Starting phenix.real_space_refine on Wed Jan 22 12:23:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dva_47194/01_2025/9dva_47194_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dva_47194/01_2025/9dva_47194.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dva_47194/01_2025/9dva_47194.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dva_47194/01_2025/9dva_47194.map" model { file = "/net/cci-nas-00/data/ceres_data/9dva_47194/01_2025/9dva_47194_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dva_47194/01_2025/9dva_47194_neut.cif" } resolution = 3.1 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= 0.003 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 10 5.49 5 Mg 5 5.21 5 S 140 5.16 5 C 11657 2.51 5 N 3161 2.21 5 O 3556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 18529 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2899 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2899 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2899 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2899 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2899 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1642 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 6, 'TRANS': 207} Chain: "G" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 610 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "H" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1642 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 6, 'TRANS': 207} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.19, per 1000 atoms: 0.66 Number of scatterers: 18529 At special positions: 0 Unit cell: (133.9, 87.55, 196.73, 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 140 16.00 P 10 15.00 Mg 5 11.99 O 3556 8.00 N 3161 7.00 C 11657 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.41 Conformation dependent library (CDL) restraints added in 2.5 seconds 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4392 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 32 sheets defined 55.9% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.50 Creating SS restraints... Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 78 through 92 removed outlier: 3.595A pdb=" N MET A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.512A pdb=" N GLU A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 97 through 101' Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.235A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU A 117 " --> pdb=" O LYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.685A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.650A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.661A pdb=" N ARG A 254 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE A 255 " --> pdb=" O ASN A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 251 through 255' Processing helix chain 'A' and resid 257 through 262 removed outlier: 3.693A pdb=" N THR A 260 " --> pdb=" O CYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 267 Processing helix chain 'A' and resid 273 through 284 removed outlier: 3.528A pdb=" N TYR A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 294 removed outlier: 3.527A pdb=" N TYR A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.138A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 359 through 366 removed outlier: 3.541A pdb=" N GLU A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 374 removed outlier: 4.333A pdb=" N ARG A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.709A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.529A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.510A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.239A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.951A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.562A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.692A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 removed outlier: 3.664A pdb=" N SER B 233 " --> pdb=" O THR B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 260 Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 261 through 262 No H-bonds generated for 'chain 'B' and resid 261 through 262' Processing helix chain 'B' and resid 263 through 267 Processing helix chain 'B' and resid 273 through 284 removed outlier: 3.518A pdb=" N THR B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.793A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 4.149A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.539A pdb=" N LEU B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 359 through 366 removed outlier: 3.572A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 374 removed outlier: 4.196A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 61 through 63 No H-bonds generated for 'chain 'C' and resid 61 through 63' Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.814A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.203A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.754A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.791A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 260 removed outlier: 3.637A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 261 through 262 No H-bonds generated for 'chain 'C' and resid 261 through 262' Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 removed outlier: 3.590A pdb=" N TYR C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.626A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 4.194A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 355 removed outlier: 4.213A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 4.208A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 61 through 63 No H-bonds generated for 'chain 'D' and resid 61 through 63' Processing helix chain 'D' and resid 78 through 91 removed outlier: 3.681A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.022A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE D 124 " --> pdb=" O THR D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.898A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.802A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 260 removed outlier: 3.594A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 261 through 262 No H-bonds generated for 'chain 'D' and resid 261 through 262' Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 removed outlier: 3.809A pdb=" N TYR D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE D 282 " --> pdb=" O THR D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 295 Processing helix chain 'D' and resid 301 through 306 removed outlier: 4.158A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.532A pdb=" N ALA D 319 " --> pdb=" O LYS D 315 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 352 through 356 removed outlier: 3.969A pdb=" N TRP D 356 " --> pdb=" O GLN D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 368 through 374 removed outlier: 4.405A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 removed outlier: 4.264A pdb=" N LYS E 84 " --> pdb=" O ASP E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.511A pdb=" N GLU E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 97 through 101' Processing helix chain 'E' and resid 112 through 126 removed outlier: 4.111A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET E 123 " --> pdb=" O MET E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 removed outlier: 3.539A pdb=" N SER E 141 " --> pdb=" O GLN E 137 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU E 142 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR E 143 " --> pdb=" O VAL E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 194 removed outlier: 3.769A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.563A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.667A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 262 Processing helix chain 'E' and resid 263 through 267 Processing helix chain 'E' and resid 273 through 284 removed outlier: 3.776A pdb=" N TYR E 279 " --> pdb=" O HIS E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 295 removed outlier: 3.790A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 306 removed outlier: 4.067A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 removed outlier: 3.638A pdb=" N LEU E 320 " --> pdb=" O GLU E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 350 through 356 removed outlier: 3.935A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TRP E 356 " --> pdb=" O GLN E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 366 Processing helix chain 'E' and resid 368 through 374 removed outlier: 3.822A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 692 through 694 No H-bonds generated for 'chain 'F' and resid 692 through 694' Processing helix chain 'F' and resid 695 through 703 Processing helix chain 'F' and resid 704 through 707 removed outlier: 4.184A pdb=" N ASP F 707 " --> pdb=" O LYS F 704 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 704 through 707' Processing helix chain 'F' and resid 711 through 730 removed outlier: 3.863A pdb=" N THR F 730 " --> pdb=" O MET F 726 " (cutoff:3.500A) Processing helix chain 'F' and resid 738 through 765 removed outlier: 3.569A pdb=" N VAL F 742 " --> pdb=" O ASN F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 770 through 805 removed outlier: 3.989A pdb=" N GLN F 774 " --> pdb=" O SER F 770 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP F 775 " --> pdb=" O ALA F 771 " (cutoff:3.500A) Processing helix chain 'F' and resid 811 through 814 removed outlier: 3.689A pdb=" N SER F 814 " --> pdb=" O GLY F 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 811 through 814' Processing helix chain 'F' and resid 815 through 843 Processing helix chain 'F' and resid 854 through 858 Processing helix chain 'F' and resid 875 through 880 Processing helix chain 'F' and resid 892 through 899 removed outlier: 3.522A pdb=" N LEU F 897 " --> pdb=" O PRO F 893 " (cutoff:3.500A) Processing helix chain 'G' and resid 1512 through 1543 removed outlier: 3.841A pdb=" N ARG G1516 " --> pdb=" O ASP G1512 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL G1531 " --> pdb=" O GLN G1527 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASP G1532 " --> pdb=" O MET G1528 " (cutoff:3.500A) Processing helix chain 'G' and resid 1548 through 1550 No H-bonds generated for 'chain 'G' and resid 1548 through 1550' Processing helix chain 'G' and resid 1551 through 1575 removed outlier: 3.583A pdb=" N LYS G1574 " --> pdb=" O GLU G1570 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASP G1575 " --> pdb=" O SER G1571 " (cutoff:3.500A) Processing helix chain 'H' and resid 691 through 703 removed outlier: 3.995A pdb=" N LYS H 695 " --> pdb=" O PHE H 691 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER H 696 " --> pdb=" O GLN H 692 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS H 697 " --> pdb=" O GLU H 693 " (cutoff:3.500A) Processing helix chain 'H' and resid 711 through 728 removed outlier: 3.524A pdb=" N ILE H 722 " --> pdb=" O GLN H 718 " (cutoff:3.500A) Processing helix chain 'H' and resid 738 through 767 removed outlier: 3.652A pdb=" N VAL H 742 " --> pdb=" O ASN H 738 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER H 754 " --> pdb=" O ALA H 750 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG H 755 " --> pdb=" O GLU H 751 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE H 763 " --> pdb=" O LEU H 759 " (cutoff:3.500A) Processing helix chain 'H' and resid 770 through 805 removed outlier: 3.674A pdb=" N TYR H 779 " --> pdb=" O ASP H 775 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU H 780 " --> pdb=" O LEU H 776 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG H 782 " --> pdb=" O ALA H 778 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA H 784 " --> pdb=" O LEU H 780 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU H 785 " --> pdb=" O GLN H 781 " (cutoff:3.500A) Processing helix chain 'H' and resid 811 through 814 removed outlier: 3.973A pdb=" N SER H 814 " --> pdb=" O GLY H 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 811 through 814' Processing helix chain 'H' and resid 815 through 843 removed outlier: 3.679A pdb=" N ALA H 821 " --> pdb=" O SER H 817 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA H 828 " --> pdb=" O ASN H 824 " (cutoff:3.500A) Processing helix chain 'H' and resid 854 through 857 Processing helix chain 'H' and resid 875 through 880 removed outlier: 4.258A pdb=" N GLN H 879 " --> pdb=" O GLN H 875 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR H 880 " --> pdb=" O ASP H 876 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 875 through 880' Processing helix chain 'H' and resid 892 through 899 removed outlier: 3.949A pdb=" N GLU H 899 " --> pdb=" O GLN H 895 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.585A pdb=" N PHE A 31 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 42 removed outlier: 3.897A pdb=" N GLN A 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 41 through 42 removed outlier: 3.897A pdb=" N GLN A 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA6, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA7, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.248A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 247 through 250 removed outlier: 6.651A pdb=" N SER A 239 " --> pdb=" O LYS H 883 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 29 through 32 removed outlier: 4.155A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.626A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'B' and resid 247 through 250 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.501A pdb=" N PHE C 31 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 9.044A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.238A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 4.109A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ASN D 12 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.327A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 4.405A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ASN E 12 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AD4, first strand: chain 'F' and resid 859 through 861 Processing sheet with id=AD5, first strand: chain 'H' and resid 859 through 861 939 hydrogen bonds defined for protein. 2511 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.95 Time building geometry restraints manager: 5.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6048 1.34 - 1.46: 4135 1.46 - 1.58: 8452 1.58 - 1.70: 15 1.70 - 1.82: 245 Bond restraints: 18895 Sorted by residual: bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.94e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.86e+00 bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.86e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.81e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.75e+00 ... (remaining 18890 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 25188 1.66 - 3.32: 290 3.32 - 4.98: 63 4.98 - 6.64: 25 6.64 - 8.30: 4 Bond angle restraints: 25570 Sorted by residual: angle pdb=" N MET G1559 " pdb=" CA MET G1559 " pdb=" CB MET G1559 " ideal model delta sigma weight residual 110.16 116.99 -6.83 1.48e+00 4.57e-01 2.13e+01 angle pdb=" N ASP D 157 " pdb=" CA ASP D 157 " pdb=" C ASP D 157 " ideal model delta sigma weight residual 113.97 108.75 5.22 1.28e+00 6.10e-01 1.66e+01 angle pdb=" N ASP C 157 " pdb=" CA ASP C 157 " pdb=" C ASP C 157 " ideal model delta sigma weight residual 113.97 109.74 4.23 1.28e+00 6.10e-01 1.09e+01 angle pdb=" CA MET G1559 " pdb=" CB MET G1559 " pdb=" CG MET G1559 " ideal model delta sigma weight residual 114.10 120.65 -6.55 2.00e+00 2.50e-01 1.07e+01 angle pdb=" N VAL C 201 " pdb=" CA VAL C 201 " pdb=" C VAL C 201 " ideal model delta sigma weight residual 113.71 110.66 3.05 9.50e-01 1.11e+00 1.03e+01 ... (remaining 25565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.33: 10878 24.33 - 48.66: 548 48.66 - 72.99: 57 72.99 - 97.32: 19 97.32 - 121.65: 2 Dihedral angle restraints: 11504 sinusoidal: 4678 harmonic: 6826 Sorted by residual: dihedral pdb=" O2A ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PA ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sinusoidal sigma weight residual 300.00 178.35 121.65 1 2.00e+01 2.50e-03 3.66e+01 dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 47.27 -107.26 1 2.00e+01 2.50e-03 3.11e+01 dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 25.35 -85.35 1 2.00e+01 2.50e-03 2.21e+01 ... (remaining 11501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1894 0.036 - 0.071: 690 0.071 - 0.107: 210 0.107 - 0.142: 56 0.142 - 0.178: 1 Chirality restraints: 2851 Sorted by residual: chirality pdb=" CA ASP D 157 " pdb=" N ASP D 157 " pdb=" C ASP D 157 " pdb=" CB ASP D 157 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.88e-01 chirality pdb=" CA ILE E 357 " pdb=" N ILE E 357 " pdb=" C ILE E 357 " pdb=" CB ILE E 357 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" C3' ADP D 401 " pdb=" C2' ADP D 401 " pdb=" C4' ADP D 401 " pdb=" O3' ADP D 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.63 0.12 2.00e-01 2.50e+01 3.80e-01 ... (remaining 2848 not shown) Planarity restraints: 3263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN E 111 " 0.038 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO E 112 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO E 112 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 112 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 111 " -0.037 5.00e-02 4.00e+02 5.64e-02 5.09e+00 pdb=" N PRO B 112 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 112 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 112 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 111 " -0.037 5.00e-02 4.00e+02 5.61e-02 5.03e+00 pdb=" N PRO C 112 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 112 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 112 " -0.031 5.00e-02 4.00e+02 ... (remaining 3260 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 139 2.64 - 3.21: 16525 3.21 - 3.77: 26630 3.77 - 4.34: 38368 4.34 - 4.90: 63970 Nonbonded interactions: 145632 Sorted by model distance: nonbonded pdb=" O2B ADP E 401 " pdb="MG MG E 402 " model vdw 2.077 2.170 nonbonded pdb=" O3B ADP D 401 " pdb="MG MG D 402 " model vdw 2.147 2.170 nonbonded pdb=" O GLY B 156 " pdb=" OG1 THR B 303 " model vdw 2.202 3.040 nonbonded pdb=" O2B ADP A 401 " pdb="MG MG A 402 " model vdw 2.213 2.170 nonbonded pdb=" O GLY A 156 " pdb=" OG1 THR A 303 " model vdw 2.229 3.040 ... (remaining 145627 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'H' } 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: 10.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 44.940 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 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 : 0.003 0.056 18895 Z= 0.187 Angle : 0.512 8.304 25570 Z= 0.249 Chirality : 0.041 0.178 2851 Planarity : 0.004 0.058 3263 Dihedral : 14.231 121.648 7112 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.18), residues: 2323 helix: -0.13 (0.16), residues: 1067 sheet: 0.58 (0.29), residues: 380 loop : 0.68 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 705 HIS 0.003 0.000 HIS A 101 PHE 0.015 0.001 PHE E 124 TYR 0.024 0.001 TYR F 779 ARG 0.005 0.000 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 330 time to evaluate : 2.003 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.8244 (mtp) cc_final: 0.7953 (mmm) REVERT: A 157 ASP cc_start: 0.7690 (t70) cc_final: 0.7192 (t0) REVERT: A 271 SER cc_start: 0.8643 (m) cc_final: 0.8203 (p) REVERT: A 374 CYS cc_start: 0.6579 (m) cc_final: 0.6335 (m) REVERT: B 68 LYS cc_start: 0.8237 (mtmm) cc_final: 0.7844 (mtmm) REVERT: B 78 ASN cc_start: 0.8667 (t0) cc_final: 0.8461 (t0) REVERT: B 118 LYS cc_start: 0.7569 (tttp) cc_final: 0.7092 (ttmt) REVERT: B 206 ARG cc_start: 0.7316 (ttp-110) cc_final: 0.6977 (ttp-170) REVERT: B 297 ASN cc_start: 0.8408 (t0) cc_final: 0.8189 (t0) REVERT: C 6 THR cc_start: 0.8247 (p) cc_final: 0.7959 (t) REVERT: C 157 ASP cc_start: 0.8299 (t70) cc_final: 0.8088 (t0) REVERT: C 246 GLN cc_start: 0.8299 (mt0) cc_final: 0.7897 (mt0) REVERT: C 325 MET cc_start: 0.8799 (mmp) cc_final: 0.8206 (mmp) REVERT: D 246 GLN cc_start: 0.7912 (mt0) cc_final: 0.7643 (mt0) REVERT: D 283 MET cc_start: 0.8063 (mmt) cc_final: 0.7827 (mmp) REVERT: D 328 LYS cc_start: 0.7801 (mtpp) cc_final: 0.7481 (tptp) REVERT: D 360 GLN cc_start: 0.8327 (pp30) cc_final: 0.8101 (pp30) REVERT: E 121 GLN cc_start: 0.8464 (tt0) cc_final: 0.7904 (tt0) REVERT: E 123 MET cc_start: 0.8544 (mmt) cc_final: 0.8025 (mmt) REVERT: E 227 MET cc_start: 0.8084 (mmt) cc_final: 0.7805 (mmt) REVERT: E 263 GLN cc_start: 0.7172 (mt0) cc_final: 0.6771 (mt0) REVERT: E 276 GLU cc_start: 0.8496 (pt0) cc_final: 0.8249 (pt0) REVERT: E 289 ILE cc_start: 0.8275 (pt) cc_final: 0.8009 (pt) REVERT: F 786 TYR cc_start: 0.8308 (m-80) cc_final: 0.7757 (m-80) REVERT: G 1559 MET cc_start: 0.7742 (mtm) cc_final: 0.7270 (mpp) REVERT: G 1569 GLN cc_start: 0.7799 (tp40) cc_final: 0.7223 (mm110) REVERT: G 1570 GLU cc_start: 0.7705 (tt0) cc_final: 0.7260 (pt0) REVERT: H 844 GLN cc_start: 0.5911 (tm-30) cc_final: 0.5711 (tp40) outliers start: 0 outliers final: 0 residues processed: 330 average time/residue: 0.3249 time to fit residues: 163.8183 Evaluate side-chains 237 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 60 optimal weight: 0.4980 chunk 119 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN C 12 ASN C 137 GLN E 225 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.131918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.108824 restraints weight = 25355.170| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.75 r_work: 0.3026 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 18895 Z= 0.296 Angle : 0.613 9.357 25570 Z= 0.312 Chirality : 0.047 0.156 2851 Planarity : 0.005 0.055 3263 Dihedral : 6.466 123.661 2602 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.90 % Allowed : 6.11 % Favored : 92.99 % 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: 0.49 (0.18), residues: 2323 helix: 0.22 (0.16), residues: 1132 sheet: 0.86 (0.29), residues: 360 loop : 0.52 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 340 HIS 0.006 0.001 HIS C 161 PHE 0.011 0.001 PHE E 255 TYR 0.012 0.001 TYR D 166 ARG 0.003 0.000 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 247 time to evaluate : 2.172 Fit side-chains REVERT: A 44 MET cc_start: 0.8872 (mtp) cc_final: 0.8508 (mmm) REVERT: A 157 ASP cc_start: 0.8345 (t0) cc_final: 0.7830 (t0) REVERT: A 271 SER cc_start: 0.8878 (m) cc_final: 0.8615 (p) REVERT: B 72 GLU cc_start: 0.8455 (pp20) cc_final: 0.7916 (tt0) REVERT: B 206 ARG cc_start: 0.8288 (ttp-110) cc_final: 0.8031 (ttp-170) REVERT: B 360 GLN cc_start: 0.7753 (tp-100) cc_final: 0.7082 (tp-100) REVERT: C 6 THR cc_start: 0.8344 (p) cc_final: 0.8088 (t) REVERT: C 157 ASP cc_start: 0.8778 (t70) cc_final: 0.8520 (t0) REVERT: C 325 MET cc_start: 0.9083 (mmp) cc_final: 0.8364 (mmp) REVERT: D 328 LYS cc_start: 0.8127 (mtpp) cc_final: 0.7820 (tptp) REVERT: E 44 MET cc_start: 0.7906 (mtp) cc_final: 0.7500 (mtt) REVERT: E 121 GLN cc_start: 0.8699 (tt0) cc_final: 0.8322 (tt0) REVERT: E 149 THR cc_start: 0.8900 (t) cc_final: 0.8629 (m) REVERT: E 227 MET cc_start: 0.8376 (mmt) cc_final: 0.7974 (mmt) REVERT: E 289 ILE cc_start: 0.8715 (pt) cc_final: 0.8490 (pt) REVERT: E 368 SER cc_start: 0.8868 (m) cc_final: 0.8658 (t) REVERT: G 1533 MET cc_start: 0.7957 (tpt) cc_final: 0.7664 (tpp) REVERT: G 1570 GLU cc_start: 0.8499 (tt0) cc_final: 0.7875 (pt0) REVERT: H 844 GLN cc_start: 0.6043 (tm-30) cc_final: 0.5792 (tp40) outliers start: 18 outliers final: 14 residues processed: 259 average time/residue: 0.3224 time to fit residues: 128.7100 Evaluate side-chains 250 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 236 time to evaluate : 2.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain F residue 733 LYS Chi-restraints excluded: chain F residue 841 THR Chi-restraints excluded: chain H residue 783 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 225 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 224 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 93 optimal weight: 0.0870 chunk 80 optimal weight: 0.0980 chunk 72 optimal weight: 0.0870 chunk 120 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 115 ASN F 879 GLN H 766 HIS H 802 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.133226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.110041 restraints weight = 25260.116| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.74 r_work: 0.3042 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18895 Z= 0.195 Angle : 0.545 7.272 25570 Z= 0.271 Chirality : 0.044 0.150 2851 Planarity : 0.004 0.047 3263 Dihedral : 6.318 128.165 2602 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.20 % Allowed : 7.56 % Favored : 91.24 % 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: 0.72 (0.18), residues: 2323 helix: 0.54 (0.16), residues: 1122 sheet: 0.70 (0.28), residues: 365 loop : 0.57 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 340 HIS 0.008 0.001 HIS H 766 PHE 0.009 0.001 PHE B 31 TYR 0.010 0.001 TYR F 779 ARG 0.002 0.000 ARG F 884 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 242 time to evaluate : 2.465 Fit side-chains REVERT: A 44 MET cc_start: 0.8868 (mtp) cc_final: 0.8555 (mmm) REVERT: A 123 MET cc_start: 0.8762 (mmt) cc_final: 0.8381 (mmt) REVERT: A 157 ASP cc_start: 0.8284 (t0) cc_final: 0.7801 (t0) REVERT: A 271 SER cc_start: 0.8850 (m) cc_final: 0.8594 (p) REVERT: B 206 ARG cc_start: 0.8281 (ttp-110) cc_final: 0.7998 (ttp-170) REVERT: B 224 GLU cc_start: 0.7466 (mp0) cc_final: 0.7205 (mp0) REVERT: B 360 GLN cc_start: 0.7769 (tp-100) cc_final: 0.7255 (tp-100) REVERT: C 6 THR cc_start: 0.8305 (p) cc_final: 0.8016 (t) REVERT: C 325 MET cc_start: 0.9064 (mmp) cc_final: 0.8363 (mmp) REVERT: E 121 GLN cc_start: 0.8704 (tt0) cc_final: 0.8371 (tt0) REVERT: E 123 MET cc_start: 0.9227 (mmt) cc_final: 0.8339 (mmt) REVERT: E 149 THR cc_start: 0.8895 (t) cc_final: 0.8605 (m) REVERT: E 227 MET cc_start: 0.8267 (mmt) cc_final: 0.7769 (mmt) REVERT: E 263 GLN cc_start: 0.8038 (mt0) cc_final: 0.7825 (mt0) REVERT: E 276 GLU cc_start: 0.8469 (pt0) cc_final: 0.8221 (pt0) REVERT: E 289 ILE cc_start: 0.8610 (pt) cc_final: 0.8396 (pt) REVERT: E 368 SER cc_start: 0.8909 (m) cc_final: 0.8690 (t) REVERT: G 1533 MET cc_start: 0.7905 (tpt) cc_final: 0.7634 (tpp) REVERT: G 1570 GLU cc_start: 0.8491 (tt0) cc_final: 0.7866 (pt0) REVERT: H 844 GLN cc_start: 0.6042 (tm-30) cc_final: 0.5749 (tp40) outliers start: 24 outliers final: 18 residues processed: 254 average time/residue: 0.3229 time to fit residues: 126.6701 Evaluate side-chains 250 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 232 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 363 ASP Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain F residue 733 LYS Chi-restraints excluded: chain F residue 841 THR Chi-restraints excluded: chain G residue 1532 ASP Chi-restraints excluded: chain G residue 1569 GLN Chi-restraints excluded: chain H residue 783 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 1 optimal weight: 0.9980 chunk 208 optimal weight: 0.9980 chunk 222 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 150 optimal weight: 0.1980 chunk 233 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 115 ASN H 802 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.132821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.109435 restraints weight = 25273.239| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.74 r_work: 0.3059 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18895 Z= 0.224 Angle : 0.547 7.023 25570 Z= 0.270 Chirality : 0.044 0.158 2851 Planarity : 0.004 0.042 3263 Dihedral : 6.274 129.896 2602 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.30 % Allowed : 8.81 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.18), residues: 2323 helix: 0.65 (0.16), residues: 1122 sheet: 0.58 (0.27), residues: 365 loop : 0.51 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 340 HIS 0.005 0.001 HIS C 161 PHE 0.009 0.001 PHE B 31 TYR 0.017 0.001 TYR F 779 ARG 0.003 0.000 ARG F 884 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 238 time to evaluate : 2.067 Fit side-chains REVERT: A 44 MET cc_start: 0.8902 (mtp) cc_final: 0.8570 (mmm) REVERT: A 137 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.6830 (mm-40) REVERT: A 157 ASP cc_start: 0.8377 (t0) cc_final: 0.7970 (t0) REVERT: A 211 ASP cc_start: 0.8614 (OUTLIER) cc_final: 0.8253 (t0) REVERT: B 72 GLU cc_start: 0.8470 (pp20) cc_final: 0.7974 (tt0) REVERT: B 206 ARG cc_start: 0.8310 (ttp-110) cc_final: 0.8037 (ttp-170) REVERT: B 360 GLN cc_start: 0.7857 (tp-100) cc_final: 0.7162 (tp-100) REVERT: C 6 THR cc_start: 0.8311 (p) cc_final: 0.8011 (t) REVERT: C 325 MET cc_start: 0.9086 (mmp) cc_final: 0.8352 (mmp) REVERT: D 83 GLU cc_start: 0.7803 (tp30) cc_final: 0.7421 (mt-10) REVERT: D 328 LYS cc_start: 0.8142 (ttmm) cc_final: 0.7778 (tttp) REVERT: E 121 GLN cc_start: 0.8698 (tt0) cc_final: 0.8422 (tt0) REVERT: E 123 MET cc_start: 0.9211 (mmt) cc_final: 0.8364 (mmt) REVERT: E 149 THR cc_start: 0.8906 (t) cc_final: 0.8635 (m) REVERT: E 263 GLN cc_start: 0.8105 (mt0) cc_final: 0.7868 (mt0) REVERT: E 289 ILE cc_start: 0.8676 (pt) cc_final: 0.8451 (pt) REVERT: G 1533 MET cc_start: 0.7965 (tpt) cc_final: 0.7744 (tpp) REVERT: G 1570 GLU cc_start: 0.8520 (tt0) cc_final: 0.7942 (pt0) REVERT: H 844 GLN cc_start: 0.6074 (tm-30) cc_final: 0.5782 (tp40) outliers start: 26 outliers final: 19 residues processed: 251 average time/residue: 0.3256 time to fit residues: 126.9452 Evaluate side-chains 251 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 230 time to evaluate : 2.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 363 ASP Chi-restraints excluded: chain C residue 372 ARG Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain F residue 733 LYS Chi-restraints excluded: chain F residue 841 THR Chi-restraints excluded: chain G residue 1532 ASP Chi-restraints excluded: chain G residue 1569 GLN Chi-restraints excluded: chain H residue 727 THR Chi-restraints excluded: chain H residue 783 ILE Chi-restraints excluded: chain H residue 803 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 214 optimal weight: 9.9990 chunk 189 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 167 optimal weight: 0.7980 chunk 231 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 115 ASN D 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.130177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.107328 restraints weight = 25496.721| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.76 r_work: 0.3002 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 18895 Z= 0.399 Angle : 0.621 7.576 25570 Z= 0.311 Chirality : 0.048 0.178 2851 Planarity : 0.005 0.044 3263 Dihedral : 6.535 130.272 2602 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.70 % Allowed : 9.46 % Favored : 88.84 % 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: 0.46 (0.17), residues: 2323 helix: 0.42 (0.16), residues: 1127 sheet: 0.51 (0.27), residues: 360 loop : 0.32 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 340 HIS 0.008 0.001 HIS C 161 PHE 0.011 0.002 PHE E 31 TYR 0.013 0.001 TYR D 143 ARG 0.005 0.000 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 235 time to evaluate : 2.206 Fit side-chains REVERT: A 113 LYS cc_start: 0.5858 (mptt) cc_final: 0.4862 (mptt) REVERT: A 123 MET cc_start: 0.9001 (tpp) cc_final: 0.8454 (mmp) REVERT: A 137 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8534 (mp10) REVERT: A 157 ASP cc_start: 0.8417 (t0) cc_final: 0.7966 (t0) REVERT: B 72 GLU cc_start: 0.8493 (pp20) cc_final: 0.7982 (tt0) REVERT: B 237 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.7936 (mt-10) REVERT: B 360 GLN cc_start: 0.7816 (tp-100) cc_final: 0.7103 (tp-100) REVERT: D 83 GLU cc_start: 0.7895 (tp30) cc_final: 0.7427 (mt-10) REVERT: D 328 LYS cc_start: 0.8176 (ttmm) cc_final: 0.7919 (mttt) REVERT: E 44 MET cc_start: 0.7961 (mtp) cc_final: 0.7550 (mtt) REVERT: E 121 GLN cc_start: 0.8744 (tt0) cc_final: 0.8432 (tt0) REVERT: E 149 THR cc_start: 0.8963 (t) cc_final: 0.8756 (m) REVERT: E 263 GLN cc_start: 0.8156 (mt0) cc_final: 0.7900 (mt0) REVERT: E 289 ILE cc_start: 0.8827 (pt) cc_final: 0.8575 (pt) REVERT: F 816 MET cc_start: 0.8191 (mmm) cc_final: 0.7780 (mmm) REVERT: G 1533 MET cc_start: 0.7995 (tpt) cc_final: 0.7718 (tpp) REVERT: G 1570 GLU cc_start: 0.8554 (tt0) cc_final: 0.7977 (pt0) REVERT: H 844 GLN cc_start: 0.6126 (tm-30) cc_final: 0.5758 (tp40) outliers start: 34 outliers final: 24 residues processed: 257 average time/residue: 0.3048 time to fit residues: 122.1887 Evaluate side-chains 254 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 228 time to evaluate : 2.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 372 ARG Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain F residue 728 ASP Chi-restraints excluded: chain F residue 733 LYS Chi-restraints excluded: chain F residue 841 THR Chi-restraints excluded: chain G residue 1569 GLN Chi-restraints excluded: chain H residue 727 THR Chi-restraints excluded: chain H residue 783 ILE Chi-restraints excluded: chain H residue 803 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 205 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 179 optimal weight: 0.6980 chunk 120 optimal weight: 0.7980 chunk 220 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 198 optimal weight: 0.5980 chunk 223 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 115 ASN D 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.132334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.109055 restraints weight = 25330.840| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.78 r_work: 0.3035 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18895 Z= 0.208 Angle : 0.550 9.089 25570 Z= 0.272 Chirality : 0.044 0.171 2851 Planarity : 0.004 0.040 3263 Dihedral : 6.330 133.286 2602 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.50 % Allowed : 10.51 % Favored : 87.99 % 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: 0.63 (0.18), residues: 2323 helix: 0.59 (0.16), residues: 1127 sheet: 0.51 (0.27), residues: 360 loop : 0.39 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 340 HIS 0.005 0.001 HIS C 161 PHE 0.009 0.001 PHE B 31 TYR 0.010 0.001 TYR F 779 ARG 0.003 0.000 ARG F 884 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 237 time to evaluate : 2.014 Fit side-chains REVERT: A 99 GLU cc_start: 0.7808 (pm20) cc_final: 0.7419 (mp0) REVERT: A 113 LYS cc_start: 0.5903 (mptt) cc_final: 0.4690 (mptt) REVERT: A 137 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.6970 (mm-40) REVERT: A 157 ASP cc_start: 0.8426 (t0) cc_final: 0.8034 (t0) REVERT: A 355 MET cc_start: 0.8757 (mtt) cc_final: 0.8554 (mtp) REVERT: B 72 GLU cc_start: 0.8450 (pp20) cc_final: 0.7932 (tt0) REVERT: B 237 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.7931 (mt-10) REVERT: B 360 GLN cc_start: 0.7841 (tp-100) cc_final: 0.7103 (tp-100) REVERT: C 325 MET cc_start: 0.9094 (mmp) cc_final: 0.8395 (mmp) REVERT: C 372 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8464 (ttm110) REVERT: D 83 GLU cc_start: 0.7918 (tp30) cc_final: 0.7516 (mt-10) REVERT: D 299 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.8697 (mtp) REVERT: D 328 LYS cc_start: 0.8080 (ttmm) cc_final: 0.7865 (mttt) REVERT: E 44 MET cc_start: 0.7895 (mtp) cc_final: 0.7518 (mtt) REVERT: E 121 GLN cc_start: 0.8732 (tt0) cc_final: 0.8450 (tt0) REVERT: E 149 THR cc_start: 0.8943 (t) cc_final: 0.8731 (m) REVERT: E 263 GLN cc_start: 0.8113 (mt0) cc_final: 0.7844 (mt0) REVERT: E 289 ILE cc_start: 0.8722 (pt) cc_final: 0.8507 (pt) REVERT: F 816 MET cc_start: 0.8182 (mmm) cc_final: 0.7786 (mmm) REVERT: G 1533 MET cc_start: 0.7958 (tpt) cc_final: 0.7706 (tpp) REVERT: G 1570 GLU cc_start: 0.8523 (tt0) cc_final: 0.8005 (tt0) REVERT: H 844 GLN cc_start: 0.5906 (tm-30) cc_final: 0.5568 (tp40) outliers start: 30 outliers final: 22 residues processed: 256 average time/residue: 0.3189 time to fit residues: 125.3220 Evaluate side-chains 256 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 230 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 372 ARG Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain F residue 728 ASP Chi-restraints excluded: chain F residue 841 THR Chi-restraints excluded: chain G residue 1532 ASP Chi-restraints excluded: chain G residue 1569 GLN Chi-restraints excluded: chain H residue 727 THR Chi-restraints excluded: chain H residue 783 ILE Chi-restraints excluded: chain H residue 803 LEU Chi-restraints excluded: chain H residue 870 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 196 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.131186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.108235 restraints weight = 25223.085| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.75 r_work: 0.3012 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 18895 Z= 0.306 Angle : 0.583 9.906 25570 Z= 0.288 Chirality : 0.046 0.175 2851 Planarity : 0.004 0.041 3263 Dihedral : 6.407 134.611 2602 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.60 % Allowed : 10.91 % Favored : 87.49 % 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 (0.18), residues: 2323 helix: 0.52 (0.16), residues: 1127 sheet: 0.49 (0.28), residues: 360 loop : 0.33 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 340 HIS 0.007 0.001 HIS C 161 PHE 0.010 0.001 PHE B 31 TYR 0.011 0.001 TYR D 143 ARG 0.004 0.000 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 228 time to evaluate : 2.232 Fit side-chains REVERT: A 113 LYS cc_start: 0.5995 (mptt) cc_final: 0.4688 (mptt) REVERT: A 137 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.6990 (mm-40) REVERT: B 72 GLU cc_start: 0.8484 (pp20) cc_final: 0.7962 (tt0) REVERT: B 237 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.7921 (mt-10) REVERT: B 297 ASN cc_start: 0.9169 (OUTLIER) cc_final: 0.8929 (m-40) REVERT: B 360 GLN cc_start: 0.7831 (tp-100) cc_final: 0.7122 (tp-100) REVERT: C 325 MET cc_start: 0.9107 (mmp) cc_final: 0.8874 (mmp) REVERT: C 372 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8479 (ttm110) REVERT: D 83 GLU cc_start: 0.7875 (tp30) cc_final: 0.7496 (mt-10) REVERT: D 299 MET cc_start: 0.9130 (OUTLIER) cc_final: 0.8708 (mtp) REVERT: D 328 LYS cc_start: 0.8115 (ttmm) cc_final: 0.7893 (mttt) REVERT: E 44 MET cc_start: 0.7914 (mtp) cc_final: 0.7514 (mtt) REVERT: E 121 GLN cc_start: 0.8739 (tt0) cc_final: 0.8463 (tt0) REVERT: E 149 THR cc_start: 0.8978 (t) cc_final: 0.8753 (m) REVERT: E 263 GLN cc_start: 0.8163 (mt0) cc_final: 0.7890 (mt0) REVERT: E 289 ILE cc_start: 0.8759 (pt) cc_final: 0.8517 (pt) REVERT: F 757 ASP cc_start: 0.8269 (t0) cc_final: 0.8064 (t0) REVERT: F 816 MET cc_start: 0.8210 (mmm) cc_final: 0.7843 (mmm) REVERT: G 1533 MET cc_start: 0.7974 (tpt) cc_final: 0.7703 (tpp) REVERT: G 1570 GLU cc_start: 0.8512 (tt0) cc_final: 0.7995 (tt0) REVERT: H 844 GLN cc_start: 0.6039 (tm-30) cc_final: 0.5697 (tp40) outliers start: 32 outliers final: 23 residues processed: 250 average time/residue: 0.3049 time to fit residues: 118.9431 Evaluate side-chains 255 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 227 time to evaluate : 2.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 372 ARG Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain F residue 728 ASP Chi-restraints excluded: chain F residue 841 THR Chi-restraints excluded: chain G residue 1532 ASP Chi-restraints excluded: chain G residue 1569 GLN Chi-restraints excluded: chain H residue 727 THR Chi-restraints excluded: chain H residue 783 ILE Chi-restraints excluded: chain H residue 803 LEU Chi-restraints excluded: chain H residue 870 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 17 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 106 optimal weight: 0.8980 chunk 79 optimal weight: 0.0970 chunk 56 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 78 optimal weight: 0.0370 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN D 12 ASN D 225 ASN H 801 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.133851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.110673 restraints weight = 25163.701| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.76 r_work: 0.3050 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 18895 Z= 0.161 Angle : 0.528 10.721 25570 Z= 0.259 Chirality : 0.043 0.161 2851 Planarity : 0.004 0.037 3263 Dihedral : 6.171 137.574 2602 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.20 % Allowed : 11.36 % Favored : 87.44 % 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: 0.80 (0.18), residues: 2323 helix: 0.74 (0.16), residues: 1127 sheet: 0.50 (0.27), residues: 360 loop : 0.51 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 340 HIS 0.004 0.001 HIS E 161 PHE 0.014 0.001 PHE C 124 TYR 0.010 0.001 TYR F 779 ARG 0.003 0.000 ARG D 28 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 233 time to evaluate : 2.087 Fit side-chains REVERT: A 99 GLU cc_start: 0.7794 (pm20) cc_final: 0.7335 (mp0) REVERT: A 113 LYS cc_start: 0.5841 (mptt) cc_final: 0.4404 (mptt) REVERT: A 157 ASP cc_start: 0.8384 (t0) cc_final: 0.7912 (t0) REVERT: B 72 GLU cc_start: 0.8384 (pp20) cc_final: 0.7849 (tt0) REVERT: B 224 GLU cc_start: 0.7666 (mp0) cc_final: 0.7396 (mp0) REVERT: B 360 GLN cc_start: 0.7794 (tp-100) cc_final: 0.7062 (mm-40) REVERT: C 325 MET cc_start: 0.9047 (mmp) cc_final: 0.8355 (mmp) REVERT: C 372 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8437 (ttm110) REVERT: D 83 GLU cc_start: 0.7807 (tp30) cc_final: 0.7380 (mt-10) REVERT: D 299 MET cc_start: 0.9056 (OUTLIER) cc_final: 0.8628 (mtp) REVERT: D 328 LYS cc_start: 0.8028 (ttmm) cc_final: 0.7800 (mttt) REVERT: D 355 MET cc_start: 0.8323 (ptp) cc_final: 0.8043 (ptm) REVERT: E 44 MET cc_start: 0.7819 (mtp) cc_final: 0.7436 (mtt) REVERT: E 121 GLN cc_start: 0.8689 (tt0) cc_final: 0.8439 (tt0) REVERT: E 149 THR cc_start: 0.8949 (t) cc_final: 0.8719 (m) REVERT: E 192 ILE cc_start: 0.8117 (mm) cc_final: 0.7868 (pt) REVERT: F 757 ASP cc_start: 0.8183 (t0) cc_final: 0.7947 (t0) REVERT: F 779 TYR cc_start: 0.8397 (m-80) cc_final: 0.8180 (m-80) REVERT: F 816 MET cc_start: 0.8078 (mmm) cc_final: 0.7744 (mmm) REVERT: G 1533 MET cc_start: 0.7782 (tpt) cc_final: 0.7522 (tpp) REVERT: G 1570 GLU cc_start: 0.8416 (tt0) cc_final: 0.7964 (tt0) REVERT: H 844 GLN cc_start: 0.6002 (tm-30) cc_final: 0.5669 (tp40) outliers start: 24 outliers final: 20 residues processed: 249 average time/residue: 0.2939 time to fit residues: 114.0831 Evaluate side-chains 246 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 224 time to evaluate : 1.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 372 ARG Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain F residue 728 ASP Chi-restraints excluded: chain F residue 841 THR Chi-restraints excluded: chain G residue 1532 ASP Chi-restraints excluded: chain G residue 1569 GLN Chi-restraints excluded: chain H residue 783 ILE Chi-restraints excluded: chain H residue 803 LEU Chi-restraints excluded: chain H residue 870 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 29 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 212 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 216 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 152 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.132083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.108662 restraints weight = 25448.821| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.78 r_work: 0.3015 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18895 Z= 0.265 Angle : 0.566 10.016 25570 Z= 0.277 Chirality : 0.045 0.170 2851 Planarity : 0.004 0.044 3263 Dihedral : 6.264 138.837 2602 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.30 % Allowed : 11.61 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.18), residues: 2323 helix: 0.66 (0.16), residues: 1127 sheet: 0.45 (0.27), residues: 360 loop : 0.41 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 340 HIS 0.006 0.001 HIS C 161 PHE 0.010 0.001 PHE B 31 TYR 0.009 0.001 TYR D 143 ARG 0.003 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 226 time to evaluate : 1.988 Fit side-chains REVERT: A 99 GLU cc_start: 0.7868 (pm20) cc_final: 0.7392 (mp0) REVERT: A 113 LYS cc_start: 0.6014 (mptt) cc_final: 0.4514 (mptt) REVERT: A 137 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.6928 (mm-40) REVERT: B 72 GLU cc_start: 0.8480 (pp20) cc_final: 0.7961 (tt0) REVERT: B 224 GLU cc_start: 0.7716 (mp0) cc_final: 0.7445 (mp0) REVERT: B 360 GLN cc_start: 0.7856 (tp-100) cc_final: 0.7167 (tp-100) REVERT: C 325 MET cc_start: 0.9096 (mmp) cc_final: 0.8855 (mmp) REVERT: C 372 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8442 (ttm110) REVERT: D 83 GLU cc_start: 0.7898 (tp30) cc_final: 0.7504 (mt-10) REVERT: D 299 MET cc_start: 0.9113 (OUTLIER) cc_final: 0.8686 (mtp) REVERT: D 328 LYS cc_start: 0.8085 (ttmm) cc_final: 0.7858 (mttt) REVERT: D 355 MET cc_start: 0.8333 (ptp) cc_final: 0.8061 (ptm) REVERT: D 372 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7840 (ptt-90) REVERT: E 44 MET cc_start: 0.7855 (mtp) cc_final: 0.7474 (mtt) REVERT: E 121 GLN cc_start: 0.8732 (tt0) cc_final: 0.8503 (tt0) REVERT: E 149 THR cc_start: 0.8975 (t) cc_final: 0.8742 (m) REVERT: E 192 ILE cc_start: 0.8221 (mm) cc_final: 0.7993 (pt) REVERT: E 289 ILE cc_start: 0.8738 (pt) cc_final: 0.8509 (pt) REVERT: F 757 ASP cc_start: 0.8213 (t0) cc_final: 0.7984 (t0) REVERT: F 779 TYR cc_start: 0.8477 (m-80) cc_final: 0.8258 (m-80) REVERT: F 816 MET cc_start: 0.8173 (mmm) cc_final: 0.7836 (mmm) REVERT: G 1570 GLU cc_start: 0.8452 (tt0) cc_final: 0.7980 (tt0) outliers start: 26 outliers final: 20 residues processed: 244 average time/residue: 0.3010 time to fit residues: 114.4506 Evaluate side-chains 249 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 225 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 372 ARG Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain F residue 728 ASP Chi-restraints excluded: chain F residue 841 THR Chi-restraints excluded: chain G residue 1532 ASP Chi-restraints excluded: chain G residue 1569 GLN Chi-restraints excluded: chain H residue 783 ILE Chi-restraints excluded: chain H residue 803 LEU Chi-restraints excluded: chain H residue 870 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 224 optimal weight: 0.8980 chunk 206 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 104 optimal weight: 0.0040 chunk 12 optimal weight: 0.9990 chunk 143 optimal weight: 0.7980 chunk 208 optimal weight: 0.6980 chunk 87 optimal weight: 0.5980 chunk 228 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 39 optimal weight: 0.0980 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.133885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.110732 restraints weight = 25218.091| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.77 r_work: 0.3077 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18895 Z= 0.163 Angle : 0.533 8.130 25570 Z= 0.260 Chirality : 0.043 0.183 2851 Planarity : 0.004 0.036 3263 Dihedral : 6.116 140.632 2602 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.30 % Allowed : 11.51 % Favored : 87.19 % 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: 0.85 (0.18), residues: 2323 helix: 0.80 (0.16), residues: 1122 sheet: 0.51 (0.27), residues: 360 loop : 0.51 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 340 HIS 0.004 0.001 HIS E 161 PHE 0.009 0.001 PHE B 31 TYR 0.009 0.001 TYR F 779 ARG 0.002 0.000 ARG B 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 228 time to evaluate : 2.073 Fit side-chains REVERT: A 99 GLU cc_start: 0.7855 (pm20) cc_final: 0.7389 (mp0) REVERT: A 113 LYS cc_start: 0.5970 (mptt) cc_final: 0.4546 (mptt) REVERT: A 137 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.6800 (mm-40) REVERT: B 72 GLU cc_start: 0.8452 (pp20) cc_final: 0.7931 (tt0) REVERT: B 224 GLU cc_start: 0.7714 (mp0) cc_final: 0.7446 (mp0) REVERT: B 237 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.7910 (mt-10) REVERT: B 360 GLN cc_start: 0.7884 (tp-100) cc_final: 0.7117 (mm110) REVERT: C 325 MET cc_start: 0.9086 (mmp) cc_final: 0.8384 (mmp) REVERT: C 372 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8442 (ttm110) REVERT: D 83 GLU cc_start: 0.7816 (tp30) cc_final: 0.7447 (mt-10) REVERT: D 299 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.8606 (mtp) REVERT: D 328 LYS cc_start: 0.8047 (ttmm) cc_final: 0.7823 (mttt) REVERT: D 355 MET cc_start: 0.8343 (ptp) cc_final: 0.8081 (ptm) REVERT: D 372 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7831 (ptt-90) REVERT: E 44 MET cc_start: 0.7962 (mtp) cc_final: 0.7593 (mtt) REVERT: E 121 GLN cc_start: 0.8718 (tt0) cc_final: 0.8510 (tt0) REVERT: E 149 THR cc_start: 0.8929 (t) cc_final: 0.8713 (m) REVERT: F 757 ASP cc_start: 0.8190 (t0) cc_final: 0.7957 (t0) REVERT: F 816 MET cc_start: 0.8138 (mmm) cc_final: 0.7773 (mmm) REVERT: G 1533 MET cc_start: 0.7839 (tpt) cc_final: 0.7595 (tpp) REVERT: G 1570 GLU cc_start: 0.8402 (tt0) cc_final: 0.7994 (tt0) outliers start: 26 outliers final: 20 residues processed: 246 average time/residue: 0.3051 time to fit residues: 116.4479 Evaluate side-chains 249 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 224 time to evaluate : 2.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 372 ARG Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain F residue 728 ASP Chi-restraints excluded: chain F residue 841 THR Chi-restraints excluded: chain G residue 1532 ASP Chi-restraints excluded: chain G residue 1569 GLN Chi-restraints excluded: chain H residue 783 ILE Chi-restraints excluded: chain H residue 803 LEU Chi-restraints excluded: chain H residue 870 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 217 optimal weight: 0.0970 chunk 210 optimal weight: 4.9990 chunk 173 optimal weight: 0.9990 chunk 158 optimal weight: 0.8980 chunk 203 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 218 optimal weight: 0.6980 chunk 213 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.132870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.109595 restraints weight = 25265.534| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.78 r_work: 0.3044 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 18895 Z= 0.224 Angle : 0.554 9.602 25570 Z= 0.271 Chirality : 0.045 0.241 2851 Planarity : 0.004 0.037 3263 Dihedral : 6.156 141.727 2602 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.40 % Allowed : 11.81 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.18), residues: 2323 helix: 0.74 (0.16), residues: 1122 sheet: 0.49 (0.27), residues: 360 loop : 0.47 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 340 HIS 0.005 0.001 HIS C 161 PHE 0.009 0.001 PHE B 31 TYR 0.020 0.001 TYR F 779 ARG 0.003 0.000 ARG F 884 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9816.44 seconds wall clock time: 180 minutes 27.19 seconds (10827.19 seconds total)