Starting phenix.real_space_refine on Fri Sep 19 05:54:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b3d_44135/09_2025/9b3d_44135.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b3d_44135/09_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_44135/09_2025/9b3d_44135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b3d_44135/09_2025/9b3d_44135.map" model { file = "/net/cci-nas-00/data/ceres_data/9b3d_44135/09_2025/9b3d_44135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b3d_44135/09_2025/9b3d_44135.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.96, per 1000 atoms: 0.21 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: 1.53 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.9 microseconds 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: 0.85 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: 4.74 Time building geometry restraints manager: 2.22 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 20.930 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.090 ------------------------------------------------------------------------------- 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 24115 Z= 0.246 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.004 0.001 ARG E 210 TYR 0.012 0.001 TYR F 240 PHE 0.029 0.002 PHE H1020 TRP 0.013 0.002 TRP G 767 HIS 0.006 0.001 HIS E 173 Details of bonding type rmsd covalent geometry : bond 0.00486 (24110) covalent geometry : angle 0.87907 (32637) hydrogen bonds : bond 0.19102 ( 1142) hydrogen bonds : angle 7.83727 ( 3120) Misc. bond : bond 0.00366 ( 5) *********************** 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 : 0.765 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: 0.7326 (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: 0.6559 (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: -0.0186 (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: 0.7388 (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: 0.1681 time to fit residues: 128.8259 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 : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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** ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN D 354 GLN ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 GLN F 59 GLN G 761 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 = 0.4053 r_free = 0.4053 target = 0.097694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.066052 restraints weight = 86247.706| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 5.78 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 24115 Z= 0.206 Angle : 0.672 9.788 32637 Z= 0.338 Chirality : 0.045 0.163 3614 Planarity : 0.006 0.074 4192 Dihedral : 10.832 169.051 3284 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.86 % Favored : 96.07 % Rotamer: Outliers : 1.49 % Allowed : 7.16 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.15), residues: 2927 helix: -0.63 (0.12), residues: 1398 sheet: -0.22 (0.26), residues: 402 loop : -0.46 (0.19), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 991 TYR 0.031 0.001 TYR H 854 PHE 0.019 0.002 PHE C 223 TRP 0.022 0.002 TRP D 79 HIS 0.010 0.001 HIS F 275 Details of bonding type rmsd covalent geometry : bond 0.00459 (24110) covalent geometry : angle 0.67244 (32637) hydrogen bonds : bond 0.03938 ( 1142) hydrogen bonds : angle 4.82175 ( 3120) Misc. bond : bond 0.00230 ( 5) *********************** 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 311 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 273 time to evaluate : 0.984 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 10 CYS cc_start: 0.7730 (t) cc_final: 0.7274 (t) REVERT: A 12 ASN cc_start: 0.8164 (m110) cc_final: 0.7499 (m110) REVERT: A 44 MET cc_start: 0.8427 (mmm) cc_final: 0.7708 (pmm) REVERT: A 82 MET cc_start: 0.9428 (tpp) cc_final: 0.9098 (tpp) REVERT: A 187 ASP cc_start: 0.8902 (m-30) cc_final: 0.8370 (t70) REVERT: A 227 MET cc_start: 0.8229 (mmm) cc_final: 0.7782 (mmm) REVERT: B 82 MET cc_start: 0.7327 (tpt) cc_final: 0.6466 (tpt) REVERT: B 104 LEU cc_start: 0.9011 (tt) cc_final: 0.8796 (tt) REVERT: B 361 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8590 (mt-10) REVERT: C 132 MET cc_start: 0.8498 (ppp) cc_final: 0.8134 (ppp) REVERT: C 223 PHE cc_start: 0.7111 (t80) cc_final: 0.6625 (t80) REVERT: C 236 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8319 (tp) REVERT: C 297 ASN cc_start: 0.8269 (OUTLIER) cc_final: 0.8007 (m110) REVERT: D 191 LYS cc_start: 0.8468 (tttm) cc_final: 0.8193 (tmtt) REVERT: E 283 MET cc_start: 0.8509 (mmm) cc_final: 0.8261 (mmm) REVERT: E 284 LYS cc_start: 0.9125 (ttmm) cc_final: 0.8862 (ttmt) REVERT: E 305 MET cc_start: 0.9049 (mmm) cc_final: 0.8553 (mmm) REVERT: E 325 MET cc_start: 0.8159 (mmt) cc_final: 0.7919 (mmt) REVERT: E 367 PRO cc_start: 0.7993 (Cg_endo) cc_final: 0.7710 (Cg_exo) REVERT: F 10 CYS cc_start: 0.8189 (t) cc_final: 0.7804 (t) REVERT: F 276 GLU cc_start: 0.8929 (mp0) cc_final: 0.8507 (mp0) REVERT: F 305 MET cc_start: 0.8973 (mmm) cc_final: 0.8500 (mmt) REVERT: G 1119 MET cc_start: 0.9070 (mmm) cc_final: 0.8827 (mmm) REVERT: H 852 MET cc_start: 0.5494 (ttm) cc_final: 0.5221 (tpp) REVERT: H 854 TYR cc_start: 0.5632 (m-10) cc_final: 0.5211 (m-10) REVERT: H 857 ILE cc_start: 0.9087 (mt) cc_final: 0.8615 (mt) REVERT: H 873 MET cc_start: 0.8531 (ttm) cc_final: 0.8285 (ptm) REVERT: H 902 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8154 (tm-30) outliers start: 38 outliers final: 23 residues processed: 300 average time/residue: 0.1537 time to fit residues: 74.1610 Evaluate side-chains 246 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 221 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ILE 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 236 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 139 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 363 ASP 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 247 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 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 191 optimal weight: 1.9990 chunk 239 optimal weight: 6.9990 chunk 235 optimal weight: 20.0000 chunk 82 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 218 optimal weight: 10.0000 chunk 226 optimal weight: 10.0000 chunk 280 optimal weight: 0.0970 chunk 38 optimal weight: 4.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 ASN ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 955 ASN G1093 ASN H1126 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.096749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.065507 restraints weight = 87461.577| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 5.63 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24115 Z= 0.180 Angle : 0.626 8.432 32637 Z= 0.310 Chirality : 0.044 0.150 3614 Planarity : 0.005 0.066 4192 Dihedral : 9.577 161.810 3284 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.45 % Favored : 96.48 % Rotamer: Outliers : 1.76 % Allowed : 9.11 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.16), residues: 2927 helix: 0.34 (0.14), residues: 1390 sheet: -0.17 (0.26), residues: 402 loop : -0.39 (0.19), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 95 TYR 0.018 0.001 TYR H 854 PHE 0.016 0.001 PHE G1107 TRP 0.018 0.001 TRP D 79 HIS 0.007 0.001 HIS F 275 Details of bonding type rmsd covalent geometry : bond 0.00400 (24110) covalent geometry : angle 0.62642 (32637) hydrogen bonds : bond 0.03479 ( 1142) hydrogen bonds : angle 4.54379 ( 3120) Misc. bond : bond 0.00155 ( 5) *********************** 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 266 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 221 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.8180 (m110) cc_final: 0.7858 (m110) REVERT: A 44 MET cc_start: 0.8439 (mmm) cc_final: 0.7573 (pmm) REVERT: A 82 MET cc_start: 0.9419 (tpp) cc_final: 0.9018 (tpp) REVERT: A 187 ASP cc_start: 0.8813 (m-30) cc_final: 0.8363 (t70) REVERT: A 269 MET cc_start: 0.8658 (mtp) cc_final: 0.8342 (mtt) REVERT: A 283 MET cc_start: 0.8609 (mmm) cc_final: 0.8068 (tpp) REVERT: A 313 MET cc_start: 0.8284 (tpt) cc_final: 0.7941 (tpt) REVERT: B 82 MET cc_start: 0.7406 (tpt) cc_final: 0.7043 (tpt) REVERT: B 361 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8584 (mt-10) REVERT: C 132 MET cc_start: 0.8587 (ppp) cc_final: 0.8200 (ppp) REVERT: C 223 PHE cc_start: 0.7040 (t80) cc_final: 0.6676 (t80) REVERT: C 297 ASN cc_start: 0.8374 (OUTLIER) cc_final: 0.8148 (m110) REVERT: C 305 MET cc_start: 0.8405 (mtp) cc_final: 0.8180 (mtp) REVERT: D 132 MET cc_start: 0.7667 (ppp) cc_final: 0.7235 (ppp) REVERT: D 190 MET cc_start: 0.7835 (mtm) cc_final: 0.7511 (mtm) REVERT: D 191 LYS cc_start: 0.8506 (tttm) cc_final: 0.8189 (tmtt) REVERT: E 305 MET cc_start: 0.9066 (mmm) cc_final: 0.8615 (mmm) REVERT: E 325 MET cc_start: 0.8272 (mmt) cc_final: 0.7958 (mmt) REVERT: E 367 PRO cc_start: 0.8052 (Cg_endo) cc_final: 0.7785 (Cg_exo) REVERT: F 10 CYS cc_start: 0.8240 (t) cc_final: 0.7857 (t) REVERT: F 154 ASP cc_start: 0.7164 (t0) cc_final: 0.6897 (t0) REVERT: F 276 GLU cc_start: 0.8829 (mp0) cc_final: 0.8395 (mp0) REVERT: F 283 MET cc_start: 0.9076 (mmm) cc_final: 0.8867 (mmm) REVERT: F 305 MET cc_start: 0.8992 (mmm) cc_final: 0.8559 (mmt) REVERT: G 1094 MET cc_start: 0.7094 (OUTLIER) cc_final: 0.6749 (tpt) REVERT: G 1119 MET cc_start: 0.9112 (mmm) cc_final: 0.8893 (mmm) REVERT: H 852 MET cc_start: 0.5300 (ttm) cc_final: 0.4944 (tpp) REVERT: H 854 TYR cc_start: 0.5605 (m-10) cc_final: 0.4942 (m-10) REVERT: H 857 ILE cc_start: 0.9054 (mt) cc_final: 0.8549 (mt) REVERT: H 873 MET cc_start: 0.8651 (ttm) cc_final: 0.8284 (ptm) REVERT: H 902 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8047 (tm-30) REVERT: H 1082 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8177 (pp20) outliers start: 45 outliers final: 29 residues processed: 252 average time/residue: 0.1475 time to fit residues: 61.0650 Evaluate side-chains 242 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 210 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 297 ASN 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 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 189 optimal weight: 9.9990 chunk 199 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 4 optimal weight: 0.0570 chunk 37 optimal weight: 10.0000 chunk 213 optimal weight: 4.9990 chunk 248 optimal weight: 8.9990 chunk 227 optimal weight: 20.0000 chunk 142 optimal weight: 5.9990 chunk 218 optimal weight: 10.0000 overall best weight: 3.6106 ------------------------------------------------------------------------------- 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 12 ASN E 162 ASN H1081 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.095735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.064357 restraints weight = 87414.417| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 5.70 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 24115 Z= 0.193 Angle : 0.629 7.706 32637 Z= 0.310 Chirality : 0.044 0.196 3614 Planarity : 0.004 0.062 4192 Dihedral : 8.798 162.629 3284 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.83 % Favored : 96.11 % Rotamer: Outliers : 1.96 % Allowed : 9.74 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.16), residues: 2927 helix: 0.64 (0.14), residues: 1398 sheet: -0.22 (0.27), residues: 402 loop : -0.24 (0.20), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 919 TYR 0.011 0.001 TYR B 306 PHE 0.017 0.001 PHE H1076 TRP 0.018 0.001 TRP D 79 HIS 0.005 0.001 HIS D 371 Details of bonding type rmsd covalent geometry : bond 0.00432 (24110) covalent geometry : angle 0.62891 (32637) hydrogen bonds : bond 0.03429 ( 1142) hydrogen bonds : angle 4.51441 ( 3120) Misc. bond : bond 0.00136 ( 5) *********************** 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 267 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 217 time to evaluate : 0.811 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: 0.8609 (mmm) cc_final: 0.7678 (pmm) REVERT: A 82 MET cc_start: 0.9429 (tpp) cc_final: 0.9019 (tpp) REVERT: A 187 ASP cc_start: 0.8829 (m-30) cc_final: 0.8403 (t70) REVERT: A 269 MET cc_start: 0.8677 (mtp) cc_final: 0.8348 (mtt) REVERT: A 313 MET cc_start: 0.8278 (tpt) cc_final: 0.8077 (tpt) REVERT: B 82 MET cc_start: 0.7425 (tpt) cc_final: 0.6591 (tpt) REVERT: B 140 LEU cc_start: 0.8882 (mt) cc_final: 0.8578 (mt) REVERT: B 190 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7863 (mtt) REVERT: B 361 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8609 (mt-10) REVERT: C 132 MET cc_start: 0.8650 (ppp) cc_final: 0.8288 (ppp) REVERT: C 223 PHE cc_start: 0.7098 (t80) cc_final: 0.6808 (t80) REVERT: C 297 ASN cc_start: 0.8423 (OUTLIER) cc_final: 0.8181 (m110) REVERT: D 190 MET cc_start: 0.7758 (mtm) cc_final: 0.7373 (mtm) REVERT: D 191 LYS cc_start: 0.8547 (tttm) cc_final: 0.8287 (tmtt) REVERT: E 283 MET cc_start: 0.8747 (mmm) cc_final: 0.8338 (mmm) REVERT: E 305 MET cc_start: 0.9102 (mmm) cc_final: 0.8736 (mmm) REVERT: E 325 MET cc_start: 0.8306 (mmt) cc_final: 0.8094 (mmt) REVERT: E 367 PRO cc_start: 0.7928 (Cg_endo) cc_final: 0.7652 (Cg_exo) REVERT: F 10 CYS cc_start: 0.8250 (t) cc_final: 0.7794 (t) REVERT: F 154 ASP cc_start: 0.7177 (t0) cc_final: 0.6869 (t0) REVERT: F 276 GLU cc_start: 0.8718 (mp0) cc_final: 0.8252 (mp0) REVERT: F 305 MET cc_start: 0.8984 (mmm) cc_final: 0.8596 (mmt) REVERT: G 873 MET cc_start: 0.8036 (ppp) cc_final: 0.7383 (ppp) REVERT: G 1087 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9178 (mm) REVERT: G 1094 MET cc_start: 0.6908 (OUTLIER) cc_final: 0.6574 (tpt) REVERT: G 1119 MET cc_start: 0.9066 (mmm) cc_final: 0.8856 (mmm) REVERT: H 852 MET cc_start: 0.5569 (ttm) cc_final: 0.5167 (ttm) REVERT: H 854 TYR cc_start: 0.5639 (m-10) cc_final: 0.4982 (m-10) REVERT: H 873 MET cc_start: 0.8753 (ttm) cc_final: 0.8362 (ptm) REVERT: H 902 GLU cc_start: 0.8321 (mt-10) cc_final: 0.8065 (tm-30) REVERT: H 951 ARG cc_start: 0.8569 (tpp80) cc_final: 0.8152 (tpp80) REVERT: H 1082 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8255 (pp20) outliers start: 50 outliers final: 33 residues processed: 255 average time/residue: 0.1469 time to fit residues: 61.2768 Evaluate side-chains 241 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 203 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE 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 190 MET 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 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 12 ASN Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 162 ASN 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 151 ILE Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain G residue 1087 LEU 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 1022 ASP 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 171 optimal weight: 8.9990 chunk 52 optimal weight: 0.0870 chunk 129 optimal weight: 1.9990 chunk 160 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 173 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 170 optimal weight: 0.9990 chunk 271 optimal weight: 30.0000 chunk 158 optimal weight: 1.9990 overall best weight: 0.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 GLN E 12 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 859 ASN H 935 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 = 0.097643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.066401 restraints weight = 86425.506| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 5.57 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 24115 Z= 0.106 Angle : 0.576 7.999 32637 Z= 0.279 Chirality : 0.042 0.196 3614 Planarity : 0.004 0.059 4192 Dihedral : 8.325 163.770 3284 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.45 % Favored : 96.48 % Rotamer: Outliers : 1.17 % Allowed : 11.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.16), residues: 2927 helix: 0.73 (0.14), residues: 1446 sheet: -0.18 (0.26), residues: 402 loop : 0.03 (0.20), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 919 TYR 0.009 0.001 TYR G1084 PHE 0.018 0.001 PHE G1107 TRP 0.017 0.001 TRP D 79 HIS 0.005 0.001 HIS D 371 Details of bonding type rmsd covalent geometry : bond 0.00240 (24110) covalent geometry : angle 0.57570 (32637) hydrogen bonds : bond 0.02963 ( 1142) hydrogen bonds : angle 4.27272 ( 3120) Misc. bond : bond 0.00112 ( 5) *********************** 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 254 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 224 time to evaluate : 0.844 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: 0.8645 (mmm) cc_final: 0.7699 (pmm) REVERT: A 82 MET cc_start: 0.9396 (tpp) cc_final: 0.8995 (tpp) REVERT: A 187 ASP cc_start: 0.8761 (m-30) cc_final: 0.8319 (t70) REVERT: A 269 MET cc_start: 0.8625 (mtp) cc_final: 0.8301 (mtt) REVERT: A 283 MET cc_start: 0.8559 (mmm) cc_final: 0.7971 (tpp) REVERT: A 313 MET cc_start: 0.8319 (tpt) cc_final: 0.8042 (tpt) REVERT: A 374 CYS cc_start: 0.6921 (m) cc_final: 0.6222 (m) REVERT: B 82 MET cc_start: 0.7365 (tpt) cc_final: 0.7033 (tpt) REVERT: B 140 LEU cc_start: 0.8833 (mt) cc_final: 0.8603 (mt) REVERT: B 190 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7861 (mtt) REVERT: B 361 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8581 (mt-10) REVERT: C 44 MET cc_start: 0.9460 (mmt) cc_final: 0.8940 (mmp) REVERT: C 132 MET cc_start: 0.8564 (ppp) cc_final: 0.8359 (ppp) REVERT: C 223 PHE cc_start: 0.6989 (t80) cc_final: 0.6755 (t80) REVERT: C 297 ASN cc_start: 0.8388 (OUTLIER) cc_final: 0.8083 (m-40) REVERT: C 325 MET cc_start: 0.8324 (mmt) cc_final: 0.8089 (mmm) REVERT: D 190 MET cc_start: 0.7662 (mtm) cc_final: 0.7284 (mtm) REVERT: D 191 LYS cc_start: 0.8460 (tttm) cc_final: 0.8198 (tmtt) REVERT: E 283 MET cc_start: 0.8569 (mmm) cc_final: 0.8147 (mmm) REVERT: E 305 MET cc_start: 0.9059 (mmm) cc_final: 0.8704 (mmm) REVERT: E 367 PRO cc_start: 0.7690 (Cg_endo) cc_final: 0.6971 (Cg_exo) REVERT: F 10 CYS cc_start: 0.8160 (t) cc_final: 0.7755 (t) REVERT: F 57 GLU cc_start: 0.7998 (mp0) cc_final: 0.7776 (pm20) REVERT: F 154 ASP cc_start: 0.6948 (t0) cc_final: 0.6735 (t0) REVERT: F 276 GLU cc_start: 0.8692 (mp0) cc_final: 0.8232 (mp0) REVERT: F 283 MET cc_start: 0.9285 (mmm) cc_final: 0.9000 (mmm) REVERT: F 305 MET cc_start: 0.8972 (mmm) cc_final: 0.8591 (mmt) REVERT: G 1094 MET cc_start: 0.6959 (OUTLIER) cc_final: 0.6687 (tpt) REVERT: H 852 MET cc_start: 0.5424 (ttm) cc_final: 0.5161 (ttm) REVERT: H 854 TYR cc_start: 0.5462 (m-10) cc_final: 0.5185 (m-10) REVERT: H 873 MET cc_start: 0.8775 (ttm) cc_final: 0.8315 (ptm) REVERT: H 902 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8085 (tm-30) REVERT: H 951 ARG cc_start: 0.8494 (tpp80) cc_final: 0.8244 (tpp80) outliers start: 30 outliers final: 17 residues processed: 243 average time/residue: 0.1539 time to fit residues: 60.8647 Evaluate side-chains 231 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 211 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 ILE 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 190 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 221 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 G residue 1094 MET 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 137 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 215 optimal weight: 10.0000 chunk 136 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 147 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 chunk 268 optimal weight: 5.9990 chunk 184 optimal weight: 10.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN E 115 ASN ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H1126 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.095770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.065225 restraints weight = 87139.135| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 5.36 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24115 Z= 0.174 Angle : 0.629 10.821 32637 Z= 0.305 Chirality : 0.044 0.209 3614 Planarity : 0.004 0.057 4192 Dihedral : 8.320 169.148 3284 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.00 % Favored : 95.93 % Rotamer: Outliers : 1.68 % Allowed : 11.38 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.16), residues: 2927 helix: 0.87 (0.14), residues: 1438 sheet: -0.22 (0.26), residues: 402 loop : -0.01 (0.20), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 919 TYR 0.011 0.001 TYR B 306 PHE 0.019 0.001 PHE G1107 TRP 0.015 0.001 TRP D 79 HIS 0.004 0.001 HIS D 371 Details of bonding type rmsd covalent geometry : bond 0.00392 (24110) covalent geometry : angle 0.62932 (32637) hydrogen bonds : bond 0.03217 ( 1142) hydrogen bonds : angle 4.37458 ( 3120) Misc. bond : bond 0.00165 ( 5) *********************** 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 252 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 209 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8477 (mmm) cc_final: 0.7600 (pmm) REVERT: A 82 MET cc_start: 0.9430 (tpp) cc_final: 0.9024 (tpp) REVERT: A 187 ASP cc_start: 0.8820 (m-30) cc_final: 0.8374 (t70) REVERT: A 283 MET cc_start: 0.8585 (mmm) cc_final: 0.8004 (tpp) REVERT: A 305 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8412 (mmt) REVERT: A 313 MET cc_start: 0.8285 (tpt) cc_final: 0.7844 (tpt) REVERT: B 82 MET cc_start: 0.7420 (tpt) cc_final: 0.6718 (tpt) REVERT: B 104 LEU cc_start: 0.9233 (tt) cc_final: 0.8409 (pp) REVERT: B 140 LEU cc_start: 0.8855 (mt) cc_final: 0.8610 (mt) REVERT: B 190 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7963 (mtt) REVERT: B 361 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8554 (mt-10) REVERT: C 132 MET cc_start: 0.8590 (ppp) cc_final: 0.8385 (ppp) REVERT: C 223 PHE cc_start: 0.7093 (t80) cc_final: 0.6780 (t80) REVERT: C 297 ASN cc_start: 0.8465 (OUTLIER) cc_final: 0.8263 (m110) REVERT: D 191 LYS cc_start: 0.8572 (tttm) cc_final: 0.8331 (tmtt) REVERT: D 299 MET cc_start: 0.8065 (mmt) cc_final: 0.7759 (mmm) REVERT: E 283 MET cc_start: 0.8635 (mmm) cc_final: 0.8257 (mmm) REVERT: E 305 MET cc_start: 0.9128 (mmm) cc_final: 0.8767 (mmm) REVERT: E 325 MET cc_start: 0.8659 (mmt) cc_final: 0.8327 (mmt) REVERT: E 367 PRO cc_start: 0.7566 (Cg_endo) cc_final: 0.7269 (Cg_exo) REVERT: F 10 CYS cc_start: 0.8236 (t) cc_final: 0.7822 (t) REVERT: F 154 ASP cc_start: 0.6919 (t0) cc_final: 0.6579 (t0) REVERT: F 276 GLU cc_start: 0.8688 (mp0) cc_final: 0.8205 (mp0) REVERT: F 283 MET cc_start: 0.9249 (mmm) cc_final: 0.8968 (mmm) REVERT: F 305 MET cc_start: 0.8997 (mmm) cc_final: 0.8629 (mmt) REVERT: G 1094 MET cc_start: 0.6970 (tpt) cc_final: 0.6709 (tpt) REVERT: H 852 MET cc_start: 0.5612 (ttm) cc_final: 0.5305 (tpp) REVERT: H 854 TYR cc_start: 0.5626 (m-10) cc_final: 0.5175 (m-10) REVERT: H 857 ILE cc_start: 0.9033 (mt) cc_final: 0.8467 (mp) REVERT: H 873 MET cc_start: 0.8818 (ttm) cc_final: 0.8473 (ptm) outliers start: 43 outliers final: 28 residues processed: 239 average time/residue: 0.1542 time to fit residues: 59.9928 Evaluate side-chains 232 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 201 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 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 159 VAL Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 212 ILE 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 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 47 MET Chi-restraints excluded: chain E residue 199 SER 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 1022 ASP Chi-restraints excluded: chain H residue 1033 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 55 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 279 optimal weight: 50.0000 chunk 126 optimal weight: 6.9990 chunk 285 optimal weight: 0.0270 chunk 124 optimal weight: 0.8980 chunk 210 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 156 optimal weight: 0.9990 chunk 240 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 overall best weight: 1.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 841 GLN ** 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 = 0.4029 r_free = 0.4029 target = 0.096522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.065423 restraints weight = 86709.792| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 5.68 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 24115 Z= 0.132 Angle : 0.612 10.180 32637 Z= 0.295 Chirality : 0.043 0.188 3614 Planarity : 0.004 0.068 4192 Dihedral : 8.182 173.872 3284 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.72 % Favored : 96.21 % Rotamer: Outliers : 1.21 % Allowed : 12.16 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.16), residues: 2927 helix: 0.91 (0.14), residues: 1438 sheet: -0.19 (0.26), residues: 402 loop : 0.10 (0.20), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 919 TYR 0.009 0.001 TYR G1084 PHE 0.019 0.001 PHE G1107 TRP 0.016 0.001 TRP D 79 HIS 0.004 0.001 HIS D 371 Details of bonding type rmsd covalent geometry : bond 0.00304 (24110) covalent geometry : angle 0.61232 (32637) hydrogen bonds : bond 0.03026 ( 1142) hydrogen bonds : angle 4.31234 ( 3120) Misc. bond : bond 0.00128 ( 5) *********************** 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 240 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 209 time to evaluate : 0.862 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: 0.8717 (mmm) cc_final: 0.7754 (pmm) REVERT: A 82 MET cc_start: 0.9436 (tpp) cc_final: 0.9046 (tpp) REVERT: A 187 ASP cc_start: 0.8783 (m-30) cc_final: 0.8342 (t70) REVERT: A 283 MET cc_start: 0.8632 (mmm) cc_final: 0.8044 (tpp) REVERT: A 305 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8413 (mmt) REVERT: A 313 MET cc_start: 0.8355 (tpt) cc_final: 0.7890 (tpt) REVERT: A 374 CYS cc_start: 0.6791 (m) cc_final: 0.6136 (m) REVERT: B 82 MET cc_start: 0.7386 (tpt) cc_final: 0.7131 (tpt) REVERT: B 104 LEU cc_start: 0.9100 (tt) cc_final: 0.8276 (pp) REVERT: B 140 LEU cc_start: 0.8827 (mt) cc_final: 0.8556 (mt) REVERT: B 190 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7976 (mtt) REVERT: B 361 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8609 (mt-10) REVERT: C 44 MET cc_start: 0.9483 (mmt) cc_final: 0.9038 (mmp) REVERT: C 223 PHE cc_start: 0.7063 (t80) cc_final: 0.6773 (t80) REVERT: C 297 ASN cc_start: 0.8365 (OUTLIER) cc_final: 0.8081 (m-40) REVERT: D 190 MET cc_start: 0.7864 (mtm) cc_final: 0.7606 (mtm) REVERT: D 191 LYS cc_start: 0.8542 (tttm) cc_final: 0.8051 (ttmm) REVERT: E 176 MET cc_start: 0.6625 (ptp) cc_final: 0.6318 (ptp) REVERT: E 283 MET cc_start: 0.8646 (mmm) cc_final: 0.8293 (mmm) REVERT: E 325 MET cc_start: 0.8660 (mmt) cc_final: 0.8315 (mmt) REVERT: E 367 PRO cc_start: 0.7529 (Cg_endo) cc_final: 0.7227 (Cg_exo) REVERT: F 10 CYS cc_start: 0.8253 (t) cc_final: 0.7827 (t) REVERT: F 154 ASP cc_start: 0.6828 (t0) cc_final: 0.6455 (t0) REVERT: F 176 MET cc_start: 0.7028 (mtp) cc_final: 0.6644 (ptp) REVERT: F 276 GLU cc_start: 0.8710 (mp0) cc_final: 0.8236 (mp0) REVERT: F 283 MET cc_start: 0.9278 (mmm) cc_final: 0.9020 (mmm) REVERT: F 305 MET cc_start: 0.8977 (mmm) cc_final: 0.8604 (mmt) REVERT: G 1094 MET cc_start: 0.6877 (tpt) cc_final: 0.6523 (tpt) REVERT: H 852 MET cc_start: 0.5621 (ttm) cc_final: 0.5300 (tpp) REVERT: H 857 ILE cc_start: 0.8912 (mt) cc_final: 0.8349 (mp) REVERT: H 873 MET cc_start: 0.8808 (ttm) cc_final: 0.8395 (ptm) outliers start: 31 outliers final: 23 residues processed: 230 average time/residue: 0.1432 time to fit residues: 53.8735 Evaluate side-chains 228 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 202 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 ILE 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 159 VAL Chi-restraints excluded: chain B residue 190 MET 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 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 E residue 47 MET Chi-restraints excluded: chain E residue 151 ILE 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 1033 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 172 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 251 optimal weight: 30.0000 chunk 175 optimal weight: 0.9990 chunk 263 optimal weight: 30.0000 chunk 226 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 236 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 971 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1026 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.095188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.064767 restraints weight = 87069.621| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 5.34 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24115 Z= 0.183 Angle : 0.654 13.541 32637 Z= 0.317 Chirality : 0.044 0.187 3614 Planarity : 0.004 0.066 4192 Dihedral : 8.271 177.928 3284 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.27 % Favored : 95.70 % Rotamer: Outliers : 1.49 % Allowed : 11.85 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.16), residues: 2927 helix: 0.84 (0.14), residues: 1445 sheet: -0.21 (0.26), residues: 402 loop : 0.06 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 764 TYR 0.013 0.001 TYR H 969 PHE 0.018 0.001 PHE G1107 TRP 0.015 0.001 TRP D 79 HIS 0.004 0.001 HIS E 371 Details of bonding type rmsd covalent geometry : bond 0.00413 (24110) covalent geometry : angle 0.65381 (32637) hydrogen bonds : bond 0.03233 ( 1142) hydrogen bonds : angle 4.47610 ( 3120) Misc. bond : bond 0.00172 ( 5) *********************** 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 245 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 207 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8555 (mmm) cc_final: 0.7603 (pmm) REVERT: A 82 MET cc_start: 0.9419 (tpp) cc_final: 0.9042 (tpp) REVERT: A 187 ASP cc_start: 0.8814 (m-30) cc_final: 0.8381 (t70) REVERT: A 283 MET cc_start: 0.8599 (mmm) cc_final: 0.8044 (tpp) REVERT: A 305 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8446 (mmt) REVERT: A 313 MET cc_start: 0.8303 (tpt) cc_final: 0.7821 (tpt) REVERT: B 82 MET cc_start: 0.7436 (tpt) cc_final: 0.7178 (tpt) REVERT: B 104 LEU cc_start: 0.9115 (tt) cc_final: 0.8318 (pp) REVERT: B 140 LEU cc_start: 0.8887 (mt) cc_final: 0.8660 (mt) REVERT: B 190 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.8007 (mtt) REVERT: B 361 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8556 (mt-10) REVERT: C 44 MET cc_start: 0.9446 (OUTLIER) cc_final: 0.9224 (mmp) REVERT: C 132 MET cc_start: 0.8594 (ppp) cc_final: 0.8188 (tmm) REVERT: C 223 PHE cc_start: 0.7123 (t80) cc_final: 0.6810 (t80) REVERT: D 44 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7723 (ppp) REVERT: D 132 MET cc_start: 0.7077 (ppp) cc_final: 0.6814 (ppp) REVERT: D 190 MET cc_start: 0.7897 (mtm) cc_final: 0.7605 (mtm) REVERT: D 191 LYS cc_start: 0.8567 (tttm) cc_final: 0.8335 (tmtt) REVERT: E 176 MET cc_start: 0.6433 (ptp) cc_final: 0.6047 (ptp) REVERT: E 283 MET cc_start: 0.8733 (mmm) cc_final: 0.8406 (mmm) REVERT: E 325 MET cc_start: 0.8666 (mmt) cc_final: 0.8345 (mmt) REVERT: E 367 PRO cc_start: 0.7405 (Cg_endo) cc_final: 0.7118 (Cg_exo) REVERT: F 10 CYS cc_start: 0.8210 (t) cc_final: 0.7763 (t) REVERT: F 132 MET cc_start: 0.9166 (tmm) cc_final: 0.8881 (tmm) REVERT: F 154 ASP cc_start: 0.6998 (t0) cc_final: 0.6618 (t0) REVERT: F 276 GLU cc_start: 0.8677 (mp0) cc_final: 0.8195 (mp0) REVERT: F 305 MET cc_start: 0.9006 (mmm) cc_final: 0.8674 (mmt) REVERT: F 373 LYS cc_start: 0.8683 (mttt) cc_final: 0.8424 (mttt) REVERT: G 1094 MET cc_start: 0.7058 (tpt) cc_final: 0.6828 (tpt) REVERT: H 852 MET cc_start: 0.5909 (ttm) cc_final: 0.5616 (tpp) REVERT: H 857 ILE cc_start: 0.8915 (mt) cc_final: 0.8429 (mp) REVERT: H 873 MET cc_start: 0.8847 (ttm) cc_final: 0.8478 (ptm) REVERT: H 970 MET cc_start: -0.6334 (ttt) cc_final: -0.6619 (ttp) outliers start: 38 outliers final: 26 residues processed: 232 average time/residue: 0.1505 time to fit residues: 57.1626 Evaluate side-chains 230 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 0.955 ------------------------------------------------------------------------------- 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 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 159 VAL Chi-restraints excluded: chain B residue 190 MET 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 D residue 44 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 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 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 881 MET Chi-restraints excluded: chain H residue 1033 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 19 optimal weight: 10.0000 chunk 200 optimal weight: 0.2980 chunk 30 optimal weight: 0.6980 chunk 201 optimal weight: 5.9990 chunk 165 optimal weight: 9.9990 chunk 2 optimal weight: 0.0980 chunk 14 optimal weight: 10.0000 chunk 181 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 291 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** E 115 ASN ** 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 = 0.4025 r_free = 0.4025 target = 0.096176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.065013 restraints weight = 86913.492| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 5.72 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24115 Z= 0.128 Angle : 0.627 12.284 32637 Z= 0.303 Chirality : 0.043 0.201 3614 Planarity : 0.004 0.067 4192 Dihedral : 7.993 166.170 3284 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.66 % Favored : 96.28 % Rotamer: Outliers : 1.49 % Allowed : 12.16 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.16), residues: 2927 helix: 0.86 (0.14), residues: 1444 sheet: -0.12 (0.26), residues: 402 loop : 0.19 (0.21), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G1088 TYR 0.020 0.001 TYR H 854 PHE 0.019 0.001 PHE G1107 TRP 0.017 0.001 TRP D 79 HIS 0.004 0.001 HIS D 371 Details of bonding type rmsd covalent geometry : bond 0.00293 (24110) covalent geometry : angle 0.62714 (32637) hydrogen bonds : bond 0.03051 ( 1142) hydrogen bonds : angle 4.38058 ( 3120) Misc. bond : bond 0.00129 ( 5) *********************** 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 246 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 208 time to evaluate : 1.050 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: 0.8745 (mmm) cc_final: 0.7759 (pmm) REVERT: A 82 MET cc_start: 0.9457 (tpp) cc_final: 0.9058 (tpp) REVERT: A 187 ASP cc_start: 0.8778 (m-30) cc_final: 0.8329 (t70) REVERT: A 283 MET cc_start: 0.8618 (mmm) cc_final: 0.8041 (tpp) REVERT: A 305 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8404 (mmt) REVERT: A 313 MET cc_start: 0.8389 (tpt) cc_final: 0.7922 (tpt) REVERT: A 355 MET cc_start: 0.8234 (ttt) cc_final: 0.7917 (tpt) REVERT: B 82 MET cc_start: 0.7368 (tpt) cc_final: 0.7120 (tpt) REVERT: B 104 LEU cc_start: 0.9098 (tt) cc_final: 0.8312 (pp) REVERT: B 140 LEU cc_start: 0.8860 (mt) cc_final: 0.8610 (mt) REVERT: B 361 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8624 (mt-10) REVERT: C 34 ILE cc_start: 0.8476 (pp) cc_final: 0.8167 (mt) REVERT: C 44 MET cc_start: 0.9509 (OUTLIER) cc_final: 0.9297 (mmp) REVERT: C 107 GLU cc_start: 0.7831 (tt0) cc_final: 0.7524 (pt0) REVERT: C 132 MET cc_start: 0.8538 (ppp) cc_final: 0.8117 (tmm) REVERT: C 223 PHE cc_start: 0.7065 (t80) cc_final: 0.6774 (t80) REVERT: D 44 MET cc_start: 0.7943 (ppp) cc_final: 0.7680 (ppp) REVERT: D 132 MET cc_start: 0.7020 (ppp) cc_final: 0.6774 (ppp) REVERT: D 191 LYS cc_start: 0.8546 (tttm) cc_final: 0.8049 (ttmm) REVERT: D 299 MET cc_start: 0.8148 (tpp) cc_final: 0.7274 (mmm) REVERT: E 176 MET cc_start: 0.6505 (ptp) cc_final: 0.6152 (ptp) REVERT: E 283 MET cc_start: 0.8701 (mmm) cc_final: 0.8368 (mmm) REVERT: E 367 PRO cc_start: 0.7603 (Cg_endo) cc_final: 0.7340 (Cg_exo) REVERT: F 10 CYS cc_start: 0.8215 (t) cc_final: 0.7754 (t) REVERT: F 154 ASP cc_start: 0.6920 (t0) cc_final: 0.6540 (t0) REVERT: F 176 MET cc_start: 0.6764 (mtp) cc_final: 0.6319 (ptp) REVERT: F 276 GLU cc_start: 0.8693 (mp0) cc_final: 0.8209 (mp0) REVERT: F 305 MET cc_start: 0.8993 (mmm) cc_final: 0.8684 (mmt) REVERT: F 373 LYS cc_start: 0.8658 (mttt) cc_final: 0.8283 (mttt) REVERT: G 1094 MET cc_start: 0.6981 (tpt) cc_final: 0.6754 (tpt) REVERT: H 852 MET cc_start: 0.6355 (ttm) cc_final: 0.6007 (ttm) REVERT: H 873 MET cc_start: 0.8837 (ttm) cc_final: 0.8390 (ptm) REVERT: H 1082 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8460 (pp20) outliers start: 38 outliers final: 27 residues processed: 231 average time/residue: 0.1474 time to fit residues: 56.0974 Evaluate side-chains 235 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 205 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 274 ILE 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 159 VAL Chi-restraints excluded: chain B residue 234 SER 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 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 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 1033 VAL Chi-restraints excluded: chain H residue 1082 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 174 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 254 optimal weight: 30.0000 chunk 270 optimal weight: 20.0000 chunk 256 optimal weight: 8.9990 chunk 193 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 206 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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** ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 971 ASN ** 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 = 0.3989 r_free = 0.3989 target = 0.094327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.063346 restraints weight = 87204.718| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 5.30 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 24115 Z= 0.212 Angle : 0.684 11.923 32637 Z= 0.334 Chirality : 0.045 0.190 3614 Planarity : 0.004 0.078 4192 Dihedral : 8.040 159.537 3284 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.41 % Favored : 95.52 % Rotamer: Outliers : 1.37 % Allowed : 12.48 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.16), residues: 2927 helix: 0.74 (0.14), residues: 1443 sheet: -0.23 (0.26), residues: 402 loop : 0.07 (0.20), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 951 TYR 0.013 0.001 TYR H1104 PHE 0.019 0.001 PHE G1107 TRP 0.015 0.002 TRP D 79 HIS 0.005 0.001 HIS E 371 Details of bonding type rmsd covalent geometry : bond 0.00478 (24110) covalent geometry : angle 0.68361 (32637) hydrogen bonds : bond 0.03383 ( 1142) hydrogen bonds : angle 4.59639 ( 3120) Misc. bond : bond 0.00185 ( 5) ********************** 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 244 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8852 (mmm) cc_final: 0.7693 (pmm) REVERT: A 82 MET cc_start: 0.9432 (tpp) cc_final: 0.9036 (tpp) REVERT: A 187 ASP cc_start: 0.8783 (m-30) cc_final: 0.8373 (t70) REVERT: A 283 MET cc_start: 0.8594 (mmm) cc_final: 0.8035 (tpp) REVERT: A 305 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8495 (mmt) REVERT: A 313 MET cc_start: 0.8400 (tpt) cc_final: 0.7926 (tpt) REVERT: B 82 MET cc_start: 0.7434 (tpt) cc_final: 0.7179 (tpt) REVERT: B 104 LEU cc_start: 0.9093 (tt) cc_final: 0.8359 (pp) REVERT: B 140 LEU cc_start: 0.8917 (mt) cc_final: 0.8646 (mt) REVERT: B 361 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8638 (mt-10) REVERT: C 44 MET cc_start: 0.9496 (OUTLIER) cc_final: 0.9123 (mmt) REVERT: C 107 GLU cc_start: 0.7908 (tt0) cc_final: 0.7579 (pt0) REVERT: C 132 MET cc_start: 0.8578 (ppp) cc_final: 0.8156 (tmm) REVERT: C 223 PHE cc_start: 0.7164 (t80) cc_final: 0.6859 (t80) REVERT: D 44 MET cc_start: 0.7919 (ppp) cc_final: 0.7658 (ppp) REVERT: D 132 MET cc_start: 0.6949 (ppp) cc_final: 0.6624 (ppp) REVERT: D 190 MET cc_start: 0.7933 (mtm) cc_final: 0.7704 (mtm) REVERT: D 191 LYS cc_start: 0.8588 (tttm) cc_final: 0.8353 (tmtt) REVERT: E 176 MET cc_start: 0.6456 (ptp) cc_final: 0.6145 (ptp) REVERT: E 283 MET cc_start: 0.8768 (mmm) cc_final: 0.8453 (mmm) REVERT: E 367 PRO cc_start: 0.7613 (Cg_endo) cc_final: 0.7341 (Cg_exo) REVERT: F 10 CYS cc_start: 0.8301 (t) cc_final: 0.7848 (t) REVERT: F 154 ASP cc_start: 0.7002 (t0) cc_final: 0.6609 (t0) REVERT: F 276 GLU cc_start: 0.8688 (mp0) cc_final: 0.8198 (mp0) REVERT: F 305 MET cc_start: 0.9008 (mmm) cc_final: 0.8703 (mmt) REVERT: F 373 LYS cc_start: 0.8554 (mttt) cc_final: 0.8131 (mttt) REVERT: G 1094 MET cc_start: 0.6960 (tpt) cc_final: 0.6646 (tpt) REVERT: H 852 MET cc_start: 0.6810 (ttm) cc_final: 0.6497 (ttm) REVERT: H 873 MET cc_start: 0.8855 (ttm) cc_final: 0.8404 (ptm) outliers start: 35 outliers final: 28 residues processed: 232 average time/residue: 0.1491 time to fit residues: 56.9693 Evaluate side-chains 230 residues out of total 2557 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 274 ILE 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 159 VAL Chi-restraints excluded: chain B residue 234 SER 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 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 47 MET Chi-restraints excluded: chain E residue 94 LEU 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 1033 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 36 optimal weight: 6.9990 chunk 247 optimal weight: 5.9990 chunk 225 optimal weight: 20.0000 chunk 170 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 187 optimal weight: 0.0970 chunk 44 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 134 optimal weight: 0.0770 chunk 88 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 overall best weight: 1.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** E 115 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 = 0.4022 r_free = 0.4022 target = 0.095938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.064899 restraints weight = 85973.137| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 5.64 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 24115 Z= 0.125 Angle : 0.647 12.305 32637 Z= 0.312 Chirality : 0.043 0.213 3614 Planarity : 0.004 0.081 4192 Dihedral : 7.627 159.793 3284 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.35 % Favored : 96.58 % Rotamer: Outliers : 1.13 % Allowed : 13.14 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.16), residues: 2927 helix: 0.78 (0.14), residues: 1443 sheet: -0.12 (0.27), residues: 402 loop : 0.20 (0.21), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 372 TYR 0.016 0.001 TYR H 854 PHE 0.019 0.001 PHE G1107 TRP 0.017 0.002 TRP D 79 HIS 0.006 0.001 HIS B 371 Details of bonding type rmsd covalent geometry : bond 0.00290 (24110) covalent geometry : angle 0.64667 (32637) hydrogen bonds : bond 0.03099 ( 1142) hydrogen bonds : angle 4.48555 ( 3120) Misc. bond : bond 0.00125 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6362.48 seconds wall clock time: 109 minutes 32.53 seconds (6572.53 seconds total)