Starting phenix.real_space_refine on Wed Jun 18 02:30:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g0z_29658/06_2025/8g0z_29658.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g0z_29658/06_2025/8g0z_29658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g0z_29658/06_2025/8g0z_29658.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g0z_29658/06_2025/8g0z_29658.map" model { file = "/net/cci-nas-00/data/ceres_data/8g0z_29658/06_2025/8g0z_29658.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g0z_29658/06_2025/8g0z_29658.cif" } resolution = 3.61 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 27 5.49 5 Mg 5 5.21 5 S 119 5.16 5 C 13244 2.51 5 N 3475 2.21 5 O 4074 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20944 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "B" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "C" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "D" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "E" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "F" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "M" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 240 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.36, per 1000 atoms: 0.73 Number of scatterers: 20944 At special positions: 0 Unit cell: (140.973, 136.857, 143.031, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 119 16.00 P 27 15.00 Mg 5 11.99 O 4074 8.00 N 3475 7.00 C 13244 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: 10.12 Conformation dependent library (CDL) restraints added in 4.4 seconds 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4920 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 15 sheets defined 55.6% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.03 Creating SS restraints... Processing helix chain 'A' and resid 1 through 11 Processing helix chain 'A' and resid 13 through 20 Processing helix chain 'A' and resid 21 through 23 No H-bonds generated for 'chain 'A' and resid 21 through 23' Processing helix chain 'A' and resid 24 through 28 Processing helix chain 'A' and resid 31 through 47 Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 66 through 79 Processing helix chain 'A' and resid 86 through 118 Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 133 through 143 Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 176 through 183 Processing helix chain 'A' and resid 204 through 217 removed outlier: 3.636A pdb=" N TYR A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU A 215 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 243 Processing helix chain 'A' and resid 245 through 252 removed outlier: 3.519A pdb=" N ILE A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 269 removed outlier: 3.550A pdb=" N LYS A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 301 Processing helix chain 'A' and resid 328 through 347 Processing helix chain 'A' and resid 357 through 363 Processing helix chain 'A' and resid 390 through 396 Processing helix chain 'B' and resid 2 through 11 Processing helix chain 'B' and resid 12 through 20 Processing helix chain 'B' and resid 21 through 23 No H-bonds generated for 'chain 'B' and resid 21 through 23' Processing helix chain 'B' and resid 24 through 28 removed outlier: 3.543A pdb=" N TYR B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE B 28 " --> pdb=" O SER B 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 24 through 28' Processing helix chain 'B' and resid 31 through 48 Processing helix chain 'B' and resid 52 through 58 Processing helix chain 'B' and resid 66 through 80 Processing helix chain 'B' and resid 88 through 119 removed outlier: 3.529A pdb=" N LEU B 119 " --> pdb=" O THR B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 133 Processing helix chain 'B' and resid 134 through 143 Processing helix chain 'B' and resid 157 through 168 Processing helix chain 'B' and resid 176 through 184 removed outlier: 3.512A pdb=" N ILE B 182 " --> pdb=" O ILE B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 217 Processing helix chain 'B' and resid 229 through 243 removed outlier: 3.767A pdb=" N CYS B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA B 234 " --> pdb=" O GLU B 230 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP B 243 " --> pdb=" O ALA B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 Processing helix chain 'B' and resid 255 through 269 Processing helix chain 'B' and resid 286 through 301 Processing helix chain 'B' and resid 327 through 347 removed outlier: 3.589A pdb=" N THR B 331 " --> pdb=" O ASN B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 376 through 381 Processing helix chain 'B' and resid 391 through 396 removed outlier: 3.628A pdb=" N ALA B 395 " --> pdb=" O GLU B 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 11 Processing helix chain 'C' and resid 13 through 20 Processing helix chain 'C' and resid 24 through 28 removed outlier: 3.769A pdb=" N PHE C 28 " --> pdb=" O SER C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 47 Processing helix chain 'C' and resid 52 through 63 Processing helix chain 'C' and resid 66 through 77 removed outlier: 4.001A pdb=" N GLY C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 119 Processing helix chain 'C' and resid 130 through 132 No H-bonds generated for 'chain 'C' and resid 130 through 132' Processing helix chain 'C' and resid 133 through 143 Processing helix chain 'C' and resid 162 through 167 Processing helix chain 'C' and resid 176 through 184 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 230 through 242 Processing helix chain 'C' and resid 245 through 252 Processing helix chain 'C' and resid 255 through 268 Processing helix chain 'C' and resid 286 through 301 Processing helix chain 'C' and resid 312 through 316 removed outlier: 3.640A pdb=" N ILE C 315 " --> pdb=" O TYR C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 347 Processing helix chain 'C' and resid 357 through 361 removed outlier: 3.653A pdb=" N TRP C 361 " --> pdb=" O LYS C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'C' and resid 375 through 381 removed outlier: 3.956A pdb=" N ALA C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 395 Processing helix chain 'D' and resid 2 through 11 Processing helix chain 'D' and resid 12 through 20 removed outlier: 3.609A pdb=" N LYS D 18 " --> pdb=" O ALA D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 23 No H-bonds generated for 'chain 'D' and resid 21 through 23' Processing helix chain 'D' and resid 24 through 28 removed outlier: 3.502A pdb=" N TYR D 27 " --> pdb=" O ASP D 24 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE D 28 " --> pdb=" O SER D 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 24 through 28' Processing helix chain 'D' and resid 31 through 48 Processing helix chain 'D' and resid 52 through 62 Processing helix chain 'D' and resid 66 through 80 Processing helix chain 'D' and resid 86 through 118 Processing helix chain 'D' and resid 130 through 132 No H-bonds generated for 'chain 'D' and resid 130 through 132' Processing helix chain 'D' and resid 133 through 143 removed outlier: 3.935A pdb=" N ILE D 137 " --> pdb=" O ALA D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 163 Processing helix chain 'D' and resid 176 through 184 Processing helix chain 'D' and resid 204 through 217 Processing helix chain 'D' and resid 229 through 243 removed outlier: 3.811A pdb=" N CYS D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 252 Processing helix chain 'D' and resid 255 through 268 Processing helix chain 'D' and resid 286 through 301 Processing helix chain 'D' and resid 312 through 316 Processing helix chain 'D' and resid 327 through 347 Processing helix chain 'D' and resid 357 through 361 Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'D' and resid 375 through 380 removed outlier: 4.005A pdb=" N ALA D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 396 Processing helix chain 'E' and resid 2 through 12 Processing helix chain 'E' and resid 12 through 20 removed outlier: 3.593A pdb=" N LYS E 18 " --> pdb=" O ALA E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 28 removed outlier: 3.560A pdb=" N PHE E 28 " --> pdb=" O SER E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 47 Processing helix chain 'E' and resid 52 through 63 Processing helix chain 'E' and resid 66 through 79 Processing helix chain 'E' and resid 86 through 118 Processing helix chain 'E' and resid 130 through 132 No H-bonds generated for 'chain 'E' and resid 130 through 132' Processing helix chain 'E' and resid 133 through 141 removed outlier: 3.695A pdb=" N ALA E 141 " --> pdb=" O ILE E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 166 Processing helix chain 'E' and resid 176 through 184 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 229 through 243 removed outlier: 3.724A pdb=" N CYS E 233 " --> pdb=" O ALA E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 251 removed outlier: 3.587A pdb=" N ASP E 250 " --> pdb=" O LEU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 269 Processing helix chain 'E' and resid 286 through 301 Processing helix chain 'E' and resid 327 through 347 removed outlier: 3.842A pdb=" N LYS E 333 " --> pdb=" O TYR E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 361 Processing helix chain 'E' and resid 376 through 381 Processing helix chain 'E' and resid 390 through 397 Processing helix chain 'F' and resid 2 through 12 Processing helix chain 'F' and resid 13 through 20 Processing helix chain 'F' and resid 21 through 23 No H-bonds generated for 'chain 'F' and resid 21 through 23' Processing helix chain 'F' and resid 24 through 28 Processing helix chain 'F' and resid 31 through 48 removed outlier: 3.759A pdb=" N ASN F 35 " --> pdb=" O GLY F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 62 Processing helix chain 'F' and resid 66 through 80 Processing helix chain 'F' and resid 88 through 118 removed outlier: 3.902A pdb=" N LYS F 92 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 132 No H-bonds generated for 'chain 'F' and resid 130 through 132' Processing helix chain 'F' and resid 133 through 142 removed outlier: 3.661A pdb=" N LEU F 142 " --> pdb=" O MET F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 167 Processing helix chain 'F' and resid 176 through 184 Processing helix chain 'F' and resid 202 through 216 Processing helix chain 'F' and resid 229 through 243 Processing helix chain 'F' and resid 245 through 252 Processing helix chain 'F' and resid 255 through 269 removed outlier: 3.706A pdb=" N LYS F 269 " --> pdb=" O LYS F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 300 Processing helix chain 'F' and resid 327 through 347 Processing helix chain 'F' and resid 376 through 381 Processing sheet with id=AA1, first strand: chain 'A' and resid 171 through 172 Processing sheet with id=AA2, first strand: chain 'A' and resid 427 through 429 removed outlier: 3.674A pdb=" N LEU A 400 " --> pdb=" O ILE A 388 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE A 388 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N MET A 384 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE A 383 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA A 353 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU A 222 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A 221 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LYS A 278 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N TYR A 223 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 152 through 153 removed outlier: 6.615A pdb=" N VAL C 221 " --> pdb=" O ILE C 276 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LYS C 278 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N TYR C 223 " --> pdb=" O LYS C 278 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ASN C 220 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ILE C 309 " --> pdb=" O ASN C 220 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU C 222 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA C 353 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE C 383 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N MET C 384 " --> pdb=" O ILE C 404 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 171 through 172 Processing sheet with id=AA5, first strand: chain 'B' and resid 275 through 279 removed outlier: 6.563A pdb=" N VAL B 221 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LYS B 278 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR B 223 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU B 222 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA B 353 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE B 383 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS B 405 " --> pdb=" O MET B 384 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 420 through 422 Processing sheet with id=AA7, first strand: chain 'C' and resid 152 through 153 removed outlier: 6.511A pdb=" N VAL D 221 " --> pdb=" O ILE D 276 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LYS D 278 " --> pdb=" O VAL D 221 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TYR D 223 " --> pdb=" O LYS D 278 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ILE D 309 " --> pdb=" O ASN D 220 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LEU D 222 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 171 through 172 Processing sheet with id=AA9, first strand: chain 'C' and resid 398 through 399 Processing sheet with id=AB1, first strand: chain 'D' and resid 152 through 153 removed outlier: 3.875A pdb=" N ALA E 353 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA E 354 " --> pdb=" O LEU E 195 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LEU E 192 " --> pdb=" O PHE E 383 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N LEU E 385 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL E 194 " --> pdb=" O LEU E 385 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N VAL E 387 " --> pdb=" O VAL E 194 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N MET E 196 " --> pdb=" O VAL E 387 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N MET E 384 " --> pdb=" O ILE E 404 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 171 through 172 Processing sheet with id=AB3, first strand: chain 'D' and resid 349 through 354 removed outlier: 6.037A pdb=" N THR D 191 " --> pdb=" O LEU D 350 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N THR D 352 " --> pdb=" O THR D 191 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASN D 193 " --> pdb=" O THR D 352 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ALA D 354 " --> pdb=" O ASN D 193 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU D 195 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU D 192 " --> pdb=" O PHE D 383 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N LEU D 385 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL D 194 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL D 387 " --> pdb=" O VAL D 194 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N MET D 196 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N MET D 384 " --> pdb=" O ILE D 404 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 171 through 172 Processing sheet with id=AB5, first strand: chain 'F' and resid 275 through 279 removed outlier: 6.986A pdb=" N LEU F 222 " --> pdb=" O ILE F 309 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE F 383 " --> pdb=" O LEU F 192 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 419 through 422 1054 hydrogen bonds defined for protein. 3030 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: 13.95 Time building geometry restraints manager: 11.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 6695 1.35 - 1.50: 5604 1.50 - 1.65: 8860 1.65 - 1.80: 95 1.80 - 1.95: 114 Bond restraints: 21368 Sorted by residual: bond pdb=" N ILE A 321 " pdb=" CA ILE A 321 " ideal model delta sigma weight residual 1.460 1.494 -0.034 8.60e-03 1.35e+04 1.54e+01 bond pdb=" CE1 HIS D 87 " pdb=" NE2 HIS D 87 " ideal model delta sigma weight residual 1.321 1.360 -0.039 1.00e-02 1.00e+04 1.50e+01 bond pdb=" CE1 HIS B 152 " pdb=" NE2 HIS B 152 " ideal model delta sigma weight residual 1.321 1.356 -0.035 1.00e-02 1.00e+04 1.23e+01 bond pdb=" N VAL E 19 " pdb=" CA VAL E 19 " ideal model delta sigma weight residual 1.452 1.492 -0.040 1.18e-02 7.18e+03 1.14e+01 bond pdb=" N SER F 225 " pdb=" CA SER F 225 " ideal model delta sigma weight residual 1.455 1.495 -0.041 1.25e-02 6.40e+03 1.07e+01 ... (remaining 21363 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 28444 2.53 - 5.06: 490 5.06 - 7.59: 24 7.59 - 10.13: 4 10.13 - 12.66: 4 Bond angle restraints: 28966 Sorted by residual: angle pdb=" N ILE A 321 " pdb=" CA ILE A 321 " pdb=" C ILE A 321 " ideal model delta sigma weight residual 113.71 107.76 5.95 9.50e-01 1.11e+00 3.92e+01 angle pdb=" N MET C 226 " pdb=" CA MET C 226 " pdb=" C MET C 226 " ideal model delta sigma weight residual 112.54 107.17 5.37 1.22e+00 6.72e-01 1.94e+01 angle pdb=" PB AGS C 501 " pdb=" O3B AGS C 501 " pdb=" PG AGS C 501 " ideal model delta sigma weight residual 120.12 132.78 -12.66 3.00e+00 1.11e-01 1.78e+01 angle pdb=" PB AGS E 501 " pdb=" O3B AGS E 501 " pdb=" PG AGS E 501 " ideal model delta sigma weight residual 120.12 131.99 -11.87 3.00e+00 1.11e-01 1.57e+01 angle pdb=" CA PHE D 383 " pdb=" CB PHE D 383 " pdb=" CG PHE D 383 " ideal model delta sigma weight residual 113.80 117.75 -3.95 1.00e+00 1.00e+00 1.56e+01 ... (remaining 28961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.84: 12745 34.84 - 69.67: 174 69.67 - 104.51: 8 104.51 - 139.35: 1 139.35 - 174.18: 3 Dihedral angle restraints: 12931 sinusoidal: 5317 harmonic: 7614 Sorted by residual: dihedral pdb=" O1A AGS F 501 " pdb=" O3A AGS F 501 " pdb=" PA AGS F 501 " pdb=" PB AGS F 501 " ideal model delta sinusoidal sigma weight residual -67.73 106.45 -174.18 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1B AGS B 501 " pdb=" O3B AGS B 501 " pdb=" PB AGS B 501 " pdb=" PG AGS B 501 " ideal model delta sinusoidal sigma weight residual 68.91 -88.55 157.46 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" O1A AGS D 501 " pdb=" O3A AGS D 501 " pdb=" PA AGS D 501 " pdb=" PB AGS D 501 " ideal model delta sinusoidal sigma weight residual -67.73 66.55 -134.28 1 3.00e+01 1.11e-03 1.81e+01 ... (remaining 12928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2317 0.044 - 0.088: 570 0.088 - 0.132: 270 0.132 - 0.176: 66 0.176 - 0.220: 23 Chirality restraints: 3246 Sorted by residual: chirality pdb=" CA VAL A 150 " pdb=" N VAL A 150 " pdb=" C VAL A 150 " pdb=" CB VAL A 150 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ILE A 388 " pdb=" N ILE A 388 " pdb=" C ILE A 388 " pdb=" CB ILE A 388 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ARG A 124 " pdb=" N ARG A 124 " pdb=" C ARG A 124 " pdb=" CB ARG A 124 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 3243 not shown) Planarity restraints: 3599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 373 " 0.016 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C GLU A 373 " -0.058 2.00e-02 2.50e+03 pdb=" O GLU A 373 " 0.021 2.00e-02 2.50e+03 pdb=" N SER A 374 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 145 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.12e+00 pdb=" C SER B 145 " -0.039 2.00e-02 2.50e+03 pdb=" O SER B 145 " 0.015 2.00e-02 2.50e+03 pdb=" N PHE B 146 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 255 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.92e+00 pdb=" C SER B 255 " 0.038 2.00e-02 2.50e+03 pdb=" O SER B 255 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR B 256 " -0.013 2.00e-02 2.50e+03 ... (remaining 3596 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 81 2.44 - 3.06: 14201 3.06 - 3.67: 31753 3.67 - 4.29: 49152 4.29 - 4.90: 80760 Nonbonded interactions: 175947 Sorted by model distance: nonbonded pdb=" O3G AGS F 501 " pdb="MG MG F 502 " model vdw 1.829 2.170 nonbonded pdb=" O2B AGS F 501 " pdb="MG MG F 502 " model vdw 2.157 2.170 nonbonded pdb=" O2B AGS D 501 " pdb="MG MG D 502 " model vdw 2.172 2.170 nonbonded pdb=" O3G AGS C 501 " pdb="MG MG C 502 " model vdw 2.188 2.170 nonbonded pdb=" O LEU C 179 " pdb=" OG1 THR C 183 " model vdw 2.208 3.040 ... (remaining 175942 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 'A' selection = (chain 'B' and resid 1 through 432) selection = (chain 'C' and resid 1 through 432) selection = (chain 'D' and resid 1 through 432) selection = (chain 'E' and resid 1 through 432) selection = (chain 'F' and resid 1 through 432) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 89.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.770 Check model and map are aligned: 0.150 Set scattering table: 0.160 Process input model: 68.830 Find NCS groups from input model: 2.040 Set up NCS constraints: 0.340 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: 0.020 Load rotamer database and sin/cos tables:4.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 166.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5721 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 : 0.005 0.052 21368 Z= 0.361 Angle : 0.743 12.657 28966 Z= 0.503 Chirality : 0.051 0.220 3246 Planarity : 0.004 0.075 3599 Dihedral : 12.134 174.183 8011 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.19 % Allowed : 6.52 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.17), residues: 2580 helix: 1.37 (0.15), residues: 1308 sheet: -0.45 (0.30), residues: 342 loop : -1.31 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 351 HIS 0.008 0.001 HIS B 152 PHE 0.022 0.002 PHE D 383 TYR 0.014 0.001 TYR E 329 ARG 0.002 0.000 ARG F 291 Details of bonding type rmsd hydrogen bonds : bond 0.16624 ( 1054) hydrogen bonds : angle 6.57383 ( 3030) covalent geometry : bond 0.00507 (21368) covalent geometry : angle 0.74281 (28966) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 435 time to evaluate : 2.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 LYS cc_start: 0.4830 (OUTLIER) cc_final: 0.4475 (tmmt) REVERT: B 43 HIS cc_start: 0.6384 (t-90) cc_final: 0.6125 (t-90) REVERT: B 155 MET cc_start: 0.6828 (tpp) cc_final: 0.6006 (ptt) REVERT: B 166 MET cc_start: 0.7525 (ptm) cc_final: 0.6853 (tpp) REVERT: D 43 HIS cc_start: 0.6779 (t-90) cc_final: 0.6517 (t-90) REVERT: D 138 MET cc_start: 0.6987 (mmm) cc_final: 0.6743 (mmm) REVERT: D 355 GLN cc_start: 0.7521 (mm-40) cc_final: 0.7154 (mm-40) REVERT: E 228 MET cc_start: 0.7540 (mtm) cc_final: 0.7305 (mtt) REVERT: E 355 GLN cc_start: 0.6268 (mm-40) cc_final: 0.6039 (mm-40) REVERT: E 380 THR cc_start: 0.6756 (OUTLIER) cc_final: 0.6463 (p) REVERT: E 388 ILE cc_start: 0.6532 (OUTLIER) cc_final: 0.6188 (pt) REVERT: F 165 TYR cc_start: 0.6929 (m-10) cc_final: 0.6186 (m-10) REVERT: F 326 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7083 (mm-30) REVERT: F 418 LEU cc_start: 0.6539 (OUTLIER) cc_final: 0.6322 (mp) REVERT: F 423 LYS cc_start: 0.6995 (mttm) cc_final: 0.6595 (mttp) outliers start: 49 outliers final: 4 residues processed: 474 average time/residue: 0.4815 time to fit residues: 353.4139 Evaluate side-chains 265 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 257 time to evaluate : 3.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain F residue 303 PHE Chi-restraints excluded: chain F residue 418 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 218 optimal weight: 0.9990 chunk 196 optimal weight: 8.9990 chunk 108 optimal weight: 0.8980 chunk 67 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 203 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 235 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 167 ASN A 355 GLN B 227 GLN B 426 GLN C 114 GLN C 227 GLN D 116 ASN D 200 ASN D 227 GLN D 422 GLN E 412 ASN F 43 HIS ** F 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.236197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.217683 restraints weight = 21059.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.217283 restraints weight = 32971.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.218616 restraints weight = 28391.878| |-----------------------------------------------------------------------------| r_work (final): 0.4387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6282 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 21368 Z= 0.193 Angle : 0.678 9.323 28966 Z= 0.359 Chirality : 0.046 0.230 3246 Planarity : 0.004 0.037 3599 Dihedral : 10.831 174.205 3011 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.08 % Allowed : 11.44 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.17), residues: 2580 helix: 0.92 (0.14), residues: 1340 sheet: -0.76 (0.29), residues: 345 loop : -1.38 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 162 HIS 0.006 0.001 HIS A 8 PHE 0.029 0.003 PHE E 11 TYR 0.031 0.002 TYR C 223 ARG 0.007 0.001 ARG F 236 Details of bonding type rmsd hydrogen bonds : bond 0.04086 ( 1054) hydrogen bonds : angle 5.10025 ( 3030) covalent geometry : bond 0.00439 (21368) covalent geometry : angle 0.67839 (28966) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 313 time to evaluate : 2.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 LYS cc_start: 0.5859 (OUTLIER) cc_final: 0.5223 (ttpt) REVERT: B 8 HIS cc_start: 0.7011 (m90) cc_final: 0.6810 (m-70) REVERT: B 181 LYS cc_start: 0.7348 (pttt) cc_final: 0.7051 (pttt) REVERT: C 168 LYS cc_start: 0.6682 (mptt) cc_final: 0.6431 (mmmt) REVERT: D 23 MET cc_start: 0.7914 (mmm) cc_final: 0.7681 (mmt) REVERT: D 43 HIS cc_start: 0.7301 (t-90) cc_final: 0.7015 (t-90) REVERT: E 158 TYR cc_start: 0.5361 (p90) cc_final: 0.5001 (p90) REVERT: F 3 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6387 (mm-30) REVERT: F 112 GLU cc_start: 0.5930 (OUTLIER) cc_final: 0.5682 (mp0) REVERT: F 155 MET cc_start: 0.5718 (ptt) cc_final: 0.5290 (ptt) REVERT: F 165 TYR cc_start: 0.6807 (m-10) cc_final: 0.6028 (m-10) outliers start: 69 outliers final: 28 residues processed: 368 average time/residue: 0.5209 time to fit residues: 310.8563 Evaluate side-chains 286 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 256 time to evaluate : 2.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 223 TYR Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 303 PHE Chi-restraints excluded: chain F residue 371 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 207 optimal weight: 0.7980 chunk 160 optimal weight: 0.9980 chunk 175 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 159 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 231 optimal weight: 10.0000 chunk 242 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 ASN D 13 GLN D 200 ASN ** D 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 GLN F 219 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.234728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.221284 restraints weight = 20873.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.220880 restraints weight = 29000.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.216819 restraints weight = 24879.549| |-----------------------------------------------------------------------------| r_work (final): 0.4346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6342 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21368 Z= 0.123 Angle : 0.551 7.602 28966 Z= 0.291 Chirality : 0.042 0.234 3246 Planarity : 0.003 0.036 3599 Dihedral : 10.395 170.136 3003 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.01 % Allowed : 13.09 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.17), residues: 2580 helix: 1.27 (0.15), residues: 1341 sheet: -0.85 (0.28), residues: 351 loop : -1.36 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 428 HIS 0.008 0.001 HIS B 43 PHE 0.018 0.002 PHE E 11 TYR 0.018 0.001 TYR E 47 ARG 0.004 0.000 ARG F 236 Details of bonding type rmsd hydrogen bonds : bond 0.03520 ( 1054) hydrogen bonds : angle 4.77255 ( 3030) covalent geometry : bond 0.00267 (21368) covalent geometry : angle 0.55100 (28966) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 271 time to evaluate : 2.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 LYS cc_start: 0.5413 (OUTLIER) cc_final: 0.4849 (ttpt) REVERT: A 368 MET cc_start: 0.2498 (ttp) cc_final: 0.2183 (ttp) REVERT: B 181 LYS cc_start: 0.7328 (pttt) cc_final: 0.7113 (pttt) REVERT: C 24 ASP cc_start: 0.7973 (m-30) cc_final: 0.7427 (m-30) REVERT: C 41 LYS cc_start: 0.7661 (mmtt) cc_final: 0.7440 (mptt) REVERT: C 168 LYS cc_start: 0.6540 (mptt) cc_final: 0.6337 (mmmt) REVERT: C 226 MET cc_start: 0.8038 (mmp) cc_final: 0.7820 (mmp) REVERT: D 43 HIS cc_start: 0.7205 (t-90) cc_final: 0.6880 (t-90) REVERT: E 138 MET cc_start: 0.7764 (tpt) cc_final: 0.7379 (tpt) REVERT: E 152 HIS cc_start: 0.6952 (OUTLIER) cc_final: 0.6652 (m-70) REVERT: E 158 TYR cc_start: 0.5392 (p90) cc_final: 0.4802 (p90) REVERT: F 3 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6128 (tm-30) REVERT: F 165 TYR cc_start: 0.7067 (m-10) cc_final: 0.6212 (m-10) REVERT: F 326 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7162 (mm-30) outliers start: 45 outliers final: 22 residues processed: 306 average time/residue: 0.3937 time to fit residues: 196.1374 Evaluate side-chains 263 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 239 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 152 HIS Chi-restraints excluded: chain E residue 164 SER Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 371 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 199 optimal weight: 2.9990 chunk 222 optimal weight: 0.9980 chunk 257 optimal weight: 6.9990 chunk 217 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 161 optimal weight: 0.0980 chunk 165 optimal weight: 6.9990 chunk 162 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN C 125 ASN C 200 ASN D 200 ASN ** D 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 425 ASN E 422 GLN E 426 GLN F 398 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.225241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.204926 restraints weight = 21097.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.204185 restraints weight = 35762.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.204119 restraints weight = 30141.083| |-----------------------------------------------------------------------------| r_work (final): 0.4251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21368 Z= 0.129 Angle : 0.558 7.846 28966 Z= 0.294 Chirality : 0.042 0.211 3246 Planarity : 0.003 0.047 3599 Dihedral : 10.266 166.780 3001 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.73 % Allowed : 14.21 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.17), residues: 2580 helix: 1.30 (0.15), residues: 1341 sheet: -0.93 (0.28), residues: 342 loop : -1.44 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 428 HIS 0.005 0.001 HIS B 43 PHE 0.019 0.002 PHE E 11 TYR 0.033 0.002 TYR F 15 ARG 0.004 0.000 ARG D 340 Details of bonding type rmsd hydrogen bonds : bond 0.03225 ( 1054) hydrogen bonds : angle 4.62198 ( 3030) covalent geometry : bond 0.00288 (21368) covalent geometry : angle 0.55841 (28966) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 293 time to evaluate : 2.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 LYS cc_start: 0.5666 (OUTLIER) cc_final: 0.5046 (ttpt) REVERT: A 389 GLU cc_start: 0.5799 (OUTLIER) cc_final: 0.5474 (tt0) REVERT: B 46 GLU cc_start: 0.6476 (tt0) cc_final: 0.6237 (mt-10) REVERT: B 138 MET cc_start: 0.7074 (mmm) cc_final: 0.6824 (mmm) REVERT: B 181 LYS cc_start: 0.7491 (pttt) cc_final: 0.7211 (pttt) REVERT: B 225 SER cc_start: 0.6583 (t) cc_final: 0.6320 (p) REVERT: C 24 ASP cc_start: 0.8025 (m-30) cc_final: 0.7503 (m-30) REVERT: C 110 ILE cc_start: 0.7167 (OUTLIER) cc_final: 0.6915 (pt) REVERT: C 168 LYS cc_start: 0.6618 (mptt) cc_final: 0.6320 (mmmt) REVERT: E 137 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8142 (tt) REVERT: E 139 ARG cc_start: 0.6261 (ttm110) cc_final: 0.6050 (ttp-170) REVERT: E 158 TYR cc_start: 0.5316 (p90) cc_final: 0.4906 (p90) REVERT: E 272 LEU cc_start: 0.8147 (tp) cc_final: 0.7769 (tp) REVERT: E 371 ILE cc_start: 0.7656 (OUTLIER) cc_final: 0.7101 (tp) REVERT: F 3 GLU cc_start: 0.6976 (mm-30) cc_final: 0.6323 (tm-30) REVERT: F 90 LEU cc_start: 0.5231 (OUTLIER) cc_final: 0.4886 (mm) REVERT: F 112 GLU cc_start: 0.6240 (OUTLIER) cc_final: 0.5963 (mp0) REVERT: F 128 MET cc_start: 0.5230 (OUTLIER) cc_final: 0.4984 (mtm) REVERT: F 241 MET cc_start: 0.7342 (mtm) cc_final: 0.7079 (mtm) REVERT: F 307 ILE cc_start: 0.8483 (mm) cc_final: 0.8177 (mp) REVERT: F 326 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7290 (mp0) outliers start: 61 outliers final: 28 residues processed: 338 average time/residue: 0.3462 time to fit residues: 185.9921 Evaluate side-chains 286 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 250 time to evaluate : 2.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 99 GLN Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 128 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 27 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 202 optimal weight: 9.9990 chunk 164 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 197 optimal weight: 0.7980 chunk 206 optimal weight: 7.9990 chunk 222 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN B 8 HIS D 200 ASN E 399 GLN F 398 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.218354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.198817 restraints weight = 20949.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.197976 restraints weight = 32855.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.199050 restraints weight = 28089.453| |-----------------------------------------------------------------------------| r_work (final): 0.4233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21368 Z= 0.136 Angle : 0.559 8.563 28966 Z= 0.294 Chirality : 0.042 0.264 3246 Planarity : 0.003 0.040 3599 Dihedral : 10.215 164.431 3001 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.73 % Allowed : 15.19 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.17), residues: 2580 helix: 1.34 (0.15), residues: 1333 sheet: -1.06 (0.28), residues: 345 loop : -1.44 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 89 HIS 0.005 0.001 HIS B 8 PHE 0.016 0.002 PHE E 11 TYR 0.031 0.002 TYR D 15 ARG 0.005 0.000 ARG F 267 Details of bonding type rmsd hydrogen bonds : bond 0.03159 ( 1054) hydrogen bonds : angle 4.59801 ( 3030) covalent geometry : bond 0.00306 (21368) covalent geometry : angle 0.55894 (28966) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 276 time to evaluate : 2.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7409 (tpt) cc_final: 0.7065 (tpt) REVERT: A 107 THR cc_start: 0.6740 (OUTLIER) cc_final: 0.6339 (m) REVERT: A 333 LYS cc_start: 0.5747 (OUTLIER) cc_final: 0.5250 (ttpt) REVERT: B 138 MET cc_start: 0.7359 (mmm) cc_final: 0.7056 (mmm) REVERT: B 181 LYS cc_start: 0.7451 (pttt) cc_final: 0.7233 (pttt) REVERT: C 24 ASP cc_start: 0.7801 (m-30) cc_final: 0.7310 (m-30) REVERT: C 168 LYS cc_start: 0.6621 (mptt) cc_final: 0.6358 (mmmt) REVERT: C 226 MET cc_start: 0.8005 (mmp) cc_final: 0.7796 (mmp) REVERT: C 384 MET cc_start: 0.7467 (ttm) cc_final: 0.7027 (mtp) REVERT: D 1 MET cc_start: 0.7158 (ppp) cc_final: 0.6739 (ppp) REVERT: D 298 LYS cc_start: 0.6629 (mmtt) cc_final: 0.6225 (mtmt) REVERT: D 406 SER cc_start: 0.7385 (t) cc_final: 0.6836 (p) REVERT: E 137 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.8267 (tt) REVERT: E 138 MET cc_start: 0.8061 (tpt) cc_final: 0.7691 (tpt) REVERT: E 158 TYR cc_start: 0.5445 (p90) cc_final: 0.5158 (p90) REVERT: E 272 LEU cc_start: 0.8281 (tp) cc_final: 0.7992 (tp) REVERT: E 371 ILE cc_start: 0.7690 (OUTLIER) cc_final: 0.7165 (tp) REVERT: F 3 GLU cc_start: 0.6862 (mm-30) cc_final: 0.6591 (tm-30) REVERT: F 128 MET cc_start: 0.5152 (OUTLIER) cc_final: 0.4827 (ttm) REVERT: F 307 ILE cc_start: 0.8558 (mm) cc_final: 0.8255 (mp) REVERT: F 326 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7374 (mp0) outliers start: 61 outliers final: 32 residues processed: 322 average time/residue: 0.3037 time to fit residues: 155.7126 Evaluate side-chains 287 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 250 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 99 GLN Chi-restraints excluded: chain F residue 128 MET Chi-restraints excluded: chain F residue 263 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 217 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 119 optimal weight: 0.6980 chunk 7 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 102 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 206 optimal weight: 9.9990 chunk 91 optimal weight: 20.0000 chunk 2 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN ** D 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.218077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 121)---------------| | r_work = 0.4205 r_free = 0.4205 target = 0.196985 restraints weight = 20950.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.195530 restraints weight = 34132.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.197122 restraints weight = 27985.991| |-----------------------------------------------------------------------------| r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21368 Z= 0.124 Angle : 0.558 8.499 28966 Z= 0.293 Chirality : 0.042 0.239 3246 Planarity : 0.003 0.037 3599 Dihedral : 10.025 157.835 3001 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.50 % Allowed : 16.35 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.17), residues: 2580 helix: 1.44 (0.15), residues: 1334 sheet: -1.12 (0.28), residues: 341 loop : -1.42 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 154 HIS 0.004 0.001 HIS A 8 PHE 0.016 0.001 PHE E 11 TYR 0.021 0.001 TYR D 15 ARG 0.002 0.000 ARG D 340 Details of bonding type rmsd hydrogen bonds : bond 0.02998 ( 1054) hydrogen bonds : angle 4.52481 ( 3030) covalent geometry : bond 0.00282 (21368) covalent geometry : angle 0.55838 (28966) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 272 time to evaluate : 2.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 THR cc_start: 0.6672 (OUTLIER) cc_final: 0.6252 (m) REVERT: A 333 LYS cc_start: 0.5712 (OUTLIER) cc_final: 0.5227 (ttpt) REVERT: C 24 ASP cc_start: 0.7789 (m-30) cc_final: 0.7298 (m-30) REVERT: C 168 LYS cc_start: 0.6552 (mptt) cc_final: 0.6269 (mmmt) REVERT: C 384 MET cc_start: 0.7515 (ttm) cc_final: 0.7104 (mtp) REVERT: D 67 GLU cc_start: 0.7831 (tp30) cc_final: 0.7620 (tp30) REVERT: D 298 LYS cc_start: 0.6402 (mmtt) cc_final: 0.5983 (mtmt) REVERT: D 406 SER cc_start: 0.7495 (t) cc_final: 0.6932 (p) REVERT: E 272 LEU cc_start: 0.8452 (tp) cc_final: 0.8144 (tp) REVERT: E 371 ILE cc_start: 0.7677 (OUTLIER) cc_final: 0.7188 (tp) REVERT: F 3 GLU cc_start: 0.6837 (mm-30) cc_final: 0.6620 (tm-30) REVERT: F 307 ILE cc_start: 0.8535 (mm) cc_final: 0.8240 (mp) outliers start: 56 outliers final: 29 residues processed: 313 average time/residue: 0.4338 time to fit residues: 214.5061 Evaluate side-chains 284 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 252 time to evaluate : 6.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 99 GLN Chi-restraints excluded: chain F residue 419 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 123 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 240 optimal weight: 9.9990 chunk 50 optimal weight: 0.8980 chunk 245 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 215 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 221 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN ** A 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 GLN A 425 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.203104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.187912 restraints weight = 21097.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.180682 restraints weight = 34182.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.176921 restraints weight = 23779.150| |-----------------------------------------------------------------------------| r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.5926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21368 Z= 0.188 Angle : 0.646 9.258 28966 Z= 0.339 Chirality : 0.045 0.272 3246 Planarity : 0.004 0.037 3599 Dihedral : 10.315 160.162 2999 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.90 % Allowed : 16.31 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.17), residues: 2580 helix: 1.09 (0.14), residues: 1336 sheet: -1.40 (0.28), residues: 352 loop : -1.51 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 20 HIS 0.004 0.001 HIS F 43 PHE 0.020 0.002 PHE D 37 TYR 0.030 0.002 TYR D 15 ARG 0.009 0.001 ARG D 340 Details of bonding type rmsd hydrogen bonds : bond 0.03403 ( 1054) hydrogen bonds : angle 4.74577 ( 3030) covalent geometry : bond 0.00438 (21368) covalent geometry : angle 0.64642 (28966) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 308 time to evaluate : 2.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6939 (tpt) REVERT: A 107 THR cc_start: 0.6789 (OUTLIER) cc_final: 0.6374 (m) REVERT: A 128 MET cc_start: 0.6651 (tpp) cc_final: 0.6438 (tpp) REVERT: A 333 LYS cc_start: 0.6082 (OUTLIER) cc_final: 0.5298 (ttpt) REVERT: B 138 MET cc_start: 0.7941 (mmm) cc_final: 0.7618 (mmm) REVERT: B 155 MET cc_start: 0.7901 (tpp) cc_final: 0.7603 (tpp) REVERT: C 24 ASP cc_start: 0.7957 (m-30) cc_final: 0.7535 (m-30) REVERT: C 145 SER cc_start: 0.8830 (p) cc_final: 0.8334 (m) REVERT: C 181 LYS cc_start: 0.8244 (ttpp) cc_final: 0.7618 (mtpt) REVERT: C 384 MET cc_start: 0.7781 (ttm) cc_final: 0.7327 (mtp) REVERT: D 1 MET cc_start: 0.7381 (ppp) cc_final: 0.7012 (ppp) REVERT: D 136 ASP cc_start: 0.7163 (t70) cc_final: 0.6957 (t0) REVERT: D 154 TRP cc_start: 0.7509 (t60) cc_final: 0.7228 (t60) REVERT: D 264 GLU cc_start: 0.7389 (mm-30) cc_final: 0.6961 (mt-10) REVERT: D 298 LYS cc_start: 0.7155 (mmtt) cc_final: 0.6559 (mtmt) REVERT: D 326 GLU cc_start: 0.7014 (mm-30) cc_final: 0.6785 (mm-30) REVERT: E 371 ILE cc_start: 0.7820 (OUTLIER) cc_final: 0.7381 (tp) REVERT: F 90 LEU cc_start: 0.5269 (OUTLIER) cc_final: 0.4981 (mm) REVERT: F 112 GLU cc_start: 0.6326 (mp0) cc_final: 0.6080 (mp0) REVERT: F 128 MET cc_start: 0.5302 (OUTLIER) cc_final: 0.5017 (ttm) REVERT: F 307 ILE cc_start: 0.8500 (mm) cc_final: 0.8238 (mp) REVERT: F 368 MET cc_start: 0.5523 (OUTLIER) cc_final: 0.5146 (ttm) outliers start: 65 outliers final: 30 residues processed: 353 average time/residue: 0.3766 time to fit residues: 210.4083 Evaluate side-chains 312 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 275 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 384 MET Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 99 GLN Chi-restraints excluded: chain F residue 128 MET Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain F residue 404 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 113 optimal weight: 1.9990 chunk 205 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 247 optimal weight: 7.9990 chunk 256 optimal weight: 0.4980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 ASN ** E 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.206109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.187020 restraints weight = 21055.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.186040 restraints weight = 32318.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.187446 restraints weight = 27668.138| |-----------------------------------------------------------------------------| r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6736 moved from start: 0.6145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21368 Z= 0.131 Angle : 0.600 9.463 28966 Z= 0.313 Chirality : 0.042 0.186 3246 Planarity : 0.003 0.048 3599 Dihedral : 10.075 156.146 2999 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.10 % Allowed : 18.81 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.17), residues: 2580 helix: 1.29 (0.15), residues: 1337 sheet: -1.40 (0.27), residues: 361 loop : -1.46 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 20 HIS 0.003 0.001 HIS F 43 PHE 0.016 0.002 PHE E 11 TYR 0.024 0.001 TYR D 15 ARG 0.009 0.000 ARG E 177 Details of bonding type rmsd hydrogen bonds : bond 0.03072 ( 1054) hydrogen bonds : angle 4.60819 ( 3030) covalent geometry : bond 0.00295 (21368) covalent geometry : angle 0.59969 (28966) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 285 time to evaluate : 2.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 THR cc_start: 0.6690 (OUTLIER) cc_final: 0.6299 (m) REVERT: A 333 LYS cc_start: 0.6034 (OUTLIER) cc_final: 0.5353 (ttpt) REVERT: B 103 MET cc_start: 0.6688 (mmm) cc_final: 0.6445 (mmm) REVERT: B 138 MET cc_start: 0.7808 (mmm) cc_final: 0.7245 (mmm) REVERT: B 155 MET cc_start: 0.7801 (tpp) cc_final: 0.7524 (tpp) REVERT: C 24 ASP cc_start: 0.7815 (m-30) cc_final: 0.7420 (m-30) REVERT: C 145 SER cc_start: 0.8723 (p) cc_final: 0.8254 (m) REVERT: C 181 LYS cc_start: 0.8078 (ttpp) cc_final: 0.7503 (mtpt) REVERT: C 384 MET cc_start: 0.7670 (ttm) cc_final: 0.7219 (mtp) REVERT: D 1 MET cc_start: 0.7467 (ppp) cc_final: 0.7181 (ppp) REVERT: D 136 ASP cc_start: 0.7049 (t70) cc_final: 0.6841 (t0) REVERT: D 264 GLU cc_start: 0.7302 (mm-30) cc_final: 0.6975 (mt-10) REVERT: D 298 LYS cc_start: 0.7117 (mmtt) cc_final: 0.6570 (mtmt) REVERT: D 326 GLU cc_start: 0.6927 (mm-30) cc_final: 0.6704 (mm-30) REVERT: D 338 GLU cc_start: 0.8222 (tp30) cc_final: 0.7142 (mt-10) REVERT: E 371 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.7354 (tp) REVERT: F 112 GLU cc_start: 0.6340 (mp0) cc_final: 0.6066 (mp0) REVERT: F 307 ILE cc_start: 0.8544 (mm) cc_final: 0.8276 (mp) REVERT: F 368 MET cc_start: 0.5405 (mtp) cc_final: 0.5094 (ttm) outliers start: 47 outliers final: 28 residues processed: 318 average time/residue: 0.3057 time to fit residues: 154.0735 Evaluate side-chains 297 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 266 time to evaluate : 2.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 384 MET Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 404 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 67 optimal weight: 8.9990 chunk 189 optimal weight: 10.0000 chunk 126 optimal weight: 0.9990 chunk 243 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 118 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 198 optimal weight: 0.9990 chunk 159 optimal weight: 0.4980 chunk 196 optimal weight: 10.0000 chunk 114 optimal weight: 0.5980 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.207164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.188001 restraints weight = 20904.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.187551 restraints weight = 31399.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.190061 restraints weight = 24732.886| |-----------------------------------------------------------------------------| r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.6305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21368 Z= 0.122 Angle : 0.592 10.077 28966 Z= 0.308 Chirality : 0.042 0.169 3246 Planarity : 0.003 0.044 3599 Dihedral : 9.968 153.001 2999 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.10 % Allowed : 18.95 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.17), residues: 2580 helix: 1.39 (0.15), residues: 1336 sheet: -1.32 (0.28), residues: 353 loop : -1.41 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP D 154 HIS 0.004 0.001 HIS A 8 PHE 0.016 0.001 PHE E 11 TYR 0.034 0.001 TYR F 165 ARG 0.010 0.000 ARG D 340 Details of bonding type rmsd hydrogen bonds : bond 0.02994 ( 1054) hydrogen bonds : angle 4.55736 ( 3030) covalent geometry : bond 0.00272 (21368) covalent geometry : angle 0.59195 (28966) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 271 time to evaluate : 2.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 THR cc_start: 0.6588 (OUTLIER) cc_final: 0.6190 (m) REVERT: A 333 LYS cc_start: 0.5878 (OUTLIER) cc_final: 0.5167 (ttpt) REVERT: B 61 GLU cc_start: 0.6989 (tt0) cc_final: 0.6707 (mt-10) REVERT: B 155 MET cc_start: 0.7805 (tpp) cc_final: 0.7448 (tpp) REVERT: C 24 ASP cc_start: 0.7830 (m-30) cc_final: 0.7442 (m-30) REVERT: C 145 SER cc_start: 0.8775 (p) cc_final: 0.8303 (m) REVERT: C 181 LYS cc_start: 0.7984 (ttpp) cc_final: 0.7447 (mtpt) REVERT: C 384 MET cc_start: 0.7745 (ttm) cc_final: 0.7286 (mtp) REVERT: D 29 GLU cc_start: 0.6841 (tm-30) cc_final: 0.6134 (pt0) REVERT: D 136 ASP cc_start: 0.7022 (t70) cc_final: 0.6803 (t0) REVERT: D 155 MET cc_start: 0.8420 (mmm) cc_final: 0.8194 (tpp) REVERT: D 264 GLU cc_start: 0.7292 (mm-30) cc_final: 0.6943 (mt-10) REVERT: D 326 GLU cc_start: 0.6881 (mm-30) cc_final: 0.6637 (mm-30) REVERT: D 338 GLU cc_start: 0.8165 (tp30) cc_final: 0.7156 (mt-10) REVERT: E 23 MET cc_start: 0.7322 (mmp) cc_final: 0.7051 (mmp) REVERT: E 155 MET cc_start: 0.4404 (tpt) cc_final: 0.4164 (mmm) REVERT: E 371 ILE cc_start: 0.7752 (OUTLIER) cc_final: 0.7251 (tp) REVERT: F 112 GLU cc_start: 0.6394 (mp0) cc_final: 0.6177 (mp0) REVERT: F 263 MET cc_start: 0.6700 (mmm) cc_final: 0.6251 (mmt) REVERT: F 307 ILE cc_start: 0.8486 (mm) cc_final: 0.8202 (mp) REVERT: F 326 GLU cc_start: 0.7757 (mp0) cc_final: 0.7003 (mp0) REVERT: F 368 MET cc_start: 0.5221 (OUTLIER) cc_final: 0.4881 (ttp) outliers start: 47 outliers final: 33 residues processed: 304 average time/residue: 0.3120 time to fit residues: 153.0147 Evaluate side-chains 298 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 261 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 384 MET Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain F residue 404 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 86 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 233 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 217 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 187 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN C 125 ASN D 422 GLN ** E 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** 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 = 0.4254 r_free = 0.4254 target = 0.201982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.182567 restraints weight = 21036.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 88)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.179797 restraints weight = 28872.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.179591 restraints weight = 18519.328| |-----------------------------------------------------------------------------| r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.6623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21368 Z= 0.148 Angle : 0.620 9.230 28966 Z= 0.322 Chirality : 0.043 0.180 3246 Planarity : 0.003 0.044 3599 Dihedral : 10.068 153.744 2999 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.92 % Allowed : 19.17 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.17), residues: 2580 helix: 1.32 (0.15), residues: 1336 sheet: -1.42 (0.28), residues: 353 loop : -1.44 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP D 154 HIS 0.004 0.001 HIS F 43 PHE 0.017 0.002 PHE C 11 TYR 0.023 0.001 TYR D 15 ARG 0.010 0.000 ARG D 340 Details of bonding type rmsd hydrogen bonds : bond 0.03103 ( 1054) hydrogen bonds : angle 4.61904 ( 3030) covalent geometry : bond 0.00345 (21368) covalent geometry : angle 0.61971 (28966) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 270 time to evaluate : 2.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7463 (tpt) cc_final: 0.7056 (tpp) REVERT: A 107 THR cc_start: 0.6590 (OUTLIER) cc_final: 0.6221 (m) REVERT: A 333 LYS cc_start: 0.5898 (OUTLIER) cc_final: 0.5137 (ttpt) REVERT: B 165 TYR cc_start: 0.7841 (m-10) cc_final: 0.7605 (m-10) REVERT: C 24 ASP cc_start: 0.7925 (m-30) cc_final: 0.7572 (m-30) REVERT: C 145 SER cc_start: 0.8809 (p) cc_final: 0.8372 (m) REVERT: C 181 LYS cc_start: 0.8098 (ttpp) cc_final: 0.7544 (mtpt) REVERT: D 155 MET cc_start: 0.8552 (mmm) cc_final: 0.8297 (tpp) REVERT: D 264 GLU cc_start: 0.7391 (mm-30) cc_final: 0.6974 (mt-10) REVERT: D 326 GLU cc_start: 0.6849 (mm-30) cc_final: 0.6556 (mm-30) REVERT: D 338 GLU cc_start: 0.8078 (tp30) cc_final: 0.6957 (mt-10) REVERT: E 138 MET cc_start: 0.8542 (tpt) cc_final: 0.8131 (tpt) REVERT: E 371 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7308 (tp) REVERT: F 112 GLU cc_start: 0.6391 (mp0) cc_final: 0.6114 (mp0) REVERT: F 326 GLU cc_start: 0.7827 (mp0) cc_final: 0.7068 (mp0) REVERT: F 368 MET cc_start: 0.5357 (OUTLIER) cc_final: 0.5067 (ttm) outliers start: 43 outliers final: 33 residues processed: 300 average time/residue: 0.2916 time to fit residues: 141.4666 Evaluate side-chains 304 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 267 time to evaluate : 2.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 265 LYS Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 398 GLN Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 368 MET Chi-restraints excluded: chain F residue 404 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 143 optimal weight: 7.9990 chunk 176 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 200 optimal weight: 0.0970 chunk 91 optimal weight: 0.9990 chunk 182 optimal weight: 0.9980 chunk 108 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.204621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.187277 restraints weight = 21058.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.186878 restraints weight = 26161.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.185708 restraints weight = 24181.608| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.6763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21368 Z= 0.123 Angle : 0.601 11.940 28966 Z= 0.309 Chirality : 0.041 0.176 3246 Planarity : 0.003 0.045 3599 Dihedral : 9.936 154.443 2999 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.70 % Allowed : 19.66 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.17), residues: 2580 helix: 1.43 (0.15), residues: 1336 sheet: -1.39 (0.28), residues: 352 loop : -1.41 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP D 154 HIS 0.004 0.001 HIS A 8 PHE 0.020 0.002 PHE B 11 TYR 0.027 0.001 TYR E 329 ARG 0.008 0.000 ARG D 340 Details of bonding type rmsd hydrogen bonds : bond 0.02939 ( 1054) hydrogen bonds : angle 4.52900 ( 3030) covalent geometry : bond 0.00278 (21368) covalent geometry : angle 0.60060 (28966) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8012.96 seconds wall clock time: 146 minutes 1.77 seconds (8761.77 seconds total)