Starting phenix.real_space_refine on Mon Jun 16 10:51:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dva_47194/06_2025/9dva_47194_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dva_47194/06_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_47194/06_2025/9dva_47194.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dva_47194/06_2025/9dva_47194.map" model { file = "/net/cci-nas-00/data/ceres_data/9dva_47194/06_2025/9dva_47194_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dva_47194/06_2025/9dva_47194_neut.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 140 5.16 5 C 11657 2.51 5 N 3161 2.21 5 O 3556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18529 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2899 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2899 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2899 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2899 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2899 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1642 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 6, 'TRANS': 207} Chain: "G" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 610 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "H" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1642 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 6, 'TRANS': 207} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.72, per 1000 atoms: 0.69 Number of scatterers: 18529 At special positions: 0 Unit cell: (133.9, 87.55, 196.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 140 16.00 P 10 15.00 Mg 5 11.99 O 3556 8.00 N 3161 7.00 C 11657 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.65 Conformation dependent library (CDL) restraints added in 2.4 seconds 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4392 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 32 sheets defined 55.9% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.36 Creating SS restraints... Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 78 through 92 removed outlier: 3.595A pdb=" N MET A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.512A pdb=" N GLU A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 97 through 101' Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.235A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU A 117 " --> pdb=" O LYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.685A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.650A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.661A pdb=" N ARG A 254 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE A 255 " --> pdb=" O ASN A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 251 through 255' Processing helix chain 'A' and resid 257 through 262 removed outlier: 3.693A pdb=" N THR A 260 " --> pdb=" O CYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 267 Processing helix chain 'A' and resid 273 through 284 removed outlier: 3.528A pdb=" N TYR A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 294 removed outlier: 3.527A pdb=" N TYR A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.138A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 359 through 366 removed outlier: 3.541A pdb=" N GLU A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 374 removed outlier: 4.333A pdb=" N ARG A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.709A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.529A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.510A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.239A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.951A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.562A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.692A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 removed outlier: 3.664A pdb=" N SER B 233 " --> pdb=" O THR B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 260 Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 261 through 262 No H-bonds generated for 'chain 'B' and resid 261 through 262' Processing helix chain 'B' and resid 263 through 267 Processing helix chain 'B' and resid 273 through 284 removed outlier: 3.518A pdb=" N THR B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.793A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 4.149A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.539A pdb=" N LEU B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 359 through 366 removed outlier: 3.572A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 374 removed outlier: 4.196A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 61 through 63 No H-bonds generated for 'chain 'C' and resid 61 through 63' Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.814A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.203A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.754A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.791A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 260 removed outlier: 3.637A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 261 through 262 No H-bonds generated for 'chain 'C' and resid 261 through 262' Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 removed outlier: 3.590A pdb=" N TYR C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.626A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 4.194A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 355 removed outlier: 4.213A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 4.208A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 61 through 63 No H-bonds generated for 'chain 'D' and resid 61 through 63' Processing helix chain 'D' and resid 78 through 91 removed outlier: 3.681A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.022A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE D 124 " --> pdb=" O THR D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.898A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.802A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 260 removed outlier: 3.594A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 261 through 262 No H-bonds generated for 'chain 'D' and resid 261 through 262' Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 removed outlier: 3.809A pdb=" N TYR D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE D 282 " --> pdb=" O THR D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 295 Processing helix chain 'D' and resid 301 through 306 removed outlier: 4.158A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.532A pdb=" N ALA D 319 " --> pdb=" O LYS D 315 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 352 through 356 removed outlier: 3.969A pdb=" N TRP D 356 " --> pdb=" O GLN D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 368 through 374 removed outlier: 4.405A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 removed outlier: 4.264A pdb=" N LYS E 84 " --> pdb=" O ASP E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.511A pdb=" N GLU E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 97 through 101' Processing helix chain 'E' and resid 112 through 126 removed outlier: 4.111A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET E 123 " --> pdb=" O MET E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 removed outlier: 3.539A pdb=" N SER E 141 " --> pdb=" O GLN E 137 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU E 142 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR E 143 " --> pdb=" O VAL E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 194 removed outlier: 3.769A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.563A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.667A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 262 Processing helix chain 'E' and resid 263 through 267 Processing helix chain 'E' and resid 273 through 284 removed outlier: 3.776A pdb=" N TYR E 279 " --> pdb=" O HIS E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 295 removed outlier: 3.790A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 306 removed outlier: 4.067A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 removed outlier: 3.638A pdb=" N LEU E 320 " --> pdb=" O GLU E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 350 through 356 removed outlier: 3.935A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TRP E 356 " --> pdb=" O GLN E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 366 Processing helix chain 'E' and resid 368 through 374 removed outlier: 3.822A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 692 through 694 No H-bonds generated for 'chain 'F' and resid 692 through 694' Processing helix chain 'F' and resid 695 through 703 Processing helix chain 'F' and resid 704 through 707 removed outlier: 4.184A pdb=" N ASP F 707 " --> pdb=" O LYS F 704 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 704 through 707' Processing helix chain 'F' and resid 711 through 730 removed outlier: 3.863A pdb=" N THR F 730 " --> pdb=" O MET F 726 " (cutoff:3.500A) Processing helix chain 'F' and resid 738 through 765 removed outlier: 3.569A pdb=" N VAL F 742 " --> pdb=" O ASN F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 770 through 805 removed outlier: 3.989A pdb=" N GLN F 774 " --> pdb=" O SER F 770 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP F 775 " --> pdb=" O ALA F 771 " (cutoff:3.500A) Processing helix chain 'F' and resid 811 through 814 removed outlier: 3.689A pdb=" N SER F 814 " --> pdb=" O GLY F 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 811 through 814' Processing helix chain 'F' and resid 815 through 843 Processing helix chain 'F' and resid 854 through 858 Processing helix chain 'F' and resid 875 through 880 Processing helix chain 'F' and resid 892 through 899 removed outlier: 3.522A pdb=" N LEU F 897 " --> pdb=" O PRO F 893 " (cutoff:3.500A) Processing helix chain 'G' and resid 1512 through 1543 removed outlier: 3.841A pdb=" N ARG G1516 " --> pdb=" O ASP G1512 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL G1531 " --> pdb=" O GLN G1527 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASP G1532 " --> pdb=" O MET G1528 " (cutoff:3.500A) Processing helix chain 'G' and resid 1548 through 1550 No H-bonds generated for 'chain 'G' and resid 1548 through 1550' Processing helix chain 'G' and resid 1551 through 1575 removed outlier: 3.583A pdb=" N LYS G1574 " --> pdb=" O GLU G1570 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASP G1575 " --> pdb=" O SER G1571 " (cutoff:3.500A) Processing helix chain 'H' and resid 691 through 703 removed outlier: 3.995A pdb=" N LYS H 695 " --> pdb=" O PHE H 691 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER H 696 " --> pdb=" O GLN H 692 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS H 697 " --> pdb=" O GLU H 693 " (cutoff:3.500A) Processing helix chain 'H' and resid 711 through 728 removed outlier: 3.524A pdb=" N ILE H 722 " --> pdb=" O GLN H 718 " (cutoff:3.500A) Processing helix chain 'H' and resid 738 through 767 removed outlier: 3.652A pdb=" N VAL H 742 " --> pdb=" O ASN H 738 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER H 754 " --> pdb=" O ALA H 750 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG H 755 " --> pdb=" O GLU H 751 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE H 763 " --> pdb=" O LEU H 759 " (cutoff:3.500A) Processing helix chain 'H' and resid 770 through 805 removed outlier: 3.674A pdb=" N TYR H 779 " --> pdb=" O ASP H 775 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU H 780 " --> pdb=" O LEU H 776 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG H 782 " --> pdb=" O ALA H 778 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA H 784 " --> pdb=" O LEU H 780 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU H 785 " --> pdb=" O GLN H 781 " (cutoff:3.500A) Processing helix chain 'H' and resid 811 through 814 removed outlier: 3.973A pdb=" N SER H 814 " --> pdb=" O GLY H 811 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 811 through 814' Processing helix chain 'H' and resid 815 through 843 removed outlier: 3.679A pdb=" N ALA H 821 " --> pdb=" O SER H 817 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA H 828 " --> pdb=" O ASN H 824 " (cutoff:3.500A) Processing helix chain 'H' and resid 854 through 857 Processing helix chain 'H' and resid 875 through 880 removed outlier: 4.258A pdb=" N GLN H 879 " --> pdb=" O GLN H 875 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR H 880 " --> pdb=" O ASP H 876 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 875 through 880' Processing helix chain 'H' and resid 892 through 899 removed outlier: 3.949A pdb=" N GLU H 899 " --> pdb=" O GLN H 895 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.585A pdb=" N PHE A 31 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 42 removed outlier: 3.897A pdb=" N GLN A 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 41 through 42 removed outlier: 3.897A pdb=" N GLN A 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA6, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA7, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.248A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 247 through 250 removed outlier: 6.651A pdb=" N SER A 239 " --> pdb=" O LYS H 883 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 29 through 32 removed outlier: 4.155A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.626A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'B' and resid 247 through 250 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.501A pdb=" N PHE C 31 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 9.044A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.238A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 4.109A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ASN D 12 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.327A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 4.405A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ASN E 12 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AD4, first strand: chain 'F' and resid 859 through 861 Processing sheet with id=AD5, first strand: chain 'H' and resid 859 through 861 939 hydrogen bonds defined for protein. 2511 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.36 Time building geometry restraints manager: 5.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6048 1.34 - 1.46: 4135 1.46 - 1.58: 8452 1.58 - 1.70: 15 1.70 - 1.82: 245 Bond restraints: 18895 Sorted by residual: bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.94e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.86e+00 bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.86e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.81e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.75e+00 ... (remaining 18890 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 25188 1.66 - 3.32: 290 3.32 - 4.98: 63 4.98 - 6.64: 25 6.64 - 8.30: 4 Bond angle restraints: 25570 Sorted by residual: angle pdb=" N MET G1559 " pdb=" CA MET G1559 " pdb=" CB MET G1559 " ideal model delta sigma weight residual 110.16 116.99 -6.83 1.48e+00 4.57e-01 2.13e+01 angle pdb=" N ASP D 157 " pdb=" CA ASP D 157 " pdb=" C ASP D 157 " ideal model delta sigma weight residual 113.97 108.75 5.22 1.28e+00 6.10e-01 1.66e+01 angle pdb=" N ASP C 157 " pdb=" CA ASP C 157 " pdb=" C ASP C 157 " ideal model delta sigma weight residual 113.97 109.74 4.23 1.28e+00 6.10e-01 1.09e+01 angle pdb=" CA MET G1559 " pdb=" CB MET G1559 " pdb=" CG MET G1559 " ideal model delta sigma weight residual 114.10 120.65 -6.55 2.00e+00 2.50e-01 1.07e+01 angle pdb=" N VAL C 201 " pdb=" CA VAL C 201 " pdb=" C VAL C 201 " ideal model delta sigma weight residual 113.71 110.66 3.05 9.50e-01 1.11e+00 1.03e+01 ... (remaining 25565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.33: 10878 24.33 - 48.66: 548 48.66 - 72.99: 57 72.99 - 97.32: 19 97.32 - 121.65: 2 Dihedral angle restraints: 11504 sinusoidal: 4678 harmonic: 6826 Sorted by residual: dihedral pdb=" O2A ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PA ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sinusoidal sigma weight residual 300.00 178.35 121.65 1 2.00e+01 2.50e-03 3.66e+01 dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 47.27 -107.26 1 2.00e+01 2.50e-03 3.11e+01 dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 25.35 -85.35 1 2.00e+01 2.50e-03 2.21e+01 ... (remaining 11501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1894 0.036 - 0.071: 690 0.071 - 0.107: 210 0.107 - 0.142: 56 0.142 - 0.178: 1 Chirality restraints: 2851 Sorted by residual: chirality pdb=" CA ASP D 157 " pdb=" N ASP D 157 " pdb=" C ASP D 157 " pdb=" CB ASP D 157 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.88e-01 chirality pdb=" CA ILE E 357 " pdb=" N ILE E 357 " pdb=" C ILE E 357 " pdb=" CB ILE E 357 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" C3' ADP D 401 " pdb=" C2' ADP D 401 " pdb=" C4' ADP D 401 " pdb=" O3' ADP D 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.63 0.12 2.00e-01 2.50e+01 3.80e-01 ... (remaining 2848 not shown) Planarity restraints: 3263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN E 111 " 0.038 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO E 112 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO E 112 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 112 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 111 " -0.037 5.00e-02 4.00e+02 5.64e-02 5.09e+00 pdb=" N PRO B 112 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 112 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 112 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 111 " -0.037 5.00e-02 4.00e+02 5.61e-02 5.03e+00 pdb=" N PRO C 112 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 112 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 112 " -0.031 5.00e-02 4.00e+02 ... (remaining 3260 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 139 2.64 - 3.21: 16525 3.21 - 3.77: 26630 3.77 - 4.34: 38368 4.34 - 4.90: 63970 Nonbonded interactions: 145632 Sorted by model distance: nonbonded pdb=" O2B ADP E 401 " pdb="MG MG E 402 " model vdw 2.077 2.170 nonbonded pdb=" O3B ADP D 401 " pdb="MG MG D 402 " model vdw 2.147 2.170 nonbonded pdb=" O GLY B 156 " pdb=" OG1 THR B 303 " model vdw 2.202 3.040 nonbonded pdb=" O2B ADP A 401 " pdb="MG MG A 402 " model vdw 2.213 2.170 nonbonded pdb=" O GLY A 156 " pdb=" OG1 THR A 303 " model vdw 2.229 3.040 ... (remaining 145627 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.730 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 46.170 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.360 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.18), residues: 2323 helix: -0.13 (0.16), residues: 1067 sheet: 0.58 (0.29), residues: 380 loop : 0.68 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 705 HIS 0.003 0.000 HIS A 101 PHE 0.015 0.001 PHE E 124 TYR 0.024 0.001 TYR F 779 ARG 0.005 0.000 ARG C 372 Details of bonding type rmsd hydrogen bonds : bond 0.27398 ( 928) hydrogen bonds : angle 7.39320 ( 2511) covalent geometry : bond 0.00281 (18895) covalent geometry : angle 0.51192 (25570) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 330 time to evaluate : 2.224 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: 0.2866 time to fit residues: 145.8292 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 : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 60 optimal weight: 0.4980 chunk 119 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 ASN C 12 ASN C 137 GLN E 225 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.131819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.108672 restraints weight = 25367.872| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.75 r_work: 0.3021 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 18895 Z= 0.193 Angle : 0.611 9.248 25570 Z= 0.312 Chirality : 0.046 0.170 2851 Planarity : 0.005 0.055 3263 Dihedral : 6.463 123.843 2602 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.85 % Allowed : 6.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.18), residues: 2323 helix: 0.23 (0.16), residues: 1132 sheet: 0.86 (0.29), residues: 360 loop : 0.53 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 340 HIS 0.006 0.001 HIS C 161 PHE 0.010 0.001 PHE E 255 TYR 0.012 0.001 TYR F 779 ARG 0.003 0.000 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.06211 ( 928) hydrogen bonds : angle 5.01939 ( 2511) covalent geometry : bond 0.00462 (18895) covalent geometry : angle 0.61128 (25570) *********************** 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 267 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 250 time to evaluate : 2.004 Fit side-chains REVERT: A 44 MET cc_start: 0.8872 (mtp) cc_final: 0.8507 (mmm) REVERT: A 157 ASP cc_start: 0.8341 (t0) cc_final: 0.7825 (t0) REVERT: A 271 SER cc_start: 0.8881 (m) cc_final: 0.8616 (p) REVERT: B 72 GLU cc_start: 0.8454 (pp20) cc_final: 0.7907 (tt0) REVERT: B 206 ARG cc_start: 0.8298 (ttp-110) cc_final: 0.8045 (ttp-170) REVERT: B 360 GLN cc_start: 0.7762 (tp-100) cc_final: 0.7091 (tp-100) REVERT: C 6 THR cc_start: 0.8345 (p) cc_final: 0.8087 (t) REVERT: C 246 GLN cc_start: 0.8952 (mt0) cc_final: 0.8750 (mt0) REVERT: C 325 MET cc_start: 0.9087 (mmp) cc_final: 0.8368 (mmp) REVERT: D 328 LYS cc_start: 0.8117 (mtpp) cc_final: 0.7812 (tptp) REVERT: E 44 MET cc_start: 0.7845 (mtp) cc_final: 0.7442 (mtt) REVERT: E 121 GLN cc_start: 0.8708 (tt0) cc_final: 0.8320 (tt0) REVERT: E 149 THR cc_start: 0.8904 (t) cc_final: 0.8629 (m) REVERT: E 227 MET cc_start: 0.8408 (mmt) cc_final: 0.8018 (mmt) REVERT: E 289 ILE cc_start: 0.8719 (pt) cc_final: 0.8493 (pt) REVERT: E 368 SER cc_start: 0.8870 (m) cc_final: 0.8662 (t) REVERT: G 1533 MET cc_start: 0.7951 (tpt) cc_final: 0.7650 (tpp) REVERT: G 1570 GLU cc_start: 0.8497 (tt0) cc_final: 0.7869 (pt0) REVERT: H 844 GLN cc_start: 0.6042 (tm-30) cc_final: 0.5784 (tp40) outliers start: 17 outliers final: 13 residues processed: 261 average time/residue: 0.2843 time to fit residues: 115.0933 Evaluate side-chains 249 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 236 time to evaluate : 1.987 ------------------------------------------------------------------------------- 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 E residue 96 VAL Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain F residue 733 LYS Chi-restraints excluded: chain F residue 841 THR Chi-restraints excluded: chain H residue 783 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 225 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 224 optimal weight: 2.9990 chunk 166 optimal weight: 0.7980 chunk 192 optimal weight: 3.9990 chunk 230 optimal weight: 0.1980 chunk 128 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3518 r_free = 0.3518 target = 0.131844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.108607 restraints weight = 25304.314| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.74 r_work: 0.3047 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18895 Z= 0.165 Angle : 0.574 7.630 25570 Z= 0.287 Chirality : 0.045 0.190 2851 Planarity : 0.004 0.049 3263 Dihedral : 6.423 126.692 2602 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.20 % Allowed : 7.71 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.18), residues: 2323 helix: 0.39 (0.16), residues: 1132 sheet: 0.67 (0.28), residues: 365 loop : 0.48 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 340 HIS 0.008 0.001 HIS H 766 PHE 0.009 0.001 PHE B 31 TYR 0.010 0.001 TYR D 143 ARG 0.003 0.000 ARG F 884 Details of bonding type rmsd hydrogen bonds : bond 0.05281 ( 928) hydrogen bonds : angle 4.69459 ( 2511) covalent geometry : bond 0.00399 (18895) covalent geometry : angle 0.57395 (25570) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 242 time to evaluate : 2.137 Fit side-chains REVERT: A 44 MET cc_start: 0.8952 (mtp) cc_final: 0.8582 (mmm) REVERT: A 123 MET cc_start: 0.8805 (mmt) cc_final: 0.8419 (mmt) REVERT: A 157 ASP cc_start: 0.8372 (t0) cc_final: 0.7886 (t0) REVERT: A 271 SER cc_start: 0.8879 (m) cc_final: 0.8665 (p) REVERT: B 72 GLU cc_start: 0.8472 (pp20) cc_final: 0.7974 (tt0) REVERT: B 206 ARG cc_start: 0.8326 (ttp-110) cc_final: 0.8063 (ttp-170) REVERT: B 360 GLN cc_start: 0.7819 (tp-100) cc_final: 0.7324 (tp-100) REVERT: C 6 THR cc_start: 0.8327 (p) cc_final: 0.8038 (t) REVERT: C 325 MET cc_start: 0.9107 (mmp) cc_final: 0.8401 (mmp) REVERT: D 328 LYS cc_start: 0.8125 (mtpp) cc_final: 0.7597 (mmtt) REVERT: E 44 MET cc_start: 0.7894 (mtp) cc_final: 0.7503 (mtt) REVERT: E 121 GLN cc_start: 0.8744 (tt0) cc_final: 0.8417 (tt0) REVERT: E 123 MET cc_start: 0.9230 (mmt) cc_final: 0.8314 (mmt) REVERT: E 149 THR cc_start: 0.8902 (t) cc_final: 0.8637 (m) REVERT: E 227 MET cc_start: 0.8402 (mmt) cc_final: 0.7881 (mmt) REVERT: E 263 GLN cc_start: 0.8102 (mt0) cc_final: 0.7896 (mt0) REVERT: E 276 GLU cc_start: 0.8502 (pt0) cc_final: 0.8244 (pt0) REVERT: E 289 ILE cc_start: 0.8725 (pt) cc_final: 0.8501 (pt) REVERT: G 1533 MET cc_start: 0.7987 (tpt) cc_final: 0.7722 (tpp) REVERT: G 1570 GLU cc_start: 0.8521 (tt0) cc_final: 0.7936 (pt0) REVERT: H 844 GLN cc_start: 0.6118 (tm-30) cc_final: 0.5819 (tp40) outliers start: 24 outliers final: 18 residues processed: 256 average time/residue: 0.2997 time to fit residues: 118.4566 Evaluate side-chains 246 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 228 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain F residue 733 LYS Chi-restraints excluded: chain F residue 841 THR Chi-restraints excluded: chain G residue 1569 GLN Chi-restraints excluded: chain H residue 727 THR Chi-restraints excluded: chain H residue 783 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 1 optimal weight: 0.6980 chunk 208 optimal weight: 0.9990 chunk 222 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 29 optimal weight: 0.1980 chunk 104 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 48 optimal weight: 0.0980 chunk 150 optimal weight: 1.9990 chunk 233 optimal weight: 0.0970 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 115 ASN H 802 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.134315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.111013 restraints weight = 25199.687| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.75 r_work: 0.3065 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18895 Z= 0.104 Angle : 0.525 7.949 25570 Z= 0.258 Chirality : 0.043 0.175 2851 Planarity : 0.004 0.041 3263 Dihedral : 6.209 130.644 2602 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.05 % Allowed : 8.81 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.18), residues: 2323 helix: 0.72 (0.16), residues: 1122 sheet: 0.62 (0.27), residues: 365 loop : 0.57 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 340 HIS 0.004 0.001 HIS E 161 PHE 0.008 0.001 PHE B 31 TYR 0.018 0.001 TYR F 779 ARG 0.002 0.000 ARG F 884 Details of bonding type rmsd hydrogen bonds : bond 0.04180 ( 928) hydrogen bonds : angle 4.41702 ( 2511) covalent geometry : bond 0.00228 (18895) covalent geometry : angle 0.52481 (25570) *********************** 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: 21 poor density : 241 time to evaluate : 2.295 Fit side-chains REVERT: A 44 MET cc_start: 0.8842 (mtp) cc_final: 0.8564 (mmm) REVERT: A 137 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.6825 (mm-40) REVERT: A 157 ASP cc_start: 0.8328 (t0) cc_final: 0.7919 (t0) REVERT: A 271 SER cc_start: 0.8883 (m) cc_final: 0.8680 (p) REVERT: B 206 ARG cc_start: 0.8276 (ttp-110) cc_final: 0.8002 (ttp-170) REVERT: B 224 GLU cc_start: 0.7560 (mp0) cc_final: 0.7334 (mp0) REVERT: B 360 GLN cc_start: 0.7857 (tp-100) cc_final: 0.7150 (tp-100) REVERT: C 6 THR cc_start: 0.8289 (p) cc_final: 0.7995 (t) REVERT: C 12 ASN cc_start: 0.7740 (OUTLIER) cc_final: 0.7475 (m-40) REVERT: C 325 MET cc_start: 0.9068 (mmp) cc_final: 0.8330 (mmp) REVERT: D 83 GLU cc_start: 0.7758 (tp30) cc_final: 0.7401 (mt-10) REVERT: E 121 GLN cc_start: 0.8687 (tt0) cc_final: 0.8431 (tt0) REVERT: E 123 MET cc_start: 0.9198 (mmt) cc_final: 0.8367 (mmt) REVERT: E 149 THR cc_start: 0.8884 (t) cc_final: 0.8612 (m) REVERT: E 227 MET cc_start: 0.8251 (mmt) cc_final: 0.7563 (mmt) REVERT: E 263 GLN cc_start: 0.8053 (mt0) cc_final: 0.7817 (mt0) REVERT: G 1533 MET cc_start: 0.7957 (tpt) cc_final: 0.7711 (tpp) REVERT: G 1570 GLU cc_start: 0.8465 (tt0) cc_final: 0.7991 (tt0) REVERT: H 844 GLN cc_start: 0.6068 (tm-30) cc_final: 0.5768 (tp40) outliers start: 21 outliers final: 14 residues processed: 253 average time/residue: 0.2985 time to fit residues: 116.2286 Evaluate side-chains 239 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 223 time to evaluate : 2.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 363 ASP Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain F residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 214 optimal weight: 10.0000 chunk 189 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 115 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 196 optimal weight: 0.0370 chunk 167 optimal weight: 1.9990 chunk 231 optimal weight: 0.0060 chunk 94 optimal weight: 1.9990 overall best weight: 0.7476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 115 ASN D 12 ASN D 225 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.133267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.110026 restraints weight = 25361.498| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.79 r_work: 0.3025 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18895 Z= 0.141 Angle : 0.544 7.985 25570 Z= 0.267 Chirality : 0.044 0.175 2851 Planarity : 0.004 0.039 3263 Dihedral : 6.209 131.789 2602 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.45 % Allowed : 9.31 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.18), residues: 2323 helix: 0.74 (0.16), residues: 1122 sheet: 0.63 (0.27), residues: 360 loop : 0.52 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 340 HIS 0.005 0.001 HIS C 161 PHE 0.009 0.001 PHE B 31 TYR 0.011 0.001 TYR F 779 ARG 0.003 0.000 ARG F 884 Details of bonding type rmsd hydrogen bonds : bond 0.04371 ( 928) hydrogen bonds : angle 4.35907 ( 2511) covalent geometry : bond 0.00342 (18895) covalent geometry : angle 0.54424 (25570) *********************** 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 262 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 233 time to evaluate : 2.041 Fit side-chains REVERT: A 99 GLU cc_start: 0.7772 (pm20) cc_final: 0.7394 (mp0) REVERT: A 113 LYS cc_start: 0.5791 (mptt) cc_final: 0.5061 (mptt) REVERT: A 137 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.6782 (mm-40) REVERT: A 157 ASP cc_start: 0.8346 (t0) cc_final: 0.7830 (t0) REVERT: A 211 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.8194 (t0) REVERT: A 271 SER cc_start: 0.8889 (m) cc_final: 0.8641 (p) REVERT: B 206 ARG cc_start: 0.8289 (ttp-110) cc_final: 0.8005 (ttp-170) REVERT: B 360 GLN cc_start: 0.7809 (tp-100) cc_final: 0.7051 (tp-100) REVERT: C 6 THR cc_start: 0.8333 (p) cc_final: 0.8015 (t) REVERT: C 132 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7997 (ttp) REVERT: C 325 MET cc_start: 0.9042 (mmp) cc_final: 0.8334 (mmp) REVERT: D 83 GLU cc_start: 0.7829 (tp30) cc_final: 0.7381 (mt-10) REVERT: D 328 LYS cc_start: 0.8129 (ttmm) cc_final: 0.7721 (tttp) REVERT: E 44 MET cc_start: 0.7890 (mtp) cc_final: 0.7493 (mtt) REVERT: E 121 GLN cc_start: 0.8665 (tt0) cc_final: 0.8397 (tt0) REVERT: E 149 THR cc_start: 0.8921 (t) cc_final: 0.8663 (m) REVERT: E 263 GLN cc_start: 0.8065 (mt0) cc_final: 0.7795 (mt0) REVERT: E 289 ILE cc_start: 0.8591 (pt) cc_final: 0.8366 (pt) REVERT: G 1533 MET cc_start: 0.7893 (tpt) cc_final: 0.7640 (tpp) REVERT: G 1570 GLU cc_start: 0.8488 (tt0) cc_final: 0.7981 (tt0) REVERT: H 844 GLN cc_start: 0.6089 (tm-30) cc_final: 0.5757 (tp40) outliers start: 29 outliers final: 21 residues processed: 251 average time/residue: 0.2983 time to fit residues: 115.8039 Evaluate side-chains 249 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 225 time to evaluate : 2.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 355 MET 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 115 ASN Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 363 ASP Chi-restraints excluded: chain C residue 372 ARG Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain F residue 728 ASP Chi-restraints excluded: chain F residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 205 optimal weight: 0.1980 chunk 68 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 179 optimal weight: 0.0570 chunk 120 optimal weight: 1.9990 chunk 220 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 198 optimal weight: 0.7980 chunk 223 optimal weight: 1.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.134088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.110705 restraints weight = 25278.719| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.74 r_work: 0.3060 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18895 Z= 0.114 Angle : 0.528 9.033 25570 Z= 0.257 Chirality : 0.043 0.169 2851 Planarity : 0.004 0.037 3263 Dihedral : 6.122 133.919 2602 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.30 % Allowed : 10.01 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.18), residues: 2323 helix: 0.82 (0.16), residues: 1122 sheet: 0.61 (0.27), residues: 360 loop : 0.56 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 340 HIS 0.004 0.001 HIS E 161 PHE 0.009 0.001 PHE B 31 TYR 0.023 0.001 TYR F 779 ARG 0.002 0.000 ARG F 884 Details of bonding type rmsd hydrogen bonds : bond 0.04041 ( 928) hydrogen bonds : angle 4.27705 ( 2511) covalent geometry : bond 0.00266 (18895) covalent geometry : angle 0.52780 (25570) *********************** 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 256 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 230 time to evaluate : 2.231 Fit side-chains REVERT: A 113 LYS cc_start: 0.5948 (mptt) cc_final: 0.5099 (mptt) REVERT: A 157 ASP cc_start: 0.8398 (t0) cc_final: 0.7968 (t0) REVERT: A 271 SER cc_start: 0.8864 (m) cc_final: 0.8663 (p) REVERT: B 206 ARG cc_start: 0.8335 (ttp-110) cc_final: 0.8072 (ttp-170) REVERT: B 224 GLU cc_start: 0.7585 (mp0) cc_final: 0.7369 (mp0) REVERT: B 237 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7913 (mt-10) REVERT: B 360 GLN cc_start: 0.7844 (tp-100) cc_final: 0.7170 (tp-100) REVERT: C 6 THR cc_start: 0.8303 (p) cc_final: 0.7985 (t) REVERT: D 83 GLU cc_start: 0.7886 (tp30) cc_final: 0.7479 (mt-10) REVERT: D 299 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8735 (mtp) REVERT: D 328 LYS cc_start: 0.8101 (ttmm) cc_final: 0.7747 (tttp) REVERT: E 121 GLN cc_start: 0.8712 (tt0) cc_final: 0.8473 (tt0) REVERT: E 149 THR cc_start: 0.8897 (t) cc_final: 0.8660 (m) REVERT: E 263 GLN cc_start: 0.8071 (mt0) cc_final: 0.7796 (mt0) REVERT: G 1533 MET cc_start: 0.7945 (tpt) cc_final: 0.7707 (tpp) REVERT: G 1570 GLU cc_start: 0.8406 (tt0) cc_final: 0.7994 (tt0) REVERT: H 844 GLN cc_start: 0.6120 (tm-30) cc_final: 0.5776 (tp40) outliers start: 26 outliers final: 22 residues processed: 246 average time/residue: 0.2939 time to fit residues: 112.2877 Evaluate side-chains 249 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 225 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 72 GLU 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 363 ASP 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 350 SER 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 196 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 219 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3528 r_free = 0.3528 target = 0.132737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.109558 restraints weight = 25153.481| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.76 r_work: 0.3031 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18895 Z= 0.152 Angle : 0.553 9.702 25570 Z= 0.271 Chirality : 0.045 0.172 2851 Planarity : 0.004 0.038 3263 Dihedral : 6.176 135.432 2602 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.55 % Allowed : 10.11 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.18), residues: 2323 helix: 0.76 (0.16), residues: 1122 sheet: 0.55 (0.27), residues: 360 loop : 0.49 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 340 HIS 0.005 0.001 HIS C 161 PHE 0.009 0.001 PHE B 31 TYR 0.016 0.001 TYR F 779 ARG 0.004 0.000 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.04407 ( 928) hydrogen bonds : angle 4.30234 ( 2511) covalent geometry : bond 0.00374 (18895) covalent geometry : angle 0.55303 (25570) *********************** 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 263 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 232 time to evaluate : 2.249 Fit side-chains REVERT: A 99 GLU cc_start: 0.7806 (pm20) cc_final: 0.7604 (mp0) REVERT: A 113 LYS cc_start: 0.5795 (mptt) cc_final: 0.4749 (mptt) REVERT: A 157 ASP cc_start: 0.8415 (t0) cc_final: 0.7993 (t0) REVERT: A 211 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8278 (t0) REVERT: A 271 SER cc_start: 0.8875 (m) cc_final: 0.8657 (p) REVERT: B 224 GLU cc_start: 0.7699 (mp0) cc_final: 0.7429 (mp0) REVERT: B 237 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.7933 (mt-10) REVERT: B 360 GLN cc_start: 0.7863 (tp-100) cc_final: 0.7189 (tp-100) REVERT: C 325 MET cc_start: 0.9098 (mmp) cc_final: 0.8423 (mmp) REVERT: C 372 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8479 (ttm110) REVERT: D 83 GLU cc_start: 0.7911 (tp30) cc_final: 0.7455 (mt-10) REVERT: D 299 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8700 (mtp) REVERT: D 328 LYS cc_start: 0.8132 (ttmm) cc_final: 0.7887 (mttt) REVERT: E 44 MET cc_start: 0.7900 (mtp) cc_final: 0.7510 (mtt) REVERT: E 121 GLN cc_start: 0.8726 (tt0) cc_final: 0.8493 (tt0) REVERT: E 149 THR cc_start: 0.8940 (t) cc_final: 0.8728 (m) REVERT: E 289 ILE cc_start: 0.8704 (pt) cc_final: 0.8476 (pt) REVERT: G 1533 MET cc_start: 0.7949 (tpt) cc_final: 0.7736 (tpp) REVERT: G 1570 GLU cc_start: 0.8408 (tt0) cc_final: 0.7984 (tt0) REVERT: H 844 GLN cc_start: 0.5932 (tm-30) cc_final: 0.5617 (tp40) outliers start: 31 outliers final: 26 residues processed: 252 average time/residue: 0.2988 time to fit residues: 118.1015 Evaluate side-chains 257 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 227 time to evaluate : 2.227 ------------------------------------------------------------------------------- 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 269 MET Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 72 GLU 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 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 D residue 299 MET Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain F residue 728 ASP Chi-restraints excluded: chain F residue 841 THR Chi-restraints excluded: chain G residue 1532 ASP Chi-restraints excluded: chain G residue 1569 GLN Chi-restraints excluded: chain H residue 727 THR Chi-restraints excluded: chain H residue 783 ILE Chi-restraints excluded: chain H residue 803 LEU Chi-restraints excluded: chain H residue 870 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 17 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 106 optimal weight: 0.0470 chunk 79 optimal weight: 2.9990 chunk 56 optimal weight: 0.2980 chunk 50 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 78 optimal weight: 0.0470 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 801 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.135288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.112195 restraints weight = 25151.733| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.76 r_work: 0.3098 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 18895 Z= 0.095 Angle : 0.507 7.538 25570 Z= 0.246 Chirality : 0.042 0.160 2851 Planarity : 0.003 0.035 3263 Dihedral : 5.959 138.855 2602 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.00 % Allowed : 10.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.18), residues: 2323 helix: 0.95 (0.17), residues: 1122 sheet: 0.60 (0.27), residues: 360 loop : 0.64 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 340 HIS 0.004 0.001 HIS E 161 PHE 0.008 0.001 PHE B 31 TYR 0.017 0.001 TYR F 779 ARG 0.002 0.000 ARG G1554 Details of bonding type rmsd hydrogen bonds : bond 0.03567 ( 928) hydrogen bonds : angle 4.14750 ( 2511) covalent geometry : bond 0.00214 (18895) covalent geometry : angle 0.50699 (25570) *********************** 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 251 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 231 time to evaluate : 2.207 Fit side-chains REVERT: A 113 LYS cc_start: 0.5807 (mptt) cc_final: 0.4650 (mptt) REVERT: A 157 ASP cc_start: 0.8393 (t0) cc_final: 0.7929 (t0) REVERT: A 355 MET cc_start: 0.8790 (mtp) cc_final: 0.8562 (mtt) REVERT: B 206 ARG cc_start: 0.8327 (ttp-110) cc_final: 0.8008 (ttp-170) REVERT: B 224 GLU cc_start: 0.7661 (mp0) cc_final: 0.7431 (mp0) REVERT: B 237 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7893 (mt-10) REVERT: B 360 GLN cc_start: 0.7886 (tp-100) cc_final: 0.7110 (mm110) REVERT: C 325 MET cc_start: 0.9093 (mmp) cc_final: 0.8351 (mmp) REVERT: C 372 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8460 (ttm110) REVERT: D 83 GLU cc_start: 0.7905 (tp30) cc_final: 0.7514 (mt-10) REVERT: D 299 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8630 (mtp) REVERT: D 328 LYS cc_start: 0.8014 (ttmm) cc_final: 0.7772 (mttt) REVERT: D 355 MET cc_start: 0.8263 (ptp) cc_final: 0.7992 (ptm) REVERT: E 149 THR cc_start: 0.8908 (t) cc_final: 0.8658 (m) REVERT: G 1533 MET cc_start: 0.7845 (tpt) cc_final: 0.7611 (tpp) REVERT: G 1570 GLU cc_start: 0.8384 (tt0) cc_final: 0.7977 (tt0) outliers start: 20 outliers final: 14 residues processed: 241 average time/residue: 0.3321 time to fit residues: 125.1520 Evaluate side-chains 240 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 223 time to evaluate : 2.126 ------------------------------------------------------------------------------- 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 201 VAL Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain C residue 372 ARG Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 299 MET 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 727 THR Chi-restraints excluded: chain H residue 783 ILE Chi-restraints excluded: chain H residue 803 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 29 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 212 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 216 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 156 optimal weight: 0.3980 chunk 18 optimal weight: 2.9990 chunk 152 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3524 r_free = 0.3524 target = 0.132325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.109149 restraints weight = 25424.228| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.77 r_work: 0.3026 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 18895 Z= 0.171 Angle : 0.568 6.779 25570 Z= 0.280 Chirality : 0.046 0.184 2851 Planarity : 0.004 0.039 3263 Dihedral : 6.150 139.525 2602 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.30 % Allowed : 11.11 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.18), residues: 2323 helix: 0.75 (0.16), residues: 1127 sheet: 0.54 (0.27), residues: 360 loop : 0.50 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 340 HIS 0.006 0.001 HIS C 161 PHE 0.009 0.001 PHE B 31 TYR 0.019 0.001 TYR F 779 ARG 0.003 0.000 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.04479 ( 928) hydrogen bonds : angle 4.28879 ( 2511) covalent geometry : bond 0.00426 (18895) covalent geometry : angle 0.56791 (25570) *********************** 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 250 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 224 time to evaluate : 1.910 Fit side-chains REVERT: A 113 LYS cc_start: 0.5736 (mptt) cc_final: 0.4617 (mptt) REVERT: A 271 SER cc_start: 0.8873 (m) cc_final: 0.8612 (p) REVERT: B 237 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.7923 (mt-10) REVERT: C 325 MET cc_start: 0.9075 (mmp) cc_final: 0.8378 (mmp) REVERT: C 372 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8438 (ttm110) REVERT: D 83 GLU cc_start: 0.7921 (tp30) cc_final: 0.7414 (mt-10) REVERT: D 299 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8691 (mtp) REVERT: D 328 LYS cc_start: 0.8031 (ttmm) cc_final: 0.7803 (mttt) REVERT: D 355 MET cc_start: 0.8273 (ptp) cc_final: 0.7988 (ptm) REVERT: E 44 MET cc_start: 0.7873 (mtp) cc_final: 0.7475 (mtt) REVERT: E 149 THR cc_start: 0.8967 (t) cc_final: 0.8746 (m) REVERT: E 289 ILE cc_start: 0.8693 (pt) cc_final: 0.8457 (pt) REVERT: G 1533 MET cc_start: 0.7730 (tpt) cc_final: 0.7496 (tpp) REVERT: G 1570 GLU cc_start: 0.8360 (tt0) cc_final: 0.7895 (tt0) outliers start: 26 outliers final: 22 residues processed: 239 average time/residue: 0.2883 time to fit residues: 108.4485 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 : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 72 GLU 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 E residue 66 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain F residue 728 ASP Chi-restraints excluded: chain F residue 841 THR Chi-restraints excluded: chain G residue 1532 ASP Chi-restraints excluded: chain G residue 1569 GLN Chi-restraints excluded: chain H residue 727 THR Chi-restraints excluded: chain H residue 783 ILE Chi-restraints excluded: chain H residue 803 LEU Chi-restraints excluded: chain H residue 870 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 224 optimal weight: 0.8980 chunk 206 optimal weight: 0.0040 chunk 88 optimal weight: 0.6980 chunk 104 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 143 optimal weight: 0.5980 chunk 208 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 228 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 39 optimal weight: 0.0050 overall best weight: 0.4006 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.134828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.111635 restraints weight = 25131.906| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.76 r_work: 0.3093 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18895 Z= 0.103 Angle : 0.526 10.356 25570 Z= 0.256 Chirality : 0.043 0.167 2851 Planarity : 0.004 0.035 3263 Dihedral : 5.965 141.109 2602 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.05 % Allowed : 11.41 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.18), residues: 2323 helix: 0.89 (0.16), residues: 1122 sheet: 0.61 (0.27), residues: 360 loop : 0.59 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 340 HIS 0.004 0.001 HIS E 161 PHE 0.009 0.001 PHE B 31 TYR 0.022 0.001 TYR F 779 ARG 0.002 0.000 ARG F 884 Details of bonding type rmsd hydrogen bonds : bond 0.03680 ( 928) hydrogen bonds : angle 4.16263 ( 2511) covalent geometry : bond 0.00236 (18895) covalent geometry : angle 0.52641 (25570) ********************** 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 245 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 224 time to evaluate : 2.076 Fit side-chains REVERT: A 113 LYS cc_start: 0.5841 (mptt) cc_final: 0.4599 (mptt) REVERT: B 206 ARG cc_start: 0.8334 (ttp-110) cc_final: 0.8012 (ttp-170) REVERT: B 237 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.7900 (mt-10) REVERT: C 325 MET cc_start: 0.9102 (mmp) cc_final: 0.8379 (mmp) REVERT: C 372 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8440 (ttm110) REVERT: D 83 GLU cc_start: 0.7965 (tp30) cc_final: 0.7525 (mt-10) REVERT: D 299 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.8630 (mtp) REVERT: D 328 LYS cc_start: 0.7995 (ttmm) cc_final: 0.7784 (mttt) REVERT: D 355 MET cc_start: 0.8293 (ptp) cc_final: 0.8033 (ptm) REVERT: E 149 THR cc_start: 0.8916 (t) cc_final: 0.8696 (m) REVERT: G 1528 MET cc_start: 0.7354 (tmm) cc_final: 0.6618 (ttp) REVERT: G 1570 GLU cc_start: 0.8387 (tt0) cc_final: 0.7983 (tt0) outliers start: 21 outliers final: 18 residues processed: 235 average time/residue: 0.3043 time to fit residues: 111.5358 Evaluate side-chains 240 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 219 time to evaluate : 2.260 ------------------------------------------------------------------------------- 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 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 211 ASP Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain F residue 728 ASP Chi-restraints excluded: chain F residue 841 THR Chi-restraints excluded: chain G residue 1532 ASP Chi-restraints excluded: chain G residue 1569 GLN Chi-restraints excluded: chain H residue 727 THR Chi-restraints excluded: chain H residue 783 ILE Chi-restraints excluded: chain H residue 803 LEU Chi-restraints excluded: chain H residue 870 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 217 optimal weight: 0.0070 chunk 210 optimal weight: 2.9990 chunk 173 optimal weight: 0.5980 chunk 158 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 chunk 189 optimal weight: 0.0570 chunk 193 optimal weight: 2.9990 chunk 218 optimal weight: 0.6980 chunk 213 optimal weight: 10.0000 chunk 118 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.135279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.112143 restraints weight = 25117.605| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.77 r_work: 0.3100 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18895 Z= 0.100 Angle : 0.520 8.913 25570 Z= 0.253 Chirality : 0.043 0.176 2851 Planarity : 0.004 0.041 3263 Dihedral : 5.906 141.433 2602 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.20 % Allowed : 11.46 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.18), residues: 2323 helix: 0.93 (0.16), residues: 1122 sheet: 0.62 (0.27), residues: 360 loop : 0.63 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 340 HIS 0.004 0.001 HIS E 161 PHE 0.012 0.001 PHE F 691 TYR 0.007 0.001 TYR B 143 ARG 0.002 0.000 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.03583 ( 928) hydrogen bonds : angle 4.12290 ( 2511) covalent geometry : bond 0.00229 (18895) covalent geometry : angle 0.52039 (25570) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10629.34 seconds wall clock time: 184 minutes 23.66 seconds (11063.66 seconds total)