Starting phenix.real_space_refine on Tue Nov 19 04:56:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9dva_47194/11_2024/9dva_47194_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9dva_47194/11_2024/9dva_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9dva_47194/11_2024/9dva_47194.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9dva_47194/11_2024/9dva_47194.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9dva_47194/11_2024/9dva_47194_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9dva_47194/11_2024/9dva_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 12.06, per 1000 atoms: 0.65 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: 4.74 Conformation dependent library (CDL) restraints added in 2.6 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: 2.58 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: 6.73 Time building geometry restraints manager: 5.45 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: 5.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 44.580 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18895 Z= 0.187 Angle : 0.512 8.304 25570 Z= 0.249 Chirality : 0.041 0.178 2851 Planarity : 0.004 0.058 3263 Dihedral : 14.231 121.648 7112 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.18), residues: 2323 helix: -0.13 (0.16), residues: 1067 sheet: 0.58 (0.29), residues: 380 loop : 0.68 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 705 HIS 0.003 0.000 HIS A 101 PHE 0.015 0.001 PHE E 124 TYR 0.024 0.001 TYR F 779 ARG 0.005 0.000 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 330 time to evaluate : 2.351 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.8244 (mtp) cc_final: 0.7953 (mmm) REVERT: A 157 ASP cc_start: 0.7690 (t70) cc_final: 0.7192 (t0) REVERT: A 271 SER cc_start: 0.8643 (m) cc_final: 0.8203 (p) REVERT: A 374 CYS cc_start: 0.6579 (m) cc_final: 0.6335 (m) REVERT: B 68 LYS cc_start: 0.8237 (mtmm) cc_final: 0.7844 (mtmm) REVERT: B 78 ASN cc_start: 0.8667 (t0) cc_final: 0.8461 (t0) REVERT: B 118 LYS cc_start: 0.7569 (tttp) cc_final: 0.7092 (ttmt) REVERT: B 206 ARG cc_start: 0.7316 (ttp-110) cc_final: 0.6977 (ttp-170) REVERT: B 297 ASN cc_start: 0.8408 (t0) cc_final: 0.8189 (t0) REVERT: C 6 THR cc_start: 0.8247 (p) cc_final: 0.7959 (t) REVERT: C 157 ASP cc_start: 0.8299 (t70) cc_final: 0.8088 (t0) REVERT: C 246 GLN cc_start: 0.8299 (mt0) cc_final: 0.7897 (mt0) REVERT: C 325 MET cc_start: 0.8799 (mmp) cc_final: 0.8206 (mmp) REVERT: D 246 GLN cc_start: 0.7912 (mt0) cc_final: 0.7643 (mt0) REVERT: D 283 MET cc_start: 0.8063 (mmt) cc_final: 0.7827 (mmp) REVERT: D 328 LYS cc_start: 0.7801 (mtpp) cc_final: 0.7481 (tptp) REVERT: D 360 GLN cc_start: 0.8327 (pp30) cc_final: 0.8101 (pp30) REVERT: E 121 GLN cc_start: 0.8464 (tt0) cc_final: 0.7904 (tt0) REVERT: E 123 MET cc_start: 0.8544 (mmt) cc_final: 0.8025 (mmt) REVERT: E 227 MET cc_start: 0.8084 (mmt) cc_final: 0.7805 (mmt) REVERT: E 263 GLN cc_start: 0.7172 (mt0) cc_final: 0.6771 (mt0) REVERT: E 276 GLU cc_start: 0.8496 (pt0) cc_final: 0.8249 (pt0) REVERT: E 289 ILE cc_start: 0.8275 (pt) cc_final: 0.8009 (pt) REVERT: F 786 TYR cc_start: 0.8308 (m-80) cc_final: 0.7757 (m-80) REVERT: G 1559 MET cc_start: 0.7742 (mtm) cc_final: 0.7270 (mpp) REVERT: G 1569 GLN cc_start: 0.7799 (tp40) cc_final: 0.7223 (mm110) REVERT: G 1570 GLU cc_start: 0.7705 (tt0) cc_final: 0.7260 (pt0) REVERT: H 844 GLN cc_start: 0.5911 (tm-30) cc_final: 0.5711 (tp40) outliers start: 0 outliers final: 0 residues processed: 330 average time/residue: 0.2994 time to fit residues: 152.0713 Evaluate side-chains 237 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 2.263 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 18895 Z= 0.296 Angle : 0.613 9.357 25570 Z= 0.312 Chirality : 0.047 0.156 2851 Planarity : 0.005 0.055 3263 Dihedral : 6.466 123.661 2602 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.90 % Allowed : 6.11 % Favored : 92.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.18), residues: 2323 helix: 0.22 (0.16), residues: 1132 sheet: 0.86 (0.29), residues: 360 loop : 0.52 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 340 HIS 0.006 0.001 HIS C 161 PHE 0.011 0.001 PHE E 255 TYR 0.012 0.001 TYR D 166 ARG 0.003 0.000 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 247 time to evaluate : 2.114 Fit side-chains REVERT: A 44 MET cc_start: 0.8399 (mtp) cc_final: 0.7973 (mmm) REVERT: A 157 ASP cc_start: 0.7864 (t0) cc_final: 0.7317 (t0) REVERT: A 271 SER cc_start: 0.8742 (m) cc_final: 0.8281 (p) REVERT: B 72 GLU cc_start: 0.7695 (pp20) cc_final: 0.7146 (tt0) REVERT: B 78 ASN cc_start: 0.8242 (t0) cc_final: 0.8030 (t0) REVERT: B 206 ARG cc_start: 0.7285 (ttp-110) cc_final: 0.6946 (ttp-170) REVERT: B 360 GLN cc_start: 0.7294 (tp-100) cc_final: 0.6629 (tp-100) REVERT: C 6 THR cc_start: 0.8232 (p) cc_final: 0.7946 (t) REVERT: C 157 ASP cc_start: 0.8480 (t70) cc_final: 0.8160 (t0) REVERT: C 246 GLN cc_start: 0.8606 (mt0) cc_final: 0.8375 (mt0) REVERT: C 325 MET cc_start: 0.8820 (mmp) cc_final: 0.8164 (mmp) REVERT: D 328 LYS cc_start: 0.7866 (mtpp) cc_final: 0.7513 (tptp) REVERT: E 44 MET cc_start: 0.7514 (mtp) cc_final: 0.7069 (mtt) REVERT: E 121 GLN cc_start: 0.8394 (tt0) cc_final: 0.7950 (tt0) REVERT: E 149 THR cc_start: 0.8836 (t) cc_final: 0.8455 (m) REVERT: E 227 MET cc_start: 0.7844 (mmt) cc_final: 0.7435 (mmt) REVERT: E 263 GLN cc_start: 0.7467 (mt0) cc_final: 0.7219 (mt0) REVERT: E 289 ILE cc_start: 0.8045 (pt) cc_final: 0.7831 (pt) REVERT: E 368 SER cc_start: 0.8749 (m) cc_final: 0.8518 (t) REVERT: G 1533 MET cc_start: 0.7631 (tpt) cc_final: 0.7397 (tpp) REVERT: G 1569 GLN cc_start: 0.7816 (tp40) cc_final: 0.7602 (tp40) REVERT: G 1570 GLU cc_start: 0.7844 (tt0) cc_final: 0.7348 (pt0) REVERT: H 844 GLN cc_start: 0.5988 (tm-30) cc_final: 0.5712 (tp40) outliers start: 18 outliers final: 14 residues processed: 259 average time/residue: 0.3129 time to fit residues: 127.1018 Evaluate side-chains 255 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 241 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain F residue 733 LYS Chi-restraints excluded: chain F residue 841 THR Chi-restraints excluded: chain H residue 783 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 212 optimal weight: 1.9990 chunk 229 optimal weight: 5.9990 chunk 189 optimal weight: 0.0970 chunk 211 optimal weight: 0.7980 chunk 72 optimal weight: 0.0870 chunk 170 optimal weight: 3.9990 overall best weight: 0.7958 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18895 Z= 0.231 Angle : 0.559 7.287 25570 Z= 0.279 Chirality : 0.045 0.153 2851 Planarity : 0.004 0.048 3263 Dihedral : 6.365 127.508 2602 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.20 % Allowed : 7.66 % Favored : 91.14 % 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: 0.66 (0.18), residues: 2323 helix: 0.49 (0.16), residues: 1122 sheet: 0.68 (0.28), residues: 365 loop : 0.53 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 340 HIS 0.007 0.001 HIS H 766 PHE 0.009 0.001 PHE B 31 TYR 0.009 0.001 TYR D 143 ARG 0.003 0.000 ARG F 884 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 246 time to evaluate : 2.217 Fit side-chains REVERT: A 44 MET cc_start: 0.8442 (mtp) cc_final: 0.8024 (mmm) REVERT: A 123 MET cc_start: 0.8607 (mmt) cc_final: 0.8151 (mmt) REVERT: A 157 ASP cc_start: 0.7859 (t0) cc_final: 0.7330 (t0) REVERT: A 271 SER cc_start: 0.8739 (m) cc_final: 0.8283 (p) REVERT: B 72 GLU cc_start: 0.7658 (pp20) cc_final: 0.7136 (tt0) REVERT: B 82 MET cc_start: 0.8868 (tpt) cc_final: 0.8659 (tpt) REVERT: B 206 ARG cc_start: 0.7289 (ttp-110) cc_final: 0.6927 (ttp-170) REVERT: B 325 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7370 (mtp) REVERT: B 360 GLN cc_start: 0.7295 (tp-100) cc_final: 0.6758 (tp-100) REVERT: C 6 THR cc_start: 0.8220 (p) cc_final: 0.7890 (t) REVERT: C 246 GLN cc_start: 0.8561 (mt0) cc_final: 0.8360 (mt0) REVERT: C 325 MET cc_start: 0.8795 (mmp) cc_final: 0.8164 (mmp) REVERT: D 328 LYS cc_start: 0.7843 (mtpp) cc_final: 0.7598 (tttp) REVERT: E 44 MET cc_start: 0.7541 (mtp) cc_final: 0.7109 (mtt) REVERT: E 57 GLU cc_start: 0.7370 (tp30) cc_final: 0.7158 (tp30) REVERT: E 121 GLN cc_start: 0.8417 (tt0) cc_final: 0.8008 (tt0) REVERT: E 123 MET cc_start: 0.8967 (mmt) cc_final: 0.8008 (mmt) REVERT: E 149 THR cc_start: 0.8840 (t) cc_final: 0.8455 (m) REVERT: E 227 MET cc_start: 0.7698 (mmt) cc_final: 0.7184 (mmt) REVERT: E 263 GLN cc_start: 0.7429 (mt0) cc_final: 0.6998 (mt0) REVERT: E 276 GLU cc_start: 0.7917 (pt0) cc_final: 0.7604 (pt0) REVERT: E 289 ILE cc_start: 0.7970 (pt) cc_final: 0.7753 (pt) REVERT: E 368 SER cc_start: 0.8781 (m) cc_final: 0.8547 (t) REVERT: G 1533 MET cc_start: 0.7591 (tpt) cc_final: 0.7370 (tpp) REVERT: G 1569 GLN cc_start: 0.7791 (tp40) cc_final: 0.7582 (tp40) REVERT: G 1570 GLU cc_start: 0.7831 (tt0) cc_final: 0.7340 (pt0) REVERT: H 844 GLN cc_start: 0.6035 (tm-30) cc_final: 0.5697 (tp40) outliers start: 24 outliers final: 16 residues processed: 259 average time/residue: 0.3154 time to fit residues: 126.0778 Evaluate side-chains 255 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 238 time to evaluate : 2.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain F residue 733 LYS Chi-restraints excluded: chain F residue 841 THR Chi-restraints excluded: chain G residue 1532 ASP Chi-restraints excluded: chain H residue 783 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 4.9990 chunk 160 optimal weight: 0.7980 chunk 110 optimal weight: 0.4980 chunk 23 optimal weight: 2.9990 chunk 101 optimal weight: 0.0980 chunk 142 optimal weight: 1.9990 chunk 213 optimal weight: 9.9990 chunk 226 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 202 optimal weight: 0.9990 chunk 60 optimal weight: 0.2980 overall best weight: 0.5382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18895 Z= 0.175 Angle : 0.531 7.502 25570 Z= 0.261 Chirality : 0.043 0.154 2851 Planarity : 0.004 0.042 3263 Dihedral : 6.231 130.531 2602 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.05 % Allowed : 8.91 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.18), residues: 2323 helix: 0.69 (0.16), residues: 1122 sheet: 0.61 (0.27), residues: 365 loop : 0.56 (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 0.009 0.001 PHE B 31 TYR 0.018 0.001 TYR F 779 ARG 0.002 0.000 ARG F 884 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 249 time to evaluate : 2.272 Fit side-chains REVERT: A 44 MET cc_start: 0.8346 (mtp) cc_final: 0.8007 (mmm) REVERT: A 137 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.6431 (mm-40) REVERT: A 157 ASP cc_start: 0.7856 (t0) cc_final: 0.7323 (t0) REVERT: A 211 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.7105 (t0) REVERT: A 271 SER cc_start: 0.8755 (m) cc_final: 0.8296 (p) REVERT: B 72 GLU cc_start: 0.7660 (pp20) cc_final: 0.7460 (pp20) REVERT: B 206 ARG cc_start: 0.7324 (ttp-110) cc_final: 0.6955 (ttp-170) REVERT: B 224 GLU cc_start: 0.6987 (mp0) cc_final: 0.6733 (mp0) REVERT: B 360 GLN cc_start: 0.7311 (tp-100) cc_final: 0.6585 (tp-100) REVERT: C 6 THR cc_start: 0.8212 (p) cc_final: 0.7875 (t) REVERT: C 325 MET cc_start: 0.8753 (mmp) cc_final: 0.8101 (mmp) REVERT: D 83 GLU cc_start: 0.7035 (tp30) cc_final: 0.6695 (mt-10) REVERT: D 328 LYS cc_start: 0.7820 (mtpp) cc_final: 0.7564 (ttmm) REVERT: E 121 GLN cc_start: 0.8383 (tt0) cc_final: 0.8033 (tt0) REVERT: E 123 MET cc_start: 0.8918 (mmt) cc_final: 0.8032 (mmt) REVERT: E 149 THR cc_start: 0.8837 (t) cc_final: 0.8448 (m) REVERT: E 263 GLN cc_start: 0.7408 (mt0) cc_final: 0.7196 (mt0) REVERT: E 289 ILE cc_start: 0.7914 (pt) cc_final: 0.7710 (pt) REVERT: E 368 SER cc_start: 0.8770 (m) cc_final: 0.8544 (t) REVERT: G 1569 GLN cc_start: 0.7786 (tp40) cc_final: 0.7574 (tp40) REVERT: G 1570 GLU cc_start: 0.7785 (tt0) cc_final: 0.7288 (tt0) REVERT: H 844 GLN cc_start: 0.6010 (tm-30) cc_final: 0.5677 (tp40) outliers start: 21 outliers final: 14 residues processed: 262 average time/residue: 0.3090 time to fit residues: 124.5504 Evaluate side-chains 248 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 232 time to evaluate : 2.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 363 ASP Chi-restraints excluded: chain D residue 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 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 188 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 203 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 115 ASN D 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 18895 Z= 0.473 Angle : 0.663 7.970 25570 Z= 0.332 Chirality : 0.050 0.184 2851 Planarity : 0.005 0.045 3263 Dihedral : 6.662 129.802 2602 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.70 % Allowed : 9.76 % Favored : 88.54 % 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: 0.34 (0.17), residues: 2323 helix: 0.32 (0.16), residues: 1127 sheet: 0.50 (0.27), residues: 360 loop : 0.24 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 340 HIS 0.009 0.002 HIS C 161 PHE 0.018 0.002 PHE F 691 TYR 0.014 0.002 TYR D 143 ARG 0.005 0.000 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 235 time to evaluate : 2.162 Fit side-chains REVERT: A 113 LYS cc_start: 0.4502 (mptt) cc_final: 0.3771 (mptt) REVERT: A 123 MET cc_start: 0.8812 (tpp) cc_final: 0.8217 (mmp) REVERT: A 137 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.6790 (mm-40) REVERT: A 271 SER cc_start: 0.8771 (m) cc_final: 0.8289 (p) REVERT: B 72 GLU cc_start: 0.7728 (pp20) cc_final: 0.7191 (tt0) REVERT: B 78 ASN cc_start: 0.8311 (t0) cc_final: 0.8073 (t0) REVERT: B 206 ARG cc_start: 0.7392 (ttp-110) cc_final: 0.7039 (ttp-170) REVERT: B 237 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7740 (mt-10) REVERT: B 283 MET cc_start: 0.7974 (mmm) cc_final: 0.7668 (mmt) REVERT: B 360 GLN cc_start: 0.7262 (tp-100) cc_final: 0.6534 (tp-100) REVERT: D 83 GLU cc_start: 0.7172 (tp30) cc_final: 0.6741 (mt-10) REVERT: D 299 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8408 (mtp) REVERT: D 328 LYS cc_start: 0.7920 (mtpp) cc_final: 0.7358 (mttm) REVERT: E 44 MET cc_start: 0.7552 (mtp) cc_final: 0.7105 (mtt) REVERT: E 121 GLN cc_start: 0.8432 (tt0) cc_final: 0.8024 (tt0) REVERT: E 149 THR cc_start: 0.8946 (t) cc_final: 0.8645 (m) REVERT: E 289 ILE cc_start: 0.8243 (pt) cc_final: 0.7980 (pt) REVERT: E 368 SER cc_start: 0.8792 (m) cc_final: 0.8575 (t) REVERT: F 816 MET cc_start: 0.7612 (mmm) cc_final: 0.7319 (mmm) REVERT: G 1569 GLN cc_start: 0.7971 (tp40) cc_final: 0.7749 (tp40) REVERT: G 1570 GLU cc_start: 0.7825 (tt0) cc_final: 0.7363 (pt0) REVERT: H 844 GLN cc_start: 0.6096 (tm-30) cc_final: 0.5693 (tp40) outliers start: 34 outliers final: 24 residues processed: 258 average time/residue: 0.3080 time to fit residues: 123.5742 Evaluate side-chains 255 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 228 time to evaluate : 2.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 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 F residue 841 THR Chi-restraints excluded: chain G residue 1532 ASP Chi-restraints excluded: chain H residue 727 THR Chi-restraints excluded: chain H residue 783 ILE Chi-restraints excluded: chain H residue 803 LEU Chi-restraints excluded: chain H residue 870 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 0.7980 chunk 203 optimal weight: 0.8980 chunk 44 optimal weight: 0.0970 chunk 132 optimal weight: 0.8980 chunk 55 optimal weight: 0.1980 chunk 226 optimal weight: 2.9990 chunk 187 optimal weight: 0.5980 chunk 104 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN H 802 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18895 Z= 0.163 Angle : 0.538 8.839 25570 Z= 0.265 Chirality : 0.043 0.168 2851 Planarity : 0.004 0.039 3263 Dihedral : 6.299 134.118 2602 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.20 % Allowed : 10.96 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.18), residues: 2323 helix: 0.64 (0.16), residues: 1122 sheet: 0.54 (0.27), residues: 360 loop : 0.36 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 340 HIS 0.004 0.001 HIS E 161 PHE 0.009 0.001 PHE B 31 TYR 0.012 0.001 TYR F 779 ARG 0.002 0.000 ARG F 884 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 234 time to evaluate : 2.199 Fit side-chains REVERT: A 99 GLU cc_start: 0.7554 (pm20) cc_final: 0.7152 (mp0) REVERT: A 113 LYS cc_start: 0.4412 (mptt) cc_final: 0.3622 (mptt) REVERT: A 137 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.6562 (mm-40) REVERT: A 157 ASP cc_start: 0.7919 (t0) cc_final: 0.7376 (t0) REVERT: A 271 SER cc_start: 0.8738 (m) cc_final: 0.8259 (p) REVERT: B 72 GLU cc_start: 0.7611 (pp20) cc_final: 0.7050 (tt0) REVERT: B 224 GLU cc_start: 0.7078 (mp0) cc_final: 0.6775 (mp0) REVERT: B 237 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7693 (mt-10) REVERT: B 283 MET cc_start: 0.7956 (mmm) cc_final: 0.7681 (mmt) REVERT: B 360 GLN cc_start: 0.7288 (tp-100) cc_final: 0.6498 (tp-100) REVERT: C 325 MET cc_start: 0.8754 (mmp) cc_final: 0.8249 (mmp) REVERT: C 372 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8299 (ttm110) REVERT: D 83 GLU cc_start: 0.7185 (tp30) cc_final: 0.6828 (mt-10) REVERT: D 328 LYS cc_start: 0.7845 (mtpp) cc_final: 0.7143 (mmtt) REVERT: E 44 MET cc_start: 0.7483 (mtp) cc_final: 0.7064 (mtt) REVERT: E 57 GLU cc_start: 0.7311 (tp30) cc_final: 0.7042 (tp30) REVERT: E 121 GLN cc_start: 0.8385 (tt0) cc_final: 0.8017 (tt0) REVERT: E 149 THR cc_start: 0.8907 (t) cc_final: 0.8606 (m) REVERT: E 289 ILE cc_start: 0.7982 (pt) cc_final: 0.7778 (pt) REVERT: F 779 TYR cc_start: 0.7854 (m-80) cc_final: 0.7536 (m-80) REVERT: F 816 MET cc_start: 0.7574 (mmm) cc_final: 0.7258 (mmm) REVERT: G 1569 GLN cc_start: 0.7829 (tp40) cc_final: 0.7622 (tp40) REVERT: G 1570 GLU cc_start: 0.7767 (tt0) cc_final: 0.7263 (tt0) REVERT: H 844 GLN cc_start: 0.5868 (tm-30) cc_final: 0.5515 (tp40) outliers start: 24 outliers final: 17 residues processed: 248 average time/residue: 0.3205 time to fit residues: 123.6378 Evaluate side-chains 247 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 227 time to evaluate : 2.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 368 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 E residue 66 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain F residue 841 THR Chi-restraints excluded: chain G residue 1532 ASP Chi-restraints excluded: chain 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 128 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 225 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 802 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 18895 Z= 0.357 Angle : 0.614 9.673 25570 Z= 0.305 Chirality : 0.047 0.181 2851 Planarity : 0.005 0.043 3263 Dihedral : 6.522 134.988 2602 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.65 % Allowed : 11.06 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.17), residues: 2323 helix: 0.43 (0.16), residues: 1127 sheet: 0.45 (0.27), residues: 360 loop : 0.25 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 340 HIS 0.007 0.001 HIS C 161 PHE 0.010 0.001 PHE B 31 TYR 0.013 0.001 TYR D 143 ARG 0.005 0.000 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 224 time to evaluate : 2.255 Fit side-chains REVERT: A 113 LYS cc_start: 0.4471 (mptt) cc_final: 0.3592 (mptt) REVERT: A 137 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.6665 (mm-40) REVERT: A 271 SER cc_start: 0.8752 (m) cc_final: 0.8262 (p) REVERT: B 72 GLU cc_start: 0.7777 (pp20) cc_final: 0.7212 (tt0) REVERT: B 78 ASN cc_start: 0.8273 (t0) cc_final: 0.8003 (t0) REVERT: B 237 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7683 (mt-10) REVERT: B 283 MET cc_start: 0.7956 (mmm) cc_final: 0.7657 (mmt) REVERT: B 297 ASN cc_start: 0.9084 (OUTLIER) cc_final: 0.8793 (m-40) REVERT: B 360 GLN cc_start: 0.7306 (tp-100) cc_final: 0.6590 (tp-100) REVERT: C 132 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7768 (ttp) REVERT: C 372 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8258 (ttm110) REVERT: D 83 GLU cc_start: 0.7271 (tp30) cc_final: 0.6833 (mt-10) REVERT: D 299 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8380 (mtp) REVERT: D 328 LYS cc_start: 0.7900 (mtpp) cc_final: 0.7183 (mmtt) REVERT: D 355 MET cc_start: 0.8085 (ptp) cc_final: 0.7727 (ptm) REVERT: E 44 MET cc_start: 0.7570 (mtp) cc_final: 0.7119 (mtt) REVERT: E 121 GLN cc_start: 0.8437 (tt0) cc_final: 0.8041 (tt0) REVERT: E 149 THR cc_start: 0.8944 (t) cc_final: 0.8652 (m) REVERT: E 289 ILE cc_start: 0.8170 (pt) cc_final: 0.7923 (pt) REVERT: F 816 MET cc_start: 0.7637 (mmm) cc_final: 0.7371 (mmm) REVERT: G 1569 GLN cc_start: 0.7964 (tp40) cc_final: 0.7740 (tp40) REVERT: G 1570 GLU cc_start: 0.7798 (tt0) cc_final: 0.7336 (pt0) REVERT: H 844 GLN cc_start: 0.5998 (tm-30) cc_final: 0.5618 (tp40) outliers start: 33 outliers final: 22 residues processed: 246 average time/residue: 0.3012 time to fit residues: 116.2187 Evaluate side-chains 249 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 221 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 372 ARG Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 0.7980 chunk 134 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 chunk 205 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 225 ASN H 802 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 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 : 0.003 0.030 18895 Z= 0.216 Angle : 0.554 10.577 25570 Z= 0.273 Chirality : 0.044 0.169 2851 Planarity : 0.004 0.038 3263 Dihedral : 6.316 138.420 2602 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.55 % Allowed : 11.56 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.18), residues: 2323 helix: 0.58 (0.16), residues: 1127 sheet: 0.48 (0.27), residues: 360 loop : 0.36 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 340 HIS 0.005 0.001 HIS C 161 PHE 0.010 0.001 PHE B 31 TYR 0.009 0.001 TYR B 240 ARG 0.003 0.000 ARG F 884 *********************** 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 256 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 225 time to evaluate : 2.270 Fit side-chains REVERT: A 99 GLU cc_start: 0.7552 (pm20) cc_final: 0.7109 (mp0) REVERT: A 113 LYS cc_start: 0.4385 (mptt) cc_final: 0.3401 (mptt) REVERT: A 137 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.6594 (mm-40) REVERT: A 271 SER cc_start: 0.8732 (m) cc_final: 0.8237 (p) REVERT: B 72 GLU cc_start: 0.7710 (pp20) cc_final: 0.7125 (tt0) REVERT: B 237 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7675 (mt-10) REVERT: B 283 MET cc_start: 0.7916 (mmm) cc_final: 0.7619 (mmt) REVERT: B 297 ASN cc_start: 0.9032 (OUTLIER) cc_final: 0.8765 (m-40) REVERT: B 360 GLN cc_start: 0.7295 (tp-100) cc_final: 0.6593 (tp-100) REVERT: C 372 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8205 (ttm110) REVERT: D 83 GLU cc_start: 0.7208 (tp30) cc_final: 0.6819 (mt-10) REVERT: D 299 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8284 (mtp) REVERT: D 328 LYS cc_start: 0.7836 (mtpp) cc_final: 0.7125 (mmtt) REVERT: D 355 MET cc_start: 0.8079 (ptp) cc_final: 0.7729 (ptm) REVERT: E 44 MET cc_start: 0.7518 (mtp) cc_final: 0.7073 (mtt) REVERT: E 121 GLN cc_start: 0.8417 (tt0) cc_final: 0.8032 (tt0) REVERT: E 149 THR cc_start: 0.8931 (t) cc_final: 0.8631 (m) REVERT: E 192 ILE cc_start: 0.7597 (mm) cc_final: 0.7173 (pt) REVERT: E 289 ILE cc_start: 0.8041 (pt) cc_final: 0.7822 (pt) REVERT: F 779 TYR cc_start: 0.7919 (m-80) cc_final: 0.7633 (m-80) REVERT: F 816 MET cc_start: 0.7605 (mmm) cc_final: 0.7323 (mmm) REVERT: G 1569 GLN cc_start: 0.7937 (tp40) cc_final: 0.7717 (tp40) REVERT: G 1570 GLU cc_start: 0.7747 (tt0) cc_final: 0.7241 (tt0) REVERT: H 724 MET cc_start: 0.7408 (mmm) cc_final: 0.7196 (mmt) outliers start: 31 outliers final: 22 residues processed: 247 average time/residue: 0.2958 time to fit residues: 114.8667 Evaluate side-chains 249 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 222 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 372 ARG Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain E residue 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 189 optimal weight: 3.9990 chunk 198 optimal weight: 0.5980 chunk 209 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 802 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 18895 Z= 0.498 Angle : 0.679 9.923 25570 Z= 0.340 Chirality : 0.050 0.185 2851 Planarity : 0.005 0.054 3263 Dihedral : 6.778 141.729 2602 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.65 % Allowed : 12.11 % Favored : 86.24 % 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: 0.14 (0.17), residues: 2323 helix: 0.21 (0.16), residues: 1127 sheet: 0.40 (0.28), residues: 360 loop : 0.06 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 340 HIS 0.009 0.002 HIS C 161 PHE 0.012 0.002 PHE C 90 TYR 0.014 0.002 TYR D 143 ARG 0.006 0.001 ARG A 62 *********************** 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 257 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 224 time to evaluate : 2.186 Fit side-chains REVERT: A 113 LYS cc_start: 0.4638 (mptt) cc_final: 0.3703 (mptt) REVERT: A 137 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.6837 (mm-40) REVERT: A 271 SER cc_start: 0.8732 (m) cc_final: 0.8216 (p) REVERT: B 78 ASN cc_start: 0.8344 (t0) cc_final: 0.8114 (t0) REVERT: B 237 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7684 (mt-10) REVERT: B 283 MET cc_start: 0.8000 (mmm) cc_final: 0.7678 (mmt) REVERT: B 297 ASN cc_start: 0.9144 (OUTLIER) cc_final: 0.8854 (m-40) REVERT: B 360 GLN cc_start: 0.7277 (tp-100) cc_final: 0.6584 (tp-100) REVERT: C 83 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7441 (mp0) REVERT: C 99 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7987 (pm20) REVERT: C 372 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.8281 (ttm110) REVERT: D 83 GLU cc_start: 0.7335 (tp30) cc_final: 0.6855 (mt-10) REVERT: D 299 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8398 (mtp) REVERT: D 328 LYS cc_start: 0.7920 (mtpp) cc_final: 0.7189 (mmtt) REVERT: D 355 MET cc_start: 0.8104 (ptp) cc_final: 0.7751 (ptm) REVERT: D 372 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7719 (ptt-90) REVERT: E 44 MET cc_start: 0.7605 (mtp) cc_final: 0.7177 (mtt) REVERT: E 121 GLN cc_start: 0.8391 (tt0) cc_final: 0.8062 (tt0) REVERT: E 149 THR cc_start: 0.8943 (t) cc_final: 0.8657 (m) REVERT: F 816 MET cc_start: 0.7559 (mmm) cc_final: 0.7343 (mmm) REVERT: G 1569 GLN cc_start: 0.7992 (tp40) cc_final: 0.7766 (tp40) REVERT: G 1570 GLU cc_start: 0.7808 (tt0) cc_final: 0.7347 (pt0) outliers start: 33 outliers final: 24 residues processed: 248 average time/residue: 0.3224 time to fit residues: 124.8233 Evaluate side-chains 254 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 223 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 372 ARG Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 372 ARG 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 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 222 optimal weight: 0.8980 chunk 135 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 154 optimal weight: 0.7980 chunk 233 optimal weight: 5.9990 chunk 214 optimal weight: 10.0000 chunk 185 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 143 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 802 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18895 Z= 0.254 Angle : 0.582 11.587 25570 Z= 0.288 Chirality : 0.045 0.177 2851 Planarity : 0.004 0.041 3263 Dihedral : 6.542 146.005 2602 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.45 % Allowed : 12.41 % Favored : 86.14 % 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: 0.37 (0.17), residues: 2323 helix: 0.42 (0.16), residues: 1127 sheet: 0.42 (0.28), residues: 360 loop : 0.19 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 340 HIS 0.006 0.001 HIS C 161 PHE 0.009 0.001 PHE B 31 TYR 0.010 0.001 TYR B 240 ARG 0.003 0.000 ARG B 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4646 Ramachandran restraints generated. 2323 Oldfield, 0 Emsley, 2323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 226 time to evaluate : 2.192 Fit side-chains REVERT: A 99 GLU cc_start: 0.7684 (pm20) cc_final: 0.7232 (mp0) REVERT: A 113 LYS cc_start: 0.4570 (mptt) cc_final: 0.3615 (mptt) REVERT: A 137 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.6648 (mm-40) REVERT: A 271 SER cc_start: 0.8707 (m) cc_final: 0.8193 (p) REVERT: B 237 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7677 (mt-10) REVERT: B 283 MET cc_start: 0.7928 (mmm) cc_final: 0.7631 (mmt) REVERT: B 297 ASN cc_start: 0.9091 (OUTLIER) cc_final: 0.8799 (m-40) REVERT: C 99 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7765 (pm20) REVERT: C 372 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8241 (ttm110) REVERT: D 83 GLU cc_start: 0.7284 (tp30) cc_final: 0.6824 (mt-10) REVERT: D 299 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8271 (mtp) REVERT: D 328 LYS cc_start: 0.7852 (mtpp) cc_final: 0.7298 (mttm) REVERT: D 355 MET cc_start: 0.8094 (ptp) cc_final: 0.7754 (ptm) REVERT: D 372 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7695 (ptt-90) REVERT: E 44 MET cc_start: 0.7562 (mtp) cc_final: 0.7121 (mtt) REVERT: E 121 GLN cc_start: 0.8422 (tt0) cc_final: 0.8022 (tt0) REVERT: E 149 THR cc_start: 0.8925 (t) cc_final: 0.8627 (m) REVERT: E 192 ILE cc_start: 0.7564 (mm) cc_final: 0.7161 (pt) REVERT: E 289 ILE cc_start: 0.8074 (pt) cc_final: 0.7840 (pt) REVERT: F 816 MET cc_start: 0.7520 (mmm) cc_final: 0.7268 (mmm) REVERT: G 1569 GLN cc_start: 0.7958 (tp40) cc_final: 0.7740 (tp40) REVERT: G 1570 GLU cc_start: 0.7799 (tt0) cc_final: 0.7330 (tt0) outliers start: 29 outliers final: 22 residues processed: 246 average time/residue: 0.3239 time to fit residues: 124.0816 Evaluate side-chains 254 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 225 time to evaluate : 2.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 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 297 ASN Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 372 ARG Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 211 ASP Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 372 ARG 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 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 197 optimal weight: 0.0370 chunk 56 optimal weight: 0.4980 chunk 171 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 51 optimal weight: 0.0070 chunk 185 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 190 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 0.2980 chunk 163 optimal weight: 3.9990 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 HIS ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 801 GLN H 802 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.135050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.111861 restraints weight = 25199.218| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.76 r_work: 0.3096 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18895 Z= 0.145 Angle : 0.531 11.095 25570 Z= 0.259 Chirality : 0.042 0.163 2851 Planarity : 0.004 0.037 3263 Dihedral : 6.173 149.047 2602 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.75 % Allowed : 13.21 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.18), residues: 2323 helix: 0.75 (0.16), residues: 1122 sheet: 0.52 (0.27), residues: 360 loop : 0.41 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 356 HIS 0.004 0.001 HIS E 161 PHE 0.009 0.001 PHE B 31 TYR 0.011 0.001 TYR F 779 ARG 0.002 0.000 ARG B 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4054.16 seconds wall clock time: 75 minutes 44.75 seconds (4544.75 seconds total)