Starting phenix.real_space_refine on Wed Jun 18 07:12:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dtp_27707/06_2025/8dtp_27707.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dtp_27707/06_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_27707/06_2025/8dtp_27707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dtp_27707/06_2025/8dtp_27707.map" model { file = "/net/cci-nas-00/data/ceres_data/8dtp_27707/06_2025/8dtp_27707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dtp_27707/06_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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20944 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "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: 12.82, per 1000 atoms: 0.61 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: 5.28 Conformation dependent library (CDL) restraints added in 2.5 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: 2.44 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: 6.88 Time building geometry restraints manager: 6.23 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: 3.860 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: 0.810 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 47.830 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.930 ------------------------------------------------------------------------------- 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 : 2.159 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: 1.4680 time to fit residues: 947.5172 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 : 2.327 ------------------------------------------------------------------------------- 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 = 23133.070| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.21 r_work: 0.3477 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 0.04032 ( 1056) hydrogen bonds : angle 4.93741 ( 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 : 2.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 ASP cc_start: 0.7519 (m-30) cc_final: 0.7169 (t0) REVERT: A 333 LYS cc_start: 0.7139 (mtpt) cc_final: 0.6739 (mmmt) REVERT: A 337 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7095 (mp0) REVERT: A 414 TRP cc_start: 0.7411 (m100) cc_final: 0.7153 (m-90) REVERT: B 49 SER cc_start: 0.8779 (t) cc_final: 0.8490 (p) REVERT: B 96 LYS cc_start: 0.8517 (mtpp) cc_final: 0.8289 (mttm) REVERT: B 109 LYS cc_start: 0.8572 (ttmm) cc_final: 0.8315 (tttt) REVERT: C 92 LYS cc_start: 0.8354 (mmmm) cc_final: 0.8101 (mppt) REVERT: C 101 ARG cc_start: 0.8610 (mmm160) cc_final: 0.8406 (mmm160) REVERT: C 184 LYS cc_start: 0.8514 (mtpp) cc_final: 0.8284 (mtpt) REVERT: D 26 GLU cc_start: 0.7756 (mp0) cc_final: 0.7460 (mm-30) REVERT: D 136 ASP cc_start: 0.7313 (t70) cc_final: 0.7103 (t0) REVERT: D 139 ARG cc_start: 0.7750 (ttp80) cc_final: 0.6938 (ttp-110) REVERT: D 153 ASP cc_start: 0.7844 (t0) cc_final: 0.7411 (t70) REVERT: D 177 ARG cc_start: 0.8107 (mtm110) cc_final: 0.7872 (mtm-85) REVERT: D 226 MET cc_start: 0.8111 (mmm) cc_final: 0.7836 (mmm) REVERT: D 331 THR cc_start: 0.7761 (p) cc_final: 0.7377 (m) REVERT: E 92 LYS cc_start: 0.8536 (tppp) cc_final: 0.8243 (ttmt) REVERT: E 109 LYS cc_start: 0.8249 (tptt) cc_final: 0.7885 (tttm) REVERT: E 170 ARG cc_start: 0.6854 (ptt-90) cc_final: 0.6140 (mtp85) REVERT: E 317 LYS cc_start: 0.7466 (OUTLIER) cc_final: 0.6611 (ptmt) REVERT: E 340 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7046 (ttp80) REVERT: E 413 LYS cc_start: 0.8069 (ttmt) cc_final: 0.7841 (mttt) REVERT: F 139 ARG cc_start: 0.8082 (ttm-80) cc_final: 0.7753 (ttp80) REVERT: F 147 ASP cc_start: 0.7790 (m-30) cc_final: 0.7327 (p0) REVERT: F 243 ASP cc_start: 0.7495 (m-30) cc_final: 0.7292 (t0) REVERT: F 247 ASP cc_start: 0.7414 (m-30) cc_final: 0.7167 (m-30) REVERT: F 302 ASN cc_start: 0.7715 (t0) cc_final: 0.7345 (t0) REVERT: F 327 ASN cc_start: 0.6901 (p0) cc_final: 0.6533 (p0) REVERT: F 333 LYS cc_start: 0.7696 (ttpp) cc_final: 0.7303 (ttmt) REVERT: F 347 GLU cc_start: 0.7306 (mp0) cc_final: 0.6956 (mm-30) REVERT: F 368 MET cc_start: 0.6079 (mtp) cc_final: 0.5805 (mtt) REVERT: F 397 GLU cc_start: 0.6926 (tp30) cc_final: 0.6205 (tm-30) REVERT: F 398 GLN cc_start: 0.7526 (mt0) cc_final: 0.6921 (mp-120) REVERT: F 407 ARG cc_start: 0.7164 (ttp-170) cc_final: 0.6487 (ttm170) REVERT: F 431 ILE cc_start: 0.7118 (pp) cc_final: 0.6623 (pt) outliers start: 87 outliers final: 25 residues processed: 406 average time/residue: 1.3514 time to fit residues: 619.5570 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 : 2.426 ------------------------------------------------------------------------------- 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: 0.9980 chunk 175 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 79 optimal weight: 0.5980 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: 0.9990 chunk 6 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.4066 r_free = 0.4066 target = 0.174874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.144033 restraints weight = 22261.841| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.06 r_work: 0.3448 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21368 Z= 0.128 Angle : 0.526 7.766 28966 Z= 0.283 Chirality : 0.041 0.227 3246 Planarity : 0.003 0.037 3599 Dihedral : 10.858 179.641 2997 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.80 % Allowed : 14.57 % 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: 0.67 (0.17), residues: 2580 helix: 1.68 (0.15), residues: 1350 sheet: 0.18 (0.30), residues: 326 loop : -1.40 (0.19), residues: 904 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 0.016 0.002 PHE D 65 TYR 0.012 0.001 TYR B 312 ARG 0.006 0.000 ARG F 177 Details of bonding type rmsd hydrogen bonds : bond 0.03666 ( 1056) hydrogen bonds : angle 4.70513 ( 3033) covalent geometry : bond 0.00284 (21368) covalent geometry : angle 0.52590 (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 390 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 305 time to evaluate : 2.256 Fit side-chains REVERT: A 79 LYS cc_start: 0.8377 (ttmp) cc_final: 0.8074 (mtpm) REVERT: A 136 ASP cc_start: 0.7346 (m-30) cc_final: 0.6874 (t0) REVERT: A 196 MET cc_start: 0.8568 (mmp) cc_final: 0.8354 (mmp) REVERT: A 333 LYS cc_start: 0.6990 (ttpt) cc_final: 0.6633 (mmmt) REVERT: A 337 GLU cc_start: 0.7392 (mt-10) cc_final: 0.6914 (mp0) REVERT: A 414 TRP cc_start: 0.7439 (m100) cc_final: 0.7111 (m-90) REVERT: B 96 LYS cc_start: 0.8524 (mtpp) cc_final: 0.8235 (mttm) REVERT: B 109 LYS cc_start: 0.8564 (ttmm) cc_final: 0.8299 (tttt) REVERT: C 92 LYS cc_start: 0.8365 (mmmm) cc_final: 0.8041 (mppt) REVERT: C 184 LYS cc_start: 0.8522 (mtpp) cc_final: 0.8316 (mtpt) REVERT: D 1 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8114 (ptm) REVERT: D 26 GLU cc_start: 0.7670 (mp0) cc_final: 0.7352 (mp0) REVERT: D 153 ASP cc_start: 0.7776 (t0) cc_final: 0.7235 (t70) REVERT: D 226 MET cc_start: 0.8127 (mmm) cc_final: 0.7830 (mmm) REVERT: D 331 THR cc_start: 0.7618 (p) cc_final: 0.7276 (m) REVERT: D 389 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7882 (tp30) REVERT: E 92 LYS cc_start: 0.8466 (tppp) cc_final: 0.8123 (ttmt) REVERT: E 109 LYS cc_start: 0.8228 (tptt) cc_final: 0.7746 (tttp) REVERT: E 170 ARG cc_start: 0.6895 (ptt-90) cc_final: 0.6034 (mtp85) REVERT: E 196 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7395 (ppp) REVERT: E 413 LYS cc_start: 0.8086 (ttmt) cc_final: 0.7777 (mttt) REVERT: F 139 ARG cc_start: 0.7997 (ttm-80) cc_final: 0.7595 (ttp80) REVERT: F 147 ASP cc_start: 0.7728 (m-30) cc_final: 0.7263 (p0) REVERT: F 177 ARG cc_start: 0.6983 (mtm-85) cc_final: 0.6761 (mtm110) REVERT: F 243 ASP cc_start: 0.7574 (m-30) cc_final: 0.7276 (t0) REVERT: F 247 ASP cc_start: 0.7390 (m-30) cc_final: 0.7160 (m-30) REVERT: F 302 ASN cc_start: 0.7735 (t0) cc_final: 0.7329 (t0) REVERT: F 327 ASN cc_start: 0.6614 (p0) cc_final: 0.6190 (p0) REVERT: F 333 LYS cc_start: 0.7584 (ttpp) cc_final: 0.7127 (ttmt) REVERT: F 347 GLU cc_start: 0.7342 (mp0) cc_final: 0.6916 (mm-30) REVERT: F 397 GLU cc_start: 0.6972 (tp30) cc_final: 0.6128 (tm-30) REVERT: F 398 GLN cc_start: 0.7592 (mt0) cc_final: 0.6919 (mp-120) REVERT: F 407 ARG cc_start: 0.7031 (ttp-170) cc_final: 0.6513 (ttm170) REVERT: F 431 ILE cc_start: 0.7077 (pp) cc_final: 0.6647 (pt) outliers start: 85 outliers final: 28 residues processed: 367 average time/residue: 1.3596 time to fit residues: 567.0200 Evaluate side-chains 310 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 279 time to evaluate : 2.198 ------------------------------------------------------------------------------- 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 88 SER 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 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 76 LEU 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 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 429 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 199 optimal weight: 0.9990 chunk 222 optimal weight: 10.0000 chunk 257 optimal weight: 5.9990 chunk 217 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 121 optimal weight: 0.8980 chunk 197 optimal weight: 5.9990 chunk 161 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 chunk 162 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN B 200 ASN B 288 ASN C 302 ASN 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 = 0.4046 r_free = 0.4046 target = 0.173114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.141692 restraints weight = 22553.351| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.18 r_work: 0.3418 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21368 Z= 0.155 Angle : 0.562 9.087 28966 Z= 0.298 Chirality : 0.042 0.199 3246 Planarity : 0.004 0.038 3599 Dihedral : 10.989 175.812 2996 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.47 % Allowed : 14.70 % Favored : 80.83 % 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: 0.61 (0.17), residues: 2580 helix: 1.60 (0.15), residues: 1354 sheet: 0.21 (0.30), residues: 332 loop : -1.40 (0.19), residues: 894 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 0.020 0.001 TYR D 312 ARG 0.006 0.000 ARG D 139 Details of bonding type rmsd hydrogen bonds : bond 0.03705 ( 1056) hydrogen bonds : angle 4.66913 ( 3033) covalent geometry : bond 0.00357 (21368) covalent geometry : angle 0.56153 (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 397 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 297 time to evaluate : 2.258 Fit side-chains REVERT: A 79 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7992 (mtpm) REVERT: A 136 ASP cc_start: 0.7369 (m-30) cc_final: 0.7157 (t0) REVERT: A 140 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7614 (mt0) REVERT: A 333 LYS cc_start: 0.7150 (ttpt) cc_final: 0.6784 (mmmt) REVERT: A 337 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7089 (mp0) REVERT: A 414 TRP cc_start: 0.7446 (m100) cc_final: 0.7193 (m-90) REVERT: A 427 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7779 (ttpp) REVERT: B 96 LYS cc_start: 0.8561 (mtpp) cc_final: 0.8245 (mttt) REVERT: B 109 LYS cc_start: 0.8591 (ttmm) cc_final: 0.8328 (tttt) REVERT: B 274 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7270 (mtm-85) REVERT: C 66 THR cc_start: 0.6468 (OUTLIER) cc_final: 0.6251 (m) REVERT: C 92 LYS cc_start: 0.8346 (mmmm) cc_final: 0.8028 (mppt) REVERT: D 1 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8171 (ptm) REVERT: D 3 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7590 (mp0) REVERT: D 26 GLU cc_start: 0.7723 (mp0) cc_final: 0.7510 (mp0) REVERT: D 86 ASP cc_start: 0.7104 (OUTLIER) cc_final: 0.6104 (t70) REVERT: D 139 ARG cc_start: 0.7785 (ttp80) cc_final: 0.7505 (ttp80) REVERT: D 153 ASP cc_start: 0.7849 (t0) cc_final: 0.7314 (t70) REVERT: D 226 MET cc_start: 0.8184 (mmm) cc_final: 0.7960 (mmm) REVERT: D 331 THR cc_start: 0.7640 (p) cc_final: 0.7320 (m) REVERT: D 384 MET cc_start: 0.9044 (mtp) cc_final: 0.8781 (mtt) REVERT: D 389 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7936 (tp30) REVERT: E 92 LYS cc_start: 0.8536 (tppp) cc_final: 0.8180 (ttmt) REVERT: E 109 LYS cc_start: 0.8294 (tptt) cc_final: 0.7812 (tttt) REVERT: E 124 ARG cc_start: 0.6557 (OUTLIER) cc_final: 0.6159 (mtm180) REVERT: E 170 ARG cc_start: 0.6899 (ptt-90) cc_final: 0.6036 (mtp85) REVERT: E 196 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7474 (ppp) REVERT: E 243 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7360 (m-30) REVERT: E 413 LYS cc_start: 0.8140 (ttmt) cc_final: 0.7877 (mttt) REVERT: F 139 ARG cc_start: 0.8032 (ttm-80) cc_final: 0.7595 (ttp80) REVERT: F 147 ASP cc_start: 0.7820 (m-30) cc_final: 0.7350 (p0) REVERT: F 188 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.8020 (mp0) REVERT: F 243 ASP cc_start: 0.7573 (m-30) cc_final: 0.7116 (t0) REVERT: F 302 ASN cc_start: 0.7755 (t0) cc_final: 0.7335 (t0) REVERT: F 327 ASN cc_start: 0.6712 (p0) cc_final: 0.6298 (p0) REVERT: F 333 LYS cc_start: 0.7633 (ttpp) cc_final: 0.7177 (ttmt) REVERT: F 347 GLU cc_start: 0.7447 (mp0) cc_final: 0.6986 (mm-30) REVERT: F 397 GLU cc_start: 0.6949 (tp30) cc_final: 0.6100 (tm-30) REVERT: F 398 GLN cc_start: 0.7636 (mt0) cc_final: 0.6931 (mp-120) REVERT: F 407 ARG cc_start: 0.7235 (ttp-170) cc_final: 0.6426 (ttm170) REVERT: F 431 ILE cc_start: 0.7137 (OUTLIER) cc_final: 0.6730 (pt) outliers start: 100 outliers final: 39 residues processed: 369 average time/residue: 1.3349 time to fit residues: 557.6705 Evaluate side-chains 330 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 278 time to evaluate : 2.332 ------------------------------------------------------------------------------- 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 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 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 1 MET Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 86 ASP 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 115 THR 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 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 157 ASP Chi-restraints excluded: chain F residue 188 GLU Chi-restraints excluded: chain F residue 321 ILE Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 431 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 27 optimal weight: 4.9990 chunk 181 optimal weight: 9.9990 chunk 138 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 202 optimal weight: 9.9990 chunk 164 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 197 optimal weight: 6.9990 chunk 206 optimal weight: 0.8980 chunk 222 optimal weight: 0.9980 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 ASN B 253 HIS C 302 ASN D 100 GLN D 200 ASN E 57 ASN E 167 ASN E 200 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 = 0.4001 r_free = 0.4001 target = 0.169169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.137913 restraints weight = 22476.565| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.12 r_work: 0.3356 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 21368 Z= 0.249 Angle : 0.666 11.087 28966 Z= 0.348 Chirality : 0.046 0.186 3246 Planarity : 0.004 0.047 3599 Dihedral : 11.380 173.673 2996 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 4.92 % Allowed : 14.92 % Favored : 80.16 % 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: 0.27 (0.16), residues: 2580 helix: 1.21 (0.14), residues: 1361 sheet: 0.12 (0.29), residues: 333 loop : -1.41 (0.19), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 162 HIS 0.008 0.002 HIS B 253 PHE 0.026 0.003 PHE D 65 TYR 0.035 0.002 TYR D 312 ARG 0.006 0.001 ARG C 407 Details of bonding type rmsd hydrogen bonds : bond 0.04332 ( 1056) hydrogen bonds : angle 4.95092 ( 3033) covalent geometry : bond 0.00591 (21368) covalent geometry : angle 0.66553 (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 395 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 285 time to evaluate : 2.348 Fit side-chains REVERT: A 79 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.8024 (mtpm) REVERT: A 140 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7670 (mt0) REVERT: A 333 LYS cc_start: 0.7187 (OUTLIER) cc_final: 0.6839 (mmmt) REVERT: A 337 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7223 (mp0) REVERT: A 370 ASP cc_start: 0.6345 (m-30) cc_final: 0.5626 (t70) REVERT: A 411 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7263 (ttmm) REVERT: A 414 TRP cc_start: 0.7546 (m100) cc_final: 0.7224 (m-90) REVERT: A 427 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7935 (ttpp) REVERT: B 96 LYS cc_start: 0.8613 (mtpp) cc_final: 0.8284 (mttt) REVERT: B 109 LYS cc_start: 0.8617 (ttmm) cc_final: 0.8377 (tttt) REVERT: B 274 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7315 (mtm-85) REVERT: C 13 GLN cc_start: 0.7454 (tp40) cc_final: 0.7243 (tp40) REVERT: C 66 THR cc_start: 0.6458 (OUTLIER) cc_final: 0.6229 (m) REVERT: C 92 LYS cc_start: 0.8375 (mmmm) cc_final: 0.8036 (mppt) REVERT: C 137 ILE cc_start: 0.7891 (OUTLIER) cc_final: 0.7674 (pp) REVERT: C 313 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7292 (pp) REVERT: D 3 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7663 (mp0) REVERT: D 26 GLU cc_start: 0.7829 (mp0) cc_final: 0.7571 (mp0) REVERT: D 153 ASP cc_start: 0.7921 (t0) cc_final: 0.7402 (t70) REVERT: D 331 THR cc_start: 0.7756 (p) cc_final: 0.7478 (m) REVERT: D 389 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7957 (tp30) REVERT: D 429 VAL cc_start: 0.8956 (OUTLIER) cc_final: 0.8565 (t) REVERT: E 26 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7848 (mt-10) REVERT: E 92 LYS cc_start: 0.8642 (tppp) cc_final: 0.8256 (ttmt) REVERT: E 109 LYS cc_start: 0.8386 (tptt) cc_final: 0.7839 (tttt) REVERT: E 170 ARG cc_start: 0.7023 (ptt-90) cc_final: 0.6065 (mtp85) REVERT: E 196 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7605 (ppp) REVERT: E 243 ASP cc_start: 0.7632 (m-30) cc_final: 0.7284 (m-30) REVERT: E 279 GLN cc_start: 0.7145 (pt0) cc_final: 0.6146 (tp40) REVERT: E 413 LYS cc_start: 0.8280 (ttmt) cc_final: 0.7945 (mttt) REVERT: F 147 ASP cc_start: 0.7941 (m-30) cc_final: 0.7405 (p0) REVERT: F 243 ASP cc_start: 0.7688 (m-30) cc_final: 0.7177 (t0) REVERT: F 302 ASN cc_start: 0.7761 (t0) cc_final: 0.7350 (t0) REVERT: F 327 ASN cc_start: 0.7079 (p0) cc_final: 0.6637 (p0) REVERT: F 333 LYS cc_start: 0.7660 (ttpp) cc_final: 0.7195 (ttmt) REVERT: F 347 GLU cc_start: 0.7441 (mp0) cc_final: 0.6990 (mm-30) REVERT: F 370 ASP cc_start: 0.6009 (m-30) cc_final: 0.5736 (m-30) REVERT: F 397 GLU cc_start: 0.7011 (tp30) cc_final: 0.6089 (tm-30) REVERT: F 398 GLN cc_start: 0.7638 (mt0) cc_final: 0.6960 (mp10) REVERT: F 407 ARG cc_start: 0.7299 (ttp-170) cc_final: 0.6533 (ttm170) REVERT: F 431 ILE cc_start: 0.7232 (pp) cc_final: 0.6795 (pt) outliers start: 110 outliers final: 49 residues processed: 360 average time/residue: 1.3991 time to fit residues: 570.0747 Evaluate side-chains 334 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 272 time to evaluate : 2.441 ------------------------------------------------------------------------------- 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 356 VAL Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 411 LYS 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 292 SER Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 380 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 66 THR Chi-restraints excluded: chain C residue 137 ILE 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 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 315 ILE 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 124 ARG Chi-restraints excluded: chain E residue 196 MET 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 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 131 VAL Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 429 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 217 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 119 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 102 optimal weight: 0.0870 chunk 28 optimal weight: 4.9990 chunk 206 optimal weight: 0.6980 chunk 91 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 F 399 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.172347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.141564 restraints weight = 22409.117| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.20 r_work: 0.3398 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2944 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= 0.138 Angle : 0.553 9.538 28966 Z= 0.293 Chirality : 0.042 0.235 3246 Planarity : 0.004 0.040 3599 Dihedral : 11.131 174.267 2996 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.62 % Allowed : 16.67 % Favored : 79.71 % 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: 1.48 (0.15), residues: 1358 sheet: 0.10 (0.29), residues: 332 loop : -1.34 (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 0.021 0.001 TYR D 312 ARG 0.008 0.000 ARG D 139 Details of bonding type rmsd hydrogen bonds : bond 0.03503 ( 1056) hydrogen bonds : angle 4.71733 ( 3033) covalent geometry : bond 0.00315 (21368) covalent geometry : angle 0.55277 (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 369 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 288 time to evaluate : 2.244 Fit side-chains REVERT: A 79 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7936 (mtpm) REVERT: A 136 ASP cc_start: 0.7307 (OUTLIER) cc_final: 0.6814 (t0) REVERT: A 140 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7506 (mt0) REVERT: A 203 LYS cc_start: 0.8101 (mtmm) cc_final: 0.7535 (mtmt) REVERT: A 333 LYS cc_start: 0.7207 (OUTLIER) cc_final: 0.6917 (mmmm) REVERT: A 337 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7147 (mp0) REVERT: A 370 ASP cc_start: 0.6258 (m-30) cc_final: 0.5470 (t70) REVERT: A 414 TRP cc_start: 0.7595 (m100) cc_final: 0.7195 (m-90) REVERT: A 427 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7899 (ttpp) REVERT: B 96 LYS cc_start: 0.8578 (mtpp) cc_final: 0.8251 (mttt) REVERT: B 200 ASN cc_start: 0.6684 (OUTLIER) cc_final: 0.6460 (m-40) REVERT: B 274 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7277 (mtm-85) REVERT: C 66 THR cc_start: 0.6465 (OUTLIER) cc_final: 0.6239 (m) REVERT: C 92 LYS cc_start: 0.8381 (mmmm) cc_final: 0.8057 (mppt) REVERT: C 128 MET cc_start: 0.7011 (OUTLIER) cc_final: 0.6534 (mtt) REVERT: D 1 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8165 (ptp) REVERT: D 153 ASP cc_start: 0.7873 (t0) cc_final: 0.7341 (t70) REVERT: D 331 THR cc_start: 0.7642 (p) cc_final: 0.7366 (m) REVERT: E 92 LYS cc_start: 0.8609 (tppp) cc_final: 0.8197 (ttmt) REVERT: E 109 LYS cc_start: 0.8341 (tptt) cc_final: 0.7907 (tptt) REVERT: E 124 ARG cc_start: 0.6551 (OUTLIER) cc_final: 0.6181 (mtm180) REVERT: E 170 ARG cc_start: 0.7061 (ptt-90) cc_final: 0.6079 (mtp85) REVERT: E 196 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.7476 (ppp) REVERT: E 243 ASP cc_start: 0.7509 (m-30) cc_final: 0.7142 (m-30) REVERT: E 254 ILE cc_start: 0.8400 (tp) cc_final: 0.8170 (tt) REVERT: E 413 LYS cc_start: 0.8180 (ttmt) cc_final: 0.7911 (mttt) REVERT: F 147 ASP cc_start: 0.7936 (m-30) cc_final: 0.7392 (p0) REVERT: F 243 ASP cc_start: 0.7613 (m-30) cc_final: 0.7068 (t0) REVERT: F 327 ASN cc_start: 0.6870 (p0) cc_final: 0.6426 (p0) REVERT: F 333 LYS cc_start: 0.7677 (ttpp) cc_final: 0.7346 (ttmt) REVERT: F 347 GLU cc_start: 0.7465 (mp0) cc_final: 0.6978 (mm-30) REVERT: F 397 GLU cc_start: 0.7022 (tp30) cc_final: 0.5997 (tm-30) REVERT: F 398 GLN cc_start: 0.7661 (mt0) cc_final: 0.6953 (mp-120) REVERT: F 407 ARG cc_start: 0.7305 (ttp-170) cc_final: 0.6661 (ttm170) REVERT: F 431 ILE cc_start: 0.7199 (OUTLIER) cc_final: 0.6802 (pt) outliers start: 81 outliers final: 39 residues processed: 346 average time/residue: 1.3556 time to fit residues: 530.9349 Evaluate side-chains 316 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 264 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 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 19 VAL 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 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 66 THR Chi-restraints excluded: chain C residue 128 MET 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 431 ILE 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 384 MET 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 123 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 240 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 245 optimal weight: 0.8980 chunk 5 optimal weight: 20.0000 chunk 215 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 221 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 C 288 ASN C 302 ASN D 62 ASN D 140 GLN D 200 ASN D 279 GLN E 140 GLN E 167 ASN E 200 ASN F 140 GLN ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 295 ASN F 355 GLN F 359 GLN ** F 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.170295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.139489 restraints weight = 22513.234| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.16 r_work: 0.3367 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 21368 Z= 0.202 Angle : 0.614 10.782 28966 Z= 0.322 Chirality : 0.044 0.235 3246 Planarity : 0.004 0.037 3599 Dihedral : 11.243 172.163 2996 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.20 % Allowed : 16.93 % Favored : 78.87 % 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: 0.38 (0.17), residues: 2580 helix: 1.34 (0.14), residues: 1360 sheet: 0.04 (0.29), residues: 332 loop : -1.36 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 162 HIS 0.006 0.001 HIS A 8 PHE 0.022 0.002 PHE D 65 TYR 0.035 0.002 TYR A 312 ARG 0.009 0.001 ARG D 139 Details of bonding type rmsd hydrogen bonds : bond 0.03876 ( 1056) hydrogen bonds : angle 4.79982 ( 3033) covalent geometry : bond 0.00477 (21368) covalent geometry : angle 0.61383 (28966) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 279 time to evaluate : 2.260 Fit side-chains REVERT: A 79 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7973 (mtpm) REVERT: A 136 ASP cc_start: 0.7390 (OUTLIER) cc_final: 0.6886 (t0) REVERT: A 140 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7558 (mt0) REVERT: A 333 LYS cc_start: 0.7216 (OUTLIER) cc_final: 0.6872 (mmmt) REVERT: A 337 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7192 (mp0) REVERT: A 370 ASP cc_start: 0.6243 (m-30) cc_final: 0.5456 (t70) REVERT: A 414 TRP cc_start: 0.7594 (m100) cc_final: 0.7209 (m-90) REVERT: A 427 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7913 (ttpp) REVERT: B 96 LYS cc_start: 0.8594 (mtpp) cc_final: 0.8260 (mttt) REVERT: B 274 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7330 (mtm-85) REVERT: B 405 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7774 (tttp) REVERT: C 13 GLN cc_start: 0.7494 (tp40) cc_final: 0.7254 (tp40) REVERT: C 66 THR cc_start: 0.6441 (OUTLIER) cc_final: 0.6184 (m) REVERT: C 92 LYS cc_start: 0.8383 (mmmm) cc_final: 0.8055 (mppt) REVERT: C 128 MET cc_start: 0.7041 (OUTLIER) cc_final: 0.6521 (mtt) REVERT: C 391 GLU cc_start: 0.7825 (mp0) cc_final: 0.7386 (mp0) REVERT: D 153 ASP cc_start: 0.7938 (t0) cc_final: 0.7409 (t70) REVERT: D 331 THR cc_start: 0.7738 (p) cc_final: 0.7457 (m) REVERT: E 92 LYS cc_start: 0.8627 (tppp) cc_final: 0.8206 (ttmt) REVERT: E 109 LYS cc_start: 0.8401 (tptt) cc_final: 0.7860 (tttp) REVERT: E 124 ARG cc_start: 0.6568 (OUTLIER) cc_final: 0.6174 (mtm180) REVERT: E 170 ARG cc_start: 0.7088 (ptt-90) cc_final: 0.6092 (mtp85) REVERT: E 196 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7578 (ppp) REVERT: E 243 ASP cc_start: 0.7505 (m-30) cc_final: 0.7128 (m-30) REVERT: E 254 ILE cc_start: 0.8375 (tp) cc_final: 0.8152 (tt) REVERT: E 317 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6429 (ptmt) REVERT: E 389 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7316 (tt0) REVERT: E 413 LYS cc_start: 0.8199 (ttmt) cc_final: 0.7893 (mttt) REVERT: F 147 ASP cc_start: 0.7952 (m-30) cc_final: 0.7402 (p0) REVERT: F 168 LYS cc_start: 0.7244 (mptm) cc_final: 0.6844 (mmpt) REVERT: F 243 ASP cc_start: 0.7569 (m-30) cc_final: 0.7029 (t0) REVERT: F 296 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6842 (tm-30) REVERT: F 327 ASN cc_start: 0.6955 (p0) cc_final: 0.6496 (p0) REVERT: F 333 LYS cc_start: 0.7648 (ttpp) cc_final: 0.7162 (ttmt) REVERT: F 347 GLU cc_start: 0.7488 (mp0) cc_final: 0.6986 (mm-30) REVERT: F 397 GLU cc_start: 0.7031 (tp30) cc_final: 0.6072 (tm-30) REVERT: F 398 GLN cc_start: 0.7716 (mt0) cc_final: 0.7005 (mp-120) REVERT: F 407 ARG cc_start: 0.7339 (ttp-170) cc_final: 0.6528 (ttm170) REVERT: F 431 ILE cc_start: 0.7228 (OUTLIER) cc_final: 0.6824 (pt) outliers start: 94 outliers final: 45 residues processed: 345 average time/residue: 1.3762 time to fit residues: 535.9172 Evaluate side-chains 331 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 271 time to evaluate : 2.377 ------------------------------------------------------------------------------- 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 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 B residue 380 THR 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 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 113 ILE 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 384 MET 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 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 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 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 66 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 157 ASP Chi-restraints excluded: chain F residue 296 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 113 optimal weight: 0.9990 chunk 205 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 176 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 247 optimal weight: 0.9980 chunk 256 optimal weight: 0.4980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 100 GLN D 140 GLN D 200 ASN D 279 GLN E 140 GLN E 167 ASN E 200 ASN F 140 GLN ** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.173623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.142659 restraints weight = 22556.278| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.10 r_work: 0.3435 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3068 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= 0.119 Angle : 0.540 10.838 28966 Z= 0.286 Chirality : 0.041 0.217 3246 Planarity : 0.003 0.036 3599 Dihedral : 11.037 174.524 2996 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.35 % Allowed : 17.78 % Favored : 78.87 % 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: 0.64 (0.17), residues: 2580 helix: 1.62 (0.15), residues: 1357 sheet: 0.09 (0.29), residues: 332 loop : -1.34 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 89 HIS 0.005 0.001 HIS B 8 PHE 0.012 0.001 PHE D 65 TYR 0.016 0.001 TYR D 312 ARG 0.010 0.000 ARG D 139 Details of bonding type rmsd hydrogen bonds : bond 0.03284 ( 1056) hydrogen bonds : angle 4.61774 ( 3033) covalent geometry : bond 0.00263 (21368) covalent geometry : angle 0.53953 (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 364 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 289 time to evaluate : 2.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.8004 (mtpp) REVERT: A 136 ASP cc_start: 0.7324 (OUTLIER) cc_final: 0.6858 (t0) REVERT: A 140 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7487 (mt0) REVERT: A 258 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6883 (tp30) REVERT: A 333 LYS cc_start: 0.7176 (OUTLIER) cc_final: 0.6873 (mmmm) REVERT: A 337 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7046 (mp0) REVERT: A 370 ASP cc_start: 0.6190 (m-30) cc_final: 0.5387 (t70) REVERT: A 414 TRP cc_start: 0.7568 (m100) cc_final: 0.7192 (m-90) REVERT: A 427 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7877 (ttpp) REVERT: B 96 LYS cc_start: 0.8554 (mtpp) cc_final: 0.8233 (mttt) REVERT: B 274 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7218 (mtm-85) REVERT: C 66 THR cc_start: 0.6366 (OUTLIER) cc_final: 0.6138 (m) REVERT: C 92 LYS cc_start: 0.8361 (mmmm) cc_final: 0.8040 (mppt) REVERT: C 128 MET cc_start: 0.6980 (OUTLIER) cc_final: 0.6519 (mtt) REVERT: C 313 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.6946 (pt) REVERT: C 391 GLU cc_start: 0.7792 (mp0) cc_final: 0.7375 (mp0) REVERT: D 1 MET cc_start: 0.8499 (ptp) cc_final: 0.8207 (ptm) REVERT: D 153 ASP cc_start: 0.7829 (t0) cc_final: 0.7485 (t0) REVERT: D 331 THR cc_start: 0.7618 (p) cc_final: 0.7332 (m) REVERT: D 389 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7890 (tp30) REVERT: E 92 LYS cc_start: 0.8591 (tppp) cc_final: 0.8175 (ttmt) REVERT: E 109 LYS cc_start: 0.8292 (tptt) cc_final: 0.7876 (tptt) REVERT: E 124 ARG cc_start: 0.6469 (OUTLIER) cc_final: 0.6086 (mtm180) REVERT: E 170 ARG cc_start: 0.6999 (ptt-90) cc_final: 0.6041 (mtp85) REVERT: E 196 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7520 (ppp) REVERT: E 243 ASP cc_start: 0.7490 (m-30) cc_final: 0.7110 (m-30) REVERT: E 389 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7245 (tt0) REVERT: E 413 LYS cc_start: 0.8117 (ttmt) cc_final: 0.7870 (mttt) REVERT: F 147 ASP cc_start: 0.7881 (m-30) cc_final: 0.7356 (p0) REVERT: F 243 ASP cc_start: 0.7456 (m-30) cc_final: 0.6918 (t0) REVERT: F 296 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6797 (tm-30) REVERT: F 302 ASN cc_start: 0.7640 (t0) cc_final: 0.7210 (t0) REVERT: F 327 ASN cc_start: 0.6852 (p0) cc_final: 0.6359 (p0) REVERT: F 333 LYS cc_start: 0.7599 (ttpp) cc_final: 0.7260 (ttmt) REVERT: F 347 GLU cc_start: 0.7471 (mp0) cc_final: 0.6985 (mm-30) REVERT: F 384 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7566 (tpp) REVERT: F 397 GLU cc_start: 0.7017 (tp30) cc_final: 0.6007 (tm-30) REVERT: F 398 GLN cc_start: 0.7673 (mt0) cc_final: 0.7021 (mp-120) REVERT: F 407 ARG cc_start: 0.7279 (ttp-170) cc_final: 0.6618 (ttm170) REVERT: F 431 ILE cc_start: 0.7213 (OUTLIER) cc_final: 0.6826 (pt) outliers start: 75 outliers final: 37 residues processed: 339 average time/residue: 1.3790 time to fit residues: 532.5163 Evaluate side-chains 317 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 264 time to evaluate : 2.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 427 LYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 267 ARG 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 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 313 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 113 ILE 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 384 MET 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 71 SER 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 389 GLU Chi-restraints excluded: chain F residue 1 MET 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 296 GLU Chi-restraints excluded: chain F residue 325 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 67 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 126 optimal weight: 0.1980 chunk 243 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 198 optimal weight: 3.9990 chunk 159 optimal weight: 6.9990 chunk 196 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 62 ASN D 200 ASN D 279 GLN E 140 GLN 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.172775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.141616 restraints weight = 22480.451| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.16 r_work: 0.3418 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21368 Z= 0.140 Angle : 0.560 11.348 28966 Z= 0.294 Chirality : 0.042 0.260 3246 Planarity : 0.003 0.033 3599 Dihedral : 11.026 173.493 2996 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.17 % Allowed : 18.01 % Favored : 78.82 % 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: 0.65 (0.17), residues: 2580 helix: 1.66 (0.15), residues: 1350 sheet: 0.08 (0.29), residues: 332 loop : -1.35 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 162 HIS 0.008 0.001 HIS B 8 PHE 0.016 0.002 PHE D 65 TYR 0.017 0.001 TYR D 312 ARG 0.009 0.000 ARG D 139 Details of bonding type rmsd hydrogen bonds : bond 0.03403 ( 1056) hydrogen bonds : angle 4.62291 ( 3033) covalent geometry : bond 0.00322 (21368) covalent geometry : angle 0.55956 (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 339 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 268 time to evaluate : 2.445 Fit side-chains revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7991 (mtpm) REVERT: A 140 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7633 (mt0) REVERT: A 333 LYS cc_start: 0.7170 (OUTLIER) cc_final: 0.6842 (mmmm) REVERT: A 337 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7058 (mp0) REVERT: A 370 ASP cc_start: 0.6184 (m-30) cc_final: 0.5417 (t70) REVERT: A 414 TRP cc_start: 0.7604 (m100) cc_final: 0.7222 (m-90) REVERT: A 427 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7899 (ttpp) REVERT: B 96 LYS cc_start: 0.8571 (mtpp) cc_final: 0.8242 (mttt) REVERT: B 274 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7283 (mtm-85) REVERT: C 66 THR cc_start: 0.6356 (OUTLIER) cc_final: 0.6107 (m) REVERT: C 92 LYS cc_start: 0.8371 (mmmm) cc_final: 0.8055 (mppt) REVERT: C 128 MET cc_start: 0.6971 (OUTLIER) cc_final: 0.6503 (mtt) REVERT: C 313 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.6961 (pt) REVERT: C 391 GLU cc_start: 0.7813 (mp0) cc_final: 0.7360 (mp0) REVERT: D 1 MET cc_start: 0.8550 (ptp) cc_final: 0.8198 (ptm) REVERT: D 153 ASP cc_start: 0.7871 (t0) cc_final: 0.7552 (t0) REVERT: D 331 THR cc_start: 0.7683 (p) cc_final: 0.7393 (m) REVERT: E 92 LYS cc_start: 0.8591 (tppp) cc_final: 0.8173 (ttmt) REVERT: E 109 LYS cc_start: 0.8322 (tptt) cc_final: 0.7892 (tptt) REVERT: E 124 ARG cc_start: 0.6489 (OUTLIER) cc_final: 0.6101 (mtm180) REVERT: E 170 ARG cc_start: 0.7030 (ptt-90) cc_final: 0.6043 (mtp85) REVERT: E 196 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7550 (ppp) REVERT: E 243 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.7086 (m-30) REVERT: E 345 GLU cc_start: 0.6802 (tm-30) cc_final: 0.6316 (tt0) REVERT: E 389 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7254 (tt0) REVERT: E 413 LYS cc_start: 0.8066 (ttmt) cc_final: 0.7829 (mttt) REVERT: F 147 ASP cc_start: 0.7920 (m-30) cc_final: 0.7385 (p0) REVERT: F 243 ASP cc_start: 0.7355 (m-30) cc_final: 0.6823 (t0) REVERT: F 251 ASP cc_start: 0.6507 (m-30) cc_final: 0.6207 (p0) REVERT: F 296 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6791 (tm-30) REVERT: F 327 ASN cc_start: 0.6872 (p0) cc_final: 0.6378 (p0) REVERT: F 333 LYS cc_start: 0.7602 (ttpp) cc_final: 0.7213 (ttmt) REVERT: F 347 GLU cc_start: 0.7486 (mp0) cc_final: 0.6989 (mm-30) REVERT: F 373 GLU cc_start: 0.6233 (mt-10) cc_final: 0.5434 (mp0) REVERT: F 384 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7771 (ttp) REVERT: F 397 GLU cc_start: 0.6999 (tp30) cc_final: 0.5971 (tm-30) REVERT: F 398 GLN cc_start: 0.7668 (mt0) cc_final: 0.6994 (mp-120) REVERT: F 431 ILE cc_start: 0.7252 (OUTLIER) cc_final: 0.6858 (pt) outliers start: 71 outliers final: 43 residues processed: 314 average time/residue: 1.3382 time to fit residues: 476.5200 Evaluate side-chains 323 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 265 time to evaluate : 2.153 ------------------------------------------------------------------------------- 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 196 MET Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain B residue 267 ARG 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 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 313 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 113 ILE 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 384 MET 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 100 GLN 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 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 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 66 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 296 GLU Chi-restraints excluded: chain F residue 325 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 86 optimal weight: 6.9990 chunk 132 optimal weight: 0.4980 chunk 33 optimal weight: 5.9990 chunk 233 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 217 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 58 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 187 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS C 302 ASN D 100 GLN D 200 ASN D 279 GLN E 140 GLN E 167 ASN E 200 ASN F 140 GLN F 200 ASN F 295 ASN F 359 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.174782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.144013 restraints weight = 22570.365| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.10 r_work: 0.3453 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3153 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= 0.115 Angle : 0.534 12.330 28966 Z= 0.282 Chirality : 0.041 0.211 3246 Planarity : 0.003 0.033 3599 Dihedral : 10.946 175.387 2996 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.90 % Allowed : 18.72 % Favored : 78.37 % 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: 0.74 (0.17), residues: 2580 helix: 1.79 (0.15), residues: 1348 sheet: 0.08 (0.29), residues: 332 loop : -1.38 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 89 HIS 0.007 0.001 HIS B 8 PHE 0.012 0.001 PHE D 65 TYR 0.021 0.001 TYR A 312 ARG 0.009 0.000 ARG D 139 Details of bonding type rmsd hydrogen bonds : bond 0.03138 ( 1056) hydrogen bonds : angle 4.53145 ( 3033) covalent geometry : bond 0.00254 (21368) covalent geometry : angle 0.53355 (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 339 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 274 time to evaluate : 2.224 Fit side-chains revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7955 (mtpm) REVERT: A 140 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7631 (mt0) REVERT: A 265 LYS cc_start: 0.7822 (ttpt) cc_final: 0.7344 (tmtt) REVERT: A 333 LYS cc_start: 0.7153 (OUTLIER) cc_final: 0.6850 (mmmm) REVERT: A 337 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7050 (mp0) REVERT: A 369 SER cc_start: 0.5890 (OUTLIER) cc_final: 0.5634 (t) REVERT: A 370 ASP cc_start: 0.6085 (m-30) cc_final: 0.5383 (t70) REVERT: A 414 TRP cc_start: 0.7584 (m100) cc_final: 0.7225 (m-90) REVERT: A 419 MET cc_start: 0.7834 (tpp) cc_final: 0.7394 (mmt) REVERT: A 427 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7856 (ttpp) REVERT: B 96 LYS cc_start: 0.8538 (mtpp) cc_final: 0.8218 (mttt) REVERT: B 274 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.7237 (mtm-85) REVERT: C 66 THR cc_start: 0.6376 (OUTLIER) cc_final: 0.6106 (m) REVERT: C 92 LYS cc_start: 0.8356 (mmmm) cc_final: 0.8052 (mppt) REVERT: C 128 MET cc_start: 0.6971 (OUTLIER) cc_final: 0.6524 (mtt) REVERT: C 391 GLU cc_start: 0.7777 (mp0) cc_final: 0.7354 (mp0) REVERT: D 1 MET cc_start: 0.8568 (ptp) cc_final: 0.8249 (ptm) REVERT: D 153 ASP cc_start: 0.7835 (t0) cc_final: 0.7510 (t0) REVERT: D 331 THR cc_start: 0.7654 (p) cc_final: 0.7352 (m) REVERT: E 92 LYS cc_start: 0.8554 (tppp) cc_final: 0.8133 (ttmt) REVERT: E 109 LYS cc_start: 0.8257 (tptt) cc_final: 0.7869 (tptt) REVERT: E 124 ARG cc_start: 0.6462 (OUTLIER) cc_final: 0.6122 (mtm180) REVERT: E 170 ARG cc_start: 0.7026 (ptt-90) cc_final: 0.6057 (mtp85) REVERT: E 196 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7493 (ppp) REVERT: E 243 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.7024 (m-30) REVERT: E 345 GLU cc_start: 0.6841 (tm-30) cc_final: 0.6352 (tt0) REVERT: E 413 LYS cc_start: 0.8005 (ttmt) cc_final: 0.7797 (mttt) REVERT: F 147 ASP cc_start: 0.7914 (m-30) cc_final: 0.7396 (p0) REVERT: F 243 ASP cc_start: 0.7315 (m-30) cc_final: 0.6824 (t0) REVERT: F 251 ASP cc_start: 0.6651 (m-30) cc_final: 0.6270 (p0) REVERT: F 296 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6763 (tm-30) REVERT: F 302 ASN cc_start: 0.7572 (t0) cc_final: 0.7134 (t0) REVERT: F 327 ASN cc_start: 0.6795 (p0) cc_final: 0.6341 (p0) REVERT: F 333 LYS cc_start: 0.7616 (ttpp) cc_final: 0.7168 (ttmt) REVERT: F 347 GLU cc_start: 0.7439 (mp0) cc_final: 0.6974 (mm-30) REVERT: F 373 GLU cc_start: 0.6203 (mt-10) cc_final: 0.5418 (mp0) REVERT: F 384 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7704 (ttp) REVERT: F 397 GLU cc_start: 0.6989 (tp30) cc_final: 0.5970 (tm-30) REVERT: F 398 GLN cc_start: 0.7638 (mt0) cc_final: 0.7011 (mp-120) REVERT: F 431 ILE cc_start: 0.7187 (OUTLIER) cc_final: 0.6849 (pt) outliers start: 65 outliers final: 36 residues processed: 322 average time/residue: 1.3503 time to fit residues: 491.5425 Evaluate side-chains 312 residues out of total 2238 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 262 time to evaluate : 2.345 ------------------------------------------------------------------------------- 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 201 VAL 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 C residue 19 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 128 MET 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 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 384 MET 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 71 SER 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 304 VAL 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 66 THR Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 296 GLU Chi-restraints excluded: chain F residue 325 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 143 optimal weight: 0.3980 chunk 176 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 128 optimal weight: 0.2980 chunk 79 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 182 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN ** B 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS C 302 ASN D 200 ASN D 279 GLN E 57 ASN E 140 GLN E 167 ASN E 200 ASN F 140 GLN F 200 ASN F 295 ASN ** 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 = 0.4057 r_free = 0.4057 target = 0.174591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.143734 restraints weight = 22653.803| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.11 r_work: 0.3450 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3188 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= 0.117 Angle : 0.541 12.957 28966 Z= 0.283 Chirality : 0.041 0.210 3246 Planarity : 0.003 0.035 3599 Dihedral : 10.910 174.950 2996 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.68 % Allowed : 18.90 % Favored : 78.42 % 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: 0.78 (0.17), residues: 2580 helix: 1.82 (0.15), residues: 1348 sheet: 0.11 (0.30), residues: 332 loop : -1.37 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 162 HIS 0.008 0.001 HIS B 8 PHE 0.024 0.001 PHE F 174 TYR 0.014 0.001 TYR D 312 ARG 0.008 0.000 ARG D 139 Details of bonding type rmsd hydrogen bonds : bond 0.03132 ( 1056) hydrogen bonds : angle 4.50495 ( 3033) covalent geometry : bond 0.00261 (21368) covalent geometry : angle 0.54082 (28966) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18444.29 seconds wall clock time: 314 minutes 11.60 seconds (18851.60 seconds total)