Starting phenix.real_space_refine on Tue Jul 23 20:04:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b3d_44135/07_2024/9b3d_44135_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b3d_44135/07_2024/9b3d_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b3d_44135/07_2024/9b3d_44135.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b3d_44135/07_2024/9b3d_44135.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b3d_44135/07_2024/9b3d_44135_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b3d_44135/07_2024/9b3d_44135_neut.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 162 5.16 5 C 14930 2.51 5 N 3979 2.21 5 O 4532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 980": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1020": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 954": "OE1" <-> "OE2" Residue "H PHE 956": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 1105": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 23621 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 3052 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 13, 'TRANS': 359} Chain breaks: 2 Chain: "H" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 3001 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 14, 'TRANS': 353} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.87, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 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: 8.68 Conformation dependent library (CDL) restraints added in 4.0 seconds 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5564 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 36 sheets defined 54.6% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.21 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: 8.83 Time building geometry restraints manager: 9.60 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: 96.81 - 104.70: 491 104.70 - 112.60: 12143 112.60 - 120.49: 10821 120.49 - 128.39: 9004 128.39 - 136.28: 178 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 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: 1.080 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: 0.040 Extract box with map and model: 1.000 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 62.060 Find NCS groups from input model: 1.890 Set up NCS constraints: 0.110 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 24110 Z= 0.312 Angle : 0.879 11.266 32637 Z= 0.480 Chirality : 0.055 0.402 3614 Planarity : 0.008 0.098 4192 Dihedral : 15.329 176.415 9068 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.72 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.13), residues: 2927 helix: -3.18 (0.08), residues: 1390 sheet: -0.57 (0.25), residues: 408 loop : -1.14 (0.17), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 767 HIS 0.006 0.001 HIS E 173 PHE 0.029 0.002 PHE H1020 TYR 0.012 0.001 TYR F 240 ARG 0.004 0.001 ARG E 210 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 496 time to evaluate : 2.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 CYS cc_start: 0.6723 (t) cc_final: 0.6457 (t) REVERT: A 12 ASN cc_start: 0.7924 (m110) cc_final: 0.7324 (m110) REVERT: A 187 ASP cc_start: 0.8145 (m-30) cc_final: 0.7724 (t70) REVERT: B 104 LEU cc_start: 0.8519 (tt) cc_final: 0.7949 (mt) REVERT: B 126 THR cc_start: 0.6861 (m) cc_final: 0.6558 (p) REVERT: C 121 GLN cc_start: 0.8370 (tt0) cc_final: 0.7974 (tt0) REVERT: F 10 CYS cc_start: 0.8092 (t) cc_final: 0.7878 (t) REVERT: F 121 GLN cc_start: 0.9163 (tt0) cc_final: 0.8661 (tm-30) REVERT: F 305 MET cc_start: 0.8689 (mmm) cc_final: 0.8409 (mmt) REVERT: H 765 PRO cc_start: 0.0791 (Cg_endo) cc_final: -0.0187 (Cg_exo) REVERT: H 852 MET cc_start: 0.5161 (ttm) cc_final: 0.4621 (ttm) REVERT: H 902 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7387 (tm-30) REVERT: H 970 MET cc_start: -0.6036 (mtp) cc_final: -0.6431 (mtm) outliers start: 0 outliers final: 0 residues processed: 496 average time/residue: 0.3607 time to fit residues: 275.5562 Evaluate side-chains 259 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 2.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 249 optimal weight: 10.0000 chunk 223 optimal weight: 30.0000 chunk 124 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 150 optimal weight: 0.9990 chunk 119 optimal weight: 9.9990 chunk 231 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 140 optimal weight: 0.7980 chunk 172 optimal weight: 10.0000 chunk 267 optimal weight: 7.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN D 137 GLN D 354 GLN E 354 GLN F 59 GLN G 935 ASN G 955 ASN ** H 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 935 ASN H 955 ASN ** H1126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 24110 Z= 0.240 Angle : 0.632 9.716 32637 Z= 0.315 Chirality : 0.043 0.156 3614 Planarity : 0.005 0.073 4192 Dihedral : 11.336 179.473 3284 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.59 % Favored : 96.34 % Rotamer: Outliers : 1.53 % Allowed : 7.35 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.15), residues: 2927 helix: -0.61 (0.12), residues: 1404 sheet: -0.23 (0.26), residues: 402 loop : -0.43 (0.19), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 86 HIS 0.010 0.001 HIS B 371 PHE 0.019 0.001 PHE H1076 TYR 0.033 0.001 TYR H 854 ARG 0.014 0.001 ARG G 991 *********************** 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 fitting. rotamer outliers: 39 poor density : 272 time to evaluate : 2.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 CYS cc_start: 0.6652 (t) cc_final: 0.6430 (t) REVERT: A 12 ASN cc_start: 0.8001 (m110) cc_final: 0.7398 (m110) REVERT: A 44 MET cc_start: 0.8392 (mmm) cc_final: 0.7823 (pmm) REVERT: A 187 ASP cc_start: 0.8348 (m-30) cc_final: 0.7963 (t70) REVERT: A 374 CYS cc_start: 0.6393 (m) cc_final: 0.6191 (m) REVERT: B 104 LEU cc_start: 0.8659 (tt) cc_final: 0.8355 (tt) REVERT: D 132 MET cc_start: 0.7411 (ppp) cc_final: 0.7064 (ppp) REVERT: E 305 MET cc_start: 0.8538 (mmm) cc_final: 0.8209 (mmm) REVERT: F 10 CYS cc_start: 0.8067 (t) cc_final: 0.7833 (t) REVERT: F 132 MET cc_start: 0.8642 (ppp) cc_final: 0.8345 (ppp) REVERT: F 276 GLU cc_start: 0.8665 (mp0) cc_final: 0.8398 (mp0) REVERT: F 305 MET cc_start: 0.8778 (mmm) cc_final: 0.8452 (mmt) REVERT: G 1119 MET cc_start: 0.8996 (mmm) cc_final: 0.8703 (mmm) REVERT: H 857 ILE cc_start: 0.9146 (mt) cc_final: 0.8750 (mt) REVERT: H 873 MET cc_start: 0.8514 (ttm) cc_final: 0.8205 (ptm) outliers start: 39 outliers final: 24 residues processed: 296 average time/residue: 0.3402 time to fit residues: 162.6474 Evaluate side-chains 249 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 225 time to evaluate : 2.781 ------------------------------------------------------------------------------- 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 106 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain D residue 25 ASP 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 E residue 12 ASN 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 247 VAL Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain H residue 872 SER Chi-restraints excluded: chain H residue 898 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 148 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 222 optimal weight: 40.0000 chunk 182 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 268 optimal weight: 10.0000 chunk 289 optimal weight: 9.9990 chunk 239 optimal weight: 9.9990 chunk 266 optimal weight: 30.0000 chunk 91 optimal weight: 3.9990 chunk 215 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 761 GLN G1012 ASN G1093 ASN ** H 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 24110 Z= 0.335 Angle : 0.671 8.724 32637 Z= 0.334 Chirality : 0.045 0.161 3614 Planarity : 0.005 0.068 4192 Dihedral : 10.124 160.629 3284 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.48 % Favored : 95.46 % Rotamer: Outliers : 2.11 % Allowed : 9.50 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.16), residues: 2927 helix: 0.31 (0.14), residues: 1398 sheet: -0.22 (0.27), residues: 402 loop : -0.51 (0.19), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 79 HIS 0.005 0.001 HIS F 275 PHE 0.017 0.002 PHE G1107 TYR 0.020 0.002 TYR H 854 ARG 0.005 0.001 ARG E 290 *********************** 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 289 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 235 time to evaluate : 2.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.8218 (m110) cc_final: 0.7934 (m110) REVERT: A 44 MET cc_start: 0.8576 (mmm) cc_final: 0.7728 (pmm) REVERT: A 187 ASP cc_start: 0.8381 (m-30) cc_final: 0.8110 (t70) REVERT: A 374 CYS cc_start: 0.6559 (m) cc_final: 0.6175 (m) REVERT: B 104 LEU cc_start: 0.8603 (tt) cc_final: 0.8402 (tt) REVERT: B 372 ARG cc_start: 0.8078 (ptt-90) cc_final: 0.7844 (ptt-90) REVERT: F 10 CYS cc_start: 0.8239 (t) cc_final: 0.8029 (t) REVERT: F 132 MET cc_start: 0.8767 (ppp) cc_final: 0.8184 (ppp) REVERT: F 276 GLU cc_start: 0.8565 (mp0) cc_final: 0.8261 (mp0) REVERT: F 283 MET cc_start: 0.9004 (mmm) cc_final: 0.8792 (mmm) REVERT: F 305 MET cc_start: 0.8774 (mmm) cc_final: 0.8520 (mmt) REVERT: G 1094 MET cc_start: 0.6472 (OUTLIER) cc_final: 0.6205 (tpt) REVERT: G 1119 MET cc_start: 0.8943 (mmm) cc_final: 0.8737 (mmm) REVERT: H 873 MET cc_start: 0.8574 (ttm) cc_final: 0.8202 (ptm) REVERT: H 1082 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7988 (pp20) outliers start: 54 outliers final: 38 residues processed: 268 average time/residue: 0.3340 time to fit residues: 146.0721 Evaluate side-chains 249 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 209 time to evaluate : 2.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 184 ASP 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 106 THR 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 248 ILE Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 25 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 E residue 12 ASN Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 89 THR 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 898 ASP 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 265 optimal weight: 10.0000 chunk 201 optimal weight: 8.9990 chunk 139 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 128 optimal weight: 0.9980 chunk 180 optimal weight: 0.0050 chunk 269 optimal weight: 10.0000 chunk 285 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 255 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 GLN D 137 GLN D 246 GLN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1081 GLN H1126 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 24110 Z= 0.156 Angle : 0.572 7.515 32637 Z= 0.277 Chirality : 0.042 0.186 3614 Planarity : 0.004 0.065 4192 Dihedral : 8.958 161.913 3284 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.38 % Favored : 96.55 % Rotamer: Outliers : 1.64 % Allowed : 10.56 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.16), residues: 2927 helix: 0.66 (0.14), residues: 1411 sheet: -0.11 (0.27), residues: 402 loop : -0.17 (0.20), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 79 HIS 0.003 0.001 HIS F 275 PHE 0.016 0.001 PHE G1107 TYR 0.015 0.001 TYR H 854 ARG 0.005 0.000 ARG H 919 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 226 time to evaluate : 2.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8665 (mmm) cc_final: 0.7832 (pmm) REVERT: A 187 ASP cc_start: 0.8266 (m-30) cc_final: 0.8048 (t70) REVERT: A 269 MET cc_start: 0.8235 (mtp) cc_final: 0.8032 (mtt) REVERT: A 283 MET cc_start: 0.8269 (mmm) cc_final: 0.7787 (tpp) REVERT: A 374 CYS cc_start: 0.6621 (m) cc_final: 0.6229 (m) REVERT: B 44 MET cc_start: 0.4547 (pmm) cc_final: 0.3632 (pmm) REVERT: B 104 LEU cc_start: 0.8510 (tt) cc_final: 0.8305 (tt) REVERT: D 132 MET cc_start: 0.7484 (ppp) cc_final: 0.7209 (ppp) REVERT: E 325 MET cc_start: 0.8435 (mmt) cc_final: 0.8157 (mmt) REVERT: F 10 CYS cc_start: 0.8193 (t) cc_final: 0.7987 (t) REVERT: F 276 GLU cc_start: 0.8511 (mp0) cc_final: 0.8204 (mp0) REVERT: F 305 MET cc_start: 0.8737 (mmm) cc_final: 0.8475 (mmt) REVERT: G 1094 MET cc_start: 0.6198 (OUTLIER) cc_final: 0.5966 (tpt) REVERT: H 873 MET cc_start: 0.8668 (ttm) cc_final: 0.8193 (ptm) REVERT: H 1082 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8166 (pp20) outliers start: 42 outliers final: 24 residues processed: 255 average time/residue: 0.3399 time to fit residues: 140.9496 Evaluate side-chains 235 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 209 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ASP 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 248 ILE Chi-restraints excluded: chain D residue 25 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 283 MET Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain G residue 1094 MET Chi-restraints excluded: chain H residue 898 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 237 optimal weight: 7.9990 chunk 161 optimal weight: 5.9990 chunk 4 optimal weight: 0.0980 chunk 212 optimal weight: 8.9990 chunk 117 optimal weight: 0.7980 chunk 243 optimal weight: 30.0000 chunk 197 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 145 optimal weight: 10.0000 chunk 255 optimal weight: 20.0000 chunk 71 optimal weight: 10.0000 overall best weight: 4.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN ** D 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 24110 Z= 0.350 Angle : 0.682 9.774 32637 Z= 0.338 Chirality : 0.045 0.186 3614 Planarity : 0.005 0.057 4192 Dihedral : 8.700 174.571 3284 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.68 % Favored : 95.25 % Rotamer: Outliers : 2.35 % Allowed : 11.81 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.16), residues: 2927 helix: 0.59 (0.14), residues: 1439 sheet: -0.19 (0.27), residues: 396 loop : -0.38 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 79 HIS 0.005 0.001 HIS F 275 PHE 0.018 0.002 PHE H1076 TYR 0.015 0.002 TYR E 279 ARG 0.006 0.001 ARG H 951 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 216 time to evaluate : 2.593 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: 0.8824 (mmm) cc_final: 0.7927 (pmm) REVERT: A 187 ASP cc_start: 0.8377 (m-30) cc_final: 0.8099 (t70) REVERT: A 269 MET cc_start: 0.8324 (mtp) cc_final: 0.8116 (mtt) REVERT: B 190 MET cc_start: 0.7800 (mtt) cc_final: 0.7582 (mtt) REVERT: E 325 MET cc_start: 0.8624 (mmt) cc_final: 0.8396 (mmt) REVERT: F 132 MET cc_start: 0.8852 (ppp) cc_final: 0.8323 (ppp) REVERT: F 276 GLU cc_start: 0.8517 (mp0) cc_final: 0.8177 (mp0) REVERT: F 373 LYS cc_start: 0.8264 (mmtt) cc_final: 0.8064 (mmtt) REVERT: G 1094 MET cc_start: 0.6258 (OUTLIER) cc_final: 0.6039 (tpt) REVERT: H 873 MET cc_start: 0.8751 (ttm) cc_final: 0.8233 (ptm) outliers start: 60 outliers final: 45 residues processed: 260 average time/residue: 0.3071 time to fit residues: 131.5954 Evaluate side-chains 248 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 202 time to evaluate : 2.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 249 THR 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 248 ILE Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 25 ASP 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 25 ASP Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 185 LEU 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 89 THR Chi-restraints excluded: chain F residue 107 GLU 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 898 ASP 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 95 optimal weight: 2.9990 chunk 256 optimal weight: 0.0870 chunk 56 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 285 optimal weight: 10.0000 chunk 236 optimal weight: 8.9990 chunk 132 optimal weight: 0.9990 chunk 23 optimal weight: 20.0000 chunk 94 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 GLN ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 983 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24110 Z= 0.177 Angle : 0.598 9.514 32637 Z= 0.287 Chirality : 0.042 0.196 3614 Planarity : 0.004 0.060 4192 Dihedral : 8.247 174.955 3284 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.55 % Favored : 96.38 % Rotamer: Outliers : 1.88 % Allowed : 13.14 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.16), residues: 2927 helix: 0.76 (0.14), residues: 1445 sheet: -0.18 (0.27), residues: 402 loop : -0.07 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 79 HIS 0.005 0.001 HIS C 88 PHE 0.019 0.001 PHE G1107 TYR 0.013 0.001 TYR D 143 ARG 0.004 0.000 ARG H1054 *********************** 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 264 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 216 time to evaluate : 2.927 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: 0.8837 (mmm) cc_final: 0.7937 (pmm) REVERT: A 187 ASP cc_start: 0.8278 (m-30) cc_final: 0.8041 (t70) REVERT: A 269 MET cc_start: 0.8280 (mtp) cc_final: 0.8077 (mtt) REVERT: A 374 CYS cc_start: 0.6570 (m) cc_final: 0.6160 (m) REVERT: C 129 VAL cc_start: 0.8251 (m) cc_final: 0.8018 (m) REVERT: F 276 GLU cc_start: 0.8500 (mp0) cc_final: 0.8163 (mp0) REVERT: F 373 LYS cc_start: 0.8326 (mmtt) cc_final: 0.8027 (mmtt) REVERT: H 852 MET cc_start: 0.7294 (tpp) cc_final: 0.6889 (tmm) REVERT: H 873 MET cc_start: 0.8728 (ttm) cc_final: 0.8218 (ptm) outliers start: 48 outliers final: 33 residues processed: 251 average time/residue: 0.3191 time to fit residues: 132.4025 Evaluate side-chains 237 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 204 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 128 ASN 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 34 ILE Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 25 ASP 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 56 ASP Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain F residue 43 VAL 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 898 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 275 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 162 optimal weight: 8.9990 chunk 208 optimal weight: 0.0370 chunk 161 optimal weight: 0.9990 chunk 240 optimal weight: 20.0000 chunk 159 optimal weight: 7.9990 chunk 284 optimal weight: 7.9990 chunk 177 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24110 Z= 0.215 Angle : 0.621 10.596 32637 Z= 0.299 Chirality : 0.043 0.206 3614 Planarity : 0.004 0.058 4192 Dihedral : 7.899 152.909 3284 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.03 % Favored : 95.90 % Rotamer: Outliers : 1.76 % Allowed : 13.65 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.16), residues: 2927 helix: 0.80 (0.14), residues: 1445 sheet: -0.16 (0.27), residues: 402 loop : -0.03 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 79 HIS 0.003 0.001 HIS C 161 PHE 0.030 0.001 PHE C 223 TYR 0.014 0.001 TYR H 854 ARG 0.004 0.000 ARG H1054 *********************** 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 261 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 216 time to evaluate : 2.675 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 24 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.6943 (m-30) REVERT: A 44 MET cc_start: 0.8805 (mmm) cc_final: 0.7879 (pmm) REVERT: A 187 ASP cc_start: 0.8292 (m-30) cc_final: 0.8054 (t70) REVERT: A 269 MET cc_start: 0.8295 (mtp) cc_final: 0.8089 (mtt) REVERT: A 374 CYS cc_start: 0.6597 (m) cc_final: 0.6155 (m) REVERT: E 325 MET cc_start: 0.8489 (mmm) cc_final: 0.7716 (mmt) REVERT: F 276 GLU cc_start: 0.8487 (mp0) cc_final: 0.8153 (mp0) REVERT: F 373 LYS cc_start: 0.8332 (mmtt) cc_final: 0.8025 (mttt) REVERT: H 859 ASN cc_start: 0.8662 (m-40) cc_final: 0.8435 (m110) REVERT: H 873 MET cc_start: 0.8742 (ttm) cc_final: 0.8224 (ptm) outliers start: 45 outliers final: 37 residues processed: 247 average time/residue: 0.3036 time to fit residues: 124.6123 Evaluate side-chains 243 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 205 time to evaluate : 3.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 25 ASP 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 56 ASP Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 184 ASP 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 898 ASP Chi-restraints excluded: chain H residue 1033 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 175 optimal weight: 0.8980 chunk 113 optimal weight: 0.4980 chunk 169 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 chunk 193 optimal weight: 8.9990 chunk 140 optimal weight: 0.9980 chunk 26 optimal weight: 0.2980 chunk 223 optimal weight: 30.0000 chunk 258 optimal weight: 50.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 HIS C 137 GLN D 161 HIS D 246 GLN ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 859 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 24110 Z= 0.151 Angle : 0.611 16.227 32637 Z= 0.291 Chirality : 0.042 0.192 3614 Planarity : 0.004 0.058 4192 Dihedral : 7.340 147.786 3284 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.55 % Favored : 96.38 % Rotamer: Outliers : 1.37 % Allowed : 14.39 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.16), residues: 2927 helix: 0.89 (0.14), residues: 1443 sheet: -0.05 (0.27), residues: 402 loop : 0.13 (0.21), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 79 HIS 0.002 0.000 HIS B 275 PHE 0.051 0.001 PHE C 223 TYR 0.009 0.001 TYR G1084 ARG 0.007 0.000 ARG H1138 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 226 time to evaluate : 2.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8813 (mmm) cc_final: 0.7911 (pmm) REVERT: A 187 ASP cc_start: 0.8270 (m-30) cc_final: 0.7992 (t70) REVERT: A 305 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8318 (mmm) REVERT: A 374 CYS cc_start: 0.6628 (m) cc_final: 0.6203 (m) REVERT: C 299 MET cc_start: 0.8183 (mmp) cc_final: 0.7863 (mmm) REVERT: E 325 MET cc_start: 0.8421 (mmm) cc_final: 0.7710 (mmt) REVERT: F 176 MET cc_start: 0.6972 (mtp) cc_final: 0.6563 (ptp) REVERT: F 276 GLU cc_start: 0.8472 (mp0) cc_final: 0.8154 (mp0) REVERT: F 299 MET cc_start: 0.7870 (ttp) cc_final: 0.7569 (mtp) REVERT: F 305 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8237 (mmm) REVERT: F 373 LYS cc_start: 0.8215 (mmtt) cc_final: 0.7795 (mttt) REVERT: G 873 MET cc_start: 0.7818 (ppp) cc_final: 0.6949 (ppp) REVERT: G 910 MET cc_start: -0.1015 (ttp) cc_final: -0.1277 (ttm) REVERT: H 873 MET cc_start: 0.8732 (ttm) cc_final: 0.8192 (ptm) outliers start: 35 outliers final: 25 residues processed: 246 average time/residue: 0.3042 time to fit residues: 124.9591 Evaluate side-chains 235 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 208 time to evaluate : 2.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain D residue 25 ASP 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 283 MET Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain F residue 43 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 F residue 305 MET Chi-restraints excluded: chain H residue 762 LEU Chi-restraints excluded: chain H residue 872 SER Chi-restraints excluded: chain H residue 881 MET Chi-restraints excluded: chain H residue 898 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 272 optimal weight: 0.9990 chunk 248 optimal weight: 10.0000 chunk 264 optimal weight: 20.0000 chunk 159 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 208 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 239 optimal weight: 6.9990 chunk 250 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 280 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1026 HIS H1123 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24110 Z= 0.260 Angle : 0.667 12.131 32637 Z= 0.325 Chirality : 0.044 0.214 3614 Planarity : 0.004 0.057 4192 Dihedral : 7.343 146.221 3284 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.17 % Favored : 95.76 % Rotamer: Outliers : 1.49 % Allowed : 14.55 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.16), residues: 2927 helix: 0.86 (0.14), residues: 1440 sheet: -0.00 (0.27), residues: 396 loop : 0.00 (0.20), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 340 HIS 0.007 0.001 HIS B 371 PHE 0.068 0.001 PHE C 223 TYR 0.010 0.001 TYR E 279 ARG 0.006 0.000 ARG H1138 *********************** 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 240 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 202 time to evaluate : 2.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.7445 (OUTLIER) cc_final: 0.7018 (m-30) REVERT: A 44 MET cc_start: 0.8886 (mmm) cc_final: 0.7839 (pmm) REVERT: A 187 ASP cc_start: 0.8287 (m-30) cc_final: 0.8057 (t70) REVERT: A 269 MET cc_start: 0.8157 (ttm) cc_final: 0.7883 (mtt) REVERT: A 305 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8412 (mmm) REVERT: E 325 MET cc_start: 0.8416 (mmm) cc_final: 0.7896 (mmt) REVERT: F 132 MET cc_start: 0.8870 (ppp) cc_final: 0.8224 (ppp) REVERT: F 276 GLU cc_start: 0.8481 (mp0) cc_final: 0.8149 (mp0) REVERT: F 299 MET cc_start: 0.8026 (ttp) cc_final: 0.7631 (mtp) REVERT: F 373 LYS cc_start: 0.8217 (mmtt) cc_final: 0.7790 (mttt) REVERT: G 910 MET cc_start: -0.0586 (ttp) cc_final: -0.0879 (ttm) REVERT: H 859 ASN cc_start: 0.9239 (t0) cc_final: 0.8677 (m-40) REVERT: H 873 MET cc_start: 0.8783 (ttm) cc_final: 0.8228 (ptm) REVERT: H 970 MET cc_start: -0.6728 (ttm) cc_final: -0.7033 (mtp) outliers start: 38 outliers final: 32 residues processed: 228 average time/residue: 0.3122 time to fit residues: 118.6278 Evaluate side-chains 234 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 200 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain D residue 25 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 247 VAL Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 179 ASP 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 898 ASP 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 171 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 194 optimal weight: 0.9980 chunk 293 optimal weight: 20.0000 chunk 270 optimal weight: 20.0000 chunk 234 optimal weight: 20.0000 chunk 24 optimal weight: 0.7980 chunk 180 optimal weight: 0.4980 chunk 143 optimal weight: 0.8980 chunk 185 optimal weight: 4.9990 chunk 249 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN D 246 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24110 Z= 0.161 Angle : 0.648 13.144 32637 Z= 0.310 Chirality : 0.043 0.281 3614 Planarity : 0.004 0.061 4192 Dihedral : 6.956 147.179 3284 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.55 % Favored : 96.38 % Rotamer: Outliers : 1.17 % Allowed : 15.10 % Favored : 83.73 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.16), residues: 2927 helix: 0.97 (0.14), residues: 1440 sheet: -0.03 (0.27), residues: 402 loop : 0.17 (0.21), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 79 HIS 0.006 0.001 HIS B 371 PHE 0.043 0.001 PHE C 223 TYR 0.011 0.001 TYR G1084 ARG 0.007 0.000 ARG G1088 ********************** 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 246 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 216 time to evaluate : 2.928 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: 0.8895 (mmm) cc_final: 0.7864 (pmm) REVERT: A 187 ASP cc_start: 0.8260 (m-30) cc_final: 0.7981 (t70) REVERT: A 269 MET cc_start: 0.8124 (ttm) cc_final: 0.7855 (mtt) REVERT: A 305 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8331 (mmm) REVERT: E 325 MET cc_start: 0.8378 (mmm) cc_final: 0.7819 (mmt) REVERT: F 47 MET cc_start: 0.5501 (ptp) cc_final: 0.5152 (ptp) REVERT: F 276 GLU cc_start: 0.8482 (mp0) cc_final: 0.8130 (mp0) REVERT: F 280 ASN cc_start: 0.9227 (m-40) cc_final: 0.9000 (m110) REVERT: F 299 MET cc_start: 0.7944 (ttp) cc_final: 0.7563 (mtp) REVERT: F 373 LYS cc_start: 0.8226 (mmtt) cc_final: 0.7763 (mttt) REVERT: H 859 ASN cc_start: 0.9242 (t0) cc_final: 0.8663 (m-40) REVERT: H 873 MET cc_start: 0.8759 (ttm) cc_final: 0.8217 (ptm) REVERT: H 970 MET cc_start: -0.6765 (ttm) cc_final: -0.7071 (mtp) outliers start: 30 outliers final: 26 residues processed: 237 average time/residue: 0.3129 time to fit residues: 122.7475 Evaluate side-chains 239 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 212 time to evaluate : 2.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain D residue 25 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 E residue 56 ASP Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain F residue 43 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 898 ASP 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 71 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 234 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 240 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 205 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 928 GLN ** H 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1012 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.094607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.063534 restraints weight = 87655.246| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 5.55 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24110 Z= 0.277 Angle : 0.701 15.745 32637 Z= 0.340 Chirality : 0.045 0.260 3614 Planarity : 0.004 0.058 4192 Dihedral : 7.142 144.533 3284 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.27 % Favored : 95.66 % Rotamer: Outliers : 1.41 % Allowed : 14.86 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.16), residues: 2927 helix: 0.91 (0.14), residues: 1434 sheet: 0.03 (0.27), residues: 396 loop : 0.02 (0.20), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 340 HIS 0.003 0.001 HIS H1091 PHE 0.059 0.001 PHE C 223 TYR 0.013 0.001 TYR E 279 ARG 0.005 0.000 ARG B 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4608.61 seconds wall clock time: 83 minutes 26.22 seconds (5006.22 seconds total)