Starting phenix.real_space_refine on Tue Jul 23 23:07:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b0k_44045/07_2024/9b0k_44045_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b0k_44045/07_2024/9b0k_44045.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b0k_44045/07_2024/9b0k_44045.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b0k_44045/07_2024/9b0k_44045.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b0k_44045/07_2024/9b0k_44045_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b0k_44045/07_2024/9b0k_44045_neut.cif" } resolution = 3.03 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= 0.008 sd= 0.032 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 154 5.16 5 C 15072 2.51 5 N 4074 2.21 5 O 4578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 896": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 23896 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: 3171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3171 Classifications: {'peptide': 398} Link IDs: {'PTRANS': 15, 'TRANS': 382} Chain breaks: 2 Chain: "H" Number of atoms: 3157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3157 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 15, 'TRANS': 380} Chain breaks: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.37, per 1000 atoms: 0.56 Number of scatterers: 23896 At special positions: 0 Unit cell: (129.6, 132.84, 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 154 16.00 P 12 15.00 Mg 6 11.99 O 4578 8.00 N 4074 7.00 C 15072 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: 9.05 Conformation dependent library (CDL) restraints added in 4.4 seconds 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5672 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 36 sheets defined 56.3% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.40 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 removed outlier: 3.596A pdb=" N MET A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.780A 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: 3.575A 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 194 removed outlier: 3.957A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 217 removed outlier: 4.123A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.720A 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: 3.749A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 268 removed outlier: 3.535A pdb=" N PHE A 266 " --> pdb=" O GLN A 263 " (cutoff:3.500A) 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: 3.659A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.570A pdb=" N MET A 305 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.608A pdb=" N ARG A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 348 removed outlier: 3.571A pdb=" N SER A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.677A pdb=" N GLN A 353 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 4.058A 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 removed outlier: 3.596A pdb=" N MET B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.723A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 101' Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.805A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.531A pdb=" N GLY B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.567A 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 194 removed outlier: 3.769A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 4.008A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.907A 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: 3.721A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 removed outlier: 3.946A pdb=" N PHE B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 268 removed outlier: 3.577A pdb=" N ILE B 267 " --> pdb=" O PRO B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.764A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.692A pdb=" N THR B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 337 through 348 removed outlier: 3.607A pdb=" N SER B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.652A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 374 removed outlier: 4.189A 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 removed outlier: 3.579A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.591A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.603A 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: 3.856A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 146 Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.748A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 217 removed outlier: 4.133A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.591A 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: 3.648A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 261 Processing helix chain 'C' and resid 263 through 268 removed outlier: 3.527A pdb=" N PHE C 266 " --> pdb=" O GLN C 263 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY C 268 " --> pdb=" O SER C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 302 through 306 removed outlier: 4.188A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.613A pdb=" N ARG C 312 " --> pdb=" O GLY C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 349 through 355 removed outlier: 3.738A pdb=" N GLN C 353 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 4.016A 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: 3.850A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.529A pdb=" N MET D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.638A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.707A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix 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: 3.953A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.534A 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: 3.607A 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 268 removed outlier: 3.540A pdb=" N ILE D 267 " --> pdb=" O PRO D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 295 Processing helix chain 'D' and resid 302 through 306 removed outlier: 4.189A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.680A pdb=" N ARG D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 350 through 355 removed outlier: 3.585A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 3.884A 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: 4.079A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) removed outlier: 3.668A 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 removed outlier: 3.558A pdb=" N MET E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.761A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.867A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 194 removed outlier: 3.706A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 216 removed outlier: 3.968A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.645A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 261 Processing helix chain 'E' and resid 263 through 268 removed outlier: 3.529A pdb=" N ILE E 267 " --> pdb=" O PRO E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 289 through 295 removed outlier: 3.680A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 305 Processing helix chain 'E' and resid 308 through 321 removed outlier: 3.659A pdb=" N ARG E 312 " --> pdb=" O GLY E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 347 removed outlier: 3.666A pdb=" N GLY E 343 " --> pdb=" O VAL E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.551A pdb=" N PHE E 352 " --> pdb=" O LEU E 349 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN E 353 " --> pdb=" O SER E 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 349 through 353' Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 368 through 374 removed outlier: 3.926A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 61 Processing helix chain 'F' and resid 78 through 92 removed outlier: 3.630A pdb=" N MET F 82 " --> pdb=" O ASN F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.695A pdb=" N GLU F 100 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 3.548A 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: 4.162A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 146 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: 3.823A pdb=" N GLU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 233 removed outlier: 3.577A pdb=" N GLU F 226 " --> pdb=" O ASP F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 257 removed outlier: 3.803A pdb=" N CYS F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 263 removed outlier: 3.859A pdb=" N PHE F 262 " --> pdb=" O PRO F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 268 removed outlier: 3.569A pdb=" N ILE F 267 " --> pdb=" O PRO F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 284 Processing helix chain 'F' and resid 289 through 295 removed outlier: 3.638A pdb=" N LEU F 293 " --> pdb=" O ILE F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 306 removed outlier: 4.085A pdb=" N TYR F 306 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 removed outlier: 3.601A pdb=" N ARG F 312 " --> pdb=" O GLY F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 348 Processing helix chain 'F' and resid 349 through 356 removed outlier: 3.516A pdb=" N PHE F 352 " --> pdb=" O LEU F 349 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN F 353 " --> pdb=" O SER F 350 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TRP F 356 " --> pdb=" O GLN F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 368 through 374 removed outlier: 4.172A pdb=" N ARG F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 573 through 578 Processing helix chain 'G' and resid 582 through 589 removed outlier: 4.506A pdb=" N SER G 586 " --> pdb=" O SER G 582 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU G 587 " --> pdb=" O MET G 583 " (cutoff:3.500A) Processing helix chain 'G' and resid 598 through 606 Processing helix chain 'G' and resid 634 through 645 Processing helix chain 'G' and resid 651 through 661 Processing helix chain 'G' and resid 668 through 678 Processing helix chain 'G' and resid 681 through 691 Processing helix chain 'G' and resid 699 through 710 Processing helix chain 'G' and resid 713 through 750 removed outlier: 3.709A pdb=" N ARG G 717 " --> pdb=" O CYS G 713 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET G 733 " --> pdb=" O ALA G 729 " (cutoff:3.500A) Proline residue: G 736 - end of helix Processing helix chain 'G' and resid 752 through 769 removed outlier: 3.752A pdb=" N ILE G 756 " --> pdb=" O ARG G 752 " (cutoff:3.500A) Processing helix chain 'G' and resid 781 through 790 removed outlier: 3.960A pdb=" N THR G 784 " --> pdb=" O LYS G 781 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU G 785 " --> pdb=" O ILE G 782 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU G 786 " --> pdb=" O SER G 783 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU G 788 " --> pdb=" O LEU G 785 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N THR G 789 " --> pdb=" O LEU G 786 " (cutoff:3.500A) Processing helix chain 'G' and resid 799 through 811 removed outlier: 3.948A pdb=" N LYS G 810 " --> pdb=" O GLU G 806 " (cutoff:3.500A) Processing helix chain 'G' and resid 812 through 816 removed outlier: 3.584A pdb=" N LEU G 815 " --> pdb=" O HIS G 812 " (cutoff:3.500A) Processing helix chain 'G' and resid 817 through 822 removed outlier: 3.809A pdb=" N ASP G 821 " --> pdb=" O GLN G 817 " (cutoff:3.500A) Processing helix chain 'G' and resid 822 through 829 Processing helix chain 'G' and resid 832 through 856 removed outlier: 3.832A pdb=" N ILE G 836 " --> pdb=" O ASN G 832 " (cutoff:3.500A) Processing helix chain 'G' and resid 858 through 897 removed outlier: 3.800A pdb=" N GLN G 864 " --> pdb=" O GLU G 860 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N GLU G 867 " --> pdb=" O GLU G 863 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ARG G 868 " --> pdb=" O GLN G 864 " (cutoff:3.500A) Processing helix chain 'G' and resid 905 through 947 removed outlier: 3.675A pdb=" N THR G 909 " --> pdb=" O SER G 905 " (cutoff:3.500A) Processing helix chain 'G' and resid 972 through 980 removed outlier: 3.706A pdb=" N ASP G 979 " --> pdb=" O ALA G 975 " (cutoff:3.500A) Processing helix chain 'G' and resid 981 through 983 No H-bonds generated for 'chain 'G' and resid 981 through 983' Processing helix chain 'H' and resid 573 through 578 Processing helix chain 'H' and resid 582 through 589 Processing helix chain 'H' and resid 598 through 606 removed outlier: 3.750A pdb=" N ILE H 602 " --> pdb=" O ASP H 598 " (cutoff:3.500A) Processing helix chain 'H' and resid 634 through 647 removed outlier: 3.824A pdb=" N GLN H 647 " --> pdb=" O ILE H 643 " (cutoff:3.500A) Processing helix chain 'H' and resid 651 through 662 removed outlier: 3.510A pdb=" N VAL H 655 " --> pdb=" O SER H 651 " (cutoff:3.500A) Processing helix chain 'H' and resid 668 through 678 removed outlier: 3.617A pdb=" N LEU H 672 " --> pdb=" O ASP H 668 " (cutoff:3.500A) Processing helix chain 'H' and resid 681 through 690 Processing helix chain 'H' and resid 694 through 698 removed outlier: 3.594A pdb=" N LYS H 697 " --> pdb=" O GLU H 694 " (cutoff:3.500A) Processing helix chain 'H' and resid 699 through 710 Processing helix chain 'H' and resid 713 through 750 removed outlier: 3.863A pdb=" N ARG H 717 " --> pdb=" O CYS H 713 " (cutoff:3.500A) Proline residue: H 736 - end of helix Processing helix chain 'H' and resid 752 through 769 removed outlier: 3.895A pdb=" N ILE H 756 " --> pdb=" O ARG H 752 " (cutoff:3.500A) Processing helix chain 'H' and resid 781 through 788 removed outlier: 3.558A pdb=" N LEU H 785 " --> pdb=" O ILE H 782 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU H 786 " --> pdb=" O SER H 783 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU H 788 " --> pdb=" O LEU H 785 " (cutoff:3.500A) Processing helix chain 'H' and resid 799 through 811 removed outlier: 3.622A pdb=" N LYS H 810 " --> pdb=" O GLU H 806 " (cutoff:3.500A) Processing helix chain 'H' and resid 812 through 816 Processing helix chain 'H' and resid 817 through 822 removed outlier: 3.570A pdb=" N ASP H 821 " --> pdb=" O GLN H 817 " (cutoff:3.500A) Processing helix chain 'H' and resid 822 through 828 Processing helix chain 'H' and resid 832 through 856 removed outlier: 3.837A pdb=" N ILE H 836 " --> pdb=" O ASN H 832 " (cutoff:3.500A) Processing helix chain 'H' and resid 858 through 897 removed outlier: 3.540A pdb=" N GLN H 862 " --> pdb=" O VAL H 858 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN H 864 " --> pdb=" O GLU H 860 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N GLU H 867 " --> pdb=" O GLU H 863 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ARG H 868 " --> pdb=" O GLN H 864 " (cutoff:3.500A) Processing helix chain 'H' and resid 905 through 947 Processing helix chain 'H' and resid 972 through 979 removed outlier: 3.824A pdb=" N ASP H 979 " --> pdb=" O ALA H 975 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.358A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (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: 6.240A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.428A 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: 3.924A 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: 6.337A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (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: 6.636A 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: 3.945A 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: 6.327A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 3.578A 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: 6.223A 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: 3.781A 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: 6.823A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.333A 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: 3.623A pdb=" N SER D 155 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 176 through 178 removed outlier: 3.740A 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: 6.813A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR E 103 " --> pdb=" O ALA E 131 " (cutoff:3.500A) removed outlier: 3.633A 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: 6.251A 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: 6.990A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR F 133 " --> pdb=" O THR F 103 " (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: 5.921A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) removed outlier: 6.269A 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 1224 hydrogen bonds defined for protein. 3330 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: 8.95 Time building geometry restraints manager: 9.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6296 1.34 - 1.46: 4622 1.46 - 1.58: 13174 1.58 - 1.70: 18 1.70 - 1.82: 262 Bond restraints: 24372 Sorted by residual: bond pdb=" N GLU G 948 " pdb=" CA GLU G 948 " ideal model delta sigma weight residual 1.456 1.504 -0.047 1.23e-02 6.61e+03 1.49e+01 bond pdb=" C GLU G 947 " pdb=" N GLU G 948 " ideal model delta sigma weight residual 1.331 1.370 -0.039 1.35e-02 5.49e+03 8.37e+00 bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.404 -0.057 2.00e-02 2.50e+03 8.25e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.404 -0.057 2.00e-02 2.50e+03 8.02e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.94e+00 ... (remaining 24367 not shown) Histogram of bond angle deviations from ideal: 97.50 - 105.25: 528 105.25 - 112.99: 12816 112.99 - 120.74: 11217 120.74 - 128.49: 8262 128.49 - 136.23: 190 Bond angle restraints: 33013 Sorted by residual: angle pdb=" N GLU B 364 " pdb=" CA GLU B 364 " pdb=" CB GLU B 364 " ideal model delta sigma weight residual 110.20 118.62 -8.42 1.49e+00 4.50e-01 3.20e+01 angle pdb=" N GLU A 364 " pdb=" CA GLU A 364 " pdb=" CB GLU A 364 " ideal model delta sigma weight residual 110.07 117.71 -7.64 1.45e+00 4.76e-01 2.77e+01 angle pdb=" CA MET C 47 " pdb=" CB MET C 47 " pdb=" CG MET C 47 " ideal model delta sigma weight residual 114.10 124.30 -10.20 2.00e+00 2.50e-01 2.60e+01 angle pdb=" CA MET F 47 " pdb=" CB MET F 47 " pdb=" CG MET F 47 " ideal model delta sigma weight residual 114.10 123.97 -9.87 2.00e+00 2.50e-01 2.44e+01 angle pdb=" CA GLU B 364 " pdb=" CB GLU B 364 " pdb=" CG GLU B 364 " ideal model delta sigma weight residual 114.10 123.60 -9.50 2.00e+00 2.50e-01 2.26e+01 ... (remaining 33008 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.07: 14140 24.07 - 48.15: 629 48.15 - 72.22: 53 72.22 - 96.30: 8 96.30 - 120.37: 3 Dihedral angle restraints: 14833 sinusoidal: 6047 harmonic: 8786 Sorted by residual: dihedral pdb=" CA GLU G 947 " pdb=" C GLU G 947 " pdb=" N GLU G 948 " pdb=" CA GLU G 948 " ideal model delta harmonic sigma weight residual -180.00 -139.87 -40.13 0 5.00e+00 4.00e-02 6.44e+01 dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual 300.00 179.63 120.37 1 2.00e+01 2.50e-03 3.61e+01 dihedral pdb=" C5' ADP E 401 " pdb=" O5' ADP E 401 " pdb=" PA ADP E 401 " pdb=" O2A ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 49.09 -109.09 1 2.00e+01 2.50e-03 3.18e+01 ... (remaining 14830 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 3254 0.088 - 0.176: 410 0.176 - 0.264: 29 0.264 - 0.352: 5 0.352 - 0.440: 2 Chirality restraints: 3700 Sorted by residual: chirality pdb=" CB ILE D 287 " pdb=" CA ILE D 287 " pdb=" CG1 ILE D 287 " pdb=" CG2 ILE D 287 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.83e+00 chirality pdb=" CB ILE C 287 " pdb=" CA ILE C 287 " pdb=" CG1 ILE C 287 " pdb=" CG2 ILE C 287 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" CB ILE G 980 " pdb=" CA ILE G 980 " pdb=" CG1 ILE G 980 " pdb=" CG2 ILE G 980 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.72e+00 ... (remaining 3697 not shown) Planarity restraints: 4237 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU G 947 " -0.034 2.00e-02 2.50e+03 6.90e-02 4.76e+01 pdb=" C GLU G 947 " 0.119 2.00e-02 2.50e+03 pdb=" O GLU G 947 " -0.046 2.00e-02 2.50e+03 pdb=" N GLU G 948 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 111 " -0.059 5.00e-02 4.00e+02 8.97e-02 1.29e+01 pdb=" N PRO A 112 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO A 112 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 112 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 896 " -0.022 2.00e-02 2.50e+03 2.20e-02 9.67e+00 pdb=" CG TYR H 896 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR H 896 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR H 896 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR H 896 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR H 896 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR H 896 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR H 896 " 0.002 2.00e-02 2.50e+03 ... (remaining 4234 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 238 2.66 - 3.22: 19918 3.22 - 3.78: 36956 3.78 - 4.34: 52000 4.34 - 4.90: 84320 Nonbonded interactions: 193432 Sorted by model distance: nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 402 " model vdw 2.097 2.170 nonbonded pdb=" O1B ADP F 401 " pdb="MG MG F 402 " model vdw 2.207 2.170 nonbonded pdb=" O1B ADP C 401 " pdb="MG MG C 402 " model vdw 2.310 2.170 nonbonded pdb=" O GLN B 314 " pdb=" OG1 THR B 318 " model vdw 2.332 2.440 nonbonded pdb=" O GLY C 156 " pdb=" OG1 THR C 303 " model vdw 2.336 2.440 ... (remaining 193427 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'G' and (resid 551 through 947 or resid 971 through 983)) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.960 Check model and map are aligned: 0.210 Set scattering table: 0.230 Process input model: 64.600 Find NCS groups from input model: 1.710 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: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 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 0.078 24372 Z= 0.331 Angle : 0.962 13.155 33013 Z= 0.508 Chirality : 0.056 0.440 3700 Planarity : 0.007 0.090 4237 Dihedral : 13.377 120.369 9161 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.06 (0.13), residues: 2978 helix: -1.72 (0.10), residues: 1484 sheet: -0.63 (0.24), residues: 396 loop : -0.77 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP H 569 HIS 0.011 0.001 HIS H 803 PHE 0.033 0.002 PHE F 223 TYR 0.053 0.002 TYR H 896 ARG 0.007 0.001 ARG D 210 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 2.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8015 (mmm) cc_final: 0.7813 (mmm) REVERT: A 82 MET cc_start: 0.8031 (tpp) cc_final: 0.7556 (tpp) REVERT: C 227 MET cc_start: 0.8693 (mmm) cc_final: 0.8373 (mmm) REVERT: E 132 MET cc_start: 0.6577 (ptt) cc_final: 0.6320 (ppp) REVERT: E 283 MET cc_start: 0.9129 (mmm) cc_final: 0.8894 (mmm) REVERT: G 703 HIS cc_start: 0.8888 (t-90) cc_final: 0.8672 (t70) REVERT: G 721 MET cc_start: 0.9164 (mmp) cc_final: 0.8882 (mmm) REVERT: G 800 LEU cc_start: 0.8867 (tt) cc_final: 0.8591 (mt) REVERT: H 554 HIS cc_start: 0.3117 (p-80) cc_final: 0.2852 (p-80) REVERT: H 682 LYS cc_start: 0.9406 (mppt) cc_final: 0.9098 (tppt) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.3440 time to fit residues: 89.9953 Evaluate side-chains 137 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 2.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 9.9990 chunk 227 optimal weight: 40.0000 chunk 126 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 chunk 153 optimal weight: 2.9990 chunk 121 optimal weight: 8.9990 chunk 235 optimal weight: 30.0000 chunk 90 optimal weight: 0.9990 chunk 142 optimal weight: 7.9990 chunk 175 optimal weight: 6.9990 chunk 272 optimal weight: 0.1980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN D 115 ASN G 703 HIS H 864 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 24372 Z= 0.255 Angle : 0.602 9.650 33013 Z= 0.293 Chirality : 0.042 0.167 3700 Planarity : 0.004 0.065 4237 Dihedral : 6.745 121.663 3350 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.35 % Allowed : 3.70 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.15), residues: 2978 helix: 0.29 (0.13), residues: 1473 sheet: -0.42 (0.25), residues: 402 loop : -0.14 (0.20), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 86 HIS 0.006 0.001 HIS B 275 PHE 0.013 0.001 PHE B 127 TYR 0.017 0.001 TYR H 714 ARG 0.006 0.000 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 140 time to evaluate : 2.856 Fit side-chains revert: symmetry clash REVERT: A 190 MET cc_start: 0.8970 (mtt) cc_final: 0.8744 (mtp) REVERT: A 355 MET cc_start: 0.8086 (mmm) cc_final: 0.7469 (tpt) REVERT: B 44 MET cc_start: 0.3698 (pmm) cc_final: 0.3221 (pmm) REVERT: C 325 MET cc_start: 0.8481 (mmt) cc_final: 0.8234 (mmm) REVERT: E 132 MET cc_start: 0.6798 (ptt) cc_final: 0.6298 (ppp) REVERT: G 721 MET cc_start: 0.9183 (mmp) cc_final: 0.8449 (mmm) REVERT: H 554 HIS cc_start: 0.2840 (p-80) cc_final: 0.2562 (p-80) REVERT: H 682 LYS cc_start: 0.9354 (mppt) cc_final: 0.9093 (tppt) outliers start: 9 outliers final: 5 residues processed: 145 average time/residue: 0.3092 time to fit residues: 75.7349 Evaluate side-chains 136 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 131 time to evaluate : 2.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain G residue 724 CYS Chi-restraints excluded: chain H residue 568 ASN Chi-restraints excluded: chain H residue 757 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 226 optimal weight: 30.0000 chunk 185 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 272 optimal weight: 6.9990 chunk 294 optimal weight: 20.0000 chunk 243 optimal weight: 20.0000 chunk 270 optimal weight: 20.0000 chunk 93 optimal weight: 3.9990 chunk 218 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN B 297 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS D 137 GLN E 40 HIS E 162 ASN F 59 GLN F 88 HIS ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 647 GLN H 683 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 24372 Z= 0.380 Angle : 0.667 9.694 33013 Z= 0.327 Chirality : 0.045 0.178 3700 Planarity : 0.004 0.048 4237 Dihedral : 7.092 141.102 3350 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.74 % Allowed : 6.07 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.16), residues: 2978 helix: 0.79 (0.14), residues: 1474 sheet: -0.26 (0.26), residues: 372 loop : -0.19 (0.19), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 584 HIS 0.014 0.001 HIS G 703 PHE 0.016 0.002 PHE D 127 TYR 0.016 0.002 TYR H 714 ARG 0.005 0.000 ARG H 981 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 136 time to evaluate : 2.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8285 (tpt) cc_final: 0.7974 (tpt) REVERT: B 44 MET cc_start: 0.2921 (pmm) cc_final: 0.2456 (pmm) REVERT: B 299 MET cc_start: 0.8348 (mtm) cc_final: 0.7873 (mtm) REVERT: C 227 MET cc_start: 0.8620 (mmm) cc_final: 0.8206 (mmm) REVERT: C 355 MET cc_start: 0.8495 (mtp) cc_final: 0.8287 (mtp) REVERT: E 28 ARG cc_start: 0.8560 (tpp80) cc_final: 0.7941 (tpp80) REVERT: F 305 MET cc_start: 0.8352 (mmm) cc_final: 0.7862 (mpp) REVERT: G 721 MET cc_start: 0.9163 (mmp) cc_final: 0.8561 (mmm) REVERT: G 865 TYR cc_start: 0.6642 (m-10) cc_final: 0.6279 (m-10) REVERT: H 554 HIS cc_start: 0.2918 (p-80) cc_final: 0.2643 (p-80) REVERT: H 682 LYS cc_start: 0.9360 (mppt) cc_final: 0.9096 (tppt) REVERT: H 757 PHE cc_start: 0.9140 (OUTLIER) cc_final: 0.8859 (m-80) outliers start: 19 outliers final: 12 residues processed: 147 average time/residue: 0.3188 time to fit residues: 78.9441 Evaluate side-chains 142 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 129 time to evaluate : 2.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 355 MET Chi-restraints excluded: chain G residue 724 CYS Chi-restraints excluded: chain H residue 568 ASN Chi-restraints excluded: chain H residue 575 ASN Chi-restraints excluded: chain H residue 757 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 10.0000 chunk 205 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 273 optimal weight: 9.9990 chunk 289 optimal weight: 20.0000 chunk 143 optimal weight: 0.9990 chunk 259 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 ASN D 161 HIS D 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24372 Z= 0.228 Angle : 0.573 8.232 33013 Z= 0.275 Chirality : 0.042 0.170 3700 Planarity : 0.003 0.042 4237 Dihedral : 6.745 135.415 3350 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.58 % Allowed : 7.74 % Favored : 91.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.16), residues: 2978 helix: 1.23 (0.14), residues: 1468 sheet: -0.41 (0.25), residues: 414 loop : 0.08 (0.20), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 79 HIS 0.004 0.001 HIS D 161 PHE 0.011 0.001 PHE B 127 TYR 0.015 0.001 TYR H 714 ARG 0.003 0.000 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 135 time to evaluate : 2.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.4407 (pmm) cc_final: 0.4002 (pmm) REVERT: B 299 MET cc_start: 0.8251 (mtm) cc_final: 0.7700 (mtm) REVERT: C 227 MET cc_start: 0.8582 (mmm) cc_final: 0.8267 (mmm) REVERT: C 355 MET cc_start: 0.8514 (mtp) cc_final: 0.8309 (mtp) REVERT: F 305 MET cc_start: 0.8349 (mmm) cc_final: 0.7911 (tpp) REVERT: G 721 MET cc_start: 0.9163 (mmp) cc_final: 0.8600 (mmm) REVERT: G 770 TYR cc_start: 0.7261 (t80) cc_final: 0.6866 (m-80) REVERT: G 865 TYR cc_start: 0.6617 (m-10) cc_final: 0.6143 (m-10) REVERT: H 554 HIS cc_start: 0.2876 (p-80) cc_final: 0.2581 (p-80) REVERT: H 682 LYS cc_start: 0.9361 (mppt) cc_final: 0.9105 (tppt) REVERT: H 757 PHE cc_start: 0.9138 (OUTLIER) cc_final: 0.8866 (m-80) outliers start: 15 outliers final: 8 residues processed: 144 average time/residue: 0.3227 time to fit residues: 78.7766 Evaluate side-chains 140 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 131 time to evaluate : 3.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 355 MET Chi-restraints excluded: chain H residue 568 ASN Chi-restraints excluded: chain H residue 575 ASN Chi-restraints excluded: chain H residue 757 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 7.9990 chunk 164 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 215 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 247 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 148 optimal weight: 10.0000 chunk 260 optimal weight: 0.2980 chunk 73 optimal weight: 0.7980 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 24372 Z= 0.266 Angle : 0.595 12.129 33013 Z= 0.285 Chirality : 0.042 0.182 3700 Planarity : 0.003 0.040 4237 Dihedral : 6.742 137.070 3350 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.01 % Allowed : 8.25 % Favored : 90.74 % 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: 0.89 (0.16), residues: 2978 helix: 1.35 (0.14), residues: 1475 sheet: -0.40 (0.25), residues: 414 loop : 0.10 (0.20), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 79 HIS 0.004 0.001 HIS D 87 PHE 0.012 0.001 PHE B 127 TYR 0.016 0.001 TYR H 865 ARG 0.005 0.000 ARG E 335 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 134 time to evaluate : 2.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.4445 (pmm) cc_final: 0.3925 (pmm) REVERT: B 299 MET cc_start: 0.8234 (mtm) cc_final: 0.7808 (mtm) REVERT: C 227 MET cc_start: 0.8577 (mmm) cc_final: 0.8255 (mmm) REVERT: F 305 MET cc_start: 0.8380 (mmm) cc_final: 0.7950 (tpp) REVERT: G 721 MET cc_start: 0.9149 (mmp) cc_final: 0.8516 (mmm) REVERT: G 770 TYR cc_start: 0.7288 (OUTLIER) cc_final: 0.6901 (m-80) REVERT: G 865 TYR cc_start: 0.6641 (m-10) cc_final: 0.6219 (m-10) REVERT: H 554 HIS cc_start: 0.2959 (p-80) cc_final: 0.2646 (p-80) REVERT: H 733 MET cc_start: 0.8791 (ppp) cc_final: 0.8473 (ppp) REVERT: H 757 PHE cc_start: 0.9150 (OUTLIER) cc_final: 0.8938 (m-80) outliers start: 26 outliers final: 17 residues processed: 152 average time/residue: 0.3138 time to fit residues: 80.4274 Evaluate side-chains 151 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 132 time to evaluate : 2.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 355 MET Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain G residue 770 TYR Chi-restraints excluded: chain H residue 568 ASN Chi-restraints excluded: chain H residue 575 ASN Chi-restraints excluded: chain H residue 757 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 2.9990 chunk 261 optimal weight: 30.0000 chunk 57 optimal weight: 2.9990 chunk 170 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 290 optimal weight: 10.0000 chunk 240 optimal weight: 6.9990 chunk 134 optimal weight: 0.9980 chunk 24 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 24372 Z= 0.296 Angle : 0.609 9.279 33013 Z= 0.293 Chirality : 0.043 0.170 3700 Planarity : 0.003 0.039 4237 Dihedral : 6.810 141.435 3350 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.21 % Allowed : 8.67 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.16), residues: 2978 helix: 1.38 (0.14), residues: 1476 sheet: -0.44 (0.25), residues: 414 loop : 0.08 (0.20), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 79 HIS 0.004 0.001 HIS D 87 PHE 0.012 0.001 PHE D 127 TYR 0.016 0.001 TYR H 714 ARG 0.007 0.000 ARG E 335 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 138 time to evaluate : 2.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8329 (tpt) cc_final: 0.7822 (tpt) REVERT: B 299 MET cc_start: 0.8210 (mtm) cc_final: 0.7719 (mtm) REVERT: C 227 MET cc_start: 0.8572 (mmm) cc_final: 0.8235 (mmm) REVERT: E 119 MET cc_start: 0.8671 (mtp) cc_final: 0.8394 (mtt) REVERT: E 305 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8497 (tpp) REVERT: F 305 MET cc_start: 0.8414 (mmm) cc_final: 0.8038 (tpp) REVERT: G 583 MET cc_start: 0.3406 (ptt) cc_final: 0.2430 (ttt) REVERT: G 721 MET cc_start: 0.9134 (mmp) cc_final: 0.8473 (mmm) REVERT: G 770 TYR cc_start: 0.7277 (t80) cc_final: 0.6988 (m-80) REVERT: G 865 TYR cc_start: 0.6679 (m-10) cc_final: 0.6266 (m-10) REVERT: H 554 HIS cc_start: 0.3121 (p-80) cc_final: 0.2791 (p-80) REVERT: H 682 LYS cc_start: 0.9375 (mppt) cc_final: 0.9117 (tppt) REVERT: H 757 PHE cc_start: 0.9151 (OUTLIER) cc_final: 0.8932 (m-80) REVERT: H 974 ASP cc_start: 0.8520 (t0) cc_final: 0.8266 (m-30) outliers start: 31 outliers final: 20 residues processed: 161 average time/residue: 0.3149 time to fit residues: 85.9278 Evaluate side-chains 154 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 132 time to evaluate : 2.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 TRP Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 355 MET Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain H residue 568 ASN Chi-restraints excluded: chain H residue 575 ASN Chi-restraints excluded: chain H residue 757 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 211 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 244 optimal weight: 9.9990 chunk 162 optimal weight: 0.9990 chunk 289 optimal weight: 20.0000 chunk 180 optimal weight: 3.9990 chunk 176 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 24372 Z= 0.263 Angle : 0.596 11.509 33013 Z= 0.284 Chirality : 0.042 0.170 3700 Planarity : 0.003 0.039 4237 Dihedral : 6.734 139.820 3350 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.17 % Allowed : 9.18 % Favored : 89.65 % 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 (0.16), residues: 2978 helix: 1.46 (0.14), residues: 1476 sheet: -0.42 (0.25), residues: 414 loop : 0.11 (0.20), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 584 HIS 0.003 0.001 HIS D 87 PHE 0.016 0.001 PHE D 124 TYR 0.015 0.001 TYR H 714 ARG 0.004 0.000 ARG B 116 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 133 time to evaluate : 2.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8316 (tpt) cc_final: 0.8043 (tpt) REVERT: B 299 MET cc_start: 0.8244 (mtm) cc_final: 0.7794 (mtm) REVERT: C 227 MET cc_start: 0.8571 (mmm) cc_final: 0.8222 (mmm) REVERT: E 119 MET cc_start: 0.8627 (mtp) cc_final: 0.8324 (mtt) REVERT: E 305 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8425 (tpp) REVERT: F 305 MET cc_start: 0.8483 (mmm) cc_final: 0.8043 (tpp) REVERT: G 721 MET cc_start: 0.9130 (mmp) cc_final: 0.8460 (mmm) REVERT: G 770 TYR cc_start: 0.7267 (t80) cc_final: 0.6964 (m-80) REVERT: G 865 TYR cc_start: 0.6678 (m-10) cc_final: 0.6228 (m-10) REVERT: H 554 HIS cc_start: 0.3137 (p-80) cc_final: 0.2822 (p-80) REVERT: H 682 LYS cc_start: 0.9324 (mppt) cc_final: 0.9061 (tppt) REVERT: H 733 MET cc_start: 0.8965 (ppp) cc_final: 0.8667 (ppp) REVERT: H 757 PHE cc_start: 0.9148 (OUTLIER) cc_final: 0.8935 (m-80) outliers start: 30 outliers final: 23 residues processed: 154 average time/residue: 0.3107 time to fit residues: 80.9766 Evaluate side-chains 156 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 2.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 TRP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 355 MET Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain H residue 575 ASN Chi-restraints excluded: chain H residue 757 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 0.0970 chunk 115 optimal weight: 0.3980 chunk 172 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 183 optimal weight: 8.9990 chunk 196 optimal weight: 4.9990 chunk 142 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 227 optimal weight: 30.0000 chunk 263 optimal weight: 30.0000 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 HIS ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24372 Z= 0.134 Angle : 0.546 11.268 33013 Z= 0.256 Chirality : 0.040 0.177 3700 Planarity : 0.003 0.037 4237 Dihedral : 6.273 121.313 3350 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.97 % Allowed : 9.57 % Favored : 89.46 % 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: 1.31 (0.16), residues: 2978 helix: 1.72 (0.14), residues: 1470 sheet: -0.26 (0.25), residues: 414 loop : 0.31 (0.20), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 79 HIS 0.003 0.000 HIS E 161 PHE 0.011 0.001 PHE D 124 TYR 0.012 0.001 TYR H 714 ARG 0.002 0.000 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 137 time to evaluate : 2.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8337 (tpt) cc_final: 0.8089 (tpt) REVERT: B 299 MET cc_start: 0.8138 (mtm) cc_final: 0.7724 (mtm) REVERT: C 47 MET cc_start: 0.7513 (pmm) cc_final: 0.7311 (pmm) REVERT: C 128 ASN cc_start: 0.7638 (OUTLIER) cc_final: 0.7423 (p0) REVERT: C 227 MET cc_start: 0.8485 (mmm) cc_final: 0.8128 (mmm) REVERT: D 375 PHE cc_start: 0.8061 (t80) cc_final: 0.7664 (t80) REVERT: E 82 MET cc_start: 0.8368 (mmm) cc_final: 0.8108 (tpt) REVERT: E 132 MET cc_start: 0.7421 (ptt) cc_final: 0.7032 (ppp) REVERT: E 305 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8379 (tpp) REVERT: F 305 MET cc_start: 0.8331 (mmm) cc_final: 0.8004 (tpp) REVERT: G 583 MET cc_start: 0.3407 (ptt) cc_final: 0.2350 (tpp) REVERT: G 721 MET cc_start: 0.9107 (mmp) cc_final: 0.8467 (mmm) REVERT: G 770 TYR cc_start: 0.7189 (t80) cc_final: 0.6883 (m-80) REVERT: G 865 TYR cc_start: 0.6632 (m-10) cc_final: 0.6220 (m-10) REVERT: H 554 HIS cc_start: 0.3084 (p-80) cc_final: 0.2751 (p-80) REVERT: H 733 MET cc_start: 0.8931 (ppp) cc_final: 0.8654 (ppp) REVERT: H 974 ASP cc_start: 0.8705 (t0) cc_final: 0.8417 (m-30) outliers start: 25 outliers final: 16 residues processed: 156 average time/residue: 0.3178 time to fit residues: 83.5099 Evaluate side-chains 150 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 3.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 TRP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 128 ASN Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain H residue 568 ASN Chi-restraints excluded: chain H residue 575 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 277 optimal weight: 20.0000 chunk 252 optimal weight: 30.0000 chunk 269 optimal weight: 10.0000 chunk 276 optimal weight: 0.8980 chunk 162 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 211 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 243 optimal weight: 30.0000 chunk 254 optimal weight: 7.9990 chunk 268 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 24372 Z= 0.328 Angle : 0.638 12.030 33013 Z= 0.305 Chirality : 0.043 0.175 3700 Planarity : 0.003 0.038 4237 Dihedral : 6.657 133.408 3350 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.36 % Allowed : 9.30 % Favored : 89.34 % 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: 1.09 (0.16), residues: 2978 helix: 1.54 (0.14), residues: 1476 sheet: -0.35 (0.25), residues: 414 loop : 0.19 (0.20), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 584 HIS 0.005 0.001 HIS D 87 PHE 0.017 0.001 PHE D 124 TYR 0.013 0.001 TYR H 714 ARG 0.004 0.000 ARG E 335 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 135 time to evaluate : 3.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8327 (tpt) cc_final: 0.8115 (tpt) REVERT: B 299 MET cc_start: 0.8308 (mtm) cc_final: 0.7893 (mtm) REVERT: C 227 MET cc_start: 0.8558 (mmm) cc_final: 0.8223 (mmm) REVERT: D 375 PHE cc_start: 0.8083 (t80) cc_final: 0.7752 (t80) REVERT: E 305 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8425 (tpp) REVERT: F 305 MET cc_start: 0.8381 (mmm) cc_final: 0.8028 (tpp) REVERT: G 721 MET cc_start: 0.9092 (mmp) cc_final: 0.8454 (mmm) REVERT: G 770 TYR cc_start: 0.7083 (t80) cc_final: 0.6821 (m-80) REVERT: G 865 TYR cc_start: 0.6692 (m-10) cc_final: 0.6260 (m-10) REVERT: H 554 HIS cc_start: 0.3194 (p-80) cc_final: 0.2860 (p-80) REVERT: H 733 MET cc_start: 0.8953 (ppp) cc_final: 0.8689 (ppp) REVERT: H 757 PHE cc_start: 0.8791 (m-80) cc_final: 0.8562 (m-80) REVERT: H 974 ASP cc_start: 0.8717 (t0) cc_final: 0.8424 (m-30) outliers start: 35 outliers final: 29 residues processed: 166 average time/residue: 0.3169 time to fit residues: 89.9852 Evaluate side-chains 164 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 134 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 TRP Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 292 ASP Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain E residue 355 MET Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain H residue 568 ASN Chi-restraints excluded: chain H residue 575 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 0.5980 chunk 284 optimal weight: 9.9990 chunk 173 optimal weight: 0.7980 chunk 135 optimal weight: 3.9990 chunk 198 optimal weight: 9.9990 chunk 298 optimal weight: 6.9990 chunk 275 optimal weight: 10.0000 chunk 237 optimal weight: 7.9990 chunk 24 optimal weight: 0.0010 chunk 183 optimal weight: 7.9990 chunk 145 optimal weight: 2.9990 overall best weight: 1.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24372 Z= 0.201 Angle : 0.586 12.607 33013 Z= 0.275 Chirality : 0.041 0.182 3700 Planarity : 0.003 0.038 4237 Dihedral : 6.447 126.359 3350 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.01 % Allowed : 9.61 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.16), residues: 2978 helix: 1.67 (0.14), residues: 1476 sheet: -0.32 (0.25), residues: 414 loop : 0.25 (0.20), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 79 HIS 0.003 0.001 HIS E 161 PHE 0.015 0.001 PHE D 124 TYR 0.013 0.001 TYR H 714 ARG 0.002 0.000 ARG B 116 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5956 Ramachandran restraints generated. 2978 Oldfield, 0 Emsley, 2978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 135 time to evaluate : 2.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8316 (tpt) cc_final: 0.8103 (tpt) REVERT: B 299 MET cc_start: 0.8208 (mtm) cc_final: 0.7819 (mtm) REVERT: C 227 MET cc_start: 0.8524 (mmm) cc_final: 0.8194 (mmm) REVERT: D 44 MET cc_start: 0.5802 (tmm) cc_final: 0.5484 (tmm) REVERT: D 375 PHE cc_start: 0.8096 (t80) cc_final: 0.7750 (t80) REVERT: E 305 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8386 (tpp) REVERT: F 305 MET cc_start: 0.8376 (mmm) cc_final: 0.8009 (tpp) REVERT: G 721 MET cc_start: 0.9088 (mmp) cc_final: 0.8407 (mmm) REVERT: G 770 TYR cc_start: 0.7031 (t80) cc_final: 0.6757 (m-80) REVERT: G 865 TYR cc_start: 0.6670 (m-10) cc_final: 0.6211 (m-10) REVERT: H 554 HIS cc_start: 0.3160 (p-80) cc_final: 0.2827 (p-80) REVERT: H 733 MET cc_start: 0.8949 (ppp) cc_final: 0.8687 (ppp) REVERT: H 974 ASP cc_start: 0.8716 (t0) cc_final: 0.8424 (m-30) outliers start: 26 outliers final: 25 residues processed: 158 average time/residue: 0.2994 time to fit residues: 80.1996 Evaluate side-chains 159 residues out of total 2571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 133 time to evaluate : 2.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 TRP Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 86 TRP Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 128 ASN Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain E residue 355 MET Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 148 THR Chi-restraints excluded: chain H residue 568 ASN Chi-restraints excluded: chain H residue 575 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 189 optimal weight: 0.0070 chunk 253 optimal weight: 20.0000 chunk 72 optimal weight: 0.8980 chunk 219 optimal weight: 0.4980 chunk 35 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 238 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 244 optimal weight: 20.0000 chunk 30 optimal weight: 9.9990 chunk 43 optimal weight: 0.3980 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN ** E 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.079726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.057815 restraints weight = 99571.891| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 3.39 r_work: 0.3197 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24372 Z= 0.175 Angle : 0.583 13.258 33013 Z= 0.272 Chirality : 0.041 0.178 3700 Planarity : 0.003 0.038 4237 Dihedral : 6.332 120.841 3350 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.17 % Allowed : 9.57 % Favored : 89.26 % 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: 1.32 (0.16), residues: 2978 helix: 1.74 (0.14), residues: 1469 sheet: -0.29 (0.25), residues: 414 loop : 0.30 (0.20), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 79 HIS 0.003 0.001 HIS E 161 PHE 0.015 0.001 PHE H 757 TYR 0.021 0.001 TYR H 896 ARG 0.003 0.000 ARG E 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4410.19 seconds wall clock time: 82 minutes 20.86 seconds (4940.86 seconds total)