Starting phenix.real_space_refine on Thu Aug 8 16:52:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b3d_44135/08_2024/9b3d_44135.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b3d_44135/08_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_44135/08_2024/9b3d_44135.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b3d_44135/08_2024/9b3d_44135.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b3d_44135/08_2024/9b3d_44135.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b3d_44135/08_2024/9b3d_44135.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 162 5.16 5 C 14930 2.51 5 N 3979 2.21 5 O 4532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 12.55, per 1000 atoms: 0.53 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: 8.77 Conformation dependent library (CDL) restraints added in 4.1 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: 3.10 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: 8.64 Time building geometry restraints manager: 9.65 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 Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'G' and (resid 750 through 803 or resid 836 through 1143)) selection = (chain 'H' and (resid 750 through 803 or resid 836 through 1143)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.910 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: 0.000 Extract box with map and model: 1.930 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 60.560 Find NCS groups from input model: 1.150 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.170 ------------------------------------------------------------------------------- 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 : 2.576 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: 0.3514 time to fit residues: 267.7610 Evaluate side-chains 259 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 2.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 249 optimal weight: 3.9990 chunk 223 optimal weight: 30.0000 chunk 124 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 chunk 231 optimal weight: 9.9990 chunk 89 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 172 optimal weight: 9.9990 chunk 267 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN D 12 ASN D 354 GLN ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 GLN F 59 GLN ** H 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 955 ASN ** H1126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24110 Z= 0.204 Angle : 0.627 9.543 32637 Z= 0.312 Chirality : 0.043 0.158 3614 Planarity : 0.005 0.076 4192 Dihedral : 11.079 173.787 3284 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.35 % Favored : 96.58 % Rotamer: Outliers : 1.25 % Allowed : 7.16 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.15), residues: 2927 helix: -0.71 (0.12), residues: 1397 sheet: -0.17 (0.26), residues: 402 loop : -0.47 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 79 HIS 0.010 0.001 HIS H1122 PHE 0.019 0.001 PHE H1076 TYR 0.034 0.001 TYR H 854 ARG 0.006 0.001 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 283 time to evaluate : 2.769 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: 0.7948 (m110) cc_final: 0.7211 (m110) REVERT: A 44 MET cc_start: 0.8336 (mmm) cc_final: 0.7851 (pmm) REVERT: A 187 ASP cc_start: 0.8276 (m-30) cc_final: 0.7930 (t70) REVERT: B 82 MET cc_start: 0.6562 (tpt) cc_final: 0.6242 (tpt) REVERT: B 104 LEU cc_start: 0.8659 (tt) cc_final: 0.8296 (tt) REVERT: D 225 ASN cc_start: 0.7663 (m-40) cc_final: 0.7456 (m110) REVERT: D 325 MET cc_start: 0.8803 (mmt) cc_final: 0.8343 (mmt) REVERT: E 367 PRO cc_start: 0.7381 (Cg_endo) cc_final: 0.6941 (Cg_exo) REVERT: F 305 MET cc_start: 0.8760 (mmm) cc_final: 0.8420 (mmt) REVERT: G 1119 MET cc_start: 0.8968 (mmm) cc_final: 0.8709 (mmm) REVERT: H 851 ARG cc_start: 0.4946 (mtt180) cc_final: 0.4483 (ttp-170) REVERT: H 857 ILE cc_start: 0.9125 (mt) cc_final: 0.8764 (mt) REVERT: H 873 MET cc_start: 0.8513 (ttm) cc_final: 0.8208 (ptm) outliers start: 32 outliers final: 17 residues processed: 304 average time/residue: 0.3249 time to fit residues: 158.9867 Evaluate side-chains 245 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 228 time to evaluate : 2.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain H residue 872 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 148 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 222 optimal weight: 40.0000 chunk 182 optimal weight: 10.0000 chunk 73 optimal weight: 0.7980 chunk 268 optimal weight: 10.0000 chunk 289 optimal weight: 20.0000 chunk 239 optimal weight: 6.9990 chunk 266 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 215 optimal weight: 6.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- 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 297 ASN ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 761 GLN G 955 ASN G1093 ASN ** G1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1126 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 24110 Z= 0.409 Angle : 0.724 10.182 32637 Z= 0.364 Chirality : 0.047 0.171 3614 Planarity : 0.005 0.068 4192 Dihedral : 9.886 160.417 3284 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.96 % Favored : 95.97 % Rotamer: Outliers : 1.96 % Allowed : 9.39 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.31 (0.16), residues: 2927 helix: 0.20 (0.14), residues: 1392 sheet: -0.18 (0.27), residues: 402 loop : -0.55 (0.19), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 79 HIS 0.009 0.001 HIS F 275 PHE 0.018 0.002 PHE H1076 TYR 0.019 0.002 TYR F 279 ARG 0.005 0.001 ARG F 177 *********************** 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 279 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 229 time to evaluate : 2.716 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: A 44 MET cc_start: 0.8549 (mmm) cc_final: 0.7786 (pmm) REVERT: A 187 ASP cc_start: 0.8383 (m-30) cc_final: 0.8118 (t70) REVERT: C 132 MET cc_start: 0.8381 (ppp) cc_final: 0.8099 (tmm) REVERT: C 299 MET cc_start: 0.8004 (mmm) cc_final: 0.7702 (mmt) REVERT: E 367 PRO cc_start: 0.7506 (Cg_endo) cc_final: 0.7263 (Cg_exo) REVERT: F 10 CYS cc_start: 0.8451 (t) cc_final: 0.8106 (t) REVERT: F 154 ASP cc_start: 0.7138 (t0) cc_final: 0.6936 (t0) REVERT: F 305 MET cc_start: 0.8781 (mmm) cc_final: 0.8552 (mmt) REVERT: G 1119 MET cc_start: 0.8949 (mmm) cc_final: 0.8745 (mmm) REVERT: H 852 MET cc_start: 0.6955 (tpp) cc_final: 0.5859 (tmm) REVERT: H 857 ILE cc_start: 0.8824 (mt) cc_final: 0.8473 (mt) REVERT: H 873 MET cc_start: 0.8569 (ttm) cc_final: 0.8190 (ptm) outliers start: 50 outliers final: 36 residues processed: 263 average time/residue: 0.3286 time to fit residues: 140.9766 Evaluate side-chains 240 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 204 time to evaluate : 2.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 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 47 MET Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 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 H residue 762 LEU Chi-restraints excluded: chain H residue 872 SER Chi-restraints excluded: chain H residue 1022 ASP Chi-restraints excluded: chain H residue 1033 VAL Chi-restraints excluded: chain H residue 1126 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 265 optimal weight: 20.0000 chunk 201 optimal weight: 0.0170 chunk 139 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 180 optimal weight: 6.9990 chunk 269 optimal weight: 0.9980 chunk 285 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 255 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 overall best weight: 0.8022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 GLN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 24110 Z= 0.155 Angle : 0.588 10.538 32637 Z= 0.285 Chirality : 0.042 0.186 3614 Planarity : 0.004 0.061 4192 Dihedral : 8.837 162.492 3284 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.31 % Favored : 96.62 % Rotamer: Outliers : 1.02 % Allowed : 10.56 % Favored : 88.42 % 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: 0.10 (0.16), residues: 2927 helix: 0.52 (0.14), residues: 1440 sheet: -0.13 (0.26), residues: 402 loop : -0.27 (0.20), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 79 HIS 0.008 0.001 HIS E 173 PHE 0.016 0.001 PHE G1107 TYR 0.012 0.001 TYR H 854 ARG 0.006 0.000 ARG H 919 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 218 time to evaluate : 2.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8627 (mmm) cc_final: 0.7865 (pmm) REVERT: A 187 ASP cc_start: 0.8234 (m-30) cc_final: 0.8028 (t70) REVERT: A 283 MET cc_start: 0.8302 (mmm) cc_final: 0.7739 (tpp) REVERT: C 44 MET cc_start: 0.8719 (mmt) cc_final: 0.8517 (mmt) REVERT: E 325 MET cc_start: 0.8445 (mmt) cc_final: 0.8177 (mmt) REVERT: E 367 PRO cc_start: 0.7350 (Cg_endo) cc_final: 0.7139 (Cg_exo) REVERT: F 10 CYS cc_start: 0.8422 (t) cc_final: 0.8055 (t) REVERT: F 154 ASP cc_start: 0.6826 (t0) cc_final: 0.6610 (t0) REVERT: F 305 MET cc_start: 0.8748 (mmm) cc_final: 0.8521 (mmt) REVERT: H 873 MET cc_start: 0.8665 (ttm) cc_final: 0.8187 (ptm) outliers start: 26 outliers final: 15 residues processed: 235 average time/residue: 0.3299 time to fit residues: 125.6072 Evaluate side-chains 224 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 209 time to evaluate : 2.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 199 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 237 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 4 optimal weight: 0.0670 chunk 212 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 243 optimal weight: 50.0000 chunk 197 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 145 optimal weight: 9.9990 chunk 255 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 overall best weight: 4.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 GLN ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 ASN ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 761 GLN ** H 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 935 ASN H1081 GLN H1126 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 24110 Z= 0.346 Angle : 0.685 10.490 32637 Z= 0.337 Chirality : 0.046 0.189 3614 Planarity : 0.005 0.058 4192 Dihedral : 8.658 164.986 3284 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.37 % Favored : 95.56 % Rotamer: Outliers : 2.03 % Allowed : 10.25 % Favored : 87.72 % 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: 0.55 (0.14), residues: 1439 sheet: -0.16 (0.27), residues: 396 loop : -0.32 (0.20), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 79 HIS 0.008 0.001 HIS F 275 PHE 0.018 0.002 PHE G1107 TYR 0.014 0.002 TYR B 306 ARG 0.005 0.001 ARG C 312 *********************** 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 261 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 209 time to evaluate : 2.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8805 (mmm) cc_final: 0.7965 (pmm) REVERT: A 187 ASP cc_start: 0.8315 (m-30) cc_final: 0.8112 (t70) REVERT: B 190 MET cc_start: 0.7756 (mtt) cc_final: 0.7513 (mtt) REVERT: D 132 MET cc_start: 0.7481 (ppp) cc_final: 0.7105 (ppp) REVERT: E 367 PRO cc_start: 0.7345 (Cg_endo) cc_final: 0.7093 (Cg_exo) REVERT: F 10 CYS cc_start: 0.8504 (t) cc_final: 0.8158 (t) REVERT: F 154 ASP cc_start: 0.6966 (t0) cc_final: 0.6718 (t0) REVERT: H 873 MET cc_start: 0.8700 (ttm) cc_final: 0.8268 (ptm) outliers start: 52 outliers final: 35 residues processed: 247 average time/residue: 0.3271 time to fit residues: 131.5583 Evaluate side-chains 233 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 198 time to evaluate : 2.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 86 TRP Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 195 GLU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 257 CYS Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 248 ILE 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 47 MET Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 89 THR 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 1033 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 95 optimal weight: 0.6980 chunk 256 optimal weight: 30.0000 chunk 56 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 285 optimal weight: 0.1980 chunk 236 optimal weight: 20.0000 chunk 132 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN B 354 GLN E 162 ASN ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1039 GLN G1091 HIS ** H 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 859 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24110 Z= 0.161 Angle : 0.604 9.123 32637 Z= 0.290 Chirality : 0.043 0.190 3614 Planarity : 0.004 0.058 4192 Dihedral : 8.246 167.034 3284 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.11 % Favored : 96.82 % Rotamer: Outliers : 1.13 % Allowed : 11.89 % Favored : 86.98 % 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: 0.40 (0.16), residues: 2927 helix: 0.75 (0.14), residues: 1445 sheet: -0.16 (0.27), residues: 402 loop : -0.02 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 79 HIS 0.005 0.001 HIS D 371 PHE 0.019 0.001 PHE G1107 TYR 0.012 0.001 TYR H1104 ARG 0.004 0.000 ARG E 206 *********************** 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 248 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 219 time to evaluate : 2.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8765 (mmm) cc_final: 0.7942 (pmm) REVERT: A 187 ASP cc_start: 0.8270 (m-30) cc_final: 0.8048 (t70) REVERT: A 283 MET cc_start: 0.8216 (mmm) cc_final: 0.7674 (tpp) REVERT: A 374 CYS cc_start: 0.6714 (m) cc_final: 0.6103 (m) REVERT: D 132 MET cc_start: 0.7257 (ppp) cc_final: 0.6912 (ppp) REVERT: D 227 MET cc_start: 0.7666 (mmm) cc_final: 0.7423 (mmm) REVERT: E 325 MET cc_start: 0.8484 (mmt) cc_final: 0.8229 (mmm) REVERT: F 10 CYS cc_start: 0.8467 (t) cc_final: 0.8088 (t) REVERT: F 154 ASP cc_start: 0.6858 (t0) cc_final: 0.6648 (t0) REVERT: H 852 MET cc_start: 0.7478 (tpp) cc_final: 0.7145 (tmm) REVERT: H 873 MET cc_start: 0.8732 (ttm) cc_final: 0.8231 (ptm) outliers start: 29 outliers final: 20 residues processed: 237 average time/residue: 0.3326 time to fit residues: 127.8161 Evaluate side-chains 224 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 204 time to evaluate : 2.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain E residue 162 ASN Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain H residue 762 LEU Chi-restraints excluded: chain H residue 1033 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 275 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 162 optimal weight: 8.9990 chunk 208 optimal weight: 0.7980 chunk 161 optimal weight: 3.9990 chunk 240 optimal weight: 7.9990 chunk 159 optimal weight: 0.9990 chunk 284 optimal weight: 6.9990 chunk 177 optimal weight: 4.9990 chunk 173 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 115 ASN ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1026 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 24110 Z= 0.237 Angle : 0.627 9.996 32637 Z= 0.303 Chirality : 0.043 0.200 3614 Planarity : 0.004 0.072 4192 Dihedral : 8.255 171.964 3284 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.79 % Favored : 96.14 % Rotamer: Outliers : 1.21 % Allowed : 12.05 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.16), residues: 2927 helix: 0.79 (0.14), residues: 1437 sheet: -0.16 (0.27), residues: 402 loop : -0.05 (0.20), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 79 HIS 0.005 0.001 HIS F 275 PHE 0.024 0.001 PHE C 223 TYR 0.025 0.001 TYR H 854 ARG 0.004 0.000 ARG C 312 *********************** 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 237 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 206 time to evaluate : 2.747 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: A 44 MET cc_start: 0.8858 (mmm) cc_final: 0.7967 (pmm) REVERT: A 187 ASP cc_start: 0.8297 (m-30) cc_final: 0.8071 (t70) REVERT: A 283 MET cc_start: 0.8304 (mmm) cc_final: 0.7711 (tpp) REVERT: A 374 CYS cc_start: 0.6771 (m) cc_final: 0.6120 (m) REVERT: B 104 LEU cc_start: 0.8870 (tt) cc_final: 0.8186 (pp) REVERT: D 132 MET cc_start: 0.7346 (ppp) cc_final: 0.7004 (ppp) REVERT: D 227 MET cc_start: 0.7738 (mmm) cc_final: 0.7525 (mmm) REVERT: E 325 MET cc_start: 0.8553 (mmt) cc_final: 0.8301 (mmm) REVERT: F 10 CYS cc_start: 0.8486 (t) cc_final: 0.8145 (t) REVERT: F 154 ASP cc_start: 0.6863 (t0) cc_final: 0.6559 (t0) REVERT: F 373 LYS cc_start: 0.8371 (mmtt) cc_final: 0.8081 (mttt) REVERT: H 873 MET cc_start: 0.8766 (ttm) cc_final: 0.8251 (ptm) outliers start: 31 outliers final: 24 residues processed: 226 average time/residue: 0.3234 time to fit residues: 118.9092 Evaluate side-chains 224 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 200 time to evaluate : 2.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 86 TRP Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 293 LEU 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 881 MET 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: 1.9990 chunk 113 optimal weight: 6.9990 chunk 169 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 180 optimal weight: 0.6980 chunk 193 optimal weight: 9.9990 chunk 140 optimal weight: 0.6980 chunk 26 optimal weight: 10.0000 chunk 223 optimal weight: 6.9990 chunk 258 optimal weight: 40.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 HIS ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1026 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24110 Z= 0.157 Angle : 0.604 11.101 32637 Z= 0.289 Chirality : 0.042 0.192 3614 Planarity : 0.004 0.068 4192 Dihedral : 8.052 179.078 3284 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.18 % Favored : 96.75 % Rotamer: Outliers : 0.90 % Allowed : 12.67 % Favored : 86.43 % 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: 0.87 (0.14), residues: 1444 sheet: -0.08 (0.27), residues: 402 loop : 0.16 (0.20), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 79 HIS 0.004 0.001 HIS D 371 PHE 0.029 0.001 PHE C 223 TYR 0.022 0.001 TYR H 854 ARG 0.003 0.000 ARG E 206 *********************** 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 246 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 223 time to evaluate : 2.715 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: 0.8845 (mmm) cc_final: 0.7909 (pmm) REVERT: A 187 ASP cc_start: 0.8258 (m-30) cc_final: 0.7965 (t70) REVERT: A 283 MET cc_start: 0.8245 (mmm) cc_final: 0.7771 (tpp) REVERT: A 374 CYS cc_start: 0.6678 (m) cc_final: 0.6068 (m) REVERT: B 104 LEU cc_start: 0.8750 (tt) cc_final: 0.8080 (pp) REVERT: C 132 MET cc_start: 0.7608 (tmm) cc_final: 0.7408 (tmm) REVERT: D 132 MET cc_start: 0.7308 (ppp) cc_final: 0.6941 (ppp) REVERT: D 227 MET cc_start: 0.7673 (mmm) cc_final: 0.7463 (mmm) REVERT: E 325 MET cc_start: 0.8517 (mmt) cc_final: 0.8307 (mmm) REVERT: F 10 CYS cc_start: 0.8466 (t) cc_final: 0.8116 (t) REVERT: F 154 ASP cc_start: 0.6863 (t0) cc_final: 0.6562 (t0) REVERT: F 373 LYS cc_start: 0.8267 (mmtt) cc_final: 0.7947 (mttt) REVERT: H 873 MET cc_start: 0.8762 (ttm) cc_final: 0.8235 (ptm) REVERT: H 970 MET cc_start: -0.6538 (ttm) cc_final: -0.6891 (mtp) outliers start: 23 outliers final: 17 residues processed: 236 average time/residue: 0.3147 time to fit residues: 121.3954 Evaluate side-chains 220 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 203 time to evaluate : 2.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain E residue 293 LEU 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 881 MET Chi-restraints excluded: chain H residue 1033 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 272 optimal weight: 6.9990 chunk 248 optimal weight: 9.9990 chunk 264 optimal weight: 50.0000 chunk 159 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 208 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 239 optimal weight: 3.9990 chunk 250 optimal weight: 7.9990 chunk 173 optimal weight: 6.9990 chunk 280 optimal weight: 0.3980 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 GLN ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1026 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 24110 Z= 0.293 Angle : 0.687 12.909 32637 Z= 0.332 Chirality : 0.045 0.197 3614 Planarity : 0.004 0.068 4192 Dihedral : 8.162 169.618 3284 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.10 % Favored : 95.83 % Rotamer: Outliers : 1.06 % Allowed : 12.98 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.16), residues: 2927 helix: 0.79 (0.14), residues: 1434 sheet: -0.22 (0.26), residues: 402 loop : -0.01 (0.20), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 79 HIS 0.006 0.001 HIS F 275 PHE 0.056 0.001 PHE C 223 TYR 0.029 0.001 TYR H 854 ARG 0.004 0.000 ARG B 196 *********************** 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 228 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 201 time to evaluate : 2.757 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: 0.8892 (mmm) cc_final: 0.7873 (pmm) REVERT: A 187 ASP cc_start: 0.8301 (m-30) cc_final: 0.8081 (t70) REVERT: A 374 CYS cc_start: 0.6566 (m) cc_final: 0.6186 (m) REVERT: B 104 LEU cc_start: 0.8877 (tt) cc_final: 0.8235 (pp) REVERT: B 137 GLN cc_start: 0.7600 (OUTLIER) cc_final: 0.7063 (mt0) REVERT: B 361 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8147 (mm-30) REVERT: D 132 MET cc_start: 0.7353 (ppp) cc_final: 0.7050 (ppp) REVERT: E 325 MET cc_start: 0.8700 (mmt) cc_final: 0.8117 (mmt) REVERT: F 10 CYS cc_start: 0.8487 (t) cc_final: 0.8140 (t) REVERT: F 154 ASP cc_start: 0.6915 (t0) cc_final: 0.6611 (t0) REVERT: F 280 ASN cc_start: 0.9273 (m-40) cc_final: 0.9022 (m110) REVERT: F 373 LYS cc_start: 0.8265 (mmtt) cc_final: 0.7813 (mttt) REVERT: G 889 MET cc_start: 0.8293 (ptp) cc_final: 0.7794 (tmm) REVERT: H 873 MET cc_start: 0.8773 (ttm) cc_final: 0.8300 (ptm) REVERT: H 970 MET cc_start: -0.6320 (ttm) cc_final: -0.6607 (mtp) outliers start: 27 outliers final: 23 residues processed: 220 average time/residue: 0.3434 time to fit residues: 122.9741 Evaluate side-chains 220 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 196 time to evaluate : 2.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 212 ILE 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 106 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain F residue 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 881 MET Chi-restraints excluded: chain H residue 1033 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 171 optimal weight: 0.0980 chunk 132 optimal weight: 0.8980 chunk 194 optimal weight: 0.7980 chunk 293 optimal weight: 20.0000 chunk 270 optimal weight: 9.9990 chunk 234 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 180 optimal weight: 0.9980 chunk 143 optimal weight: 0.9990 chunk 185 optimal weight: 9.9990 chunk 249 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS ** 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24110 Z= 0.159 Angle : 0.641 13.742 32637 Z= 0.307 Chirality : 0.043 0.231 3614 Planarity : 0.004 0.069 4192 Dihedral : 7.730 159.410 3284 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.25 % Favored : 96.69 % Rotamer: Outliers : 0.86 % Allowed : 13.45 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.16), residues: 2927 helix: 0.84 (0.14), residues: 1447 sheet: -0.12 (0.26), residues: 402 loop : 0.19 (0.20), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 79 HIS 0.005 0.001 HIS B 371 PHE 0.033 0.001 PHE C 223 TYR 0.035 0.001 TYR H 854 ARG 0.003 0.000 ARG E 206 ********************** 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 232 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 210 time to evaluate : 2.677 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: 0.8901 (mmm) cc_final: 0.7901 (pmm) REVERT: A 187 ASP cc_start: 0.8253 (m-30) cc_final: 0.7953 (t70) REVERT: A 374 CYS cc_start: 0.6608 (m) cc_final: 0.6255 (m) REVERT: B 104 LEU cc_start: 0.8770 (tt) cc_final: 0.8125 (pp) REVERT: B 192 ILE cc_start: 0.8512 (pt) cc_final: 0.8100 (mm) REVERT: D 132 MET cc_start: 0.7332 (ppp) cc_final: 0.6957 (ppp) REVERT: E 325 MET cc_start: 0.8407 (mmt) cc_final: 0.7955 (mmt) REVERT: F 10 CYS cc_start: 0.8492 (t) cc_final: 0.8157 (t) REVERT: F 47 MET cc_start: 0.5570 (ptp) cc_final: 0.5143 (ptp) REVERT: F 154 ASP cc_start: 0.6877 (t0) cc_final: 0.6563 (t0) REVERT: F 176 MET cc_start: 0.7317 (mtp) cc_final: 0.7074 (ptp) REVERT: F 280 ASN cc_start: 0.9234 (m-40) cc_final: 0.8996 (m110) REVERT: F 373 LYS cc_start: 0.8270 (mmtt) cc_final: 0.7815 (mttt) REVERT: G 889 MET cc_start: 0.8281 (ptp) cc_final: 0.7818 (tmm) REVERT: H 873 MET cc_start: 0.8775 (ttm) cc_final: 0.8251 (ptm) REVERT: H 970 MET cc_start: -0.6375 (ttm) cc_final: -0.6708 (mtp) outliers start: 22 outliers final: 16 residues processed: 222 average time/residue: 0.3210 time to fit residues: 115.9817 Evaluate side-chains 216 residues out of total 2557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 200 time to evaluate : 2.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 190 MET Chi-restraints excluded: chain H residue 762 LEU Chi-restraints excluded: chain H residue 881 MET Chi-restraints excluded: chain H residue 1033 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 71 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 chunk 34 optimal weight: 9.9990 chunk 65 optimal weight: 0.0870 chunk 234 optimal weight: 30.0000 chunk 98 optimal weight: 4.9990 chunk 240 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 chunk 205 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.096749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.065912 restraints weight = 87014.610| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 5.80 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24110 Z= 0.178 Angle : 0.653 15.520 32637 Z= 0.310 Chirality : 0.043 0.181 3614 Planarity : 0.004 0.069 4192 Dihedral : 7.450 156.485 3284 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.45 % Favored : 96.48 % Rotamer: Outliers : 0.90 % Allowed : 13.84 % Favored : 85.26 % 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: 0.65 (0.16), residues: 2927 helix: 0.88 (0.14), residues: 1447 sheet: -0.07 (0.26), residues: 402 loop : 0.24 (0.21), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 79 HIS 0.005 0.001 HIS B 371 PHE 0.036 0.001 PHE C 223 TYR 0.032 0.001 TYR H 854 ARG 0.008 0.000 ARG H1054 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4682.54 seconds wall clock time: 85 minutes 12.52 seconds (5112.52 seconds total)