Starting phenix.real_space_refine on Thu Sep 18 17:03:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dva_47194/09_2025/9dva_47194_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dva_47194/09_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_47194/09_2025/9dva_47194.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dva_47194/09_2025/9dva_47194.map" model { file = "/net/cci-nas-00/data/ceres_data/9dva_47194/09_2025/9dva_47194_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dva_47194/09_2025/9dva_47194_neut.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.31, per 1000 atoms: 0.23 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: 1.15 Conformation dependent library (CDL) restraints added in 786.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.01 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: 2.97 Time building geometry restraints manager: 1.53 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 16.730 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.820 ------------------------------------------------------------------------------- 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= 0.131 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.000 ARG C 372 TYR 0.024 0.001 TYR F 779 PHE 0.015 0.001 PHE E 124 TRP 0.008 0.001 TRP H 705 HIS 0.003 0.000 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00281 (18895) covalent geometry : angle 0.51192 (25570) hydrogen bonds : bond 0.27398 ( 928) hydrogen bonds : angle 7.39320 ( 2511) *********************** 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 : 0.614 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 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: 0.7644 (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: 0.7905 (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: 0.8250 (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: 0.1323 time to fit residues: 67.7557 Evaluate side-chains 238 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.6980 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.132796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.109855 restraints weight = 25282.813| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.76 r_work: 0.3069 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18895 Z= 0.166 Angle : 0.593 9.154 25570 Z= 0.301 Chirality : 0.045 0.166 2851 Planarity : 0.004 0.055 3263 Dihedral : 6.415 124.499 2602 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.90 % Allowed : 6.01 % Favored : 93.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.18), residues: 2323 helix: 0.27 (0.16), residues: 1132 sheet: 0.87 (0.29), residues: 360 loop : 0.58 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 372 TYR 0.013 0.001 TYR F 779 PHE 0.010 0.001 PHE E 255 TRP 0.012 0.001 TRP B 340 HIS 0.006 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00389 (18895) covalent geometry : angle 0.59264 (25570) hydrogen bonds : bond 0.05859 ( 928) hydrogen bonds : angle 4.97092 ( 2511) *********************** 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 269 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 251 time to evaluate : 0.683 Fit side-chains REVERT: A 44 MET cc_start: 0.8871 (mtp) cc_final: 0.8551 (mmm) REVERT: A 157 ASP cc_start: 0.8352 (t0) cc_final: 0.7860 (t0) REVERT: A 271 SER cc_start: 0.8877 (m) cc_final: 0.8664 (p) REVERT: B 72 GLU cc_start: 0.8525 (pp20) cc_final: 0.7997 (tt0) REVERT: B 206 ARG cc_start: 0.8331 (ttp-110) cc_final: 0.8082 (ttp-170) REVERT: B 360 GLN cc_start: 0.7838 (tp-100) cc_final: 0.7352 (tp-100) REVERT: C 6 THR cc_start: 0.8340 (p) cc_final: 0.8105 (t) REVERT: C 325 MET cc_start: 0.9111 (mmp) cc_final: 0.8414 (mmp) REVERT: D 328 LYS cc_start: 0.8116 (mtpp) cc_final: 0.7838 (tptp) REVERT: E 121 GLN cc_start: 0.8720 (tt0) cc_final: 0.8367 (tt0) REVERT: E 149 THR cc_start: 0.8875 (t) cc_final: 0.8620 (m) REVERT: E 227 MET cc_start: 0.8467 (mmt) cc_final: 0.8038 (mmt) REVERT: E 289 ILE cc_start: 0.8723 (pt) cc_final: 0.8505 (pt) REVERT: G 1533 MET cc_start: 0.7979 (tpt) cc_final: 0.7697 (tpp) REVERT: G 1570 GLU cc_start: 0.8419 (tt0) cc_final: 0.7863 (pt0) REVERT: H 844 GLN cc_start: 0.6005 (tm-30) cc_final: 0.5803 (tp40) outliers start: 18 outliers final: 14 residues processed: 262 average time/residue: 0.1240 time to fit residues: 50.9002 Evaluate side-chains 243 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 229 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 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 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 H residue 783 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 87 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 204 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 226 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3509 r_free = 0.3509 target = 0.131112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.107769 restraints weight = 25379.149| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.75 r_work: 0.3035 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 18895 Z= 0.193 Angle : 0.595 7.413 25570 Z= 0.297 Chirality : 0.046 0.190 2851 Planarity : 0.004 0.049 3263 Dihedral : 6.473 126.671 2602 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.25 % Allowed : 7.81 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.18), residues: 2323 helix: 0.40 (0.16), residues: 1122 sheet: 0.67 (0.28), residues: 365 loop : 0.46 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 62 TYR 0.011 0.001 TYR D 143 PHE 0.009 0.001 PHE C 31 TRP 0.014 0.002 TRP B 340 HIS 0.008 0.001 HIS H 766 Details of bonding type rmsd covalent geometry : bond 0.00478 (18895) covalent geometry : angle 0.59469 (25570) hydrogen bonds : bond 0.05557 ( 928) hydrogen bonds : angle 4.72329 ( 2511) *********************** 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 258 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 233 time to evaluate : 0.623 Fit side-chains REVERT: A 44 MET cc_start: 0.8987 (mtp) cc_final: 0.8552 (mmm) REVERT: A 157 ASP cc_start: 0.8387 (t0) cc_final: 0.7890 (t0) REVERT: A 271 SER cc_start: 0.8878 (m) cc_final: 0.8661 (p) REVERT: B 72 GLU cc_start: 0.8486 (pp20) cc_final: 0.7992 (tt0) REVERT: B 325 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7433 (mtp) REVERT: B 360 GLN cc_start: 0.7831 (tp-100) cc_final: 0.7332 (tp-100) REVERT: C 6 THR cc_start: 0.8321 (p) cc_final: 0.8029 (t) REVERT: C 325 MET cc_start: 0.9098 (mmp) cc_final: 0.8340 (mmp) REVERT: D 283 MET cc_start: 0.9000 (mmt) cc_final: 0.8410 (mmt) REVERT: D 328 LYS cc_start: 0.8167 (mtpp) cc_final: 0.7632 (mmtt) REVERT: E 44 MET cc_start: 0.7882 (mtp) cc_final: 0.7488 (mtt) REVERT: E 121 GLN cc_start: 0.8745 (tt0) cc_final: 0.8405 (tt0) REVERT: E 149 THR cc_start: 0.8920 (t) cc_final: 0.8650 (m) REVERT: E 227 MET cc_start: 0.8369 (mmt) cc_final: 0.7759 (mmt) REVERT: E 263 GLN cc_start: 0.8132 (mt0) cc_final: 0.7931 (mt0) REVERT: E 276 GLU cc_start: 0.8544 (pt0) cc_final: 0.8282 (pt0) REVERT: E 289 ILE cc_start: 0.8776 (pt) cc_final: 0.8541 (pt) REVERT: G 1533 MET cc_start: 0.8010 (tpt) cc_final: 0.7731 (tpp) REVERT: G 1570 GLU cc_start: 0.8533 (tt0) cc_final: 0.7953 (pt0) REVERT: H 844 GLN cc_start: 0.6107 (tm-30) cc_final: 0.5788 (tp40) outliers start: 25 outliers final: 17 residues processed: 248 average time/residue: 0.1325 time to fit residues: 51.0420 Evaluate side-chains 244 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 226 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 325 MET 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 D residue 100 GLU 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 128 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 224 optimal weight: 0.7980 chunk 203 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 227 optimal weight: 0.7980 chunk 138 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 225 ASN H 802 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.131952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.108586 restraints weight = 25507.852| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.76 r_work: 0.3016 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18895 Z= 0.157 Angle : 0.564 7.029 25570 Z= 0.280 Chirality : 0.045 0.184 2851 Planarity : 0.004 0.044 3263 Dihedral : 6.387 129.420 2602 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.35 % Allowed : 9.06 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.18), residues: 2323 helix: 0.54 (0.16), residues: 1122 sheet: 0.63 (0.28), residues: 360 loop : 0.45 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 884 TYR 0.015 0.001 TYR F 779 PHE 0.009 0.001 PHE B 31 TRP 0.013 0.001 TRP D 340 HIS 0.005 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00381 (18895) covalent geometry : angle 0.56378 (25570) hydrogen bonds : bond 0.04842 ( 928) hydrogen bonds : angle 4.53154 ( 2511) *********************** 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 262 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 235 time to evaluate : 0.646 Fit side-chains REVERT: A 113 LYS cc_start: 0.5683 (mptt) cc_final: 0.5005 (mptt) REVERT: A 137 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.6890 (mm-40) REVERT: A 157 ASP cc_start: 0.8325 (t0) cc_final: 0.7913 (t0) REVERT: A 271 SER cc_start: 0.8873 (m) cc_final: 0.8621 (p) REVERT: B 72 GLU cc_start: 0.8415 (pp20) cc_final: 0.7898 (tt0) REVERT: B 360 GLN cc_start: 0.7777 (tp-100) cc_final: 0.7063 (tp-100) REVERT: C 6 THR cc_start: 0.8332 (p) cc_final: 0.8004 (t) REVERT: C 132 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.8071 (ttp) REVERT: C 325 MET cc_start: 0.9058 (mmp) cc_final: 0.8311 (mmp) REVERT: D 83 GLU cc_start: 0.7801 (tp30) cc_final: 0.7348 (mt-10) REVERT: D 328 LYS cc_start: 0.8119 (mtpp) cc_final: 0.7539 (mmtt) REVERT: E 44 MET cc_start: 0.7912 (mtp) cc_final: 0.7516 (mtt) REVERT: E 121 GLN cc_start: 0.8672 (tt0) cc_final: 0.8370 (tt0) REVERT: E 123 MET cc_start: 0.9182 (mmt) cc_final: 0.8299 (mmt) REVERT: E 149 THR cc_start: 0.8935 (t) cc_final: 0.8686 (m) REVERT: E 263 GLN cc_start: 0.8073 (mt0) cc_final: 0.7819 (mt0) REVERT: E 276 GLU cc_start: 0.8425 (pt0) cc_final: 0.8137 (pt0) REVERT: E 289 ILE cc_start: 0.8675 (pt) cc_final: 0.8453 (pt) REVERT: G 1533 MET cc_start: 0.7918 (tpt) cc_final: 0.7649 (tpp) REVERT: G 1570 GLU cc_start: 0.8516 (tt0) cc_final: 0.7894 (pt0) REVERT: H 844 GLN cc_start: 0.6062 (tm-30) cc_final: 0.5710 (tp40) outliers start: 27 outliers final: 21 residues processed: 251 average time/residue: 0.1306 time to fit residues: 51.3373 Evaluate side-chains 254 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 231 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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 288 ASP 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 12 ASN Chi-restraints excluded: chain C residue 115 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 100 GLU 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 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 164 optimal weight: 0.9980 chunk 229 optimal weight: 7.9990 chunk 166 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 E 225 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.130592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.107350 restraints weight = 25361.026| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.76 r_work: 0.3001 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 18895 Z= 0.219 Angle : 0.604 7.519 25570 Z= 0.301 Chirality : 0.047 0.191 2851 Planarity : 0.004 0.044 3263 Dihedral : 6.508 130.403 2602 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.75 % Allowed : 10.01 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.18), residues: 2323 helix: 0.44 (0.16), residues: 1127 sheet: 0.51 (0.28), residues: 360 loop : 0.35 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 62 TYR 0.012 0.001 TYR D 143 PHE 0.011 0.001 PHE B 31 TRP 0.015 0.002 TRP B 340 HIS 0.007 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00547 (18895) covalent geometry : angle 0.60399 (25570) hydrogen bonds : bond 0.05277 ( 928) hydrogen bonds : angle 4.56095 ( 2511) *********************** 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 266 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 231 time to evaluate : 0.777 Fit side-chains REVERT: A 113 LYS cc_start: 0.5896 (mptt) cc_final: 0.4775 (mptt) REVERT: A 137 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8539 (mp10) REVERT: A 157 ASP cc_start: 0.8424 (t0) cc_final: 0.7977 (t0) REVERT: A 271 SER cc_start: 0.8907 (m) cc_final: 0.8683 (p) REVERT: B 72 GLU cc_start: 0.8495 (pp20) cc_final: 0.7974 (tt0) REVERT: B 237 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.7945 (mt-10) REVERT: B 360 GLN cc_start: 0.7834 (tp-100) cc_final: 0.7111 (tp-100) REVERT: D 83 GLU cc_start: 0.7899 (tp30) cc_final: 0.7453 (mt-10) REVERT: D 328 LYS cc_start: 0.8178 (mtpp) cc_final: 0.7740 (mttm) REVERT: E 44 MET cc_start: 0.7960 (mtp) cc_final: 0.7555 (mtt) REVERT: E 121 GLN cc_start: 0.8729 (tt0) cc_final: 0.8428 (tt0) REVERT: E 149 THR cc_start: 0.8961 (t) cc_final: 0.8749 (m) REVERT: E 263 GLN cc_start: 0.8164 (mt0) cc_final: 0.7911 (mt0) REVERT: E 289 ILE cc_start: 0.8806 (pt) cc_final: 0.8560 (pt) REVERT: F 757 ASP cc_start: 0.8285 (t0) cc_final: 0.8080 (t0) REVERT: F 816 MET cc_start: 0.8205 (mmm) cc_final: 0.7804 (mmm) REVERT: G 1533 MET cc_start: 0.8029 (tpt) cc_final: 0.7754 (tpp) REVERT: G 1570 GLU cc_start: 0.8556 (tt0) cc_final: 0.7968 (pt0) REVERT: H 844 GLN cc_start: 0.6137 (tm-30) cc_final: 0.5768 (tp40) outliers start: 35 outliers final: 27 residues processed: 254 average time/residue: 0.1278 time to fit residues: 50.9441 Evaluate side-chains 258 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 229 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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 288 ASP Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 34 ILE 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 12 ASN Chi-restraints excluded: chain C residue 115 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 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 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 Chi-restraints excluded: chain H residue 870 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 192 optimal weight: 2.9990 chunk 220 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 158 optimal weight: 0.6980 chunk 205 optimal weight: 0.4980 chunk 50 optimal weight: 0.5980 chunk 69 optimal weight: 0.0770 chunk 125 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 10 optimal weight: 0.0670 chunk 51 optimal weight: 0.8980 overall best weight: 0.3876 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.133893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.110767 restraints weight = 25030.055| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.77 r_work: 0.3063 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2009 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= 0.103 Angle : 0.525 8.974 25570 Z= 0.257 Chirality : 0.043 0.175 2851 Planarity : 0.004 0.039 3263 Dihedral : 6.201 134.557 2602 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.10 % Allowed : 11.06 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.18), residues: 2323 helix: 0.75 (0.16), residues: 1122 sheet: 0.53 (0.27), residues: 360 loop : 0.49 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 116 TYR 0.012 0.001 TYR F 779 PHE 0.009 0.001 PHE B 31 TRP 0.010 0.001 TRP D 340 HIS 0.004 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00232 (18895) covalent geometry : angle 0.52506 (25570) hydrogen bonds : bond 0.04003 ( 928) hydrogen bonds : angle 4.30878 ( 2511) *********************** 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 262 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 240 time to evaluate : 0.637 Fit side-chains REVERT: A 99 GLU cc_start: 0.7792 (pm20) cc_final: 0.7378 (mp0) REVERT: A 113 LYS cc_start: 0.5842 (mptt) cc_final: 0.4657 (mptt) REVERT: A 137 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.6915 (mm-40) REVERT: A 157 ASP cc_start: 0.8395 (t0) cc_final: 0.7977 (t0) REVERT: A 271 SER cc_start: 0.8894 (m) cc_final: 0.8675 (p) REVERT: B 72 GLU cc_start: 0.8424 (pp20) cc_final: 0.7902 (tt0) REVERT: B 237 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.7928 (mt-10) REVERT: B 360 GLN cc_start: 0.7858 (tp-100) cc_final: 0.7094 (tp-100) REVERT: C 325 MET cc_start: 0.9086 (mmp) cc_final: 0.8408 (mmp) REVERT: C 372 ARG cc_start: 0.8677 (ttp-110) cc_final: 0.8435 (ttm110) REVERT: D 83 GLU cc_start: 0.7893 (tp30) cc_final: 0.7504 (mt-10) REVERT: D 328 LYS cc_start: 0.8104 (mtpp) cc_final: 0.7551 (mmtt) REVERT: E 44 MET cc_start: 0.7845 (mtp) cc_final: 0.7469 (mtt) REVERT: E 57 GLU cc_start: 0.7938 (tp30) cc_final: 0.7728 (tp30) REVERT: E 121 GLN cc_start: 0.8700 (tt0) cc_final: 0.8439 (tt0) REVERT: E 149 THR cc_start: 0.8935 (t) cc_final: 0.8706 (m) REVERT: E 192 ILE cc_start: 0.8067 (mm) cc_final: 0.7853 (pt) REVERT: E 263 GLN cc_start: 0.8109 (mt0) cc_final: 0.7837 (mt0) REVERT: F 816 MET cc_start: 0.8157 (mmm) cc_final: 0.7742 (mmm) REVERT: G 1533 MET cc_start: 0.7974 (tpt) cc_final: 0.7724 (tpp) REVERT: G 1570 GLU cc_start: 0.8476 (tt0) cc_final: 0.8006 (tt0) REVERT: H 844 GLN cc_start: 0.5931 (tm-30) cc_final: 0.5607 (tp40) outliers start: 22 outliers final: 14 residues processed: 255 average time/residue: 0.1321 time to fit residues: 52.4690 Evaluate side-chains 242 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 226 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 350 SER 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 363 ASP 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 234 SER Chi-restraints excluded: chain E residue 358 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 50 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 chunk 232 optimal weight: 0.0020 chunk 226 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 193 optimal weight: 0.0970 chunk 0 optimal weight: 4.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.133654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.110631 restraints weight = 25318.115| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.74 r_work: 0.3076 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18895 Z= 0.120 Angle : 0.533 9.846 25570 Z= 0.260 Chirality : 0.043 0.173 2851 Planarity : 0.004 0.038 3263 Dihedral : 6.113 135.923 2602 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.15 % Allowed : 11.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.18), residues: 2323 helix: 0.79 (0.16), residues: 1127 sheet: 0.53 (0.27), residues: 360 loop : 0.53 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 28 TYR 0.022 0.001 TYR F 779 PHE 0.009 0.001 PHE B 31 TRP 0.010 0.001 TRP D 340 HIS 0.004 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00284 (18895) covalent geometry : angle 0.53343 (25570) hydrogen bonds : bond 0.04017 ( 928) hydrogen bonds : angle 4.24200 ( 2511) *********************** 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 250 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 227 time to evaluate : 0.789 Fit side-chains REVERT: A 99 GLU cc_start: 0.7800 (pm20) cc_final: 0.7406 (mp0) REVERT: A 113 LYS cc_start: 0.5996 (mptt) cc_final: 0.4655 (mptt) REVERT: A 137 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8531 (mp10) REVERT: A 157 ASP cc_start: 0.8441 (t0) cc_final: 0.7999 (t0) REVERT: A 271 SER cc_start: 0.8889 (m) cc_final: 0.8680 (p) REVERT: B 72 GLU cc_start: 0.8452 (pp20) cc_final: 0.7932 (tt0) REVERT: B 237 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7949 (mt-10) REVERT: B 360 GLN cc_start: 0.7855 (tp-100) cc_final: 0.7176 (tp-100) REVERT: C 83 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8324 (mt-10) REVERT: C 325 MET cc_start: 0.9102 (mmp) cc_final: 0.8412 (mmp) REVERT: C 372 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8480 (ttm110) REVERT: D 83 GLU cc_start: 0.7913 (tp30) cc_final: 0.7509 (mt-10) REVERT: D 299 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8738 (mtp) REVERT: D 328 LYS cc_start: 0.8071 (mtpp) cc_final: 0.7561 (mmtt) REVERT: E 44 MET cc_start: 0.7843 (mtp) cc_final: 0.7470 (mtt) REVERT: E 57 GLU cc_start: 0.7955 (tp30) cc_final: 0.7735 (tp30) REVERT: E 121 GLN cc_start: 0.8718 (tt0) cc_final: 0.8477 (tt0) REVERT: E 149 THR cc_start: 0.8941 (t) cc_final: 0.8716 (m) REVERT: F 816 MET cc_start: 0.8124 (mmm) cc_final: 0.7732 (mmm) REVERT: G 1533 MET cc_start: 0.7846 (tpt) cc_final: 0.7621 (tpp) REVERT: G 1570 GLU cc_start: 0.8388 (tt0) cc_final: 0.7978 (tt0) REVERT: H 844 GLN cc_start: 0.6027 (tm-30) cc_final: 0.5686 (tp40) outliers start: 23 outliers final: 18 residues processed: 243 average time/residue: 0.1337 time to fit residues: 51.0510 Evaluate side-chains 244 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 222 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 142 LEU 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 94 optimal weight: 0.5980 chunk 178 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 227 optimal weight: 0.5980 chunk 161 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 26 optimal weight: 0.0060 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 12 ASN H 801 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.133886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.110900 restraints weight = 25208.923| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.77 r_work: 0.3079 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18895 Z= 0.114 Angle : 0.527 7.376 25570 Z= 0.256 Chirality : 0.043 0.223 2851 Planarity : 0.004 0.040 3263 Dihedral : 6.057 137.160 2602 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.40 % Allowed : 11.46 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.18), residues: 2323 helix: 0.84 (0.16), residues: 1122 sheet: 0.54 (0.27), residues: 360 loop : 0.53 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 256 TYR 0.022 0.001 TYR F 779 PHE 0.009 0.001 PHE B 31 TRP 0.010 0.001 TRP D 340 HIS 0.004 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00267 (18895) covalent geometry : angle 0.52654 (25570) hydrogen bonds : bond 0.03897 ( 928) hydrogen bonds : angle 4.21098 ( 2511) *********************** 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 252 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 224 time to evaluate : 0.756 Fit side-chains REVERT: A 99 GLU cc_start: 0.7814 (pm20) cc_final: 0.7427 (mp0) REVERT: A 113 LYS cc_start: 0.6038 (mptt) cc_final: 0.4647 (mptt) REVERT: A 157 ASP cc_start: 0.8438 (t0) cc_final: 0.8011 (t0) REVERT: A 271 SER cc_start: 0.8891 (m) cc_final: 0.8682 (p) REVERT: B 224 GLU cc_start: 0.7666 (mp0) cc_final: 0.7454 (mp0) REVERT: B 237 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7944 (mt-10) REVERT: B 360 GLN cc_start: 0.7862 (tp-100) cc_final: 0.7109 (mm110) REVERT: C 325 MET cc_start: 0.9094 (mmp) cc_final: 0.8348 (mmp) REVERT: C 372 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8468 (ttm110) REVERT: D 83 GLU cc_start: 0.7840 (tp30) cc_final: 0.7478 (mt-10) REVERT: D 299 MET cc_start: 0.9082 (OUTLIER) cc_final: 0.8705 (mtp) REVERT: D 328 LYS cc_start: 0.8076 (mtpp) cc_final: 0.7559 (mmtt) REVERT: D 355 MET cc_start: 0.8307 (ptp) cc_final: 0.8045 (ptm) REVERT: D 372 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7857 (ptt-90) REVERT: E 44 MET cc_start: 0.7832 (mtp) cc_final: 0.7464 (mtt) REVERT: E 57 GLU cc_start: 0.7934 (tp30) cc_final: 0.7678 (tp30) REVERT: E 121 GLN cc_start: 0.8726 (tt0) cc_final: 0.8508 (tt0) REVERT: E 149 THR cc_start: 0.8941 (t) cc_final: 0.8715 (m) REVERT: F 816 MET cc_start: 0.8134 (mmm) cc_final: 0.7741 (mmm) REVERT: G 1533 MET cc_start: 0.7845 (tpt) cc_final: 0.7604 (tpp) REVERT: G 1570 GLU cc_start: 0.8388 (tt0) cc_final: 0.7981 (tt0) outliers start: 28 outliers final: 21 residues processed: 244 average time/residue: 0.1391 time to fit residues: 52.9972 Evaluate side-chains 245 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 220 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 142 LEU 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 363 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 191 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 199 optimal weight: 0.4980 chunk 175 optimal weight: 1.9990 chunk 152 optimal weight: 0.3980 chunk 201 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 200 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 212 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.3538 r_free = 0.3538 target = 0.133549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.110537 restraints weight = 25264.470| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.76 r_work: 0.3091 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18895 Z= 0.125 Angle : 0.542 12.721 25570 Z= 0.263 Chirality : 0.044 0.279 2851 Planarity : 0.004 0.037 3263 Dihedral : 6.061 138.200 2602 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.30 % Allowed : 11.76 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.18), residues: 2323 helix: 0.83 (0.16), residues: 1122 sheet: 0.54 (0.27), residues: 360 loop : 0.52 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 884 TYR 0.020 0.001 TYR F 779 PHE 0.009 0.001 PHE B 31 TRP 0.010 0.001 TRP D 340 HIS 0.005 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00300 (18895) covalent geometry : angle 0.54208 (25570) hydrogen bonds : bond 0.03984 ( 928) hydrogen bonds : angle 4.20841 ( 2511) *********************** 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 247 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 221 time to evaluate : 0.699 Fit side-chains REVERT: A 113 LYS cc_start: 0.5947 (mptt) cc_final: 0.4540 (mptt) REVERT: A 157 ASP cc_start: 0.8433 (t0) cc_final: 0.7997 (t0) REVERT: A 271 SER cc_start: 0.8891 (m) cc_final: 0.8671 (p) REVERT: B 237 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.7950 (mt-10) REVERT: B 360 GLN cc_start: 0.7848 (tp-100) cc_final: 0.7089 (mm110) REVERT: C 325 MET cc_start: 0.9093 (mmp) cc_final: 0.8403 (mmp) REVERT: C 372 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8436 (ttm110) REVERT: D 83 GLU cc_start: 0.7831 (tp30) cc_final: 0.7464 (mt-10) REVERT: D 299 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8711 (mtp) REVERT: D 328 LYS cc_start: 0.8068 (mtpp) cc_final: 0.7547 (mmtt) REVERT: D 355 MET cc_start: 0.8300 (ptp) cc_final: 0.8033 (ptm) REVERT: D 372 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7864 (ptt-90) REVERT: E 44 MET cc_start: 0.7816 (mtp) cc_final: 0.7443 (mtt) REVERT: E 57 GLU cc_start: 0.7933 (tp30) cc_final: 0.7671 (tp30) REVERT: E 121 GLN cc_start: 0.8722 (tt0) cc_final: 0.8502 (tt0) REVERT: E 149 THR cc_start: 0.8949 (t) cc_final: 0.8719 (m) REVERT: F 816 MET cc_start: 0.8125 (mmm) cc_final: 0.7747 (mmm) REVERT: G 1533 MET cc_start: 0.7833 (tpt) cc_final: 0.7582 (tpp) REVERT: G 1570 GLU cc_start: 0.8382 (tt0) cc_final: 0.7966 (tt0) outliers start: 26 outliers final: 22 residues processed: 239 average time/residue: 0.1387 time to fit residues: 51.8101 Evaluate side-chains 246 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 220 time to evaluate : 0.737 ------------------------------------------------------------------------------- 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 142 LEU 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 363 ASP 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 3 optimal weight: 0.6980 chunk 180 optimal weight: 0.0010 chunk 227 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 168 optimal weight: 0.8980 chunk 225 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.133338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.110272 restraints weight = 25288.414| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.78 r_work: 0.3053 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18895 Z= 0.130 Angle : 0.550 13.800 25570 Z= 0.267 Chirality : 0.044 0.293 2851 Planarity : 0.004 0.037 3263 Dihedral : 6.066 139.303 2602 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.25 % Allowed : 11.76 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.18), residues: 2323 helix: 0.81 (0.16), residues: 1122 sheet: 0.54 (0.27), residues: 360 loop : 0.51 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 884 TYR 0.019 0.001 TYR F 779 PHE 0.009 0.001 PHE B 31 TRP 0.011 0.001 TRP D 340 HIS 0.005 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00314 (18895) covalent geometry : angle 0.54991 (25570) hydrogen bonds : bond 0.04043 ( 928) hydrogen bonds : angle 4.21508 ( 2511) ********************** 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 248 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 223 time to evaluate : 0.736 Fit side-chains REVERT: A 99 GLU cc_start: 0.7819 (pm20) cc_final: 0.7324 (mp0) REVERT: A 113 LYS cc_start: 0.5978 (mptt) cc_final: 0.4572 (mptt) REVERT: A 271 SER cc_start: 0.8879 (m) cc_final: 0.8663 (p) REVERT: B 237 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7955 (mt-10) REVERT: B 360 GLN cc_start: 0.7872 (tp-100) cc_final: 0.7115 (mm110) REVERT: C 325 MET cc_start: 0.9096 (mmp) cc_final: 0.8364 (mmp) REVERT: C 372 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8426 (ttm110) REVERT: D 83 GLU cc_start: 0.7834 (tp30) cc_final: 0.7481 (mt-10) REVERT: D 299 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.8728 (mtp) REVERT: D 328 LYS cc_start: 0.8079 (mtpp) cc_final: 0.7545 (mmtt) REVERT: D 355 MET cc_start: 0.8292 (ptp) cc_final: 0.8023 (ptm) REVERT: D 372 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7857 (ptt-90) REVERT: E 44 MET cc_start: 0.7825 (mtp) cc_final: 0.7456 (mtt) REVERT: E 57 GLU cc_start: 0.7963 (tp30) cc_final: 0.7706 (tp30) REVERT: E 121 GLN cc_start: 0.8728 (tt0) cc_final: 0.8518 (tt0) REVERT: E 149 THR cc_start: 0.8943 (t) cc_final: 0.8719 (m) REVERT: F 816 MET cc_start: 0.8155 (mmm) cc_final: 0.7776 (mmm) REVERT: G 1533 MET cc_start: 0.7850 (tpt) cc_final: 0.7614 (tpp) REVERT: G 1570 GLU cc_start: 0.8392 (tt0) cc_final: 0.7986 (tt0) outliers start: 25 outliers final: 21 residues processed: 240 average time/residue: 0.1387 time to fit residues: 52.0880 Evaluate side-chains 247 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 222 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 72 GLU Chi-restraints excluded: chain B residue 142 LEU 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 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 21 optimal weight: 1.9990 chunk 167 optimal weight: 0.0370 chunk 123 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 193 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 49 optimal weight: 0.0470 chunk 229 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 overall best weight: 0.5556 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.134039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.110853 restraints weight = 25220.097| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.77 r_work: 0.3049 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2191 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= 0.115 Angle : 0.537 15.253 25570 Z= 0.260 Chirality : 0.043 0.259 2851 Planarity : 0.004 0.036 3263 Dihedral : 5.997 141.061 2602 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.40 % Allowed : 11.71 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.18), residues: 2323 helix: 0.85 (0.16), residues: 1122 sheet: 0.56 (0.27), residues: 360 loop : 0.56 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 884 TYR 0.022 0.001 TYR F 779 PHE 0.009 0.001 PHE B 31 TRP 0.010 0.001 TRP D 340 HIS 0.004 0.001 HIS E 161 Details of bonding type rmsd covalent geometry : bond 0.00272 (18895) covalent geometry : angle 0.53735 (25570) hydrogen bonds : bond 0.03844 ( 928) hydrogen bonds : angle 4.16501 ( 2511) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4968.13 seconds wall clock time: 85 minutes 43.19 seconds (5143.19 seconds total)