Starting phenix.real_space_refine on Wed May 21 03:42:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dtp_27707/05_2025/8dtp_27707.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dtp_27707/05_2025/8dtp_27707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dtp_27707/05_2025/8dtp_27707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dtp_27707/05_2025/8dtp_27707.map" model { file = "/net/cci-nas-00/data/ceres_data/8dtp_27707/05_2025/8dtp_27707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dtp_27707/05_2025/8dtp_27707.cif" } resolution = 2.7 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= 0.004 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 3469 2.21 5 O 4080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: "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: 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: "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: 12.09, per 1000 atoms: 0.58 Number of scatterers: 20944 At special positions: 0 Unit cell: (112.608, 134.136, 141.588, 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 4080 8.00 N 3469 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: 4.75 Conformation dependent library (CDL) restraints added in 2.4 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 16 sheets defined 55.7% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.36 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 202 through 217 removed outlier: 4.527A pdb=" N GLY A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 207 " --> pdb=" O LYS A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 243 Processing helix chain 'A' and resid 245 through 252 removed outlier: 3.520A 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: 3.549A 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: 3.568A 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 removed outlier: 3.844A pdb=" N LYS B 269 " --> pdb=" O LYS B 265 " (cutoff:3.500A) 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 229 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: 3.639A 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: 3.503A 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: 3.936A 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 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: 4.004A 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: 3.534A 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 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: 3.843A 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: 3.660A 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 302 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 152 through 153 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: 6.224A 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: 3.626A 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=AA2, first strand: chain 'A' and resid 171 through 172 Processing sheet with id=AA3, first strand: chain 'A' and resid 427 through 429 removed outlier: 6.512A pdb=" N MET A 384 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU A 192 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N LEU A 385 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL A 194 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N VAL A 387 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N MET A 196 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N THR A 191 " --> pdb=" O LEU A 350 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N THR A 352 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ASN A 193 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ALA A 354 " --> pdb=" O ASN A 193 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU A 195 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 4.452A 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: 6.656A 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: 6.337A pdb=" N TYR A 223 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 152 through 153 removed outlier: 6.614A 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: 6.242A 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: 7.639A 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: 6.431A pdb=" N MET C 384 " --> pdb=" O ILE C 404 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 171 through 172 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: 6.324A pdb=" N VAL E 194 " --> pdb=" O LEU E 385 " (cutoff:3.500A) removed outlier: 7.859A 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: 6.502A 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: 6.038A 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: 6.346A 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: 6.439A 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 349 through 352 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 275 through 279 removed outlier: 6.325A pdb=" N LEU F 222 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 419 through 422 1056 hydrogen bonds defined for protein. 3033 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.15 Time building geometry restraints manager: 5.57 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: 5600 1.50 - 1.65: 8864 1.65 - 1.80: 98 1.80 - 1.95: 111 Bond restraints: 21368 Sorted by residual: bond pdb=" CE1 HIS C 253 " pdb=" NE2 HIS C 253 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.66e+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 1.52e+01 bond pdb=" CE1 HIS B 152 " pdb=" NE2 HIS B 152 " ideal model delta sigma weight residual 1.321 1.357 -0.036 1.00e-02 1.00e+04 1.27e+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 1.13e+01 bond pdb=" N VAL A 323 " pdb=" CA VAL A 323 " ideal model delta sigma weight residual 1.457 1.494 -0.038 1.19e-02 7.06e+03 9.93e+00 ... (remaining 21363 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 27833 1.56 - 3.12: 966 3.12 - 4.69: 141 4.69 - 6.25: 25 6.25 - 7.81: 1 Bond angle restraints: 28966 Sorted by residual: angle pdb=" N ASP A 82 " pdb=" CA ASP A 82 " pdb=" C ASP A 82 " ideal model delta sigma weight residual 112.57 108.09 4.48 1.13e+00 7.83e-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 113.80 117.73 -3.93 1.00e+00 1.00e+00 1.54e+01 angle pdb=" C GLY F 151 " pdb=" N HIS F 152 " pdb=" CA HIS F 152 " ideal model delta sigma weight residual 122.30 117.08 5.22 1.35e+00 5.49e-01 1.50e+01 angle pdb=" N ASP F 382 " pdb=" CA ASP F 382 " pdb=" C ASP F 382 " ideal model delta sigma weight residual 114.31 109.48 4.83 1.29e+00 6.01e-01 1.40e+01 angle pdb=" N GLU A 122 " pdb=" CA GLU A 122 " pdb=" C GLU A 122 " ideal model delta sigma weight residual 111.71 107.41 4.30 1.15e+00 7.56e-01 1.40e+01 ... (remaining 28961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 12753 35.65 - 71.31: 169 71.31 - 106.96: 4 106.96 - 142.61: 1 142.61 - 178.27: 4 Dihedral angle restraints: 12931 sinusoidal: 5317 harmonic: 7614 Sorted by residual: dihedral pdb=" O1B AGS E 501 " pdb=" O3B AGS E 501 " pdb=" PB AGS E 501 " pdb=" PG AGS E 501 " ideal model delta sinusoidal sigma weight residual 68.91 -112.82 -178.27 1 3.00e+01 1.11e-03 2.13e+01 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 -67.73 106.47 -174.20 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 -88.57 157.48 1 3.00e+01 1.11e-03 2.05e+01 ... (remaining 12928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2404 0.044 - 0.088: 561 0.088 - 0.132: 237 0.132 - 0.175: 33 0.175 - 0.219: 11 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 1.20e+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 2.73 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA ILE A 371 " pdb=" N ILE A 371 " pdb=" C ILE A 371 " pdb=" CB ILE A 371 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+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 3.34e-02 1.11e+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 2.27e-02 5.14e+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 GLU A 122 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.36e+00 pdb=" C GLU A 122 " -0.036 2.00e-02 2.50e+03 pdb=" O GLU A 122 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS A 123 " 0.012 2.00e-02 2.50e+03 ... (remaining 3596 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 157 2.56 - 3.14: 16858 3.14 - 3.73: 33356 3.73 - 4.31: 46831 4.31 - 4.90: 78026 Nonbonded interactions: 175228 Sorted by model distance: nonbonded pdb=" O3B AGS B 501 " pdb="MG MG B 502 " model vdw 1.973 2.170 nonbonded pdb=" OE2 GLU B 227 " pdb="MG MG B 502 " model vdw 1.979 2.170 nonbonded pdb=" O2G AGS E 501 " pdb="MG MG E 502 " model vdw 1.984 2.170 nonbonded pdb=" O2B AGS F 501 " pdb="MG MG F 502 " model vdw 1.993 2.170 nonbonded pdb=" OE2 GLU C 227 " pdb="MG MG C 502 " model vdw 2.005 2.170 ... (remaining 175223 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 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: 0.010 Extract box with map and model: 0.770 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 44.350 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21368 Z= 0.292 Angle : 0.633 7.809 28966 Z= 0.424 Chirality : 0.046 0.219 3246 Planarity : 0.004 0.075 3599 Dihedral : 12.189 178.266 8011 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.92 % Allowed : 6.26 % Favored : 91.82 % 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: 0.52 (0.17), residues: 2580 helix: 1.58 (0.15), residues: 1317 sheet: -0.15 (0.30), residues: 345 loop : -1.28 (0.20), residues: 918 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 0.023 0.002 PHE D 383 TYR 0.014 0.001 TYR E 329 ARG 0.002 0.000 ARG D 274 Details of bonding type rmsd hydrogen bonds : bond 0.15695 ( 1056) hydrogen bonds : angle 6.38349 ( 3033) covalent geometry : bond 0.00421 (21368) covalent geometry : angle 0.63325 (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 592 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 549 time to evaluate : 2.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8240 (tpt) cc_final: 0.7270 (tpt) REVERT: A 70 TYR cc_start: 0.6704 (t80) cc_final: 0.6445 (t80) REVERT: A 203 LYS cc_start: 0.7948 (mttm) cc_final: 0.7714 (mtmm) REVERT: A 312 TYR cc_start: 0.4815 (t80) cc_final: 0.4605 (t80) REVERT: A 337 GLU cc_start: 0.6337 (mt-10) cc_final: 0.6019 (mt-10) REVERT: B 13 GLN cc_start: 0.7676 (tp40) cc_final: 0.7476 (mp10) REVERT: B 53 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7569 (mm) REVERT: B 57 ASN cc_start: 0.7789 (p0) cc_final: 0.7453 (p0) REVERT: B 71 SER cc_start: 0.8308 (t) cc_final: 0.8103 (m) REVERT: B 96 LYS cc_start: 0.8296 (mtpp) cc_final: 0.7997 (mttm) REVERT: B 109 LYS cc_start: 0.8213 (ttmm) cc_final: 0.7952 (tttt) REVERT: B 330 THR cc_start: 0.7601 (t) cc_final: 0.7358 (m) REVERT: C 92 LYS cc_start: 0.8106 (mmmm) cc_final: 0.7751 (mppt) REVERT: C 177 ARG cc_start: 0.7692 (mtm110) cc_final: 0.7478 (mtm110) REVERT: C 184 LYS cc_start: 0.7702 (mtpp) cc_final: 0.7454 (mtpt) REVERT: C 236 ARG cc_start: 0.8321 (mtt-85) cc_final: 0.7974 (mtp180) REVERT: C 279 GLN cc_start: 0.8193 (tt0) cc_final: 0.7879 (tt0) REVERT: C 313 LEU cc_start: 0.6143 (pp) cc_final: 0.5875 (tt) REVERT: C 317 LYS cc_start: 0.7867 (pttt) cc_final: 0.7623 (pttm) REVERT: D 86 ASP cc_start: 0.6867 (OUTLIER) cc_final: 0.5885 (t70) REVERT: D 101 ARG cc_start: 0.8152 (mmm160) cc_final: 0.7935 (mmm160) REVERT: D 153 ASP cc_start: 0.7384 (t0) cc_final: 0.7168 (t70) REVERT: D 177 ARG cc_start: 0.7803 (mtm110) cc_final: 0.7562 (mtm-85) REVERT: D 226 MET cc_start: 0.7580 (mmm) cc_final: 0.7264 (mmm) REVERT: D 227 GLU cc_start: 0.7202 (tt0) cc_final: 0.6784 (pm20) REVERT: D 238 ASP cc_start: 0.8633 (m-30) cc_final: 0.8401 (m-30) REVERT: D 279 GLN cc_start: 0.7722 (tt0) cc_final: 0.6829 (tm130) REVERT: D 331 THR cc_start: 0.7402 (p) cc_final: 0.6992 (m) REVERT: E 92 LYS cc_start: 0.8450 (tppp) cc_final: 0.8158 (ttmt) REVERT: E 109 LYS cc_start: 0.8056 (tptt) cc_final: 0.7715 (tttm) REVERT: E 170 ARG cc_start: 0.6466 (ptt-90) cc_final: 0.6036 (mtp85) REVERT: E 228 MET cc_start: 0.6478 (mmp) cc_final: 0.6160 (mmm) REVERT: E 265 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7756 (mppt) REVERT: E 274 ARG cc_start: 0.8026 (mtp180) cc_final: 0.7708 (mmm-85) REVERT: E 279 GLN cc_start: 0.7177 (pt0) cc_final: 0.6106 (tp40) REVERT: E 384 MET cc_start: 0.6712 (ttm) cc_final: 0.6492 (mtp) REVERT: E 392 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7136 (pm20) REVERT: E 413 LYS cc_start: 0.7861 (ttmt) cc_final: 0.7575 (mttt) REVERT: F 139 ARG cc_start: 0.7500 (ttm-80) cc_final: 0.6925 (ttp-110) REVERT: F 147 ASP cc_start: 0.7469 (m-30) cc_final: 0.7219 (p0) REVERT: F 247 ASP cc_start: 0.7450 (m-30) cc_final: 0.7111 (m-30) REVERT: F 302 ASN cc_start: 0.7693 (t0) cc_final: 0.7382 (t0) REVERT: F 327 ASN cc_start: 0.7051 (p0) cc_final: 0.6696 (p0) REVERT: F 333 LYS cc_start: 0.7406 (ttpp) cc_final: 0.6800 (ttmm) REVERT: F 347 GLU cc_start: 0.7100 (mp0) cc_final: 0.6882 (mm-30) REVERT: F 397 GLU cc_start: 0.6503 (tp30) cc_final: 0.6164 (tm-30) REVERT: F 398 GLN cc_start: 0.7540 (mt0) cc_final: 0.6941 (mp-120) REVERT: F 404 ILE cc_start: 0.8258 (mt) cc_final: 0.7976 (mm) REVERT: F 407 ARG cc_start: 0.6875 (ttp-170) cc_final: 0.6113 (ttm170) outliers start: 43 outliers final: 2 residues processed: 577 average time/residue: 1.4296 time to fit residues: 921.6872 Evaluate side-chains 327 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 322 time to evaluate : 2.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 265 LYS Chi-restraints excluded: chain E residue 380 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 218 optimal weight: 4.9990 chunk 196 optimal weight: 0.6980 chunk 108 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 203 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 151 optimal weight: 0.0970 chunk 235 optimal weight: 8.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN A 216 GLN C 116 ASN C 302 ASN D 116 ASN D 200 ASN E 167 ASN F 62 ASN F 140 GLN F 200 ASN F 295 ASN F 359 GLN ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.175847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.146032 restraints weight = 23133.062| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.21 r_work: 0.3478 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21368 Z= 0.165 Angle : 0.588 8.599 28966 Z= 0.312 Chirality : 0.043 0.211 3246 Planarity : 0.004 0.039 3599 Dihedral : 10.992 178.837 3005 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.89 % Allowed : 12.91 % Favored : 83.20 % 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: 0.54 (0.17), residues: 2580 helix: 1.52 (0.15), residues: 1347 sheet: -0.13 (0.29), residues: 354 loop : -1.26 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 162 HIS 0.005 0.001 HIS A 8 PHE 0.021 0.002 PHE D 65 TYR 0.021 0.002 TYR A 70 ARG 0.005 0.001 ARG A 101 Details of bonding type rmsd hydrogen bonds : bond 0.04031 ( 1056) hydrogen bonds : angle 4.93740 ( 3033) covalent geometry : bond 0.00377 (21368) covalent geometry : angle 0.58755 (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 436 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 349 time to evaluate : 2.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 ASP cc_start: 0.7516 (m-30) cc_final: 0.7167 (t0) REVERT: A 333 LYS cc_start: 0.7132 (mtpt) cc_final: 0.6733 (mmmt) REVERT: A 337 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7098 (mp0) REVERT: A 414 TRP cc_start: 0.7414 (m100) cc_final: 0.7151 (m-90) REVERT: B 49 SER cc_start: 0.8782 (t) cc_final: 0.8491 (p) REVERT: B 96 LYS cc_start: 0.8519 (mtpp) cc_final: 0.8291 (mttm) REVERT: B 109 LYS cc_start: 0.8571 (ttmm) cc_final: 0.8315 (tttt) REVERT: C 92 LYS cc_start: 0.8359 (mmmm) cc_final: 0.8105 (mppt) REVERT: C 101 ARG cc_start: 0.8615 (mmm160) cc_final: 0.8411 (mmm160) REVERT: C 184 LYS cc_start: 0.8515 (mtpp) cc_final: 0.8285 (mtpt) REVERT: D 26 GLU cc_start: 0.7753 (mp0) cc_final: 0.7457 (mm-30) REVERT: D 136 ASP cc_start: 0.7311 (t70) cc_final: 0.7102 (t0) REVERT: D 139 ARG cc_start: 0.7749 (ttp80) cc_final: 0.6937 (ttp-110) REVERT: D 153 ASP cc_start: 0.7845 (t0) cc_final: 0.7409 (t70) REVERT: D 177 ARG cc_start: 0.8109 (mtm110) cc_final: 0.7874 (mtm-85) REVERT: D 226 MET cc_start: 0.8108 (mmm) cc_final: 0.7833 (mmm) REVERT: D 331 THR cc_start: 0.7759 (p) cc_final: 0.7375 (m) REVERT: E 92 LYS cc_start: 0.8538 (tppp) cc_final: 0.8244 (ttmt) REVERT: E 109 LYS cc_start: 0.8249 (tptt) cc_final: 0.7884 (tttm) REVERT: E 170 ARG cc_start: 0.6855 (ptt-90) cc_final: 0.6139 (mtp85) REVERT: E 317 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.6608 (ptmt) REVERT: E 340 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.7042 (ttp80) REVERT: E 413 LYS cc_start: 0.8068 (ttmt) cc_final: 0.7840 (mttt) REVERT: F 139 ARG cc_start: 0.8081 (ttm-80) cc_final: 0.7754 (ttp80) REVERT: F 147 ASP cc_start: 0.7785 (m-30) cc_final: 0.7324 (p0) REVERT: F 243 ASP cc_start: 0.7494 (m-30) cc_final: 0.7289 (t0) REVERT: F 247 ASP cc_start: 0.7410 (m-30) cc_final: 0.7163 (m-30) REVERT: F 302 ASN cc_start: 0.7712 (t0) cc_final: 0.7342 (t0) REVERT: F 327 ASN cc_start: 0.6901 (p0) cc_final: 0.6534 (p0) REVERT: F 333 LYS cc_start: 0.7696 (ttpp) cc_final: 0.7302 (ttmt) REVERT: F 347 GLU cc_start: 0.7302 (mp0) cc_final: 0.6954 (mm-30) REVERT: F 368 MET cc_start: 0.6079 (mtp) cc_final: 0.5804 (mtt) REVERT: F 397 GLU cc_start: 0.6925 (tp30) cc_final: 0.6202 (tm-30) REVERT: F 398 GLN cc_start: 0.7526 (mt0) cc_final: 0.6919 (mp-120) REVERT: F 407 ARG cc_start: 0.7161 (ttp-170) cc_final: 0.6485 (ttm170) REVERT: F 431 ILE cc_start: 0.7117 (pp) cc_final: 0.6623 (pt) outliers start: 87 outliers final: 25 residues processed: 406 average time/residue: 1.3002 time to fit residues: 597.2190 Evaluate side-chains 308 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 281 time to evaluate : 2.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 317 LYS Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 131 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 207 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 chunk 175 optimal weight: 0.4980 chunk 63 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 159 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 231 optimal weight: 5.9990 chunk 242 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 ASN C 288 ASN C 302 ASN D 13 GLN D 100 GLN D 200 ASN E 167 ASN F 140 GLN F 200 ASN F 295 ASN F 359 GLN ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.176383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.146820 restraints weight = 23040.711| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.10 r_work: 0.3490 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21368 Z= 0.127 Angle : 0.526 7.737 28966 Z= 0.283 Chirality : 0.041 0.222 3246 Planarity : 0.003 0.037 3599 Dihedral : 10.855 179.798 2997 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.66 % Allowed : 14.70 % Favored : 81.64 % 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: 0.66 (0.17), residues: 2580 helix: 1.68 (0.15), residues: 1350 sheet: 0.06 (0.30), residues: 338 loop : -1.37 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 162 HIS 0.005 0.001 HIS A 8 PHE 0.015 0.002 PHE D 65 TYR 0.012 0.001 TYR A 312 ARG 0.006 0.000 ARG F 177 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 1056) hydrogen bonds : angle 4.71746 ( 3033) covalent geometry : bond 0.00280 (21368) covalent geometry : angle 0.52589 (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 384 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 302 time to evaluate : 2.390 Fit side-chains REVERT: A 79 LYS cc_start: 0.8398 (ttmp) cc_final: 0.8080 (mtpm) REVERT: A 136 ASP cc_start: 0.7381 (m-30) cc_final: 0.7002 (t0) REVERT: A 333 LYS cc_start: 0.7092 (mtpt) cc_final: 0.6750 (mmmt) REVERT: A 337 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7036 (mp0) REVERT: A 414 TRP cc_start: 0.7446 (m100) cc_final: 0.7151 (m-90) REVERT: B 96 LYS cc_start: 0.8519 (mtpp) cc_final: 0.8284 (mttm) REVERT: B 109 LYS cc_start: 0.8524 (ttmm) cc_final: 0.8304 (tttt) REVERT: C 92 LYS cc_start: 0.8344 (mmmm) cc_final: 0.8099 (mppt) REVERT: D 1 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8130 (ptm) REVERT: D 26 GLU cc_start: 0.7632 (mp0) cc_final: 0.7407 (mp0) REVERT: D 153 ASP cc_start: 0.7838 (t0) cc_final: 0.7363 (t70) REVERT: D 226 MET cc_start: 0.8171 (mmm) cc_final: 0.7901 (mmm) REVERT: D 300 LYS cc_start: 0.7406 (mtpt) cc_final: 0.7206 (mttt) REVERT: D 331 THR cc_start: 0.7705 (p) cc_final: 0.7344 (m) REVERT: D 389 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7855 (tp30) REVERT: E 92 LYS cc_start: 0.8484 (tppp) cc_final: 0.8200 (ttmt) REVERT: E 109 LYS cc_start: 0.8225 (tptt) cc_final: 0.7804 (tttp) REVERT: E 170 ARG cc_start: 0.6892 (ptt-90) cc_final: 0.6151 (mtp85) REVERT: E 196 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7258 (ppp) REVERT: E 340 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.6850 (ttp80) REVERT: E 413 LYS cc_start: 0.8053 (ttmt) cc_final: 0.7807 (mttt) REVERT: F 139 ARG cc_start: 0.8048 (ttm-80) cc_final: 0.7754 (ttp80) REVERT: F 147 ASP cc_start: 0.7774 (m-30) cc_final: 0.7320 (p0) REVERT: F 177 ARG cc_start: 0.6954 (mtm-85) cc_final: 0.6715 (mtm110) REVERT: F 243 ASP cc_start: 0.7544 (m-30) cc_final: 0.7327 (t0) REVERT: F 247 ASP cc_start: 0.7390 (m-30) cc_final: 0.7146 (m-30) REVERT: F 302 ASN cc_start: 0.7760 (t0) cc_final: 0.7381 (t0) REVERT: F 327 ASN cc_start: 0.6736 (p0) cc_final: 0.6321 (p0) REVERT: F 333 LYS cc_start: 0.7697 (ttpp) cc_final: 0.7250 (ttmt) REVERT: F 347 GLU cc_start: 0.7348 (mp0) cc_final: 0.6980 (mm-30) REVERT: F 397 GLU cc_start: 0.7005 (tp30) cc_final: 0.6222 (tm-30) REVERT: F 398 GLN cc_start: 0.7626 (mt0) cc_final: 0.6980 (mp-120) REVERT: F 407 ARG cc_start: 0.6997 (ttp-170) cc_final: 0.6551 (ttm170) REVERT: F 431 ILE cc_start: 0.7076 (pp) cc_final: 0.6636 (pt) outliers start: 82 outliers final: 29 residues processed: 363 average time/residue: 1.3263 time to fit residues: 544.0797 Evaluate side-chains 310 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 277 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 269 LYS Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 429 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 199 optimal weight: 5.9990 chunk 222 optimal weight: 6.9990 chunk 257 optimal weight: 5.9990 chunk 217 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 121 optimal weight: 1.9990 chunk 197 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 chunk 165 optimal weight: 0.9980 chunk 162 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN B 57 ASN B 288 ASN C 302 ASN D 100 GLN D 200 ASN E 57 ASN E 167 ASN F 140 GLN F 200 ASN F 295 ASN F 359 GLN ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.171527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.140001 restraints weight = 22561.668| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.17 r_work: 0.3393 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 21368 Z= 0.193 Angle : 0.600 10.093 28966 Z= 0.317 Chirality : 0.044 0.201 3246 Planarity : 0.004 0.039 3599 Dihedral : 11.106 173.997 2996 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 5.05 % Allowed : 13.94 % Favored : 81.01 % 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: 0.48 (0.17), residues: 2580 helix: 1.43 (0.15), residues: 1359 sheet: 0.17 (0.30), residues: 332 loop : -1.39 (0.19), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 162 HIS 0.005 0.001 HIS A 8 PHE 0.024 0.002 PHE D 65 TYR 0.019 0.002 TYR B 312 ARG 0.004 0.001 ARG C 407 Details of bonding type rmsd hydrogen bonds : bond 0.03995 ( 1056) hydrogen bonds : angle 4.77680 ( 3033) covalent geometry : bond 0.00455 (21368) covalent geometry : angle 0.60012 (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 412 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 299 time to evaluate : 2.194 Fit side-chains REVERT: A 79 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.8010 (mtpm) REVERT: A 140 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7623 (mt0) REVERT: A 333 LYS cc_start: 0.7172 (ttpt) cc_final: 0.6757 (mmmt) REVERT: A 337 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7113 (mp0) REVERT: A 411 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7296 (ttmm) REVERT: A 414 TRP cc_start: 0.7475 (m100) cc_final: 0.7196 (m-90) REVERT: A 427 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7790 (ttpp) REVERT: B 96 LYS cc_start: 0.8587 (mtpp) cc_final: 0.8258 (mttt) REVERT: B 109 LYS cc_start: 0.8604 (ttmm) cc_final: 0.8325 (tttt) REVERT: B 200 ASN cc_start: 0.6562 (OUTLIER) cc_final: 0.6310 (m-40) REVERT: B 274 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7300 (mtm-85) REVERT: C 66 THR cc_start: 0.6507 (OUTLIER) cc_final: 0.6303 (m) REVERT: C 92 LYS cc_start: 0.8351 (mmmm) cc_final: 0.8030 (mppt) REVERT: C 101 ARG cc_start: 0.8643 (mmm160) cc_final: 0.8401 (mmm160) REVERT: C 236 ARG cc_start: 0.8585 (mtt-85) cc_final: 0.8379 (mtp180) REVERT: D 3 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7587 (mp0) REVERT: D 26 GLU cc_start: 0.7742 (mp0) cc_final: 0.7510 (mp0) REVERT: D 86 ASP cc_start: 0.7179 (OUTLIER) cc_final: 0.6143 (t70) REVERT: D 153 ASP cc_start: 0.7862 (t0) cc_final: 0.7347 (t70) REVERT: D 226 MET cc_start: 0.8197 (mmm) cc_final: 0.7978 (mmm) REVERT: D 279 GLN cc_start: 0.8234 (tt0) cc_final: 0.8004 (tt0) REVERT: D 331 THR cc_start: 0.7706 (p) cc_final: 0.7391 (m) REVERT: D 389 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7968 (tp30) REVERT: E 26 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7762 (mp0) REVERT: E 92 LYS cc_start: 0.8548 (tppp) cc_final: 0.8197 (ttmt) REVERT: E 109 LYS cc_start: 0.8324 (tptt) cc_final: 0.7831 (tttt) REVERT: E 124 ARG cc_start: 0.6596 (OUTLIER) cc_final: 0.6168 (mtm180) REVERT: E 170 ARG cc_start: 0.6918 (ptt-90) cc_final: 0.6041 (mtp85) REVERT: E 196 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7514 (ppp) REVERT: E 413 LYS cc_start: 0.8176 (ttmt) cc_final: 0.7845 (mttt) REVERT: F 139 ARG cc_start: 0.8011 (ttm-80) cc_final: 0.7681 (ttp80) REVERT: F 147 ASP cc_start: 0.7877 (m-30) cc_final: 0.7384 (p0) REVERT: F 188 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8057 (mp0) REVERT: F 243 ASP cc_start: 0.7617 (m-30) cc_final: 0.7150 (t0) REVERT: F 302 ASN cc_start: 0.7789 (t0) cc_final: 0.7359 (t0) REVERT: F 327 ASN cc_start: 0.6805 (p0) cc_final: 0.6392 (p0) REVERT: F 333 LYS cc_start: 0.7666 (ttpp) cc_final: 0.7198 (ttmt) REVERT: F 347 GLU cc_start: 0.7472 (mp0) cc_final: 0.6997 (mm-30) REVERT: F 397 GLU cc_start: 0.6972 (tp30) cc_final: 0.6083 (tm-30) REVERT: F 398 GLN cc_start: 0.7617 (mt0) cc_final: 0.6924 (mp-120) REVERT: F 407 ARG cc_start: 0.7269 (ttp-170) cc_final: 0.6475 (ttm170) REVERT: F 431 ILE cc_start: 0.7141 (pp) cc_final: 0.6704 (pt) outliers start: 113 outliers final: 44 residues processed: 380 average time/residue: 1.2995 time to fit residues: 558.7930 Evaluate side-chains 334 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 277 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 427 LYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 330 THR 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 50 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 124 ARG Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 301 LYS Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 188 GLU Chi-restraints excluded: chain F residue 321 ILE Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 429 VAL 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: 10.0000 chunk 138 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 197 optimal weight: 6.9990 chunk 206 optimal weight: 0.8980 chunk 222 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 253 HIS C 302 ASN D 100 GLN D 200 ASN E 167 ASN E 200 ASN F 140 GLN F 200 ASN ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 295 ASN F 359 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.172707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.141691 restraints weight = 22516.354| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.16 r_work: 0.3416 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21368 Z= 0.144 Angle : 0.546 8.569 28966 Z= 0.291 Chirality : 0.042 0.184 3246 Planarity : 0.003 0.036 3599 Dihedral : 11.074 176.027 2996 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 4.11 % Allowed : 15.68 % Favored : 80.21 % 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: 0.57 (0.17), residues: 2580 helix: 1.57 (0.15), residues: 1357 sheet: 0.11 (0.29), residues: 334 loop : -1.40 (0.19), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 162 HIS 0.007 0.001 HIS B 253 PHE 0.017 0.002 PHE D 65 TYR 0.013 0.001 TYR B 312 ARG 0.004 0.000 ARG D 139 Details of bonding type rmsd hydrogen bonds : bond 0.03577 ( 1056) hydrogen bonds : angle 4.68707 ( 3033) covalent geometry : bond 0.00329 (21368) covalent geometry : angle 0.54554 (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 380 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 288 time to evaluate : 2.181 Fit side-chains REVERT: A 79 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7983 (mtpm) REVERT: A 140 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7633 (mt0) REVERT: A 333 LYS cc_start: 0.7152 (OUTLIER) cc_final: 0.6895 (mmmt) REVERT: A 337 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7198 (mp0) REVERT: A 414 TRP cc_start: 0.7478 (m100) cc_final: 0.7120 (m-90) REVERT: A 427 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7807 (ttpp) REVERT: B 96 LYS cc_start: 0.8548 (mtpp) cc_final: 0.8227 (mttt) REVERT: B 109 LYS cc_start: 0.8562 (ttmm) cc_final: 0.8335 (tttt) REVERT: B 274 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7264 (mtm-85) REVERT: C 66 THR cc_start: 0.6433 (OUTLIER) cc_final: 0.6217 (m) REVERT: C 92 LYS cc_start: 0.8355 (mmmm) cc_final: 0.8035 (mppt) REVERT: C 128 MET cc_start: 0.6999 (OUTLIER) cc_final: 0.6522 (mtt) REVERT: C 313 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7051 (pt) REVERT: D 1 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8170 (ptm) REVERT: D 3 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7577 (mp0) REVERT: D 26 GLU cc_start: 0.7721 (mp0) cc_final: 0.7506 (mp0) REVERT: D 86 ASP cc_start: 0.7207 (OUTLIER) cc_final: 0.6180 (t70) REVERT: D 139 ARG cc_start: 0.7815 (ttp80) cc_final: 0.7475 (ttp80) REVERT: D 153 ASP cc_start: 0.7848 (t0) cc_final: 0.7317 (t70) REVERT: D 331 THR cc_start: 0.7628 (p) cc_final: 0.7331 (m) REVERT: D 389 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7928 (tp30) REVERT: E 92 LYS cc_start: 0.8522 (tppp) cc_final: 0.8166 (ttmt) REVERT: E 109 LYS cc_start: 0.8295 (tptt) cc_final: 0.7809 (tttt) REVERT: E 124 ARG cc_start: 0.6536 (OUTLIER) cc_final: 0.6136 (mtm180) REVERT: E 170 ARG cc_start: 0.6982 (ptt-90) cc_final: 0.6029 (mtp85) REVERT: E 196 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7494 (ppp) REVERT: E 243 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.7270 (m-30) REVERT: E 317 LYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6368 (ptmt) REVERT: E 413 LYS cc_start: 0.8157 (ttmt) cc_final: 0.7877 (mttt) REVERT: F 139 ARG cc_start: 0.7971 (ttm-80) cc_final: 0.7551 (ttp80) REVERT: F 147 ASP cc_start: 0.7849 (m-30) cc_final: 0.7354 (p0) REVERT: F 184 LYS cc_start: 0.6675 (mmtp) cc_final: 0.6030 (mtpt) REVERT: F 188 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8155 (mp0) REVERT: F 243 ASP cc_start: 0.7537 (m-30) cc_final: 0.7073 (t0) REVERT: F 302 ASN cc_start: 0.7746 (t0) cc_final: 0.7333 (t0) REVERT: F 327 ASN cc_start: 0.6793 (p0) cc_final: 0.6371 (p0) REVERT: F 333 LYS cc_start: 0.7632 (ttpp) cc_final: 0.7251 (ttmt) REVERT: F 347 GLU cc_start: 0.7445 (mp0) cc_final: 0.6989 (mm-30) REVERT: F 397 GLU cc_start: 0.7020 (tp30) cc_final: 0.6046 (tm-30) REVERT: F 398 GLN cc_start: 0.7642 (mt0) cc_final: 0.6910 (mp-120) REVERT: F 407 ARG cc_start: 0.7200 (ttp-170) cc_final: 0.6475 (ttm170) REVERT: F 431 ILE cc_start: 0.7124 (OUTLIER) cc_final: 0.6733 (pt) outliers start: 92 outliers final: 39 residues processed: 354 average time/residue: 1.3486 time to fit residues: 541.0728 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 : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 427 LYS Chi-restraints excluded: chain B residue 18 LYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 330 THR 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 50 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 124 ARG Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 301 LYS Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 317 LYS Chi-restraints excluded: chain E residue 333 LYS Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 188 GLU Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 431 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 217 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 119 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 17 optimal weight: 0.0370 chunk 102 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 206 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 overall best weight: 2.5464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 GLN B 200 ASN B 253 HIS C 302 ASN D 200 ASN E 167 ASN E 200 ASN F 140 GLN F 200 ASN ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 295 ASN F 359 GLN ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.170411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.140799 restraints weight = 22448.888| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.11 r_work: 0.3357 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 21368 Z= 0.199 Angle : 0.609 10.141 28966 Z= 0.320 Chirality : 0.044 0.155 3246 Planarity : 0.004 0.037 3599 Dihedral : 11.259 172.914 2996 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.65 % Allowed : 15.46 % Favored : 79.89 % 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: 0.42 (0.17), residues: 2580 helix: 1.37 (0.14), residues: 1361 sheet: 0.11 (0.29), residues: 334 loop : -1.36 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 162 HIS 0.007 0.001 HIS B 253 PHE 0.023 0.002 PHE D 65 TYR 0.019 0.002 TYR A 312 ARG 0.004 0.001 ARG C 407 Details of bonding type rmsd hydrogen bonds : bond 0.03906 ( 1056) hydrogen bonds : angle 4.80776 ( 3033) covalent geometry : bond 0.00469 (21368) covalent geometry : angle 0.60930 (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 386 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 282 time to evaluate : 2.387 Fit side-chains REVERT: A 79 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7951 (mtpm) REVERT: A 140 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7469 (mt0) REVERT: A 333 LYS cc_start: 0.7159 (OUTLIER) cc_final: 0.6819 (mmmt) REVERT: A 337 GLU cc_start: 0.7353 (mt-10) cc_final: 0.7042 (mp0) REVERT: A 370 ASP cc_start: 0.6306 (m-30) cc_final: 0.5665 (t70) REVERT: A 414 TRP cc_start: 0.7408 (m100) cc_final: 0.7145 (m-90) REVERT: A 427 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7833 (ttpp) REVERT: B 96 LYS cc_start: 0.8458 (mtpp) cc_final: 0.8163 (mttt) REVERT: B 274 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7231 (mtm-85) REVERT: C 66 THR cc_start: 0.6443 (OUTLIER) cc_final: 0.6171 (m) REVERT: C 92 LYS cc_start: 0.8204 (mmmm) cc_final: 0.7925 (mppt) REVERT: C 128 MET cc_start: 0.7029 (OUTLIER) cc_final: 0.6510 (mtt) REVERT: D 1 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.8047 (ptp) REVERT: D 120 PRO cc_start: 0.5493 (Cg_endo) cc_final: 0.5293 (Cg_exo) REVERT: D 153 ASP cc_start: 0.7755 (t0) cc_final: 0.7263 (t70) REVERT: D 331 THR cc_start: 0.7647 (p) cc_final: 0.7360 (m) REVERT: D 429 VAL cc_start: 0.8876 (OUTLIER) cc_final: 0.8497 (t) REVERT: E 92 LYS cc_start: 0.8501 (tppp) cc_final: 0.8113 (ttmt) REVERT: E 109 LYS cc_start: 0.8246 (tptt) cc_final: 0.7728 (tttt) REVERT: E 124 ARG cc_start: 0.6565 (OUTLIER) cc_final: 0.6223 (mtm180) REVERT: E 170 ARG cc_start: 0.6914 (ptt-90) cc_final: 0.6099 (mtp180) REVERT: E 196 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7335 (ppp) REVERT: E 243 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.6996 (m-30) REVERT: E 317 LYS cc_start: 0.7256 (OUTLIER) cc_final: 0.6524 (ptmt) REVERT: E 389 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7196 (tt0) REVERT: E 413 LYS cc_start: 0.8124 (ttmt) cc_final: 0.7888 (mttt) REVERT: F 147 ASP cc_start: 0.7705 (m-30) cc_final: 0.7340 (p0) REVERT: F 243 ASP cc_start: 0.7415 (m-30) cc_final: 0.6999 (t0) REVERT: F 302 ASN cc_start: 0.7686 (t0) cc_final: 0.7286 (t0) REVERT: F 327 ASN cc_start: 0.6931 (p0) cc_final: 0.6496 (p0) REVERT: F 333 LYS cc_start: 0.7588 (ttpp) cc_final: 0.7160 (ttmt) REVERT: F 347 GLU cc_start: 0.7357 (mp0) cc_final: 0.6974 (mm-30) REVERT: F 397 GLU cc_start: 0.6946 (tp30) cc_final: 0.6027 (tm-30) REVERT: F 398 GLN cc_start: 0.7622 (mt0) cc_final: 0.6979 (mp-120) REVERT: F 407 ARG cc_start: 0.7169 (ttp-170) cc_final: 0.6531 (ttm170) REVERT: F 431 ILE cc_start: 0.7134 (OUTLIER) cc_final: 0.6738 (pt) outliers start: 104 outliers final: 49 residues processed: 353 average time/residue: 1.3189 time to fit residues: 526.0726 Evaluate side-chains 330 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 266 time to evaluate : 2.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 427 LYS Chi-restraints excluded: chain B residue 18 LYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 330 THR 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 50 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 124 ARG Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 243 ASP Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 301 LYS Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 317 LYS Chi-restraints excluded: chain E residue 333 LYS Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 389 GLU Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 431 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 123 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 240 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 245 optimal weight: 0.9990 chunk 5 optimal weight: 20.0000 chunk 215 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 221 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 ASN B 253 HIS C 288 ASN C 302 ASN D 100 GLN D 200 ASN E 167 ASN E 200 ASN F 140 GLN ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 295 ASN F 359 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.172426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.141551 restraints weight = 22543.467| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.17 r_work: 0.3414 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21368 Z= 0.136 Angle : 0.551 9.854 28966 Z= 0.291 Chirality : 0.041 0.169 3246 Planarity : 0.003 0.037 3599 Dihedral : 11.120 174.354 2996 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.49 % Allowed : 16.71 % Favored : 79.80 % 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: 0.59 (0.17), residues: 2580 helix: 1.57 (0.15), residues: 1356 sheet: 0.08 (0.29), residues: 334 loop : -1.35 (0.19), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 162 HIS 0.007 0.001 HIS B 253 PHE 0.016 0.002 PHE D 65 TYR 0.012 0.001 TYR E 158 ARG 0.009 0.000 ARG D 139 Details of bonding type rmsd hydrogen bonds : bond 0.03440 ( 1056) hydrogen bonds : angle 4.67150 ( 3033) covalent geometry : bond 0.00308 (21368) covalent geometry : angle 0.55127 (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 363 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 285 time to evaluate : 2.318 Fit side-chains revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7957 (mtpm) REVERT: A 140 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7644 (mt0) REVERT: A 333 LYS cc_start: 0.7142 (OUTLIER) cc_final: 0.6853 (mmmm) REVERT: A 337 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7077 (mp0) REVERT: A 370 ASP cc_start: 0.6242 (m-30) cc_final: 0.5465 (t70) REVERT: A 414 TRP cc_start: 0.7535 (m100) cc_final: 0.7129 (m-90) REVERT: A 427 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7873 (ttpp) REVERT: B 96 LYS cc_start: 0.8557 (mtpp) cc_final: 0.8227 (mttt) REVERT: B 274 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7253 (mtm-85) REVERT: C 66 THR cc_start: 0.6455 (OUTLIER) cc_final: 0.6222 (m) REVERT: C 92 LYS cc_start: 0.8363 (mmmm) cc_final: 0.8038 (mppt) REVERT: C 128 MET cc_start: 0.6986 (OUTLIER) cc_final: 0.6516 (mtt) REVERT: C 313 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7059 (pt) REVERT: C 391 GLU cc_start: 0.7792 (mp0) cc_final: 0.7375 (mp0) REVERT: D 153 ASP cc_start: 0.7881 (t0) cc_final: 0.7343 (t70) REVERT: D 300 LYS cc_start: 0.7471 (mtpt) cc_final: 0.7240 (mtmt) REVERT: D 331 THR cc_start: 0.7677 (p) cc_final: 0.7396 (m) REVERT: E 92 LYS cc_start: 0.8591 (tppp) cc_final: 0.8171 (ttmt) REVERT: E 109 LYS cc_start: 0.8334 (tptt) cc_final: 0.7888 (tptt) REVERT: E 124 ARG cc_start: 0.6450 (OUTLIER) cc_final: 0.6173 (mtm180) REVERT: E 170 ARG cc_start: 0.7052 (ptt-90) cc_final: 0.6086 (mtp180) REVERT: E 196 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7505 (ppp) REVERT: E 413 LYS cc_start: 0.8134 (ttmt) cc_final: 0.7870 (mttt) REVERT: F 147 ASP cc_start: 0.7915 (m-30) cc_final: 0.7386 (p0) REVERT: F 243 ASP cc_start: 0.7479 (m-30) cc_final: 0.6952 (t0) REVERT: F 302 ASN cc_start: 0.7697 (t0) cc_final: 0.7269 (t0) REVERT: F 327 ASN cc_start: 0.6827 (p0) cc_final: 0.6383 (p0) REVERT: F 333 LYS cc_start: 0.7644 (ttpp) cc_final: 0.7197 (ttmt) REVERT: F 347 GLU cc_start: 0.7470 (mp0) cc_final: 0.6984 (mm-30) REVERT: F 384 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7552 (tpp) REVERT: F 397 GLU cc_start: 0.6962 (tp30) cc_final: 0.6054 (tm-30) REVERT: F 398 GLN cc_start: 0.7665 (mt0) cc_final: 0.7001 (mp-120) REVERT: F 407 ARG cc_start: 0.7280 (ttp-170) cc_final: 0.6668 (ttm170) REVERT: F 431 ILE cc_start: 0.7142 (OUTLIER) cc_final: 0.6766 (pt) outliers start: 78 outliers final: 44 residues processed: 338 average time/residue: 1.3030 time to fit residues: 498.1963 Evaluate side-chains 325 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 269 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 427 LYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 330 THR 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 50 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 124 ARG Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 301 LYS Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 333 LYS Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 384 MET Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 431 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 113 optimal weight: 0.9990 chunk 205 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 chunk 164 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 176 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 247 optimal weight: 9.9990 chunk 256 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 ASN B 253 HIS C 302 ASN D 62 ASN D 100 GLN D 140 GLN D 200 ASN D 279 GLN E 167 ASN E 200 ASN F 140 GLN F 200 ASN ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 295 ASN F 359 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.170076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.139191 restraints weight = 22562.751| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.20 r_work: 0.3369 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 21368 Z= 0.203 Angle : 0.617 11.962 28966 Z= 0.323 Chirality : 0.044 0.207 3246 Planarity : 0.004 0.038 3599 Dihedral : 11.288 172.376 2996 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 4.07 % Allowed : 16.40 % Favored : 79.54 % 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: 0.39 (0.17), residues: 2580 helix: 1.35 (0.14), residues: 1362 sheet: 0.06 (0.29), residues: 332 loop : -1.37 (0.19), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 162 HIS 0.007 0.001 HIS B 253 PHE 0.022 0.002 PHE D 65 TYR 0.016 0.002 TYR B 312 ARG 0.010 0.001 ARG D 139 Details of bonding type rmsd hydrogen bonds : bond 0.03885 ( 1056) hydrogen bonds : angle 4.80461 ( 3033) covalent geometry : bond 0.00479 (21368) covalent geometry : angle 0.61745 (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 369 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 278 time to evaluate : 2.807 Fit side-chains REVERT: A 79 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7976 (mtpm) REVERT: A 136 ASP cc_start: 0.7376 (OUTLIER) cc_final: 0.6890 (t0) REVERT: A 140 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7591 (mt0) REVERT: A 333 LYS cc_start: 0.7176 (OUTLIER) cc_final: 0.6864 (mmmm) REVERT: A 337 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7176 (mp0) REVERT: A 370 ASP cc_start: 0.6211 (m-30) cc_final: 0.5416 (t70) REVERT: A 414 TRP cc_start: 0.7617 (m100) cc_final: 0.7196 (m-90) REVERT: A 427 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7894 (ttpp) REVERT: B 96 LYS cc_start: 0.8598 (mtpp) cc_final: 0.8260 (mttt) REVERT: B 274 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7344 (mtm-85) REVERT: B 405 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8060 (tttt) REVERT: C 13 GLN cc_start: 0.7498 (tp40) cc_final: 0.7268 (tp40) REVERT: C 66 THR cc_start: 0.6388 (OUTLIER) cc_final: 0.6129 (m) REVERT: C 92 LYS cc_start: 0.8380 (mmmm) cc_final: 0.8045 (mppt) REVERT: C 128 MET cc_start: 0.7029 (OUTLIER) cc_final: 0.6535 (mtt) REVERT: D 1 MET cc_start: 0.8562 (ptp) cc_final: 0.8239 (ptm) REVERT: D 153 ASP cc_start: 0.7898 (t0) cc_final: 0.7559 (t0) REVERT: D 331 THR cc_start: 0.7697 (p) cc_final: 0.7411 (m) REVERT: E 92 LYS cc_start: 0.8620 (tppp) cc_final: 0.8223 (ttmt) REVERT: E 109 LYS cc_start: 0.8421 (tptt) cc_final: 0.7851 (tttp) REVERT: E 124 ARG cc_start: 0.6520 (OUTLIER) cc_final: 0.6147 (mtm180) REVERT: E 170 ARG cc_start: 0.7073 (ptt-90) cc_final: 0.6097 (mtp180) REVERT: E 196 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7644 (ppp) REVERT: E 413 LYS cc_start: 0.8167 (ttmt) cc_final: 0.7875 (mttt) REVERT: F 123 LYS cc_start: 0.6966 (tmtm) cc_final: 0.6760 (ttmt) REVERT: F 147 ASP cc_start: 0.7955 (m-30) cc_final: 0.7412 (p0) REVERT: F 170 ARG cc_start: 0.6275 (OUTLIER) cc_final: 0.5467 (ttm170) REVERT: F 243 ASP cc_start: 0.7509 (m-30) cc_final: 0.6969 (t0) REVERT: F 302 ASN cc_start: 0.7702 (t0) cc_final: 0.7261 (t0) REVERT: F 327 ASN cc_start: 0.6868 (p0) cc_final: 0.6399 (p0) REVERT: F 333 LYS cc_start: 0.7618 (ttpp) cc_final: 0.7188 (ttmt) REVERT: F 347 GLU cc_start: 0.7477 (mp0) cc_final: 0.6975 (mm-30) REVERT: F 397 GLU cc_start: 0.7012 (tp30) cc_final: 0.6067 (tm-30) REVERT: F 398 GLN cc_start: 0.7657 (mt0) cc_final: 0.7011 (mp-120) REVERT: F 431 ILE cc_start: 0.7201 (OUTLIER) cc_final: 0.6806 (pt) outliers start: 91 outliers final: 50 residues processed: 344 average time/residue: 1.3336 time to fit residues: 523.7602 Evaluate side-chains 331 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 268 time to evaluate : 2.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 427 LYS Chi-restraints excluded: chain B residue 18 LYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 405 LYS Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 124 ARG Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 301 LYS Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 333 LYS Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 170 ARG Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 431 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 67 optimal weight: 0.9980 chunk 189 optimal weight: 0.8980 chunk 126 optimal weight: 0.1980 chunk 243 optimal weight: 6.9990 chunk 132 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 198 optimal weight: 6.9990 chunk 159 optimal weight: 5.9990 chunk 196 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN C 302 ASN D 100 GLN D 140 GLN D 200 ASN E 167 ASN E 200 ASN F 140 GLN F 200 ASN ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 295 ASN F 359 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.172650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.141628 restraints weight = 22457.557| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.14 r_work: 0.3417 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21368 Z= 0.134 Angle : 0.556 11.916 28966 Z= 0.295 Chirality : 0.041 0.177 3246 Planarity : 0.003 0.033 3599 Dihedral : 11.141 174.261 2996 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.44 % Allowed : 17.52 % Favored : 79.04 % 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: 0.57 (0.17), residues: 2580 helix: 1.58 (0.15), residues: 1357 sheet: 0.05 (0.29), residues: 332 loop : -1.38 (0.19), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 162 HIS 0.005 0.001 HIS A 8 PHE 0.015 0.002 PHE D 65 TYR 0.033 0.001 TYR A 312 ARG 0.011 0.000 ARG D 139 Details of bonding type rmsd hydrogen bonds : bond 0.03412 ( 1056) hydrogen bonds : angle 4.66618 ( 3033) covalent geometry : bond 0.00305 (21368) covalent geometry : angle 0.55642 (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 360 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 283 time to evaluate : 2.503 Fit side-chains REVERT: A 79 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7962 (mtpm) REVERT: A 140 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7658 (mt0) REVERT: A 333 LYS cc_start: 0.7130 (OUTLIER) cc_final: 0.6835 (mmmm) REVERT: A 337 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7105 (mp0) REVERT: A 414 TRP cc_start: 0.7563 (m100) cc_final: 0.7172 (m-90) REVERT: A 427 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7880 (ttpp) REVERT: B 96 LYS cc_start: 0.8569 (mtpp) cc_final: 0.8233 (mttt) REVERT: B 274 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7257 (mtm-85) REVERT: B 405 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7839 (tttm) REVERT: C 66 THR cc_start: 0.6359 (OUTLIER) cc_final: 0.6116 (m) REVERT: C 92 LYS cc_start: 0.8350 (mmmm) cc_final: 0.8018 (mppt) REVERT: C 128 MET cc_start: 0.6983 (OUTLIER) cc_final: 0.6521 (mtt) REVERT: C 391 GLU cc_start: 0.7776 (mp0) cc_final: 0.7354 (mp0) REVERT: D 1 MET cc_start: 0.8561 (ptp) cc_final: 0.8277 (ptm) REVERT: D 153 ASP cc_start: 0.7875 (t0) cc_final: 0.7531 (t0) REVERT: D 300 LYS cc_start: 0.7482 (mtpt) cc_final: 0.7255 (mtmt) REVERT: D 331 THR cc_start: 0.7679 (p) cc_final: 0.7397 (m) REVERT: E 92 LYS cc_start: 0.8602 (tppp) cc_final: 0.8180 (ttmt) REVERT: E 109 LYS cc_start: 0.8357 (tptt) cc_final: 0.7822 (tttp) REVERT: E 124 ARG cc_start: 0.6444 (OUTLIER) cc_final: 0.6153 (mtm180) REVERT: E 170 ARG cc_start: 0.7053 (ptt-90) cc_final: 0.6072 (mtp85) REVERT: E 196 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7523 (ppp) REVERT: E 228 MET cc_start: 0.6366 (mmm) cc_final: 0.6128 (ptt) REVERT: E 345 GLU cc_start: 0.6709 (tm-30) cc_final: 0.6270 (tt0) REVERT: E 413 LYS cc_start: 0.8115 (ttmt) cc_final: 0.7862 (mttt) REVERT: F 147 ASP cc_start: 0.7923 (m-30) cc_final: 0.7393 (p0) REVERT: F 243 ASP cc_start: 0.7419 (m-30) cc_final: 0.6895 (t0) REVERT: F 302 ASN cc_start: 0.7652 (t0) cc_final: 0.7211 (t0) REVERT: F 327 ASN cc_start: 0.6905 (p0) cc_final: 0.6396 (p0) REVERT: F 333 LYS cc_start: 0.7600 (ttpp) cc_final: 0.7243 (ttmt) REVERT: F 347 GLU cc_start: 0.7462 (mp0) cc_final: 0.6971 (mm-30) REVERT: F 397 GLU cc_start: 0.7033 (tp30) cc_final: 0.6126 (tm-30) REVERT: F 398 GLN cc_start: 0.7406 (mt0) cc_final: 0.6822 (mp-120) REVERT: F 431 ILE cc_start: 0.7207 (OUTLIER) cc_final: 0.6825 (pt) outliers start: 77 outliers final: 45 residues processed: 342 average time/residue: 1.2735 time to fit residues: 494.3761 Evaluate side-chains 319 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 263 time to evaluate : 2.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 427 LYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 405 LYS Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 402 LYS Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 124 ARG Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 333 LYS Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 431 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 86 optimal weight: 2.9990 chunk 132 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 233 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 217 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 chunk 58 optimal weight: 0.0470 chunk 63 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 187 optimal weight: 0.8980 overall best weight: 0.5280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN C 302 ASN D 200 ASN D 279 GLN E 140 GLN E 167 ASN E 200 ASN F 140 GLN F 200 ASN F 295 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.175499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.144893 restraints weight = 22617.411| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.10 r_work: 0.3466 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21368 Z= 0.108 Angle : 0.532 13.869 28966 Z= 0.282 Chirality : 0.040 0.180 3246 Planarity : 0.003 0.033 3599 Dihedral : 10.924 176.476 2996 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.14 % Allowed : 18.90 % 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: 0.76 (0.17), residues: 2580 helix: 1.79 (0.15), residues: 1356 sheet: 0.05 (0.29), residues: 333 loop : -1.36 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 89 HIS 0.007 0.001 HIS B 8 PHE 0.010 0.001 PHE D 65 TYR 0.018 0.001 TYR E 158 ARG 0.010 0.000 ARG D 139 Details of bonding type rmsd hydrogen bonds : bond 0.03053 ( 1056) hydrogen bonds : angle 4.51005 ( 3033) covalent geometry : bond 0.00234 (21368) covalent geometry : angle 0.53243 (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 332 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 284 time to evaluate : 2.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7965 (mtpm) REVERT: A 140 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7606 (mt0) REVERT: A 265 LYS cc_start: 0.7810 (ttpt) cc_final: 0.7336 (tmtt) REVERT: A 333 LYS cc_start: 0.7196 (ttpt) cc_final: 0.6557 (mmmm) REVERT: A 337 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7045 (mp0) REVERT: A 369 SER cc_start: 0.6120 (OUTLIER) cc_final: 0.5878 (t) REVERT: A 370 ASP cc_start: 0.6085 (m-30) cc_final: 0.5341 (t70) REVERT: A 414 TRP cc_start: 0.7525 (m100) cc_final: 0.7154 (m-90) REVERT: A 419 MET cc_start: 0.7826 (tpp) cc_final: 0.7396 (mmt) REVERT: A 427 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7863 (ttpp) REVERT: B 96 LYS cc_start: 0.8543 (mtpp) cc_final: 0.8219 (mttt) REVERT: C 66 THR cc_start: 0.6357 (OUTLIER) cc_final: 0.6071 (m) REVERT: C 92 LYS cc_start: 0.8344 (mmmm) cc_final: 0.8045 (mppt) REVERT: C 128 MET cc_start: 0.6964 (OUTLIER) cc_final: 0.6526 (mtt) REVERT: D 1 MET cc_start: 0.8565 (ptp) cc_final: 0.8259 (ptm) REVERT: D 153 ASP cc_start: 0.7806 (t0) cc_final: 0.7487 (t0) REVERT: D 331 THR cc_start: 0.7629 (p) cc_final: 0.7320 (m) REVERT: D 384 MET cc_start: 0.8884 (mtp) cc_final: 0.8652 (mtt) REVERT: E 92 LYS cc_start: 0.8556 (tppp) cc_final: 0.8137 (ttmt) REVERT: E 109 LYS cc_start: 0.8238 (tptt) cc_final: 0.7855 (tptt) REVERT: E 124 ARG cc_start: 0.6466 (OUTLIER) cc_final: 0.6181 (mtm180) REVERT: E 170 ARG cc_start: 0.7050 (ptt-90) cc_final: 0.6118 (mtp180) REVERT: E 345 GLU cc_start: 0.6780 (tm-30) cc_final: 0.6312 (tt0) REVERT: F 147 ASP cc_start: 0.7885 (m-30) cc_final: 0.7385 (p0) REVERT: F 243 ASP cc_start: 0.7324 (m-30) cc_final: 0.6813 (t0) REVERT: F 251 ASP cc_start: 0.6712 (m-30) cc_final: 0.6344 (p0) REVERT: F 302 ASN cc_start: 0.7589 (t0) cc_final: 0.7149 (t0) REVERT: F 327 ASN cc_start: 0.6853 (p0) cc_final: 0.6401 (p0) REVERT: F 333 LYS cc_start: 0.7610 (ttpp) cc_final: 0.7180 (ttmt) REVERT: F 347 GLU cc_start: 0.7450 (mp0) cc_final: 0.6977 (mm-30) REVERT: F 359 GLN cc_start: 0.6931 (pm20) cc_final: 0.6724 (pm20) REVERT: F 373 GLU cc_start: 0.6172 (mt-10) cc_final: 0.5452 (mp0) REVERT: F 397 GLU cc_start: 0.6997 (tp30) cc_final: 0.6124 (tm-30) REVERT: F 398 GLN cc_start: 0.7413 (mt0) cc_final: 0.6907 (mp-120) REVERT: F 431 ILE cc_start: 0.7162 (OUTLIER) cc_final: 0.6804 (pt) outliers start: 48 outliers final: 28 residues processed: 320 average time/residue: 1.2984 time to fit residues: 472.4680 Evaluate side-chains 300 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 264 time to evaluate : 2.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 427 LYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 363 SER Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 100 GLN Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 124 ARG Chi-restraints excluded: chain E residue 365 ASP Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 431 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 143 optimal weight: 2.9990 chunk 176 optimal weight: 7.9990 chunk 115 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 128 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 200 optimal weight: 10.0000 chunk 91 optimal weight: 0.7980 chunk 182 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN B 140 GLN ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN C 302 ASN D 62 ASN D 100 GLN D 200 ASN E 140 GLN E 167 ASN E 200 ASN F 140 GLN F 200 ASN F 295 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.174729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.144107 restraints weight = 22685.217| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.16 r_work: 0.3446 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21368 Z= 0.119 Angle : 0.547 12.813 28966 Z= 0.286 Chirality : 0.041 0.195 3246 Planarity : 0.003 0.034 3599 Dihedral : 10.898 175.597 2996 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.50 % Allowed : 18.77 % Favored : 78.73 % 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: 0.79 (0.17), residues: 2580 helix: 1.81 (0.15), residues: 1355 sheet: 0.09 (0.30), residues: 333 loop : -1.35 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 162 HIS 0.007 0.001 HIS B 8 PHE 0.022 0.001 PHE F 174 TYR 0.015 0.001 TYR E 256 ARG 0.012 0.000 ARG D 139 Details of bonding type rmsd hydrogen bonds : bond 0.03137 ( 1056) hydrogen bonds : angle 4.50994 ( 3033) covalent geometry : bond 0.00267 (21368) covalent geometry : angle 0.54741 (28966) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17334.31 seconds wall clock time: 298 minutes 19.06 seconds (17899.06 seconds total)