Starting phenix.real_space_refine on Tue Jun 24 11:06:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qba_13885/06_2025/7qba_13885.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qba_13885/06_2025/7qba_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_13885/06_2025/7qba_13885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qba_13885/06_2025/7qba_13885.map" model { file = "/net/cci-nas-00/data/ceres_data/7qba_13885/06_2025/7qba_13885.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qba_13885/06_2025/7qba_13885.cif" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.081 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.36, per 1000 atoms: 0.64 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: 5.04 Conformation dependent library (CDL) restraints added in 3.0 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: 2.61 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: 7.90 Time building geometry restraints manager: 6.02 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 638 or resid 701)) selection = (chain 'I' and (resid 58 through 136 or resid 138 through 601 or resid 603 throu \ gh 638 or resid 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: 0.000 Normalize map: mean=0, sd=1: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.010 Extract box with map and model: 0.880 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 49.820 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.110 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.790 ------------------------------------------------------------------------------- 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 : 16.56 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (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 TRP 0.064 0.003 TRP H 74 HIS 0.013 0.002 HIS H 494 PHE 0.044 0.002 PHE H 385 TYR 0.045 0.002 TYR H 256 ARG 0.008 0.001 ARG H 459 Details of bonding type rmsd hydrogen bonds : bond 0.17494 ( 835) hydrogen bonds : angle 7.75268 ( 2399) covalent geometry : bond 0.00593 (21438) covalent geometry : angle 1.07357 (29093) *********************** 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 : 2.154 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: 0.8099 (p) REVERT: A 126 ARG cc_start: 0.7299 (ttp-170) cc_final: 0.7072 (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: 0.6078 (tt0) REVERT: B 115 GLN cc_start: 0.8040 (tt0) cc_final: 0.7097 (mt0) REVERT: C 127 LYS cc_start: 0.8687 (tttt) cc_final: 0.8410 (tptm) REVERT: C 216 ARG cc_start: 0.7685 (mtp85) cc_final: 0.7372 (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: 0.8506 (mt) REVERT: H 267 MET cc_start: 0.8465 (mtt) cc_final: 0.8227 (mtt) REVERT: H 298 SER cc_start: 0.8893 (t) cc_final: 0.8460 (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: 0.6531 (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: 0.7943 (tpp80) REVERT: H 526 LYS cc_start: 0.8403 (mmtt) cc_final: 0.8031 (mmmt) REVERT: H 551 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7823 (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: 0.8331 (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: 0.8394 (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: 0.3184 time to fit residues: 377.5669 Evaluate side-chains 649 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 644 time to evaluate : 2.158 ------------------------------------------------------------------------------- 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 224 optimal weight: 6.9990 chunk 201 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 68 optimal weight: 0.1980 chunk 135 optimal weight: 8.9990 chunk 107 optimal weight: 0.9990 chunk 208 optimal weight: 0.0370 chunk 80 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 chunk 155 optimal weight: 4.9990 chunk 241 optimal weight: 0.9980 overall best weight: 0.8462 ------------------------------------------------------------------------------- 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 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 ASN ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 196 ASN D 225 ASN ** H 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 626 HIS I 132 HIS I 148 ASN ** I 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 187 HIS ** I 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 574 ASN I 583 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.151075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.122525 restraints weight = 33950.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.126163 restraints weight = 15480.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.128477 restraints weight = 8718.021| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21438 Z= 0.141 Angle : 0.685 12.684 29093 Z= 0.348 Chirality : 0.047 0.196 3253 Planarity : 0.005 0.079 3755 Dihedral : 6.886 70.754 2983 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.82 % Favored : 95.07 % Rotamer: Outliers : 2.55 % Allowed : 12.51 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.16), residues: 2678 helix: 0.66 (0.18), residues: 792 sheet: -0.71 (0.22), residues: 539 loop : -1.68 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 98 HIS 0.006 0.001 HIS B 97 PHE 0.043 0.002 PHE H 385 TYR 0.019 0.002 TYR B 78 ARG 0.005 0.001 ARG B 74 Details of bonding type rmsd hydrogen bonds : bond 0.03894 ( 835) hydrogen bonds : angle 5.72338 ( 2399) covalent geometry : bond 0.00319 (21438) covalent geometry : angle 0.68540 (29093) *********************** 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 692 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 635 time to evaluate : 2.173 Fit side-chains revert: symmetry clash REVERT: A 94 THR cc_start: 0.8387 (m) cc_final: 0.7790 (p) REVERT: A 141 GLN cc_start: 0.7877 (mt0) cc_final: 0.7612 (mt0) REVERT: A 157 ASP cc_start: 0.8094 (t0) cc_final: 0.7868 (t0) REVERT: A 174 HIS cc_start: 0.8101 (m90) cc_final: 0.7842 (m90) REVERT: A 219 ASN cc_start: 0.8901 (m-40) cc_final: 0.8480 (m-40) REVERT: A 241 ASN cc_start: 0.8391 (m-40) cc_final: 0.8103 (m-40) REVERT: A 403 ARG cc_start: 0.6757 (ptp-170) cc_final: 0.6384 (mtm110) REVERT: B 16 MET cc_start: 0.6783 (ttt) cc_final: 0.6266 (mmt) REVERT: B 73 ARG cc_start: 0.8816 (mtm180) cc_final: 0.8476 (mtm-85) REVERT: B 75 GLN cc_start: 0.7970 (mm110) cc_final: 0.7296 (mm110) REVERT: B 295 MET cc_start: 0.7717 (tpp) cc_final: 0.7259 (tpp) REVERT: C 11 GLN cc_start: 0.7775 (tp40) cc_final: 0.7447 (tp40) REVERT: C 127 LYS cc_start: 0.8671 (tttt) cc_final: 0.8323 (tptm) REVERT: C 211 SER cc_start: 0.7905 (p) cc_final: 0.7617 (p) REVERT: C 216 ARG cc_start: 0.7654 (mtp85) cc_final: 0.7360 (ttm-80) REVERT: D 38 LEU cc_start: 0.8197 (mt) cc_final: 0.7909 (mm) REVERT: D 66 MET cc_start: 0.8265 (tpt) cc_final: 0.8065 (tpt) REVERT: D 211 TRP cc_start: 0.7638 (OUTLIER) cc_final: 0.6856 (m100) REVERT: E 9 ARG cc_start: 0.8418 (ptm160) cc_final: 0.7785 (ptm160) REVERT: E 272 ARG cc_start: 0.7325 (mtm180) cc_final: 0.6749 (mtt180) REVERT: H 94 MET cc_start: 0.8557 (tpt) cc_final: 0.8264 (tpt) REVERT: H 144 TYR cc_start: 0.8577 (m-80) cc_final: 0.8207 (m-80) REVERT: H 308 LYS cc_start: 0.7495 (tppt) cc_final: 0.6436 (ttmm) REVERT: H 512 ARG cc_start: 0.8386 (mmm160) cc_final: 0.7832 (tpp80) REVERT: H 526 LYS cc_start: 0.8112 (mmtt) cc_final: 0.7713 (mmmt) REVERT: H 551 MET cc_start: 0.8637 (ttt) cc_final: 0.8367 (ttp) REVERT: H 567 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7989 (mt-10) REVERT: H 593 SER cc_start: 0.9007 (t) cc_final: 0.8798 (m) REVERT: H 629 MET cc_start: 0.7757 (mtp) cc_final: 0.7498 (mtp) REVERT: I 68 ASP cc_start: 0.7508 (m-30) cc_final: 0.7258 (m-30) REVERT: I 440 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8471 (mm-30) REVERT: I 523 MET cc_start: 0.7842 (ttm) cc_final: 0.7632 (ttm) REVERT: I 558 GLN cc_start: 0.7954 (mt0) cc_final: 0.7666 (mt0) outliers start: 57 outliers final: 38 residues processed: 652 average time/residue: 0.3119 time to fit residues: 320.9611 Evaluate side-chains 615 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 576 time to evaluate : 2.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 184 ILE 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 C residue 23 ASN Chi-restraints excluded: chain C residue 53 LEU 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 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 63 THR 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 287 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 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 532 ASP Chi-restraints excluded: chain I residue 563 LYS Chi-restraints excluded: chain I residue 572 ILE Chi-restraints excluded: chain I residue 574 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 29 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 chunk 128 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 175 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 174 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS B 108 GLN B 135 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN ** H 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 626 HIS I 148 ASN ** I 382 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 = 0.3431 r_free = 0.3431 target = 0.141673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.111437 restraints weight = 42393.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.115290 restraints weight = 18643.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.117690 restraints weight = 10276.525| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 21438 Z= 0.240 Angle : 0.711 12.539 29093 Z= 0.366 Chirality : 0.047 0.178 3253 Planarity : 0.005 0.052 3755 Dihedral : 7.025 67.759 2979 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.94 % Favored : 93.98 % Rotamer: Outliers : 3.72 % Allowed : 16.45 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.16), residues: 2678 helix: 0.54 (0.18), residues: 799 sheet: -0.81 (0.22), residues: 553 loop : -1.69 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 141 HIS 0.005 0.001 HIS A 311 PHE 0.044 0.002 PHE H 385 TYR 0.017 0.002 TYR B 13 ARG 0.004 0.001 ARG H 459 Details of bonding type rmsd hydrogen bonds : bond 0.04189 ( 835) hydrogen bonds : angle 5.59569 ( 2399) covalent geometry : bond 0.00554 (21438) covalent geometry : angle 0.71147 (29093) *********************** 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 688 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 605 time to evaluate : 2.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8415 (tt) REVERT: A 141 GLN cc_start: 0.7901 (mt0) cc_final: 0.7639 (mt0) REVERT: A 174 HIS cc_start: 0.8196 (m90) cc_final: 0.7931 (m90) REVERT: A 204 TYR cc_start: 0.8895 (m-80) cc_final: 0.8693 (m-10) REVERT: A 219 ASN cc_start: 0.8949 (m-40) cc_final: 0.8592 (m-40) REVERT: A 241 ASN cc_start: 0.8702 (m-40) cc_final: 0.8432 (m-40) REVERT: B 16 MET cc_start: 0.6756 (ttt) cc_final: 0.6282 (mmt) REVERT: B 73 ARG cc_start: 0.8978 (mtm180) cc_final: 0.8519 (mtm-85) REVERT: B 125 ARG cc_start: 0.6809 (OUTLIER) cc_final: 0.6029 (mtt-85) REVERT: C 11 GLN cc_start: 0.7807 (tp40) cc_final: 0.7554 (tp40) REVERT: C 23 ASN cc_start: 0.7111 (OUTLIER) cc_final: 0.6881 (p0) REVERT: C 50 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8861 (mm) REVERT: C 127 LYS cc_start: 0.8682 (tttt) cc_final: 0.8324 (tptm) REVERT: C 216 ARG cc_start: 0.7682 (mtp85) cc_final: 0.7360 (mtp-110) REVERT: D 102 LEU cc_start: 0.8618 (mt) cc_final: 0.8365 (mm) REVERT: D 211 TRP cc_start: 0.7751 (OUTLIER) cc_final: 0.7173 (m100) REVERT: D 236 MET cc_start: 0.6060 (mmp) cc_final: 0.4809 (mmm) REVERT: E 147 MET cc_start: 0.6485 (mmt) cc_final: 0.5798 (mmp) REVERT: E 272 ARG cc_start: 0.7528 (mtm180) cc_final: 0.6738 (mtp180) REVERT: H 144 TYR cc_start: 0.8685 (m-80) cc_final: 0.8229 (m-80) REVERT: H 335 LYS cc_start: 0.7487 (mtpp) cc_final: 0.7190 (mtmt) REVERT: H 492 GLU cc_start: 0.8184 (tt0) cc_final: 0.7842 (tp30) REVERT: H 501 ARG cc_start: 0.8281 (ttt180) cc_final: 0.7867 (ttt-90) REVERT: H 551 MET cc_start: 0.8645 (ttt) cc_final: 0.8424 (ttp) REVERT: H 567 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7904 (mt-10) REVERT: I 95 ARG cc_start: 0.8014 (mtp-110) cc_final: 0.7686 (mtp-110) REVERT: I 135 MET cc_start: 0.8047 (ptp) cc_final: 0.7387 (ptp) REVERT: I 300 THR cc_start: 0.9239 (m) cc_final: 0.8934 (p) REVERT: I 414 LYS cc_start: 0.8098 (mmmt) cc_final: 0.6518 (mtpt) REVERT: I 422 LYS cc_start: 0.8570 (mttt) cc_final: 0.8337 (mttt) REVERT: I 440 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8517 (mm-30) REVERT: I 511 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7603 (t70) REVERT: I 517 PHE cc_start: 0.9193 (OUTLIER) cc_final: 0.8922 (p90) REVERT: I 532 ASP cc_start: 0.8695 (OUTLIER) cc_final: 0.7811 (t70) outliers start: 83 outliers final: 56 residues processed: 635 average time/residue: 0.3119 time to fit residues: 313.8368 Evaluate side-chains 647 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 583 time to evaluate : 2.196 ------------------------------------------------------------------------------- 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 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 108 GLN Chi-restraints excluded: chain B residue 125 ARG Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 139 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 100 ILE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 199 LEU 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 174 VAL Chi-restraints excluded: chain H residue 207 VAL Chi-restraints excluded: chain H residue 258 SER Chi-restraints excluded: chain H residue 313 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 105 THR Chi-restraints excluded: chain I residue 134 SER 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 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 517 PHE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 229 optimal weight: 4.9990 chunk 145 optimal weight: 0.0770 chunk 127 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 192 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 264 optimal weight: 5.9990 overall best weight: 2.1744 ------------------------------------------------------------------------------- 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 254 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN C 165 GLN D 225 ASN ** H 614 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 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 626 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 = 0.3438 r_free = 0.3438 target = 0.142340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.111819 restraints weight = 46032.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.115776 restraints weight = 19601.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.118315 restraints weight = 10622.202| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21438 Z= 0.186 Angle : 0.651 11.387 29093 Z= 0.333 Chirality : 0.046 0.176 3253 Planarity : 0.005 0.044 3755 Dihedral : 6.822 76.470 2979 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.90 % Favored : 94.02 % Rotamer: Outliers : 3.90 % Allowed : 17.84 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.16), residues: 2678 helix: 0.62 (0.18), residues: 803 sheet: -0.88 (0.22), residues: 571 loop : -1.60 (0.16), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 141 HIS 0.007 0.001 HIS B 97 PHE 0.035 0.002 PHE H 385 TYR 0.025 0.002 TYR B 78 ARG 0.007 0.000 ARG H 95 Details of bonding type rmsd hydrogen bonds : bond 0.03707 ( 835) hydrogen bonds : angle 5.40161 ( 2399) covalent geometry : bond 0.00434 (21438) covalent geometry : angle 0.65052 (29093) *********************** 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 674 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 587 time to evaluate : 2.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8572 (tt) REVERT: A 141 GLN cc_start: 0.7844 (mt0) cc_final: 0.7638 (mt0) REVERT: A 174 HIS cc_start: 0.8183 (m90) cc_final: 0.7949 (m90) REVERT: A 219 ASN cc_start: 0.8970 (m-40) cc_final: 0.8574 (m-40) REVERT: B 16 MET cc_start: 0.6873 (ttt) cc_final: 0.6330 (mmt) REVERT: C 50 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8798 (mm) REVERT: C 127 LYS cc_start: 0.8680 (tttt) cc_final: 0.8335 (tptm) REVERT: C 135 GLN cc_start: 0.8555 (tp-100) cc_final: 0.8254 (tp-100) REVERT: C 216 ARG cc_start: 0.7668 (mtp85) cc_final: 0.7304 (mtp-110) REVERT: D 211 TRP cc_start: 0.7764 (OUTLIER) cc_final: 0.7236 (m100) REVERT: D 236 MET cc_start: 0.6016 (mmp) cc_final: 0.4814 (mmm) REVERT: E 272 ARG cc_start: 0.7529 (mtm180) cc_final: 0.6894 (mtt180) REVERT: H 144 TYR cc_start: 0.8662 (m-80) cc_final: 0.8245 (m-80) REVERT: H 228 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7519 (mm-30) REVERT: H 397 ILE cc_start: 0.8809 (mt) cc_final: 0.8460 (mt) REVERT: H 492 GLU cc_start: 0.8208 (tt0) cc_final: 0.7853 (tp30) REVERT: H 501 ARG cc_start: 0.8295 (ttt180) cc_final: 0.7973 (ttt-90) REVERT: H 512 ARG cc_start: 0.8745 (mmm160) cc_final: 0.8139 (tpp80) REVERT: H 551 MET cc_start: 0.8565 (ttt) cc_final: 0.8351 (ttp) REVERT: I 94 MET cc_start: 0.8491 (tpt) cc_final: 0.8199 (tpt) REVERT: I 135 MET cc_start: 0.7995 (ptp) cc_final: 0.7541 (ptp) REVERT: I 229 MET cc_start: 0.8095 (mmt) cc_final: 0.7887 (mmt) REVERT: I 300 THR cc_start: 0.9318 (m) cc_final: 0.9042 (p) REVERT: I 422 LYS cc_start: 0.8603 (mttt) cc_final: 0.8230 (mttt) REVERT: I 511 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7536 (t0) REVERT: I 532 ASP cc_start: 0.8670 (OUTLIER) cc_final: 0.7880 (t0) REVERT: I 627 MET cc_start: 0.7534 (mmp) cc_final: 0.7208 (mmm) outliers start: 87 outliers final: 52 residues processed: 625 average time/residue: 0.3071 time to fit residues: 303.2922 Evaluate side-chains 622 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 565 time to evaluate : 2.159 ------------------------------------------------------------------------------- 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 134 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 184 ILE 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 18 VAL 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 C residue 50 LEU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain D residue 16 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 168 VAL Chi-restraints excluded: chain D residue 211 TRP Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain H residue 93 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 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 H residue 595 GLU Chi-restraints excluded: chain I residue 112 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 198 ILE 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 9 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 238 optimal weight: 7.9990 chunk 262 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 175 optimal weight: 4.9990 chunk 147 optimal weight: 10.0000 chunk 221 optimal weight: 3.9990 chunk 192 optimal weight: 0.4980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 GLN C 23 ASN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 564 GLN ** H 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 ASN I 178 HIS I 211 GLN I 382 HIS ** I 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.140860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.111542 restraints weight = 35582.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.115013 restraints weight = 16368.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.117216 restraints weight = 9320.124| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 21438 Z= 0.205 Angle : 0.665 12.723 29093 Z= 0.340 Chirality : 0.046 0.174 3253 Planarity : 0.004 0.042 3755 Dihedral : 6.826 86.647 2979 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.13 % Favored : 93.80 % Rotamer: Outliers : 4.62 % Allowed : 18.69 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.16), residues: 2678 helix: 0.63 (0.18), residues: 802 sheet: -0.91 (0.22), residues: 571 loop : -1.60 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 98 HIS 0.006 0.001 HIS B 97 PHE 0.032 0.002 PHE H 385 TYR 0.022 0.002 TYR A 204 ARG 0.005 0.000 ARG B 74 Details of bonding type rmsd hydrogen bonds : bond 0.03752 ( 835) hydrogen bonds : angle 5.35637 ( 2399) covalent geometry : bond 0.00477 (21438) covalent geometry : angle 0.66490 (29093) *********************** 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 680 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 577 time to evaluate : 2.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8599 (tt) REVERT: A 141 GLN cc_start: 0.7828 (mt0) cc_final: 0.7610 (mt0) REVERT: A 174 HIS cc_start: 0.8180 (m90) cc_final: 0.7924 (m90) REVERT: A 219 ASN cc_start: 0.8941 (m-40) cc_final: 0.8666 (m-40) REVERT: B 16 MET cc_start: 0.6835 (ttt) cc_final: 0.6308 (mmt) REVERT: C 50 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8866 (mm) REVERT: C 127 LYS cc_start: 0.8647 (tttt) cc_final: 0.8275 (tptm) REVERT: C 135 GLN cc_start: 0.8566 (tp-100) cc_final: 0.8215 (tp-100) REVERT: C 216 ARG cc_start: 0.7609 (mtp85) cc_final: 0.7229 (mtp-110) REVERT: D 135 GLU cc_start: 0.7329 (tm-30) cc_final: 0.6869 (tm-30) REVERT: D 211 TRP cc_start: 0.7791 (OUTLIER) cc_final: 0.7315 (m100) REVERT: D 236 MET cc_start: 0.6050 (mmp) cc_final: 0.4869 (mmm) REVERT: H 144 TYR cc_start: 0.8691 (m-80) cc_final: 0.8242 (m-80) REVERT: H 397 ILE cc_start: 0.8801 (mt) cc_final: 0.8523 (mt) REVERT: H 492 GLU cc_start: 0.8215 (tt0) cc_final: 0.7907 (tp30) REVERT: H 501 ARG cc_start: 0.8327 (ttt180) cc_final: 0.7991 (ttt-90) REVERT: H 512 ARG cc_start: 0.8856 (mmm160) cc_final: 0.8143 (tpp80) REVERT: H 551 MET cc_start: 0.8551 (ttt) cc_final: 0.8332 (ttp) REVERT: H 567 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7692 (mt-10) REVERT: I 94 MET cc_start: 0.8495 (tpt) cc_final: 0.8202 (tpt) REVERT: I 135 MET cc_start: 0.7999 (ptp) cc_final: 0.7743 (ptp) REVERT: I 300 THR cc_start: 0.9337 (m) cc_final: 0.9058 (p) REVERT: I 335 LYS cc_start: 0.8866 (ptmm) cc_final: 0.8487 (ptmm) REVERT: I 382 HIS cc_start: 0.7154 (t70) cc_final: 0.6768 (t70) REVERT: I 414 LYS cc_start: 0.8165 (tppt) cc_final: 0.6778 (ttpt) REVERT: I 422 LYS cc_start: 0.8610 (mttt) cc_final: 0.8238 (mttt) REVERT: I 440 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8482 (mm-30) REVERT: I 511 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7545 (t0) REVERT: I 532 ASP cc_start: 0.8666 (OUTLIER) cc_final: 0.7756 (t0) REVERT: I 561 THR cc_start: 0.8942 (OUTLIER) cc_final: 0.8475 (t) REVERT: I 595 GLU cc_start: 0.7308 (tm-30) cc_final: 0.7025 (tm-30) outliers start: 103 outliers final: 73 residues processed: 622 average time/residue: 0.3539 time to fit residues: 350.3235 Evaluate side-chains 632 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 553 time to evaluate : 2.162 ------------------------------------------------------------------------------- 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 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 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 A residue 420 MET Chi-restraints excluded: chain B residue 18 VAL 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 187 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 185 SER 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 100 ILE Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 200 SER 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 102 LEU Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain H residue 93 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 215 SER Chi-restraints excluded: chain H residue 223 ASP Chi-restraints excluded: chain H residue 258 SER Chi-restraints excluded: chain H residue 270 ASN 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 112 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 198 ILE 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 49 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 168 optimal weight: 0.7980 chunk 160 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 142 optimal weight: 3.9990 chunk 265 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 108 GLN C 38 ASN ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 419 ASN ** H 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 ASN ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 326 HIS ** I 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 626 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 = 0.3445 r_free = 0.3445 target = 0.143004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.111972 restraints weight = 51779.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.116137 restraints weight = 21182.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.118825 restraints weight = 11234.052| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21438 Z= 0.152 Angle : 0.629 11.742 29093 Z= 0.320 Chirality : 0.045 0.215 3253 Planarity : 0.004 0.041 3755 Dihedral : 6.639 86.089 2979 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.75 % Favored : 94.17 % Rotamer: Outliers : 4.08 % Allowed : 20.08 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.16), residues: 2678 helix: 0.74 (0.18), residues: 800 sheet: -0.92 (0.21), residues: 588 loop : -1.54 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 141 HIS 0.007 0.001 HIS H 626 PHE 0.030 0.002 PHE H 262 TYR 0.018 0.002 TYR A 204 ARG 0.004 0.000 ARG B 73 Details of bonding type rmsd hydrogen bonds : bond 0.03446 ( 835) hydrogen bonds : angle 5.23877 ( 2399) covalent geometry : bond 0.00355 (21438) covalent geometry : angle 0.62882 (29093) *********************** 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 658 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 567 time to evaluate : 2.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8571 (tt) REVERT: A 141 GLN cc_start: 0.7829 (mt0) cc_final: 0.7624 (mt0) REVERT: A 157 ASP cc_start: 0.8174 (t0) cc_final: 0.7717 (t0) REVERT: A 174 HIS cc_start: 0.8146 (m90) cc_final: 0.7915 (m90) REVERT: A 219 ASN cc_start: 0.8902 (m-40) cc_final: 0.8641 (m-40) REVERT: B 16 MET cc_start: 0.6864 (ttt) cc_final: 0.6290 (mmt) REVERT: B 214 GLN cc_start: 0.7626 (mt0) cc_final: 0.7264 (mt0) REVERT: C 50 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8884 (mm) REVERT: C 127 LYS cc_start: 0.8616 (tttt) cc_final: 0.8243 (tptm) REVERT: C 135 GLN cc_start: 0.8530 (tp-100) cc_final: 0.8159 (tp-100) REVERT: C 216 ARG cc_start: 0.7616 (mtp85) cc_final: 0.7234 (mtp-110) REVERT: C 221 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7563 (tt) REVERT: D 135 GLU cc_start: 0.7348 (tm-30) cc_final: 0.6863 (tm-30) REVERT: D 211 TRP cc_start: 0.7748 (OUTLIER) cc_final: 0.7353 (m100) REVERT: D 236 MET cc_start: 0.6065 (mmp) cc_final: 0.4902 (mmm) REVERT: H 144 TYR cc_start: 0.8655 (m-80) cc_final: 0.8204 (m-80) REVERT: H 228 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7541 (mm-30) REVERT: H 397 ILE cc_start: 0.8789 (mt) cc_final: 0.8480 (mt) REVERT: H 501 ARG cc_start: 0.8323 (ttt180) cc_final: 0.7994 (ttt-90) REVERT: H 512 ARG cc_start: 0.8767 (mmm160) cc_final: 0.8159 (tpp80) REVERT: H 551 MET cc_start: 0.8510 (ttt) cc_final: 0.8295 (ttp) REVERT: I 94 MET cc_start: 0.8484 (tpt) cc_final: 0.8192 (tpt) REVERT: I 135 MET cc_start: 0.7954 (ptp) cc_final: 0.7696 (ptp) REVERT: I 300 THR cc_start: 0.9321 (m) cc_final: 0.8999 (p) REVERT: I 335 LYS cc_start: 0.8865 (ptmm) cc_final: 0.8524 (ptmm) REVERT: I 382 HIS cc_start: 0.7071 (t70) cc_final: 0.6759 (t70) REVERT: I 422 LYS cc_start: 0.8623 (mttt) cc_final: 0.8224 (mttt) REVERT: I 440 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8442 (mm-30) REVERT: I 511 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7728 (t70) REVERT: I 532 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.7905 (t0) REVERT: I 561 THR cc_start: 0.8982 (OUTLIER) cc_final: 0.8515 (t) REVERT: I 595 GLU cc_start: 0.7133 (tm-30) cc_final: 0.6882 (tm-30) REVERT: I 627 MET cc_start: 0.7763 (mmp) cc_final: 0.7305 (mmm) outliers start: 91 outliers final: 67 residues processed: 606 average time/residue: 0.3459 time to fit residues: 331.5760 Evaluate side-chains 620 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 546 time to evaluate : 3.870 ------------------------------------------------------------------------------- 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 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 248 ASN Chi-restraints excluded: chain A residue 257 THR 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 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 187 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 185 SER 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 11 GLU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 102 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 207 VAL Chi-restraints excluded: chain H residue 217 THR 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 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 H residue 626 HIS 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 198 ILE Chi-restraints excluded: chain I residue 220 ASN Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 274 TRP 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 43 optimal weight: 10.0000 chunk 204 optimal weight: 0.9990 chunk 145 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 188 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 158 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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** B 108 GLN C 38 ASN ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 ASN ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 626 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 = 0.3453 r_free = 0.3453 target = 0.143720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.113792 restraints weight = 41875.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.117630 restraints weight = 18335.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.120078 restraints weight = 10034.246| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3162 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21438 Z= 0.150 Angle : 0.627 11.369 29093 Z= 0.318 Chirality : 0.045 0.247 3253 Planarity : 0.004 0.042 3755 Dihedral : 6.557 84.496 2978 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.49 % Favored : 94.43 % Rotamer: Outliers : 4.30 % Allowed : 20.53 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.16), residues: 2678 helix: 0.80 (0.18), residues: 800 sheet: -0.93 (0.21), residues: 588 loop : -1.52 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 141 HIS 0.005 0.001 HIS H 626 PHE 0.036 0.002 PHE H 250 TYR 0.015 0.002 TYR A 204 ARG 0.004 0.000 ARG H 269 Details of bonding type rmsd hydrogen bonds : bond 0.03378 ( 835) hydrogen bonds : angle 5.18507 ( 2399) covalent geometry : bond 0.00350 (21438) covalent geometry : angle 0.62692 (29093) *********************** 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 646 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 550 time to evaluate : 2.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8592 (tt) REVERT: A 141 GLN cc_start: 0.7825 (mt0) cc_final: 0.7622 (mt0) REVERT: A 157 ASP cc_start: 0.8182 (t0) cc_final: 0.7726 (t0) REVERT: A 174 HIS cc_start: 0.8153 (m90) cc_final: 0.7914 (m90) REVERT: A 219 ASN cc_start: 0.8885 (m-40) cc_final: 0.8647 (m-40) REVERT: B 16 MET cc_start: 0.6811 (ttt) cc_final: 0.6313 (mmt) REVERT: B 73 ARG cc_start: 0.8895 (ttm110) cc_final: 0.8659 (ttp-110) REVERT: B 203 LYS cc_start: 0.7187 (ptpt) cc_final: 0.6984 (ptpt) REVERT: B 214 GLN cc_start: 0.7639 (mt0) cc_final: 0.7263 (mt0) REVERT: C 50 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8886 (mm) REVERT: C 127 LYS cc_start: 0.8620 (tttt) cc_final: 0.8226 (tptm) REVERT: C 135 GLN cc_start: 0.8507 (tp-100) cc_final: 0.8151 (tp-100) REVERT: C 216 ARG cc_start: 0.7643 (mtp85) cc_final: 0.7237 (mtp-110) REVERT: C 221 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7571 (tt) REVERT: D 135 GLU cc_start: 0.7337 (tm-30) cc_final: 0.6864 (tm-30) REVERT: D 211 TRP cc_start: 0.7722 (OUTLIER) cc_final: 0.7396 (m100) REVERT: D 236 MET cc_start: 0.6045 (mmp) cc_final: 0.4893 (mmm) REVERT: E 158 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8230 (mp) REVERT: H 144 TYR cc_start: 0.8643 (m-80) cc_final: 0.8190 (m-80) REVERT: H 228 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7550 (mm-30) REVERT: H 397 ILE cc_start: 0.8779 (mt) cc_final: 0.8481 (mt) REVERT: H 454 LYS cc_start: 0.8556 (mmmm) cc_final: 0.8346 (mmmm) REVERT: H 501 ARG cc_start: 0.8327 (ttt180) cc_final: 0.7992 (ttt-90) REVERT: H 512 ARG cc_start: 0.8761 (mmm160) cc_final: 0.8067 (tpp80) REVERT: I 94 MET cc_start: 0.8484 (tpt) cc_final: 0.8177 (tpt) REVERT: I 135 MET cc_start: 0.7978 (ptp) cc_final: 0.7700 (ptp) REVERT: I 300 THR cc_start: 0.9307 (m) cc_final: 0.8986 (p) REVERT: I 335 LYS cc_start: 0.8856 (ptmm) cc_final: 0.8491 (ptmm) REVERT: I 422 LYS cc_start: 0.8647 (mttt) cc_final: 0.8347 (mttt) REVERT: I 511 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7712 (t70) REVERT: I 532 ASP cc_start: 0.8662 (OUTLIER) cc_final: 0.7893 (m-30) REVERT: I 561 THR cc_start: 0.8996 (OUTLIER) cc_final: 0.8493 (p) REVERT: I 595 GLU cc_start: 0.7113 (tm-30) cc_final: 0.6862 (tm-30) REVERT: I 634 MET cc_start: 0.7763 (mmm) cc_final: 0.7293 (tpt) outliers start: 96 outliers final: 74 residues processed: 599 average time/residue: 0.3382 time to fit residues: 322.1595 Evaluate side-chains 626 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 544 time to evaluate : 4.257 ------------------------------------------------------------------------------- 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 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 248 ASN Chi-restraints excluded: chain A residue 257 THR 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 420 MET 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 187 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 146 GLU 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 102 LEU Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 165 SER 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 207 VAL Chi-restraints excluded: chain H residue 217 THR 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 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 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 220 ASN Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 239 LEU Chi-restraints excluded: chain I residue 274 TRP 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 398 ASP 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 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 68 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 197 optimal weight: 9.9990 chunk 174 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 chunk 65 optimal weight: 50.0000 chunk 17 optimal weight: 0.7980 chunk 163 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 ASN ** I 152 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 626 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 = 0.3439 r_free = 0.3439 target = 0.142409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.112314 restraints weight = 45888.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.116286 restraints weight = 19593.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.118803 restraints weight = 10566.329| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21438 Z= 0.182 Angle : 0.651 11.669 29093 Z= 0.329 Chirality : 0.046 0.308 3253 Planarity : 0.004 0.042 3755 Dihedral : 6.601 83.829 2978 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.09 % Favored : 93.83 % Rotamer: Outliers : 4.08 % Allowed : 21.38 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.16), residues: 2678 helix: 0.75 (0.18), residues: 800 sheet: -0.96 (0.21), residues: 588 loop : -1.54 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 141 HIS 0.005 0.001 HIS H 626 PHE 0.038 0.002 PHE H 250 TYR 0.015 0.002 TYR B 78 ARG 0.005 0.000 ARG B 175 Details of bonding type rmsd hydrogen bonds : bond 0.03523 ( 835) hydrogen bonds : angle 5.21655 ( 2399) covalent geometry : bond 0.00428 (21438) covalent geometry : angle 0.65099 (29093) *********************** 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 642 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 551 time to evaluate : 2.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8555 (tt) REVERT: A 141 GLN cc_start: 0.7823 (mt0) cc_final: 0.7617 (mt0) REVERT: A 157 ASP cc_start: 0.8235 (t0) cc_final: 0.7792 (t0) REVERT: A 174 HIS cc_start: 0.8168 (m90) cc_final: 0.7926 (m90) REVERT: A 219 ASN cc_start: 0.8910 (m-40) cc_final: 0.8673 (m-40) REVERT: B 16 MET cc_start: 0.6777 (ttt) cc_final: 0.6268 (mmt) REVERT: B 30 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7613 (mt-10) REVERT: B 73 ARG cc_start: 0.8918 (ttm110) cc_final: 0.8691 (ttp-110) REVERT: B 214 GLN cc_start: 0.7631 (mt0) cc_final: 0.7254 (mt0) REVERT: C 50 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8904 (mm) REVERT: C 127 LYS cc_start: 0.8635 (tttt) cc_final: 0.8237 (tptm) REVERT: C 135 GLN cc_start: 0.8520 (tp-100) cc_final: 0.8163 (tp-100) REVERT: C 216 ARG cc_start: 0.7649 (mtp85) cc_final: 0.7237 (mtp-110) REVERT: C 221 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7607 (tt) REVERT: D 135 GLU cc_start: 0.7444 (tm-30) cc_final: 0.6949 (tm-30) REVERT: D 211 TRP cc_start: 0.7785 (OUTLIER) cc_final: 0.7403 (m100) REVERT: D 236 MET cc_start: 0.6073 (mmp) cc_final: 0.4929 (mmm) REVERT: E 158 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8176 (mp) REVERT: H 144 TYR cc_start: 0.8654 (m-80) cc_final: 0.8170 (m-80) REVERT: H 501 ARG cc_start: 0.8332 (ttt180) cc_final: 0.7976 (ttt-90) REVERT: H 512 ARG cc_start: 0.8787 (mmm160) cc_final: 0.8192 (tpp80) REVERT: H 525 LYS cc_start: 0.7852 (mptt) cc_final: 0.7516 (mppt) REVERT: H 567 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7818 (mt-10) REVERT: I 94 MET cc_start: 0.8536 (tpt) cc_final: 0.8263 (tpt) REVERT: I 135 MET cc_start: 0.8017 (ptp) cc_final: 0.7746 (ptp) REVERT: I 300 THR cc_start: 0.9347 (m) cc_final: 0.9021 (p) REVERT: I 335 LYS cc_start: 0.8861 (ptmm) cc_final: 0.8477 (ptmm) REVERT: I 422 LYS cc_start: 0.8647 (mttt) cc_final: 0.8370 (mttt) REVERT: I 440 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8416 (mm-30) REVERT: I 532 ASP cc_start: 0.8696 (OUTLIER) cc_final: 0.8325 (m-30) REVERT: I 561 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8496 (p) REVERT: I 595 GLU cc_start: 0.7092 (tm-30) cc_final: 0.6816 (tm-30) REVERT: I 627 MET cc_start: 0.7822 (mmp) cc_final: 0.7375 (mmm) REVERT: I 634 MET cc_start: 0.7782 (mmm) cc_final: 0.7327 (tpt) outliers start: 91 outliers final: 77 residues processed: 595 average time/residue: 0.4247 time to fit residues: 410.4393 Evaluate side-chains 626 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 542 time to evaluate : 3.732 ------------------------------------------------------------------------------- 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 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 248 ASN Chi-restraints excluded: chain A residue 257 THR 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 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 130 SER Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 146 GLU 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 102 LEU Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 165 SER 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 217 THR Chi-restraints excluded: chain H residue 223 ASP Chi-restraints excluded: chain H residue 258 SER Chi-restraints excluded: chain H residue 270 ASN 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 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 198 ILE Chi-restraints excluded: chain I residue 220 ASN Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 239 LEU Chi-restraints excluded: chain I residue 274 TRP 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 398 ASP Chi-restraints excluded: chain I residue 428 HIS Chi-restraints excluded: chain I residue 439 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 232 optimal weight: 7.9990 chunk 206 optimal weight: 0.5980 chunk 198 optimal weight: 6.9990 chunk 196 optimal weight: 8.9990 chunk 124 optimal weight: 0.9990 chunk 214 optimal weight: 7.9990 chunk 257 optimal weight: 4.9990 chunk 260 optimal weight: 0.9990 chunk 175 optimal weight: 7.9990 chunk 184 optimal weight: 0.6980 chunk 203 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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** B 108 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS C 38 ASN ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 ASN ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 626 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.143268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.115138 restraints weight = 31011.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.118430 restraints weight = 14754.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.120463 restraints weight = 8580.648| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21438 Z= 0.158 Angle : 0.641 10.766 29093 Z= 0.323 Chirality : 0.045 0.175 3253 Planarity : 0.004 0.042 3755 Dihedral : 6.554 82.125 2978 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.83 % Favored : 94.10 % Rotamer: Outliers : 3.94 % Allowed : 21.92 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.16), residues: 2678 helix: 0.81 (0.18), residues: 800 sheet: -0.95 (0.21), residues: 587 loop : -1.55 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 141 HIS 0.005 0.001 HIS C 37 PHE 0.038 0.002 PHE H 250 TYR 0.014 0.002 TYR A 204 ARG 0.006 0.000 ARG A 403 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 835) hydrogen bonds : angle 5.17783 ( 2399) covalent geometry : bond 0.00370 (21438) covalent geometry : angle 0.64138 (29093) *********************** 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 628 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 540 time to evaluate : 2.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8548 (tt) REVERT: A 157 ASP cc_start: 0.8187 (t0) cc_final: 0.7739 (t0) REVERT: A 174 HIS cc_start: 0.8153 (m90) cc_final: 0.7924 (m90) REVERT: A 204 TYR cc_start: 0.8892 (m-80) cc_final: 0.8606 (m-10) REVERT: A 219 ASN cc_start: 0.8825 (m-40) cc_final: 0.8605 (m-40) REVERT: A 308 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9027 (tt) REVERT: B 16 MET cc_start: 0.6747 (ttt) cc_final: 0.6206 (mmt) REVERT: B 73 ARG cc_start: 0.8913 (ttm110) cc_final: 0.8688 (ttp-110) REVERT: B 203 LYS cc_start: 0.7198 (OUTLIER) cc_final: 0.6963 (ptpt) REVERT: B 214 GLN cc_start: 0.7588 (mt0) cc_final: 0.7235 (mt0) REVERT: C 50 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8901 (mm) REVERT: C 127 LYS cc_start: 0.8613 (tttt) cc_final: 0.8211 (tptm) REVERT: C 135 GLN cc_start: 0.8468 (tp-100) cc_final: 0.8123 (tp-100) REVERT: C 216 ARG cc_start: 0.7653 (mtp85) cc_final: 0.7237 (mtp-110) REVERT: C 221 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7563 (tt) REVERT: D 135 GLU cc_start: 0.7448 (tm-30) cc_final: 0.6977 (tm-30) REVERT: D 211 TRP cc_start: 0.7772 (OUTLIER) cc_final: 0.7393 (m100) REVERT: D 236 MET cc_start: 0.6062 (mmp) cc_final: 0.4921 (mmm) REVERT: E 158 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8192 (mp) REVERT: H 144 TYR cc_start: 0.8627 (m-80) cc_final: 0.8210 (m-80) REVERT: H 501 ARG cc_start: 0.8323 (ttt180) cc_final: 0.7975 (ttt-90) REVERT: H 512 ARG cc_start: 0.8769 (mmm160) cc_final: 0.8193 (tpp80) REVERT: H 567 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7816 (mt-10) REVERT: I 94 MET cc_start: 0.8535 (tpt) cc_final: 0.8255 (tpt) REVERT: I 135 MET cc_start: 0.7977 (ptp) cc_final: 0.7674 (ptp) REVERT: I 300 THR cc_start: 0.9317 (m) cc_final: 0.8981 (p) REVERT: I 335 LYS cc_start: 0.8853 (ptmm) cc_final: 0.8482 (ptmm) REVERT: I 422 LYS cc_start: 0.8648 (mttt) cc_final: 0.8354 (mttt) REVERT: I 532 ASP cc_start: 0.8667 (OUTLIER) cc_final: 0.8297 (m-30) REVERT: I 627 MET cc_start: 0.7706 (mmp) cc_final: 0.7234 (mmm) REVERT: I 634 MET cc_start: 0.7679 (mmm) cc_final: 0.7444 (tpt) outliers start: 88 outliers final: 77 residues processed: 584 average time/residue: 0.3652 time to fit residues: 342.1293 Evaluate side-chains 622 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 537 time to evaluate : 2.342 ------------------------------------------------------------------------------- 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 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 248 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 308 LEU 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 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 B residue 188 LEU Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 146 GLU 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 11 GLU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 165 SER 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 207 VAL Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain H residue 223 ASP Chi-restraints excluded: chain H residue 258 SER Chi-restraints excluded: chain H residue 270 ASN 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 220 ASN Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 274 TRP 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 398 ASP Chi-restraints excluded: chain I residue 428 HIS Chi-restraints excluded: chain I residue 439 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 44 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 67 optimal weight: 50.0000 chunk 198 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 241 optimal weight: 7.9990 chunk 197 optimal weight: 4.9990 chunk 101 optimal weight: 0.4980 chunk 41 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 ASN C 38 ASN ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 626 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 = 0.3443 r_free = 0.3443 target = 0.142859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.113785 restraints weight = 35403.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.117345 restraints weight = 16295.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.119564 restraints weight = 9209.609| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21438 Z= 0.169 Angle : 0.649 11.370 29093 Z= 0.327 Chirality : 0.045 0.173 3253 Planarity : 0.004 0.042 3755 Dihedral : 6.497 84.612 2978 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.05 % Favored : 93.87 % Rotamer: Outliers : 3.99 % Allowed : 22.01 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.16), residues: 2678 helix: 0.81 (0.18), residues: 800 sheet: -0.97 (0.21), residues: 587 loop : -1.55 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 141 HIS 0.004 0.001 HIS H 201 PHE 0.054 0.002 PHE H 250 TYR 0.017 0.002 TYR B 78 ARG 0.006 0.000 ARG A 403 Details of bonding type rmsd hydrogen bonds : bond 0.03425 ( 835) hydrogen bonds : angle 5.16613 ( 2399) covalent geometry : bond 0.00396 (21438) covalent geometry : angle 0.64881 (29093) ********************** 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 627 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 538 time to evaluate : 2.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8525 (tt) REVERT: A 157 ASP cc_start: 0.8200 (t0) cc_final: 0.7772 (t0) REVERT: A 174 HIS cc_start: 0.8154 (m90) cc_final: 0.7926 (m90) REVERT: A 204 TYR cc_start: 0.8880 (m-80) cc_final: 0.8589 (m-10) REVERT: A 219 ASN cc_start: 0.8820 (m-40) cc_final: 0.8613 (m-40) REVERT: B 16 MET cc_start: 0.6772 (ttt) cc_final: 0.6445 (mmt) REVERT: B 73 ARG cc_start: 0.8910 (ttm110) cc_final: 0.8682 (ttp-110) REVERT: B 203 LYS cc_start: 0.7205 (OUTLIER) cc_final: 0.6959 (ptpt) REVERT: B 214 GLN cc_start: 0.7598 (mt0) cc_final: 0.7239 (mt0) REVERT: C 50 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8908 (mm) REVERT: C 127 LYS cc_start: 0.8618 (tttt) cc_final: 0.8218 (tptm) REVERT: C 135 GLN cc_start: 0.8469 (tp-100) cc_final: 0.8124 (tp-100) REVERT: C 216 ARG cc_start: 0.7620 (mtp85) cc_final: 0.7199 (mtp-110) REVERT: C 221 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7603 (tt) REVERT: D 135 GLU cc_start: 0.7469 (tm-30) cc_final: 0.6992 (tm-30) REVERT: D 211 TRP cc_start: 0.7783 (OUTLIER) cc_final: 0.7409 (m100) REVERT: D 236 MET cc_start: 0.6062 (mmp) cc_final: 0.4928 (mmm) REVERT: E 158 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8190 (mp) REVERT: H 144 TYR cc_start: 0.8637 (m-80) cc_final: 0.8206 (m-80) REVERT: H 246 TYR cc_start: 0.7898 (m-10) cc_final: 0.7650 (m-80) REVERT: H 454 LYS cc_start: 0.8684 (mmmm) cc_final: 0.7735 (mmmm) REVERT: H 501 ARG cc_start: 0.8299 (ttt180) cc_final: 0.7948 (ttt-90) REVERT: H 512 ARG cc_start: 0.8794 (mmm160) cc_final: 0.8228 (tpp80) REVERT: H 525 LYS cc_start: 0.7910 (mptt) cc_final: 0.7688 (mppt) REVERT: H 567 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7824 (mt-10) REVERT: I 94 MET cc_start: 0.8539 (tpt) cc_final: 0.8269 (tpt) REVERT: I 135 MET cc_start: 0.7977 (ptp) cc_final: 0.7686 (ptp) REVERT: I 300 THR cc_start: 0.9312 (m) cc_final: 0.8969 (p) REVERT: I 335 LYS cc_start: 0.8853 (ptmm) cc_final: 0.8469 (ptmm) REVERT: I 422 LYS cc_start: 0.8649 (mttt) cc_final: 0.8390 (mttt) REVERT: I 440 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8377 (mm-30) REVERT: I 505 LYS cc_start: 0.8369 (pttt) cc_final: 0.7541 (tptt) REVERT: I 532 ASP cc_start: 0.8678 (OUTLIER) cc_final: 0.8361 (m-30) REVERT: I 627 MET cc_start: 0.7731 (mmp) cc_final: 0.7276 (mmm) outliers start: 89 outliers final: 76 residues processed: 582 average time/residue: 0.3295 time to fit residues: 301.5569 Evaluate side-chains 619 residues out of total 2227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 536 time to evaluate : 2.358 ------------------------------------------------------------------------------- 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 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 248 ASN Chi-restraints excluded: chain A residue 257 THR 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 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 B residue 188 LEU Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 146 GLU 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 11 GLU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 165 SER 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 207 VAL Chi-restraints excluded: chain H residue 217 THR Chi-restraints excluded: chain H residue 223 ASP Chi-restraints excluded: chain H residue 258 SER Chi-restraints excluded: chain H residue 270 ASN 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 H residue 626 HIS Chi-restraints excluded: chain I residue 105 THR 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 274 TRP 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 398 ASP Chi-restraints excluded: chain I residue 428 HIS Chi-restraints excluded: chain I residue 439 CYS 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 629 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 127 optimal weight: 2.9990 chunk 79 optimal weight: 0.0060 chunk 55 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 223 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 190 optimal weight: 0.9980 overall best weight: 1.7400 ------------------------------------------------------------------------------- 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 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 ASN ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 574 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 626 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 = 0.3445 r_free = 0.3445 target = 0.142972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.114222 restraints weight = 35000.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.117718 restraints weight = 16068.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.119943 restraints weight = 9096.312| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 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 = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21438 Z= 0.163 Angle : 0.652 11.254 29093 Z= 0.328 Chirality : 0.045 0.173 3253 Planarity : 0.004 0.042 3755 Dihedral : 6.466 88.739 2978 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.87 % Favored : 94.06 % Rotamer: Outliers : 4.03 % Allowed : 22.01 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.16), residues: 2678 helix: 0.84 (0.18), residues: 800 sheet: -0.94 (0.22), residues: 576 loop : -1.54 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 141 HIS 0.008 0.001 HIS H 78 PHE 0.030 0.002 PHE H 262 TYR 0.014 0.002 TYR A 204 ARG 0.006 0.000 ARG A 403 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 835) hydrogen bonds : angle 5.14465 ( 2399) covalent geometry : bond 0.00382 (21438) covalent geometry : angle 0.65212 (29093) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10616.15 seconds wall clock time: 189 minutes 27.42 seconds (11367.42 seconds total)