Starting phenix.real_space_refine on Sat Jan 25 16:11:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b3d_44135/01_2025/9b3d_44135.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b3d_44135/01_2025/9b3d_44135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b3d_44135/01_2025/9b3d_44135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b3d_44135/01_2025/9b3d_44135.map" model { file = "/net/cci-nas-00/data/ceres_data/9b3d_44135/01_2025/9b3d_44135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b3d_44135/01_2025/9b3d_44135.cif" } resolution = 3.41 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= 0.002 sd= 0.025 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 12 5.49 5 Mg 6 5.21 5 S 162 5.16 5 C 14930 2.51 5 N 3979 2.21 5 O 4532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 23621 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} 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: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} 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: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} 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: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} 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: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} 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: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} 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: "G" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 3052 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 13, 'TRANS': 359} Chain breaks: 2 Chain: "H" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 3001 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 14, 'TRANS': 353} Chain breaks: 1 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} Chain: "F" 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: 13.16, per 1000 atoms: 0.56 Number of scatterers: 23621 At special positions: 0 Unit cell: (135, 138.24, 222.48, 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 162 16.00 P 12 15.00 Mg 6 11.99 O 4532 8.00 N 3979 7.00 C 14930 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.17 Conformation dependent library (CDL) restraints added in 2.7 seconds 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5564 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 36 sheets defined 54.6% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.35 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.075A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.727A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.942A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.716A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 263 removed outlier: 3.854A pdb=" N PHE A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.915A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.647A pdb=" N ARG A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 349 through 355 removed outlier: 3.624A pdb=" N GLN A 353 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.868A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.838A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 202 through 216 removed outlier: 4.034A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.691A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 261 removed outlier: 3.628A pdb=" N LEU B 261 " --> pdb=" O PRO B 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 258 through 261' Processing helix chain 'B' and resid 263 through 267 removed outlier: 3.605A pdb=" N PHE B 266 " --> pdb=" O GLN B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 289 through 294 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.665A pdb=" N ARG B 312 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 349 through 355 removed outlier: 3.525A pdb=" N PHE B 352 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 374 removed outlier: 4.323A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.585A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.893A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.774A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for '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: 3.886A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.726A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 removed outlier: 3.534A pdb=" N PHE C 266 " --> pdb=" O GLN C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.661A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.771A pdb=" N GLN C 353 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 4.176A 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: 4.091A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS C 374 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.733A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.930A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.657A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.528A pdb=" N ARG D 206 " --> pdb=" O THR D 202 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.746A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 261 Processing helix chain 'D' and resid 263 through 267 removed outlier: 3.609A pdb=" N PHE D 266 " --> pdb=" O GLN D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 289 through 295 Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.540A pdb=" N ARG D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 347 Processing helix chain 'D' and resid 349 through 355 removed outlier: 3.647A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 368 through 374 removed outlier: 4.152A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS D 374 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.646A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.957A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.931A 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) removed outlier: 3.758A pdb=" N CYS E 217 " --> pdb=" O LYS E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.619A 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 Processing helix chain 'E' and resid 289 through 295 removed outlier: 3.818A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 306 removed outlier: 4.203A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 321 removed outlier: 3.546A pdb=" N ARG E 312 " --> pdb=" O GLY E 308 " (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 removed outlier: 3.866A pdb=" N GLY E 343 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER E 348 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 356 removed outlier: 3.583A pdb=" N GLN E 353 " --> pdb=" O SER E 350 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TRP E 356 " --> pdb=" O GLN E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 368 through 374 removed outlier: 3.869A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N CYS E 374 " --> pdb=" O VAL E 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 61 Processing helix chain 'F' and resid 78 through 92 removed outlier: 3.625A pdb=" N MET F 82 " --> pdb=" O ASN F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.664A pdb=" N GLU F 100 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N HIS F 101 " --> pdb=" O PRO F 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 97 through 101' Processing helix chain 'F' and resid 112 through 126 removed outlier: 4.039A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 Processing helix chain 'F' and resid 181 through 193 Processing helix chain 'F' and resid 194 through 196 No H-bonds generated for 'chain 'F' and resid 194 through 196' Processing helix chain 'F' and resid 202 through 217 removed outlier: 3.848A pdb=" N GLU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS F 217 " --> pdb=" O LYS F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 233 Processing helix chain 'F' and resid 252 through 257 removed outlier: 3.646A pdb=" N CYS F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 263 removed outlier: 3.838A pdb=" N PHE F 262 " --> pdb=" O PRO F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 267 Processing helix chain 'F' and resid 273 through 284 Processing helix chain 'F' and resid 289 through 296 removed outlier: 3.856A pdb=" N LEU F 293 " --> pdb=" O ILE F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 306 removed outlier: 4.126A pdb=" N TYR F 306 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 removed outlier: 3.501A pdb=" N ARG F 312 " --> pdb=" O GLY F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 349 Processing helix chain 'F' and resid 350 through 355 removed outlier: 3.577A pdb=" N GLN F 353 " --> pdb=" O SER F 350 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 368 through 374 removed outlier: 4.212A pdb=" N ARG F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 780 through 784 removed outlier: 3.665A pdb=" N VAL G 784 " --> pdb=" O TRP G 781 " (cutoff:3.500A) Processing helix chain 'G' and resid 785 through 790 Processing helix chain 'G' and resid 791 through 802 Processing helix chain 'G' and resid 836 through 851 removed outlier: 3.513A pdb=" N SER G 844 " --> pdb=" O ALA G 840 " (cutoff:3.500A) Processing helix chain 'G' and resid 853 through 864 Processing helix chain 'G' and resid 870 through 880 removed outlier: 3.524A pdb=" N ILE G 874 " --> pdb=" O THR G 870 " (cutoff:3.500A) Processing helix chain 'G' and resid 883 through 892 Processing helix chain 'G' and resid 893 through 897 removed outlier: 3.542A pdb=" N GLU G 896 " --> pdb=" O LEU G 893 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR G 897 " --> pdb=" O LYS G 894 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 893 through 897' Processing helix chain 'G' and resid 901 through 911 Processing helix chain 'G' and resid 915 through 948 removed outlier: 3.520A pdb=" N ASN G 921 " --> pdb=" O ARG G 917 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER G 930 " --> pdb=" O LYS G 926 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLU G 931 " --> pdb=" O LEU G 927 " (cutoff:3.500A) Proline residue: G 938 - end of helix Processing helix chain 'G' and resid 953 through 971 removed outlier: 3.772A pdb=" N SER G 958 " --> pdb=" O GLU G 954 " (cutoff:3.500A) Processing helix chain 'G' and resid 983 through 991 removed outlier: 3.520A pdb=" N LEU G 987 " --> pdb=" O ILE G 984 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N CYS G 988 " --> pdb=" O SER G 985 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU G 990 " --> pdb=" O LEU G 987 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG G 991 " --> pdb=" O CYS G 988 " (cutoff:3.500A) Processing helix chain 'G' and resid 1001 through 1013 Processing helix chain 'G' and resid 1016 through 1018 No H-bonds generated for 'chain 'G' and resid 1016 through 1018' Processing helix chain 'G' and resid 1019 through 1024 removed outlier: 3.568A pdb=" N GLU G1023 " --> pdb=" O LYS G1019 " (cutoff:3.500A) Processing helix chain 'G' and resid 1035 through 1058 removed outlier: 3.622A pdb=" N GLN G1039 " --> pdb=" O ALA G1035 " (cutoff:3.500A) Processing helix chain 'G' and resid 1068 through 1105 removed outlier: 3.577A pdb=" N MET G1073 " --> pdb=" O PHE G1069 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR G1074 " --> pdb=" O VAL G1070 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR G1104 " --> pdb=" O GLU G1100 " (cutoff:3.500A) Processing helix chain 'G' and resid 1114 through 1143 Processing helix chain 'H' and resid 746 through 750 removed outlier: 3.912A pdb=" N GLY H 749 " --> pdb=" O LEU H 746 " (cutoff:3.500A) Processing helix chain 'H' and resid 780 through 784 removed outlier: 3.740A pdb=" N VAL H 784 " --> pdb=" O TRP H 781 " (cutoff:3.500A) Processing helix chain 'H' and resid 785 through 790 Processing helix chain 'H' and resid 791 through 802 Processing helix chain 'H' and resid 837 through 851 Processing helix chain 'H' and resid 853 through 864 Processing helix chain 'H' and resid 870 through 880 removed outlier: 3.537A pdb=" N GLN H 880 " --> pdb=" O ASN H 876 " (cutoff:3.500A) Processing helix chain 'H' and resid 883 through 892 Processing helix chain 'H' and resid 893 through 897 removed outlier: 3.552A pdb=" N GLU H 896 " --> pdb=" O LEU H 893 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR H 897 " --> pdb=" O LYS H 894 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 893 through 897' Processing helix chain 'H' and resid 901 through 913 removed outlier: 3.830A pdb=" N VAL H 913 " --> pdb=" O VAL H 909 " (cutoff:3.500A) Processing helix chain 'H' and resid 920 through 928 Processing helix chain 'H' and resid 928 through 950 Proline residue: H 938 - end of helix Processing helix chain 'H' and resid 957 through 971 removed outlier: 3.710A pdb=" N GLU H 961 " --> pdb=" O SER H 957 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR H 969 " --> pdb=" O LEU H 965 " (cutoff:3.500A) Processing helix chain 'H' and resid 983 through 991 removed outlier: 4.056A pdb=" N CYS H 988 " --> pdb=" O SER H 985 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU H 990 " --> pdb=" O LEU H 987 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG H 991 " --> pdb=" O CYS H 988 " (cutoff:3.500A) Processing helix chain 'H' and resid 1001 through 1013 Processing helix chain 'H' and resid 1016 through 1020 removed outlier: 3.814A pdb=" N LYS H1019 " --> pdb=" O GLU H1016 " (cutoff:3.500A) Processing helix chain 'H' and resid 1036 through 1058 removed outlier: 4.016A pdb=" N LYS H1040 " --> pdb=" O GLU H1036 " (cutoff:3.500A) Processing helix chain 'H' and resid 1068 through 1105 removed outlier: 4.061A pdb=" N LYS H1072 " --> pdb=" O LYS H1068 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR H1074 " --> pdb=" O VAL H1070 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER H1075 " --> pdb=" O GLU H1071 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU H1082 " --> pdb=" O LYS H1078 " (cutoff:3.500A) Processing helix chain 'H' and resid 1114 through 1143 removed outlier: 3.932A pdb=" N ASP H1120 " --> pdb=" O GLU H1116 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU H1121 " --> pdb=" O PHE H1117 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.390A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.187A 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 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178 removed outlier: 6.581A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 176 through 178 removed outlier: 3.923A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.495A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR B 133 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 176 through 178 removed outlier: 6.157A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 176 through 178 removed outlier: 4.015A pdb=" N GLN D 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.457A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR C 133 " --> pdb=" O THR C 103 " (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 176 through 178 removed outlier: 6.166A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 176 through 178 removed outlier: 3.755A pdb=" N GLN E 41 " --> pdb=" O ALA C 170 " (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: 6.755A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N CYS D 10 " --> 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 176 through 178 removed outlier: 6.175A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 176 through 178 removed outlier: 3.821A pdb=" N GLN F 41 " --> pdb=" O ALA D 170 " (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: 6.674A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR E 133 " --> pdb=" O THR E 103 " (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 removed outlier: 6.204A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) 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 29 through 32 removed outlier: 6.829A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR F 103 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N ALA F 135 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU F 105 " --> pdb=" O ALA F 135 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AD6, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AD7, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AD8, first strand: chain 'F' and resid 169 through 170 removed outlier: 6.104A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 238 through 241 1162 hydrogen bonds defined for protein. 3120 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: 9.68 Time building geometry restraints manager: 5.96 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: 6738 1.34 - 1.46: 4017 1.46 - 1.57: 13050 1.57 - 1.69: 19 1.69 - 1.81: 286 Bond restraints: 24110 Sorted by residual: bond pdb=" C ARG G 917 " pdb=" N PRO G 918 " ideal model delta sigma weight residual 1.336 1.390 -0.054 1.20e-02 6.94e+03 2.06e+01 bond pdb=" C ARG H 917 " pdb=" N PRO H 918 " ideal model delta sigma weight residual 1.334 1.411 -0.077 2.34e-02 1.83e+03 1.09e+01 bond pdb=" C CYS B 257 " pdb=" N PRO B 258 " ideal model delta sigma weight residual 1.331 1.354 -0.023 7.90e-03 1.60e+04 8.18e+00 bond pdb=" CE1 HIC F 73 " pdb=" NE2 HIC F 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.85e+00 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 7.83e+00 ... (remaining 24105 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 31619 2.25 - 4.51: 856 4.51 - 6.76: 120 6.76 - 9.01: 30 9.01 - 11.27: 12 Bond angle restraints: 32637 Sorted by residual: angle pdb=" N ASN B 128 " pdb=" CA ASN B 128 " pdb=" C ASN B 128 " ideal model delta sigma weight residual 110.30 118.19 -7.89 1.50e+00 4.44e-01 2.77e+01 angle pdb=" C PHE H1105 " pdb=" N VAL H1106 " pdb=" CA VAL H1106 " ideal model delta sigma weight residual 121.97 131.16 -9.19 1.80e+00 3.09e-01 2.61e+01 angle pdb=" CA PRO H 918 " pdb=" N PRO H 918 " pdb=" CD PRO H 918 " ideal model delta sigma weight residual 112.00 104.87 7.13 1.40e+00 5.10e-01 2.60e+01 angle pdb=" C PRO H 914 " pdb=" N ARG H 915 " pdb=" CA ARG H 915 " ideal model delta sigma weight residual 121.54 130.97 -9.43 1.91e+00 2.74e-01 2.44e+01 angle pdb=" N ASN D 128 " pdb=" CA ASN D 128 " pdb=" C ASN D 128 " ideal model delta sigma weight residual 110.10 116.98 -6.88 1.49e+00 4.50e-01 2.13e+01 ... (remaining 32632 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 14385 35.28 - 70.57: 214 70.57 - 105.85: 16 105.85 - 141.13: 7 141.13 - 176.42: 10 Dihedral angle restraints: 14632 sinusoidal: 6002 harmonic: 8630 Sorted by residual: dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 116.41 -176.42 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP F 401 " pdb=" O5' ADP F 401 " pdb=" PA ADP F 401 " pdb=" O2A ADP F 401 " ideal model delta sinusoidal sigma weight residual 300.00 125.38 174.63 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 109.82 -169.82 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 14629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 3188 0.080 - 0.161: 372 0.161 - 0.241: 39 0.241 - 0.322: 13 0.322 - 0.402: 2 Chirality restraints: 3614 Sorted by residual: chirality pdb=" CB VAL H1106 " pdb=" CA VAL H1106 " pdb=" CG1 VAL H1106 " pdb=" CG2 VAL H1106 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 4.04e+00 chirality pdb=" CB ILE C 151 " pdb=" CA ILE C 151 " pdb=" CG1 ILE C 151 " pdb=" CG2 ILE C 151 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CB ILE B 151 " pdb=" CA ILE B 151 " pdb=" CG1 ILE B 151 " pdb=" CG2 ILE B 151 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.48e+00 ... (remaining 3611 not shown) Planarity restraints: 4192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 111 " 0.065 5.00e-02 4.00e+02 9.78e-02 1.53e+01 pdb=" N PRO B 112 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO B 112 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO B 112 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG H 917 " 0.065 5.00e-02 4.00e+02 9.71e-02 1.51e+01 pdb=" N PRO H 918 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO H 918 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO H 918 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 111 " 0.059 5.00e-02 4.00e+02 8.91e-02 1.27e+01 pdb=" N PRO C 112 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO C 112 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 112 " 0.048 5.00e-02 4.00e+02 ... (remaining 4189 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 285 2.66 - 3.22: 19517 3.22 - 3.78: 35728 3.78 - 4.34: 50689 4.34 - 4.90: 81712 Nonbonded interactions: 187931 Sorted by model distance: nonbonded pdb=" O2A ADP E 401 " pdb="MG MG E 402 " model vdw 2.099 2.170 nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 402 " model vdw 2.100 2.170 nonbonded pdb=" O2A ADP A 401 " pdb="MG MG A 402 " model vdw 2.112 2.170 nonbonded pdb=" O3A ADP F 401 " pdb="MG MG F 402 " model vdw 2.131 2.170 nonbonded pdb=" O2B ADP A 401 " pdb="MG MG A 402 " model vdw 2.186 2.170 ... (remaining 187926 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' selection = chain 'F' } ncs_group { reference = (chain 'G' and (resid 750 through 803 or resid 836 through 1143)) selection = (chain 'H' and (resid 750 through 803 or resid 836 through 1143)) } 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: 0.690 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: 0.880 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 51.510 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.160 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 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 : 0.005 0.077 24110 Z= 0.312 Angle : 0.879 11.266 32637 Z= 0.480 Chirality : 0.055 0.402 3614 Planarity : 0.008 0.098 4192 Dihedral : 15.329 176.415 9068 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.72 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.30 (0.13), residues: 2927 helix: -3.18 (0.08), residues: 1390 sheet: -0.57 (0.25), residues: 408 loop : -1.14 (0.17), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 767 HIS 0.006 0.001 HIS E 173 PHE 0.029 0.002 PHE H1020 TYR 0.012 0.001 TYR F 240 ARG 0.004 0.001 ARG E 210 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 496 time to evaluate : 2.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 CYS cc_start: 0.6723 (t) cc_final: 0.6457 (t) REVERT: A 12 ASN cc_start: 0.7924 (m110) cc_final: 0.7324 (m110) REVERT: A 187 ASP cc_start: 0.8145 (m-30) cc_final: 0.7724 (t70) REVERT: B 104 LEU cc_start: 0.8519 (tt) cc_final: 0.7949 (mt) REVERT: B 126 THR cc_start: 0.6861 (m) cc_final: 0.6558 (p) REVERT: C 121 GLN cc_start: 0.8370 (tt0) cc_final: 0.7974 (tt0) REVERT: F 10 CYS cc_start: 0.8092 (t) cc_final: 0.7878 (t) REVERT: F 121 GLN cc_start: 0.9163 (tt0) cc_final: 0.8661 (tm-30) REVERT: F 305 MET cc_start: 0.8689 (mmm) cc_final: 0.8409 (mmt) REVERT: H 765 PRO cc_start: 0.0791 (Cg_endo) cc_final: -0.0187 (Cg_exo) REVERT: H 852 MET cc_start: 0.5161 (ttm) cc_final: 0.4621 (ttm) REVERT: H 902 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7387 (tm-30) REVERT: H 970 MET cc_start: -0.6036 (mtp) cc_final: -0.6431 (mtm) outliers start: 0 outliers final: 0 residues processed: 496 average time/residue: 0.3795 time to fit residues: 289.1244 Evaluate side-chains 259 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 2.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 249 optimal weight: 3.9990 chunk 223 optimal weight: 30.0000 chunk 124 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 chunk 231 optimal weight: 9.9990 chunk 89 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 172 optimal weight: 9.9990 chunk 267 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN D 12 ASN D 354 GLN ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 GLN F 59 GLN ** H 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 955 ASN ** H1126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.100022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.069243 restraints weight = 85633.150| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 5.37 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24110 Z= 0.204 Angle : 0.627 9.543 32637 Z= 0.312 Chirality : 0.043 0.158 3614 Planarity : 0.005 0.076 4192 Dihedral : 11.079 173.787 3284 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.35 % Favored : 96.58 % Rotamer: Outliers : 1.25 % Allowed : 7.16 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.15), residues: 2927 helix: -0.71 (0.12), residues: 1397 sheet: -0.17 (0.26), residues: 402 loop : -0.47 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 79 HIS 0.010 0.001 HIS H1122 PHE 0.019 0.001 PHE H1076 TYR 0.034 0.001 TYR H 854 ARG 0.006 0.001 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 283 time to evaluate : 2.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 CYS cc_start: 0.7593 (t) cc_final: 0.7205 (t) REVERT: A 12 ASN cc_start: 0.8029 (m110) cc_final: 0.7233 (m110) REVERT: A 44 MET cc_start: 0.8351 (mmm) cc_final: 0.7639 (pmm) REVERT: A 65 LEU cc_start: 0.8763 (mt) cc_final: 0.8553 (mt) REVERT: A 82 MET cc_start: 0.9414 (tpp) cc_final: 0.9067 (tpp) REVERT: A 187 ASP cc_start: 0.8847 (m-30) cc_final: 0.8292 (t70) REVERT: B 76 ILE cc_start: 0.8593 (mt) cc_final: 0.8341 (mt) REVERT: B 82 MET cc_start: 0.7258 (tpt) cc_final: 0.6353 (tpt) REVERT: B 104 LEU cc_start: 0.8933 (tt) cc_final: 0.8611 (tt) REVERT: B 111 ASN cc_start: 0.8415 (t0) cc_final: 0.8202 (t0) REVERT: C 121 GLN cc_start: 0.9388 (tt0) cc_final: 0.8821 (pt0) REVERT: C 132 MET cc_start: 0.8365 (ppp) cc_final: 0.8078 (ppp) REVERT: C 223 PHE cc_start: 0.6921 (t80) cc_final: 0.6696 (t80) REVERT: C 297 ASN cc_start: 0.8122 (OUTLIER) cc_final: 0.7874 (m-40) REVERT: D 54 VAL cc_start: 0.8592 (t) cc_final: 0.8328 (m) REVERT: D 57 GLU cc_start: 0.8328 (mp0) cc_final: 0.8127 (pm20) REVERT: D 78 ASN cc_start: 0.8711 (t0) cc_final: 0.8345 (t0) REVERT: D 190 MET cc_start: 0.7838 (mtm) cc_final: 0.7608 (mtm) REVERT: D 225 ASN cc_start: 0.8635 (m-40) cc_final: 0.8203 (m110) REVERT: D 297 ASN cc_start: 0.8476 (t0) cc_final: 0.8222 (t0) REVERT: D 325 MET cc_start: 0.8962 (mmt) cc_final: 0.8510 (mmt) REVERT: E 283 MET cc_start: 0.8454 (mmm) cc_final: 0.8214 (mmm) REVERT: E 284 LYS cc_start: 0.9118 (ttmm) cc_final: 0.8837 (ttmt) REVERT: E 367 PRO cc_start: 0.7889 (Cg_endo) cc_final: 0.7199 (Cg_exo) REVERT: F 305 MET cc_start: 0.8937 (mmm) cc_final: 0.8406 (mmt) REVERT: G 1119 MET cc_start: 0.9119 (mmm) cc_final: 0.8873 (mmm) REVERT: H 851 ARG cc_start: 0.5027 (mtt180) cc_final: 0.4564 (ttp-170) REVERT: H 852 MET cc_start: 0.5273 (ttm) cc_final: 0.4792 (tpp) REVERT: H 857 ILE cc_start: 0.9032 (mt) cc_final: 0.8587 (mt) REVERT: H 873 MET cc_start: 0.8635 (ttm) cc_final: 0.8366 (ptm) outliers start: 32 outliers final: 17 residues processed: 304 average time/residue: 0.3346 time to fit residues: 163.3029 Evaluate side-chains 251 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 233 time to evaluate : 3.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 297 ASN Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain H residue 872 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 15 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 167 optimal weight: 8.9990 chunk 293 optimal weight: 10.0000 chunk 269 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 128 optimal weight: 8.9990 chunk 118 optimal weight: 3.9990 chunk 182 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN B 297 ASN ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 761 GLN G 955 ASN G1093 ASN ** H 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1126 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.096671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.065597 restraints weight = 86696.626| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 5.75 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 24110 Z= 0.298 Angle : 0.651 8.869 32637 Z= 0.323 Chirality : 0.045 0.153 3614 Planarity : 0.005 0.068 4192 Dihedral : 9.651 159.987 3284 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.66 % Favored : 96.28 % Rotamer: Outliers : 1.84 % Allowed : 8.88 % Favored : 89.28 % 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: -0.17 (0.16), residues: 2927 helix: 0.26 (0.14), residues: 1404 sheet: -0.09 (0.27), residues: 390 loop : -0.40 (0.19), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 79 HIS 0.008 0.001 HIS F 275 PHE 0.017 0.001 PHE G1107 TYR 0.019 0.002 TYR H 854 ARG 0.007 0.001 ARG H 919 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 233 time to evaluate : 2.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 CYS cc_start: 0.7876 (t) cc_final: 0.7668 (t) REVERT: A 12 ASN cc_start: 0.8140 (m110) cc_final: 0.7825 (m110) REVERT: A 44 MET cc_start: 0.8421 (mmm) cc_final: 0.7557 (pmm) REVERT: A 82 MET cc_start: 0.9441 (tpp) cc_final: 0.9027 (tpp) REVERT: A 187 ASP cc_start: 0.8914 (m-30) cc_final: 0.8417 (t70) REVERT: A 283 MET cc_start: 0.8532 (mmm) cc_final: 0.7990 (tpp) REVERT: B 82 MET cc_start: 0.7441 (tpt) cc_final: 0.6671 (tpt) REVERT: B 140 LEU cc_start: 0.8854 (mt) cc_final: 0.8642 (mt) REVERT: C 82 MET cc_start: 0.8014 (tpt) cc_final: 0.7593 (tpt) REVERT: C 132 MET cc_start: 0.8586 (ppp) cc_final: 0.8229 (ppp) REVERT: C 223 PHE cc_start: 0.7155 (t80) cc_final: 0.6791 (t80) REVERT: C 236 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8271 (tt) REVERT: C 297 ASN cc_start: 0.8379 (OUTLIER) cc_final: 0.8132 (m110) REVERT: C 299 MET cc_start: 0.8384 (mmm) cc_final: 0.7924 (mmt) REVERT: D 190 MET cc_start: 0.7873 (mtm) cc_final: 0.7606 (mtm) REVERT: D 191 LYS cc_start: 0.8439 (tttm) cc_final: 0.8164 (tmtt) REVERT: D 195 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7938 (mt-10) REVERT: D 325 MET cc_start: 0.9129 (mmt) cc_final: 0.8292 (mmt) REVERT: E 283 MET cc_start: 0.8626 (mmm) cc_final: 0.8360 (mmm) REVERT: E 305 MET cc_start: 0.9060 (mmm) cc_final: 0.8832 (mmm) REVERT: E 325 MET cc_start: 0.8724 (mmt) cc_final: 0.8493 (mmt) REVERT: E 367 PRO cc_start: 0.7769 (Cg_endo) cc_final: 0.7462 (Cg_exo) REVERT: F 10 CYS cc_start: 0.8669 (t) cc_final: 0.8152 (t) REVERT: F 154 ASP cc_start: 0.7233 (t0) cc_final: 0.6947 (t0) REVERT: F 283 MET cc_start: 0.9134 (mmm) cc_final: 0.8929 (mmm) REVERT: F 305 MET cc_start: 0.9015 (mmm) cc_final: 0.8549 (mmt) REVERT: G 1094 MET cc_start: 0.6859 (OUTLIER) cc_final: 0.6509 (tpt) REVERT: G 1119 MET cc_start: 0.9116 (mmm) cc_final: 0.8893 (mmm) REVERT: H 852 MET cc_start: 0.5269 (ttm) cc_final: 0.4917 (tpp) REVERT: H 857 ILE cc_start: 0.8983 (mt) cc_final: 0.8433 (mt) REVERT: H 873 MET cc_start: 0.8691 (ttm) cc_final: 0.8376 (ptm) REVERT: H 1082 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8190 (pp20) outliers start: 47 outliers final: 30 residues processed: 265 average time/residue: 0.3362 time to fit residues: 144.3047 Evaluate side-chains 245 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 211 time to evaluate : 3.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 297 ASN Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain G residue 1094 MET Chi-restraints excluded: chain H residue 762 LEU Chi-restraints excluded: chain H residue 872 SER Chi-restraints excluded: chain H residue 1033 VAL Chi-restraints excluded: chain H residue 1082 GLU Chi-restraints excluded: chain H residue 1126 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 4 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 278 optimal weight: 50.0000 chunk 191 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 210 optimal weight: 0.5980 chunk 254 optimal weight: 20.0000 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.096448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.065456 restraints weight = 87278.492| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 5.77 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24110 Z= 0.246 Angle : 0.609 7.908 32637 Z= 0.299 Chirality : 0.043 0.190 3614 Planarity : 0.004 0.060 4192 Dihedral : 8.873 162.333 3284 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.69 % Favored : 96.24 % Rotamer: Outliers : 1.72 % Allowed : 9.93 % Favored : 88.35 % 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: 0.08 (0.16), residues: 2927 helix: 0.54 (0.14), residues: 1439 sheet: -0.18 (0.27), residues: 390 loop : -0.33 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 79 HIS 0.006 0.001 HIS F 275 PHE 0.016 0.001 PHE H1076 TYR 0.010 0.001 TYR H 854 ARG 0.006 0.000 ARG H 919 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 215 time to evaluate : 2.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 CYS cc_start: 0.7809 (t) cc_final: 0.7560 (t) REVERT: A 12 ASN cc_start: 0.8263 (m110) cc_final: 0.7914 (m110) REVERT: A 44 MET cc_start: 0.8615 (mmm) cc_final: 0.7691 (pmm) REVERT: A 82 MET cc_start: 0.9431 (tpp) cc_final: 0.9004 (tpp) REVERT: A 187 ASP cc_start: 0.8811 (m-30) cc_final: 0.8379 (t70) REVERT: A 269 MET cc_start: 0.8668 (mtp) cc_final: 0.8345 (mtt) REVERT: B 82 MET cc_start: 0.7399 (tpt) cc_final: 0.7115 (tpt) REVERT: C 132 MET cc_start: 0.8580 (ppp) cc_final: 0.8375 (ppp) REVERT: C 223 PHE cc_start: 0.7098 (t80) cc_final: 0.6826 (t80) REVERT: C 236 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8332 (tt) REVERT: C 297 ASN cc_start: 0.8387 (OUTLIER) cc_final: 0.8009 (m-40) REVERT: D 191 LYS cc_start: 0.8469 (tttm) cc_final: 0.8174 (tmtt) REVERT: D 195 GLU cc_start: 0.8212 (mt-10) cc_final: 0.8004 (mt-10) REVERT: E 305 MET cc_start: 0.9076 (mmm) cc_final: 0.8716 (mmm) REVERT: E 367 PRO cc_start: 0.7758 (Cg_endo) cc_final: 0.7456 (Cg_exo) REVERT: F 10 CYS cc_start: 0.8656 (t) cc_final: 0.8195 (t) REVERT: F 154 ASP cc_start: 0.7163 (t0) cc_final: 0.6853 (t0) REVERT: F 176 MET cc_start: 0.6488 (mtt) cc_final: 0.6170 (mpp) REVERT: F 305 MET cc_start: 0.8978 (mmm) cc_final: 0.8578 (mmt) REVERT: G 1119 MET cc_start: 0.9100 (mmm) cc_final: 0.8886 (mmm) REVERT: H 852 MET cc_start: 0.5423 (ttm) cc_final: 0.5045 (ttm) REVERT: H 873 MET cc_start: 0.8745 (ttm) cc_final: 0.8385 (ptm) REVERT: H 1082 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8284 (pp20) outliers start: 44 outliers final: 28 residues processed: 247 average time/residue: 0.3356 time to fit residues: 134.2809 Evaluate side-chains 240 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 209 time to evaluate : 2.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 297 ASN Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain H residue 872 SER Chi-restraints excluded: chain H residue 1033 VAL Chi-restraints excluded: chain H residue 1082 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 129 optimal weight: 4.9990 chunk 196 optimal weight: 2.9990 chunk 267 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 260 optimal weight: 8.9990 chunk 175 optimal weight: 0.1980 chunk 160 optimal weight: 9.9990 chunk 126 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 222 optimal weight: 0.0030 chunk 209 optimal weight: 9.9990 overall best weight: 1.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 GLN C 41 GLN ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1081 GLN H1126 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.097513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.066806 restraints weight = 86353.370| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 5.24 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24110 Z= 0.175 Angle : 0.581 7.723 32637 Z= 0.281 Chirality : 0.042 0.194 3614 Planarity : 0.004 0.059 4192 Dihedral : 8.352 163.213 3284 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.52 % Favored : 96.41 % Rotamer: Outliers : 1.29 % Allowed : 11.07 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.16), residues: 2927 helix: 0.72 (0.14), residues: 1445 sheet: -0.16 (0.26), residues: 390 loop : -0.06 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 79 HIS 0.005 0.001 HIS D 371 PHE 0.018 0.001 PHE G1107 TYR 0.019 0.001 TYR H 854 ARG 0.004 0.000 ARG H 951 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 222 time to evaluate : 2.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.8292 (m110) cc_final: 0.7747 (m110) REVERT: A 44 MET cc_start: 0.8577 (mmm) cc_final: 0.7657 (pmm) REVERT: A 82 MET cc_start: 0.9391 (tpp) cc_final: 0.8978 (tpp) REVERT: A 187 ASP cc_start: 0.8790 (m-30) cc_final: 0.8341 (t70) REVERT: A 269 MET cc_start: 0.8627 (mtp) cc_final: 0.8290 (mtt) REVERT: A 283 MET cc_start: 0.8611 (mmm) cc_final: 0.8009 (tpp) REVERT: A 374 CYS cc_start: 0.6991 (m) cc_final: 0.6273 (m) REVERT: B 82 MET cc_start: 0.7371 (tpt) cc_final: 0.7124 (tpt) REVERT: C 44 MET cc_start: 0.9414 (mmt) cc_final: 0.8853 (mmt) REVERT: C 132 MET cc_start: 0.8593 (ppp) cc_final: 0.8376 (ppp) REVERT: C 223 PHE cc_start: 0.7039 (t80) cc_final: 0.6772 (t80) REVERT: C 236 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8309 (tt) REVERT: C 297 ASN cc_start: 0.8355 (OUTLIER) cc_final: 0.8031 (m-40) REVERT: D 132 MET cc_start: 0.6830 (ptt) cc_final: 0.6575 (ppp) REVERT: D 191 LYS cc_start: 0.8453 (tttm) cc_final: 0.8135 (tmtt) REVERT: D 195 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8067 (mt-10) REVERT: E 283 MET cc_start: 0.8642 (mmm) cc_final: 0.8201 (mmm) REVERT: E 305 MET cc_start: 0.9084 (mmm) cc_final: 0.8709 (mmm) REVERT: E 325 MET cc_start: 0.8667 (mmt) cc_final: 0.8115 (mmt) REVERT: E 367 PRO cc_start: 0.7608 (Cg_endo) cc_final: 0.7323 (Cg_exo) REVERT: F 154 ASP cc_start: 0.6946 (t0) cc_final: 0.6723 (t0) REVERT: F 176 MET cc_start: 0.6381 (mtt) cc_final: 0.5886 (mpp) REVERT: F 305 MET cc_start: 0.8996 (mmm) cc_final: 0.8593 (mmt) REVERT: G 1119 MET cc_start: 0.9166 (mmm) cc_final: 0.8962 (mmm) REVERT: H 852 MET cc_start: 0.5558 (ttm) cc_final: 0.5350 (ttm) REVERT: H 873 MET cc_start: 0.8809 (ttm) cc_final: 0.8397 (ptm) REVERT: H 916 LEU cc_start: 0.0725 (OUTLIER) cc_final: 0.0511 (pp) outliers start: 33 outliers final: 19 residues processed: 246 average time/residue: 0.3593 time to fit residues: 146.4154 Evaluate side-chains 227 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 2.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 297 ASN Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain H residue 762 LEU Chi-restraints excluded: chain H residue 916 LEU Chi-restraints excluded: chain H residue 1033 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 158 optimal weight: 1.9990 chunk 258 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 149 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 226 optimal weight: 7.9990 chunk 161 optimal weight: 4.9990 chunk 164 optimal weight: 7.9990 chunk 123 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 256 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 12 ASN ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 935 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.095854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.064512 restraints weight = 86659.662| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 5.63 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24110 Z= 0.255 Angle : 0.618 8.535 32637 Z= 0.301 Chirality : 0.044 0.179 3614 Planarity : 0.004 0.063 4192 Dihedral : 8.321 164.592 3284 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.96 % Favored : 95.97 % Rotamer: Outliers : 1.84 % Allowed : 10.79 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.16), residues: 2927 helix: 0.82 (0.14), residues: 1439 sheet: -0.22 (0.26), residues: 402 loop : -0.03 (0.20), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 79 HIS 0.006 0.001 HIS F 275 PHE 0.019 0.001 PHE G1107 TYR 0.031 0.001 TYR H 854 ARG 0.004 0.000 ARG H 919 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 208 time to evaluate : 3.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8643 (mmm) cc_final: 0.7709 (pmm) REVERT: A 82 MET cc_start: 0.9434 (tpp) cc_final: 0.9008 (tpp) REVERT: A 187 ASP cc_start: 0.8799 (m-30) cc_final: 0.8358 (t70) REVERT: A 283 MET cc_start: 0.8599 (mmm) cc_final: 0.8024 (tpp) REVERT: B 82 MET cc_start: 0.7426 (tpt) cc_final: 0.6769 (tpt) REVERT: C 223 PHE cc_start: 0.7102 (t80) cc_final: 0.6826 (t80) REVERT: D 191 LYS cc_start: 0.8561 (tttm) cc_final: 0.8341 (tmtt) REVERT: D 195 GLU cc_start: 0.8305 (mt-10) cc_final: 0.8102 (mt-10) REVERT: E 283 MET cc_start: 0.8652 (mmm) cc_final: 0.8208 (mmm) REVERT: E 305 MET cc_start: 0.9121 (mmm) cc_final: 0.8765 (mmm) REVERT: E 325 MET cc_start: 0.8670 (mmt) cc_final: 0.8210 (mmt) REVERT: E 367 PRO cc_start: 0.7668 (Cg_endo) cc_final: 0.7359 (Cg_exo) REVERT: F 57 GLU cc_start: 0.8145 (mp0) cc_final: 0.7860 (pm20) REVERT: F 154 ASP cc_start: 0.6923 (t0) cc_final: 0.6555 (t0) REVERT: F 305 MET cc_start: 0.8993 (mmm) cc_final: 0.8632 (mmt) REVERT: F 373 LYS cc_start: 0.8630 (mmtt) cc_final: 0.8374 (mmtt) REVERT: G 1119 MET cc_start: 0.9121 (mmm) cc_final: 0.8920 (mmm) REVERT: H 852 MET cc_start: 0.5886 (ttm) cc_final: 0.5239 (ttm) REVERT: H 873 MET cc_start: 0.8824 (ttm) cc_final: 0.8337 (ptm) REVERT: H 1082 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8346 (pp20) outliers start: 47 outliers final: 31 residues processed: 240 average time/residue: 0.3433 time to fit residues: 133.4555 Evaluate side-chains 235 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 203 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain H residue 762 LEU Chi-restraints excluded: chain H residue 872 SER Chi-restraints excluded: chain H residue 881 MET Chi-restraints excluded: chain H residue 1022 ASP Chi-restraints excluded: chain H residue 1033 VAL Chi-restraints excluded: chain H residue 1082 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 74 optimal weight: 10.0000 chunk 284 optimal weight: 20.0000 chunk 105 optimal weight: 3.9990 chunk 230 optimal weight: 20.0000 chunk 2 optimal weight: 1.9990 chunk 151 optimal weight: 10.0000 chunk 170 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 227 optimal weight: 30.0000 chunk 270 optimal weight: 20.0000 chunk 215 optimal weight: 5.9990 overall best weight: 5.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 GLN D 162 ASN ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 761 GLN ** H 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 859 ASN H1026 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.093062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.062167 restraints weight = 87822.941| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 5.70 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 24110 Z= 0.414 Angle : 0.748 16.214 32637 Z= 0.369 Chirality : 0.047 0.242 3614 Planarity : 0.005 0.067 4192 Dihedral : 8.725 172.082 3284 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.75 % Favored : 95.22 % Rotamer: Outliers : 1.96 % Allowed : 11.22 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.16), residues: 2927 helix: 0.56 (0.14), residues: 1430 sheet: -0.50 (0.26), residues: 402 loop : -0.34 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 79 HIS 0.006 0.001 HIS F 275 PHE 0.019 0.002 PHE G1107 TYR 0.024 0.002 TYR H 854 ARG 0.006 0.001 ARG H 951 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 207 time to evaluate : 2.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8747 (mmm) cc_final: 0.7733 (pmm) REVERT: A 82 MET cc_start: 0.9466 (tpp) cc_final: 0.9077 (tpp) REVERT: A 187 ASP cc_start: 0.8804 (m-30) cc_final: 0.8406 (t70) REVERT: A 313 MET cc_start: 0.8358 (tpt) cc_final: 0.8108 (tpt) REVERT: B 82 MET cc_start: 0.7457 (tpt) cc_final: 0.6769 (tpt) REVERT: B 104 LEU cc_start: 0.8970 (tt) cc_final: 0.8334 (pp) REVERT: C 34 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8440 (pp) REVERT: C 107 GLU cc_start: 0.7938 (tt0) cc_final: 0.7623 (pt0) REVERT: C 132 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8082 (tmm) REVERT: C 223 PHE cc_start: 0.7200 (t80) cc_final: 0.6930 (t80) REVERT: D 44 MET cc_start: 0.8163 (ppp) cc_final: 0.7902 (ppp) REVERT: D 132 MET cc_start: 0.7282 (ptt) cc_final: 0.7064 (ptt) REVERT: D 190 MET cc_start: 0.7897 (mtm) cc_final: 0.7671 (mtm) REVERT: D 191 LYS cc_start: 0.8630 (tttm) cc_final: 0.8141 (ttmm) REVERT: E 176 MET cc_start: 0.6563 (ptp) cc_final: 0.6317 (ptp) REVERT: E 283 MET cc_start: 0.8803 (mmm) cc_final: 0.8451 (mmm) REVERT: E 325 MET cc_start: 0.8572 (mmt) cc_final: 0.8229 (mmt) REVERT: E 367 PRO cc_start: 0.7866 (Cg_endo) cc_final: 0.7598 (Cg_exo) REVERT: F 154 ASP cc_start: 0.6995 (t0) cc_final: 0.6581 (t0) REVERT: F 305 MET cc_start: 0.9026 (mmm) cc_final: 0.8747 (mmt) REVERT: F 373 LYS cc_start: 0.8608 (mmtt) cc_final: 0.8111 (mttt) REVERT: G 1119 MET cc_start: 0.9043 (mmm) cc_final: 0.8827 (mmm) REVERT: H 852 MET cc_start: 0.6115 (ttm) cc_final: 0.5870 (ttm) REVERT: H 873 MET cc_start: 0.8857 (ttm) cc_final: 0.8467 (ptm) outliers start: 50 outliers final: 33 residues processed: 244 average time/residue: 0.3319 time to fit residues: 132.6397 Evaluate side-chains 226 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 191 time to evaluate : 2.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain H residue 762 LEU Chi-restraints excluded: chain H residue 872 SER Chi-restraints excluded: chain H residue 1022 ASP Chi-restraints excluded: chain H residue 1033 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 256 optimal weight: 6.9990 chunk 208 optimal weight: 5.9990 chunk 277 optimal weight: 30.0000 chunk 231 optimal weight: 4.9990 chunk 217 optimal weight: 6.9990 chunk 160 optimal weight: 7.9990 chunk 288 optimal weight: 20.0000 chunk 162 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 290 optimal weight: 8.9990 chunk 285 optimal weight: 0.0670 overall best weight: 2.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 GLN ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1026 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.094747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.063522 restraints weight = 86735.531| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 5.70 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 24110 Z= 0.240 Angle : 0.654 10.969 32637 Z= 0.319 Chirality : 0.044 0.193 3614 Planarity : 0.004 0.066 4192 Dihedral : 8.479 177.234 3284 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.89 % Favored : 96.07 % Rotamer: Outliers : 1.33 % Allowed : 12.55 % Favored : 86.12 % 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 (0.16), residues: 2927 helix: 0.69 (0.14), residues: 1437 sheet: -0.41 (0.26), residues: 402 loop : -0.11 (0.20), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 79 HIS 0.006 0.001 HIS D 371 PHE 0.020 0.001 PHE G1107 TYR 0.032 0.001 TYR H 854 ARG 0.004 0.000 ARG H1138 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 200 time to evaluate : 2.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8818 (mmm) cc_final: 0.7808 (pmm) REVERT: A 82 MET cc_start: 0.9417 (tpp) cc_final: 0.9029 (tpp) REVERT: A 187 ASP cc_start: 0.8766 (m-30) cc_final: 0.8363 (t70) REVERT: A 305 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8572 (mmm) REVERT: A 313 MET cc_start: 0.8289 (tpt) cc_final: 0.8027 (tpt) REVERT: B 82 MET cc_start: 0.7422 (tpt) cc_final: 0.7183 (tpt) REVERT: B 104 LEU cc_start: 0.9033 (tt) cc_final: 0.8289 (pp) REVERT: B 137 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7752 (mt0) REVERT: B 325 MET cc_start: 0.8099 (mmm) cc_final: 0.7823 (mmm) REVERT: C 82 MET cc_start: 0.7875 (tpt) cc_final: 0.7545 (tpt) REVERT: C 107 GLU cc_start: 0.7853 (tt0) cc_final: 0.7526 (pt0) REVERT: C 132 MET cc_start: 0.8519 (ppp) cc_final: 0.8090 (tmm) REVERT: C 223 PHE cc_start: 0.7220 (t80) cc_final: 0.6957 (t80) REVERT: D 44 MET cc_start: 0.8085 (ppp) cc_final: 0.7834 (ppp) REVERT: D 132 MET cc_start: 0.7107 (ptt) cc_final: 0.6825 (ptt) REVERT: D 191 LYS cc_start: 0.8580 (tttm) cc_final: 0.8310 (tmtt) REVERT: E 176 MET cc_start: 0.6592 (ptp) cc_final: 0.6307 (ptp) REVERT: E 283 MET cc_start: 0.8726 (mmm) cc_final: 0.8374 (mmm) REVERT: E 325 MET cc_start: 0.8549 (mmt) cc_final: 0.8258 (mmt) REVERT: E 367 PRO cc_start: 0.7802 (Cg_endo) cc_final: 0.7562 (Cg_exo) REVERT: F 154 ASP cc_start: 0.6975 (t0) cc_final: 0.6580 (t0) REVERT: F 276 GLU cc_start: 0.8736 (mp0) cc_final: 0.8427 (mp0) REVERT: F 305 MET cc_start: 0.9020 (mmm) cc_final: 0.8756 (mmt) REVERT: F 373 LYS cc_start: 0.8520 (mmtt) cc_final: 0.8035 (mttt) REVERT: G 1119 MET cc_start: 0.9044 (mmm) cc_final: 0.8827 (mmm) REVERT: H 852 MET cc_start: 0.6678 (ttm) cc_final: 0.6017 (ttm) REVERT: H 859 ASN cc_start: 0.8679 (m110) cc_final: 0.8428 (p0) REVERT: H 873 MET cc_start: 0.8810 (ttm) cc_final: 0.8371 (ptm) REVERT: H 1136 GLN cc_start: 0.4241 (OUTLIER) cc_final: 0.3512 (tt0) outliers start: 34 outliers final: 25 residues processed: 222 average time/residue: 0.3137 time to fit residues: 114.9350 Evaluate side-chains 220 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 2.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain H residue 762 LEU Chi-restraints excluded: chain H residue 881 MET Chi-restraints excluded: chain H residue 1033 VAL Chi-restraints excluded: chain H residue 1136 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 83 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 191 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 chunk 146 optimal weight: 3.9990 chunk 99 optimal weight: 0.0050 chunk 15 optimal weight: 10.0000 chunk 279 optimal weight: 40.0000 chunk 249 optimal weight: 6.9990 chunk 153 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 overall best weight: 1.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1039 GLN G1091 HIS ** G1126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1026 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.095772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.064615 restraints weight = 86234.215| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 5.73 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 24110 Z= 0.178 Angle : 0.641 11.988 32637 Z= 0.312 Chirality : 0.043 0.213 3614 Planarity : 0.004 0.061 4192 Dihedral : 8.191 173.471 3284 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.66 % Favored : 96.31 % Rotamer: Outliers : 1.06 % Allowed : 12.98 % Favored : 85.96 % 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: 0.45 (0.16), residues: 2927 helix: 0.80 (0.14), residues: 1443 sheet: -0.32 (0.26), residues: 402 loop : 0.08 (0.20), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 79 HIS 0.006 0.001 HIS B 371 PHE 0.020 0.001 PHE G1107 TYR 0.027 0.001 TYR H 854 ARG 0.004 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 211 time to evaluate : 3.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8820 (mmm) cc_final: 0.7729 (pmm) REVERT: A 82 MET cc_start: 0.9433 (tpp) cc_final: 0.9047 (tpp) REVERT: A 187 ASP cc_start: 0.8770 (m-30) cc_final: 0.8324 (t70) REVERT: A 305 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8508 (mmm) REVERT: A 313 MET cc_start: 0.8176 (tpt) cc_final: 0.7863 (tpt) REVERT: A 374 CYS cc_start: 0.6855 (m) cc_final: 0.6116 (m) REVERT: B 82 MET cc_start: 0.7366 (tpt) cc_final: 0.7121 (tpt) REVERT: B 104 LEU cc_start: 0.9045 (tt) cc_final: 0.8267 (pp) REVERT: B 325 MET cc_start: 0.8027 (mmm) cc_final: 0.7754 (mmm) REVERT: C 107 GLU cc_start: 0.7827 (tt0) cc_final: 0.7509 (pt0) REVERT: C 132 MET cc_start: 0.8535 (ppp) cc_final: 0.8112 (tmm) REVERT: D 191 LYS cc_start: 0.8547 (tttm) cc_final: 0.8024 (ttmm) REVERT: E 132 MET cc_start: 0.8781 (tmm) cc_final: 0.8509 (tmm) REVERT: E 176 MET cc_start: 0.6546 (ptp) cc_final: 0.6246 (ptp) REVERT: E 283 MET cc_start: 0.8710 (mmm) cc_final: 0.8333 (mmm) REVERT: E 325 MET cc_start: 0.8482 (mmt) cc_final: 0.8166 (mmt) REVERT: E 367 PRO cc_start: 0.7714 (Cg_endo) cc_final: 0.7492 (Cg_exo) REVERT: F 123 MET cc_start: 0.9003 (mtp) cc_final: 0.8795 (mtt) REVERT: F 154 ASP cc_start: 0.6908 (t0) cc_final: 0.6552 (t0) REVERT: F 276 GLU cc_start: 0.8738 (mp0) cc_final: 0.8209 (mp0) REVERT: F 299 MET cc_start: 0.8044 (ttp) cc_final: 0.7702 (mtp) REVERT: F 305 MET cc_start: 0.9001 (mmm) cc_final: 0.8672 (mmt) REVERT: F 373 LYS cc_start: 0.8554 (mmtt) cc_final: 0.8038 (mttt) REVERT: G 1119 MET cc_start: 0.9103 (mmm) cc_final: 0.8898 (mmm) REVERT: H 852 MET cc_start: 0.6592 (ttm) cc_final: 0.6007 (ttm) REVERT: H 859 ASN cc_start: 0.8676 (m110) cc_final: 0.8433 (p0) REVERT: H 873 MET cc_start: 0.8845 (ttm) cc_final: 0.8362 (ptm) REVERT: H 1136 GLN cc_start: 0.4139 (OUTLIER) cc_final: 0.3675 (mp10) outliers start: 27 outliers final: 21 residues processed: 228 average time/residue: 0.3295 time to fit residues: 123.1899 Evaluate side-chains 229 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 2.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain H residue 762 LEU Chi-restraints excluded: chain H residue 872 SER Chi-restraints excluded: chain H residue 881 MET Chi-restraints excluded: chain H residue 1136 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 108 optimal weight: 9.9990 chunk 219 optimal weight: 7.9990 chunk 198 optimal weight: 9.9990 chunk 157 optimal weight: 5.9990 chunk 209 optimal weight: 9.9990 chunk 101 optimal weight: 0.9980 chunk 268 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 290 optimal weight: 1.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 GLN ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 971 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.094056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.063484 restraints weight = 87453.350| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 5.31 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 24110 Z= 0.289 Angle : 0.691 13.315 32637 Z= 0.338 Chirality : 0.045 0.193 3614 Planarity : 0.004 0.065 4192 Dihedral : 8.182 164.195 3284 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.44 % Favored : 95.52 % Rotamer: Outliers : 1.17 % Allowed : 12.91 % Favored : 85.92 % 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: 0.36 (0.16), residues: 2927 helix: 0.75 (0.14), residues: 1443 sheet: -0.36 (0.26), residues: 402 loop : -0.01 (0.20), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 79 HIS 0.007 0.001 HIS B 371 PHE 0.020 0.001 PHE G1107 TYR 0.022 0.001 TYR H 854 ARG 0.007 0.000 ARG B 196 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 2.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8705 (mmm) cc_final: 0.7605 (pmm) REVERT: A 82 MET cc_start: 0.9410 (tpp) cc_final: 0.9018 (tpp) REVERT: A 187 ASP cc_start: 0.8788 (m-30) cc_final: 0.8368 (t70) REVERT: A 283 MET cc_start: 0.8652 (tpp) cc_final: 0.8124 (tpp) REVERT: A 313 MET cc_start: 0.8285 (tpt) cc_final: 0.8007 (tpt) REVERT: B 82 MET cc_start: 0.7449 (tpt) cc_final: 0.7191 (tpt) REVERT: B 104 LEU cc_start: 0.9054 (tt) cc_final: 0.8303 (pp) REVERT: B 361 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8707 (mm-30) REVERT: C 82 MET cc_start: 0.7892 (tpt) cc_final: 0.7508 (tpt) REVERT: C 107 GLU cc_start: 0.7896 (tt0) cc_final: 0.7599 (pt0) REVERT: C 132 MET cc_start: 0.8573 (ppp) cc_final: 0.8140 (tmm) REVERT: C 299 MET cc_start: 0.8480 (mmm) cc_final: 0.8245 (mmm) REVERT: D 191 LYS cc_start: 0.8570 (tttm) cc_final: 0.8075 (ttmm) REVERT: E 176 MET cc_start: 0.6461 (ptp) cc_final: 0.6182 (ptp) REVERT: E 283 MET cc_start: 0.8774 (mmm) cc_final: 0.8424 (mmm) REVERT: E 325 MET cc_start: 0.8551 (mmt) cc_final: 0.8233 (mmt) REVERT: E 367 PRO cc_start: 0.7637 (Cg_endo) cc_final: 0.7414 (Cg_exo) REVERT: F 132 MET cc_start: 0.9237 (tmm) cc_final: 0.9035 (tmm) REVERT: F 154 ASP cc_start: 0.7015 (t0) cc_final: 0.6613 (t0) REVERT: F 276 GLU cc_start: 0.8738 (mp0) cc_final: 0.8209 (mp0) REVERT: F 299 MET cc_start: 0.8101 (ttp) cc_final: 0.7682 (mtp) REVERT: F 305 MET cc_start: 0.9026 (mmm) cc_final: 0.8713 (mmt) REVERT: F 373 LYS cc_start: 0.8488 (mmtt) cc_final: 0.7999 (mttt) REVERT: H 852 MET cc_start: 0.7043 (ttm) cc_final: 0.6843 (ttm) REVERT: H 873 MET cc_start: 0.8863 (ttm) cc_final: 0.8455 (ptm) REVERT: H 1136 GLN cc_start: 0.4172 (OUTLIER) cc_final: 0.3581 (mp10) outliers start: 30 outliers final: 23 residues processed: 220 average time/residue: 0.3318 time to fit residues: 120.2870 Evaluate side-chains 218 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 2.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain H residue 762 LEU Chi-restraints excluded: chain H residue 872 SER Chi-restraints excluded: chain H residue 881 MET Chi-restraints excluded: chain H residue 1136 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 269 optimal weight: 3.9990 chunk 162 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 277 optimal weight: 40.0000 chunk 183 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 174 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 194 optimal weight: 0.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 HIS ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 971 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.095889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.065364 restraints weight = 86959.966| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 5.44 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 24110 Z= 0.174 Angle : 0.656 13.341 32637 Z= 0.317 Chirality : 0.043 0.230 3614 Planarity : 0.004 0.057 4192 Dihedral : 7.756 164.638 3284 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.45 % Favored : 96.48 % Rotamer: Outliers : 0.82 % Allowed : 13.41 % Favored : 85.76 % 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: 0.50 (0.16), residues: 2927 helix: 0.81 (0.14), residues: 1448 sheet: -0.27 (0.26), residues: 402 loop : 0.14 (0.20), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 79 HIS 0.005 0.001 HIS G1091 PHE 0.026 0.001 PHE C 223 TYR 0.028 0.001 TYR H 854 ARG 0.007 0.000 ARG B 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13032.83 seconds wall clock time: 233 minutes 1.43 seconds (13981.43 seconds total)