 chunk 221 optimal weight: 6.9990 chunk 156 optimal weight: 6.9990 chunk 121 optimal weight: 20.0000 chunk 72 optimal weight: 4.9990 chunk 250 optimal weight: 0.0980 chunk 109 optimal weight: 0.7980 chunk 257 optimal weight: 5.9990 chunk 197 optimal weight: 9.9990 chunk 195 optimal weight: 0.0980 chunk 188 optimal weight: 0.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 GLN B 283 HIS C 23 ASN ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.141038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.112228 restraints weight = 33644.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.115615 restraints weight = 15733.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.117772 restraints weight = 9024.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.119148 restraints weight = 6055.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.120005 restraints weight = 4582.457| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3159 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.240 21438 Z= 0.227 Angle : 0.900 59.187 29093 Z= 0.509 Chirality : 0.058 1.738 3253 Planarity : 0.005 0.140 3755 Dihedral : 6.808 84.302 2978 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.50 % Favored : 93.39 % Rotamer: Outliers : 3.05 % Allowed : 22.50 % Favored : 74.45 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.16), residues: 2678 helix: 0.83 (0.18), residues: 801 sheet: -0.75 (0.22), residues: 579 loop : -1.56 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 9 TYR 0.015 0.002 TYR H 336 PHE 0.036 0.002 PHE H 250 TRP 0.028 0.002 TRP I 74 HIS 0.006 0.001 HIS A 311 Details of bonding type rmsd covalent geometry : bond 0.00545 (21438) covalent geometry : angle 0.90018 (29093) hydrogen bonds : bond 0.03720 ( 835) hydrogen bonds : angle 5.22882 ( 2399) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4491.37 seconds wall clock time: 78 minutes 3.25 seconds (4683.25 seconds total)