Starting phenix.real_space_refine on Fri Aug 9 17:14:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0y_32929/08_2024/7x0y_32929_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0y_32929/08_2024/7x0y_32929.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0y_32929/08_2024/7x0y_32929.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0y_32929/08_2024/7x0y_32929.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0y_32929/08_2024/7x0y_32929_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0y_32929/08_2024/7x0y_32929_trim.cif" } resolution = 3.89 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= 0.004 sd= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 14118 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 64 5.16 5 C 9842 2.51 5 N 2582 2.21 5 O 2746 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 16": "NH1" <-> "NH2" Residue "C PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 73": "OD1" <-> "OD2" Residue "C ARG 91": "NH1" <-> "NH2" Residue "C PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 139": "OE1" <-> "OE2" Residue "C PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 266": "NH1" <-> "NH2" Residue "C PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 324": "OD1" <-> "OD2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C ARG 335": "NH1" <-> "NH2" Residue "C GLU 347": "OE1" <-> "OE2" Residue "C PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 389": "OD1" <-> "OD2" Residue "C ASP 450": "OD1" <-> "OD2" Residue "B ARG 16": "NH1" <-> "NH2" Residue "B GLU 43": "OE1" <-> "OE2" Residue "B ASP 73": "OD1" <-> "OD2" Residue "B ARG 91": "NH1" <-> "NH2" Residue "B ASP 105": "OD1" <-> "OD2" Residue "B TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B GLU 223": "OE1" <-> "OE2" Residue "B ASP 231": "OD1" <-> "OD2" Residue "B ARG 266": "NH1" <-> "NH2" Residue "B PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 332": "NH1" <-> "NH2" Residue "B ARG 335": "NH1" <-> "NH2" Residue "B GLU 347": "OE1" <-> "OE2" Residue "B ASP 387": "OD1" <-> "OD2" Residue "B ASP 389": "OD1" <-> "OD2" Residue "B GLU 391": "OE1" <-> "OE2" Residue "B TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 475": "OD1" <-> "OD2" Residue "A ASP 14": "OD1" <-> "OD2" Residue "A ARG 16": "NH1" <-> "NH2" Residue "A PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 218": "OD1" <-> "OD2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 266": "NH1" <-> "NH2" Residue "A PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 322": "OD1" <-> "OD2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A ARG 335": "NH1" <-> "NH2" Residue "A GLU 347": "OE1" <-> "OE2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A GLU 428": "OE1" <-> "OE2" Residue "A ASP 475": "OD1" <-> "OD2" Residue "D ARG 16": "NH1" <-> "NH2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "D PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 91": "NH1" <-> "NH2" Residue "D TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 197": "OE1" <-> "OE2" Residue "D TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 255": "OE1" <-> "OE2" Residue "D ARG 266": "NH1" <-> "NH2" Residue "D GLU 281": "OE1" <-> "OE2" Residue "D PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 322": "OD1" <-> "OD2" Residue "D ASP 324": "OD1" <-> "OD2" Residue "D ASP 326": "OD1" <-> "OD2" Residue "D ARG 332": "NH1" <-> "NH2" Residue "D ARG 335": "NH1" <-> "NH2" Residue "D PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 426": "OE1" <-> "OE2" Residue "D GLU 436": "OE1" <-> "OE2" Residue "D ASP 473": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 15242 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 3718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3718 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 25, 'TRANS': 430} Chain breaks: 2 Chain: "B" Number of atoms: 3739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3739 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 25, 'TRANS': 434} Chain breaks: 1 Chain: "A" Number of atoms: 3742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3742 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 25, 'TRANS': 434} Chain breaks: 1 Chain: "D" Number of atoms: 3751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3751 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 25, 'TRANS': 436} Chain breaks: 1 Chain: "E" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.16, per 1000 atoms: 0.54 Number of scatterers: 15242 At special positions: 0 Unit cell: (81.75, 119.9, 131.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 64 16.00 P 8 15.00 O 2746 8.00 N 2582 7.00 C 9842 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=0, symmetry=0 Time building additional restraints: 6.30 Conformation dependent library (CDL) restraints added in 2.5 seconds 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3506 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 5 sheets defined 55.5% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'C' and resid 23 through 28 removed outlier: 3.671A pdb=" N ALA C 27 " --> pdb=" O LEU C 23 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 23 through 28' Processing helix chain 'C' and resid 43 through 47 removed outlier: 4.019A pdb=" N TYR C 47 " --> pdb=" O GLY C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 68 removed outlier: 3.738A pdb=" N LYS C 57 " --> pdb=" O ARG C 53 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLN C 58 " --> pdb=" O TRP C 54 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER C 59 " --> pdb=" O TRP C 55 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 60 " --> pdb=" O MET C 56 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA C 61 " --> pdb=" O LYS C 57 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN C 65 " --> pdb=" O ALA C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 71 No H-bonds generated for 'chain 'C' and resid 69 through 71' Processing helix chain 'C' and resid 81 through 94 removed outlier: 3.969A pdb=" N ALA C 85 " --> pdb=" O ASN C 81 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE C 86 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU C 87 " --> pdb=" O ILE C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 123 removed outlier: 3.996A pdb=" N VAL C 110 " --> pdb=" O PRO C 106 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ARG C 111 " --> pdb=" O VAL C 107 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP C 112 " --> pdb=" O SER C 108 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N HIS C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL C 120 " --> pdb=" O LYS C 116 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N GLU C 121 " --> pdb=" O GLU C 117 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 161 removed outlier: 3.794A pdb=" N TYR C 154 " --> pdb=" O SER C 150 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N CYS C 158 " --> pdb=" O TYR C 154 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU C 159 " --> pdb=" O TRP C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 209 removed outlier: 3.931A pdb=" N LEU C 205 " --> pdb=" O SER C 202 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 206 " --> pdb=" O ASN C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 228 removed outlier: 3.616A pdb=" N ALA C 217 " --> pdb=" O GLY C 213 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP C 218 " --> pdb=" O TRP C 214 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LYS C 219 " --> pdb=" O SER C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 247 through 253 Processing helix chain 'C' and resid 257 through 275 removed outlier: 3.537A pdb=" N ASP C 275 " --> pdb=" O ILE C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 304 removed outlier: 3.549A pdb=" N GLU C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE C 287 " --> pdb=" O SER C 283 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG C 294 " --> pdb=" O GLY C 290 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU C 295 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG C 298 " --> pdb=" O ARG C 294 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN C 303 " --> pdb=" O TYR C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 309 Processing helix chain 'C' and resid 325 through 332 removed outlier: 3.722A pdb=" N TRP C 331 " --> pdb=" O LYS C 327 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG C 332 " --> pdb=" O PHE C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 352 removed outlier: 4.029A pdb=" N GLY C 344 " --> pdb=" O LEU C 340 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG C 346 " --> pdb=" O ASP C 342 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU C 347 " --> pdb=" O ALA C 343 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA C 350 " --> pdb=" O ARG C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 369 removed outlier: 3.842A pdb=" N PHE C 365 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA C 366 " --> pdb=" O VAL C 362 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL C 367 " --> pdb=" O SER C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 385 removed outlier: 4.435A pdb=" N TYR C 380 " --> pdb=" O TRP C 376 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP C 383 " --> pdb=" O LYS C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 401 removed outlier: 4.699A pdb=" N LEU C 395 " --> pdb=" O GLU C 391 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER C 401 " --> pdb=" O TRP C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 434 Processing helix chain 'C' and resid 435 through 438 removed outlier: 4.160A pdb=" N ALA C 438 " --> pdb=" O PRO C 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 435 through 438' Processing helix chain 'C' and resid 447 through 452 Proline residue: C 452 - end of helix Processing helix chain 'C' and resid 453 through 458 removed outlier: 3.582A pdb=" N LYS C 457 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA C 458 " --> pdb=" O THR C 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 453 through 458' Processing helix chain 'B' and resid 20 through 28 removed outlier: 3.652A pdb=" N ALA B 25 " --> pdb=" O PRO B 21 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ALA B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 70 removed outlier: 4.192A pdb=" N ALA B 61 " --> pdb=" O LYS B 57 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B 66 " --> pdb=" O HIS B 62 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 70 " --> pdb=" O SER B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 91 removed outlier: 4.001A pdb=" N ARG B 91 " --> pdb=" O LEU B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 121 removed outlier: 4.191A pdb=" N VAL B 110 " --> pdb=" O PRO B 106 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR B 114 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 115 " --> pdb=" O ARG B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 159 Processing helix chain 'B' and resid 181 through 185 removed outlier: 4.321A pdb=" N ILE B 184 " --> pdb=" O ALA B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'B' and resid 213 through 226 removed outlier: 3.559A pdb=" N ALA B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP B 218 " --> pdb=" O TRP B 214 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS B 219 " --> pdb=" O SER B 215 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU B 223 " --> pdb=" O LYS B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 235 removed outlier: 3.565A pdb=" N TYR B 232 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ALA B 233 " --> pdb=" O ILE B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 253 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 266 through 275 removed outlier: 4.905A pdb=" N TRP B 272 " --> pdb=" O LYS B 268 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA B 273 " --> pdb=" O GLN B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 285 removed outlier: 3.806A pdb=" N ASP B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 302 removed outlier: 3.596A pdb=" N GLY B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG B 298 " --> pdb=" O ARG B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 332 removed outlier: 3.814A pdb=" N ARG B 332 " --> pdb=" O PHE B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 352 removed outlier: 3.809A pdb=" N GLU B 347 " --> pdb=" O ALA B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 359 No H-bonds generated for 'chain 'B' and resid 357 through 359' Processing helix chain 'B' and resid 360 through 369 removed outlier: 3.766A pdb=" N SER B 364 " --> pdb=" O VAL B 360 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE B 369 " --> pdb=" O PHE B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 385 removed outlier: 3.683A pdb=" N LYS B 379 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR B 380 " --> pdb=" O TRP B 376 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE B 381 " --> pdb=" O GLY B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 399 removed outlier: 3.820A pdb=" N LEU B 395 " --> pdb=" O GLU B 391 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY B 396 " --> pdb=" O CYS B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 423 removed outlier: 4.143A pdb=" N LYS B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR B 423 " --> pdb=" O GLN B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 434 removed outlier: 3.782A pdb=" N TRP B 433 " --> pdb=" O TYR B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 438 Processing helix chain 'B' and resid 441 through 446 removed outlier: 4.370A pdb=" N HIS B 446 " --> pdb=" O THR B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 451 removed outlier: 3.761A pdb=" N ASP B 450 " --> pdb=" O HIS B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 459 removed outlier: 3.546A pdb=" N LEU B 456 " --> pdb=" O PRO B 452 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS B 457 " --> pdb=" O LEU B 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 26 removed outlier: 3.901A pdb=" N ALA A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 47 Processing helix chain 'A' and resid 49 through 69 removed outlier: 3.652A pdb=" N TRP A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET A 56 " --> pdb=" O SER A 52 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA A 61 " --> pdb=" O LYS A 57 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N HIS A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN A 65 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER A 66 " --> pdb=" O HIS A 62 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 69 " --> pdb=" O GLN A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 93 removed outlier: 3.558A pdb=" N ASP A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 92 " --> pdb=" O ASP A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 120 removed outlier: 3.630A pdb=" N ARG A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU A 117 " --> pdb=" O HIS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 123 No H-bonds generated for 'chain 'A' and resid 121 through 123' Processing helix chain 'A' and resid 151 through 156 removed outlier: 3.907A pdb=" N LYS A 156 " --> pdb=" O ASN A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 160 removed outlier: 4.080A pdb=" N ASP A 160 " --> pdb=" O LYS A 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 160' Processing helix chain 'A' and resid 199 through 204 removed outlier: 3.526A pdb=" N ASN A 203 " --> pdb=" O GLU A 199 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 204 " --> pdb=" O LYS A 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 199 through 204' Processing helix chain 'A' and resid 205 through 209 removed outlier: 3.649A pdb=" N ARG A 208 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 229 removed outlier: 3.583A pdb=" N LYS A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 247 through 254 Processing helix chain 'A' and resid 257 through 276 removed outlier: 3.881A pdb=" N GLN A 263 " --> pdb=" O ARG A 259 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS A 268 " --> pdb=" O CYS A 264 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE A 271 " --> pdb=" O MET A 267 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TRP A 272 " --> pdb=" O LYS A 268 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 304 removed outlier: 3.517A pdb=" N ALA A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 324 through 332 removed outlier: 4.227A pdb=" N PHE A 328 " --> pdb=" O ASP A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 352 removed outlier: 3.560A pdb=" N MET A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG A 346 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ALA A 350 " --> pdb=" O ARG A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 368 removed outlier: 3.537A pdb=" N ILE A 361 " --> pdb=" O ARG A 357 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 364 " --> pdb=" O VAL A 360 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 removed outlier: 3.555A pdb=" N GLY A 377 " --> pdb=" O PRO A 373 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR A 380 " --> pdb=" O TRP A 376 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 400 removed outlier: 3.574A pdb=" N ILE A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 395 " --> pdb=" O GLU A 391 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE A 400 " --> pdb=" O GLY A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 424 removed outlier: 3.608A pdb=" N GLN A 419 " --> pdb=" O ASN A 415 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ALA A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 434 removed outlier: 3.621A pdb=" N TRP A 433 " --> pdb=" O TYR A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 446 removed outlier: 4.517A pdb=" N HIS A 446 " --> pdb=" O THR A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 451 removed outlier: 3.523A pdb=" N ASP A 450 " --> pdb=" O HIS A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'D' and resid 22 through 30 removed outlier: 3.607A pdb=" N ALA D 26 " --> pdb=" O ALA D 22 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA D 27 " --> pdb=" O LEU D 23 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N HIS D 28 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU D 29 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY D 30 " --> pdb=" O ALA D 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 22 through 30' Processing helix chain 'D' and resid 51 through 68 removed outlier: 3.575A pdb=" N LEU D 60 " --> pdb=" O MET D 56 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ALA D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS D 68 " --> pdb=" O SER D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 94 Processing helix chain 'D' and resid 108 through 118 removed outlier: 3.576A pdb=" N HIS D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 123 removed outlier: 3.775A pdb=" N ARG D 122 " --> pdb=" O LEU D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 160 Processing helix chain 'D' and resid 204 through 208 removed outlier: 3.874A pdb=" N ARG D 208 " --> pdb=" O LEU D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 229 removed outlier: 3.657A pdb=" N LYS D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU D 226 " --> pdb=" O ASN D 222 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 254 removed outlier: 3.718A pdb=" N LEU D 251 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE D 253 " --> pdb=" O PRO D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 262 Processing helix chain 'D' and resid 262 through 276 removed outlier: 4.593A pdb=" N LYS D 268 " --> pdb=" O CYS D 264 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ILE D 271 " --> pdb=" O MET D 267 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA D 273 " --> pdb=" O GLN D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 304 removed outlier: 3.631A pdb=" N ASP D 285 " --> pdb=" O GLU D 281 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU D 286 " --> pdb=" O GLU D 282 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE D 287 " --> pdb=" O SER D 283 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG D 294 " --> pdb=" O GLY D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 removed outlier: 3.764A pdb=" N GLN D 310 " --> pdb=" O THR D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 334 removed outlier: 3.922A pdb=" N ARG D 332 " --> pdb=" O PHE D 328 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN D 333 " --> pdb=" O LYS D 329 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY D 334 " --> pdb=" O ALA D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 352 removed outlier: 3.591A pdb=" N GLY D 344 " --> pdb=" O LEU D 340 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N MET D 345 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG D 346 " --> pdb=" O ASP D 342 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU D 347 " --> pdb=" O ALA D 343 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP D 349 " --> pdb=" O MET D 345 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA D 350 " --> pdb=" O ARG D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 369 removed outlier: 4.006A pdb=" N VAL D 360 " --> pdb=" O ASN D 356 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER D 364 " --> pdb=" O VAL D 360 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA D 366 " --> pdb=" O VAL D 362 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL D 367 " --> pdb=" O SER D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 385 removed outlier: 3.734A pdb=" N TYR D 380 " --> pdb=" O TRP D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 400 removed outlier: 3.705A pdb=" N ILE D 394 " --> pdb=" O LEU D 390 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN D 398 " --> pdb=" O ILE D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 424 removed outlier: 3.949A pdb=" N GLN D 419 " --> pdb=" O ASN D 415 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY D 420 " --> pdb=" O PRO D 416 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA D 421 " --> pdb=" O ALA D 417 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 438 Processing helix chain 'D' and resid 452 through 459 removed outlier: 3.750A pdb=" N LEU D 456 " --> pdb=" O PRO D 452 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS D 457 " --> pdb=" O LEU D 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 6 Processing helix chain 'F' and resid 2 through 6 Processing sheet with id=AA1, first strand: chain 'C' and resid 98 through 101 removed outlier: 6.573A pdb=" N VAL C 98 " --> pdb=" O GLN C 127 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N TYR C 129 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N PHE C 100 " --> pdb=" O TYR C 129 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 36 through 38 Processing sheet with id=AA3, first strand: chain 'A' and resid 31 through 33 removed outlier: 4.057A pdb=" N PHE A 33 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL A 9 " --> pdb=" O PHE A 33 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 8 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A 99 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL A 98 " --> pdb=" O GLN A 127 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N TYR A 129 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N PHE A 100 " --> pdb=" O TYR A 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 35 through 38 Processing sheet with id=AA5, first strand: chain 'D' and resid 75 through 78 removed outlier: 8.930A pdb=" N THR D 75 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ILE D 77 " --> pdb=" O PRO D 34 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N PHE D 36 " --> pdb=" O ILE D 77 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR D 7 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE D 33 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL D 9 " --> pdb=" O PHE D 33 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ILE D 37 " --> pdb=" O PHE D 11 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS D 97 " --> pdb=" O LYS D 6 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ASN D 101 " --> pdb=" O TRP D 10 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N TYR D 129 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE D 100 " --> pdb=" O TYR D 129 " (cutoff:3.500A) 470 hydrogen bonds defined for protein. 1314 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: 3.62 Time building geometry restraints manager: 6.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4793 1.34 - 1.46: 3786 1.46 - 1.58: 7031 1.58 - 1.69: 5 1.69 - 1.81: 96 Bond restraints: 15711 Sorted by residual: bond pdb=" O5B FAD A 701 " pdb=" PA FAD A 701 " ideal model delta sigma weight residual 1.634 1.516 0.118 2.00e-02 2.50e+03 3.51e+01 bond pdb=" O3P FAD A 701 " pdb=" P FAD A 701 " ideal model delta sigma weight residual 1.660 1.558 0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" O3P FAD D 701 " pdb=" P FAD D 701 " ideal model delta sigma weight residual 1.660 1.561 0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" O5B FAD B 701 " pdb=" PA FAD B 701 " ideal model delta sigma weight residual 1.634 1.543 0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" O5B FAD D 701 " pdb=" PA FAD D 701 " ideal model delta sigma weight residual 1.634 1.545 0.089 2.00e-02 2.50e+03 1.96e+01 ... (remaining 15706 not shown) Histogram of bond angle deviations from ideal: 99.98 - 106.80: 599 106.80 - 113.62: 8708 113.62 - 120.44: 6258 120.44 - 127.26: 5522 127.26 - 134.08: 314 Bond angle restraints: 21401 Sorted by residual: angle pdb=" C ASN B 303 " pdb=" N PHE B 304 " pdb=" CA PHE B 304 " ideal model delta sigma weight residual 120.69 104.82 15.87 2.95e+00 1.15e-01 2.89e+01 angle pdb=" N VAL B 325 " pdb=" CA VAL B 325 " pdb=" C VAL B 325 " ideal model delta sigma weight residual 112.12 108.74 3.38 8.40e-01 1.42e+00 1.62e+01 angle pdb=" N ARG D 317 " pdb=" CA ARG D 317 " pdb=" C ARG D 317 " ideal model delta sigma weight residual 114.62 110.10 4.52 1.14e+00 7.69e-01 1.57e+01 angle pdb=" C ASN B 81 " pdb=" N THR B 82 " pdb=" CA THR B 82 " ideal model delta sigma weight residual 120.82 126.31 -5.49 1.50e+00 4.44e-01 1.34e+01 angle pdb=" C ASP A 414 " pdb=" N ASN A 415 " pdb=" CA ASN A 415 " ideal model delta sigma weight residual 121.27 132.96 -11.69 3.40e+00 8.65e-02 1.18e+01 ... (remaining 21396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.61: 9075 34.61 - 69.22: 177 69.22 - 103.83: 21 103.83 - 138.44: 2 138.44 - 173.05: 2 Dihedral angle restraints: 9277 sinusoidal: 3864 harmonic: 5413 Sorted by residual: dihedral pdb=" CA ALA C 183 " pdb=" C ALA C 183 " pdb=" N ILE C 184 " pdb=" CA ILE C 184 " ideal model delta harmonic sigma weight residual -180.00 -138.62 -41.38 0 5.00e+00 4.00e-02 6.85e+01 dihedral pdb=" CA LEU A 312 " pdb=" C LEU A 312 " pdb=" N LEU A 313 " pdb=" CA LEU A 313 " ideal model delta harmonic sigma weight residual 180.00 -144.54 -35.46 0 5.00e+00 4.00e-02 5.03e+01 dihedral pdb=" O5' FAD D 701 " pdb=" O3P FAD D 701 " pdb=" P FAD D 701 " pdb=" PA FAD D 701 " ideal model delta sinusoidal sigma weight residual -61.77 111.28 -173.05 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 9274 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1744 0.053 - 0.107: 454 0.107 - 0.160: 56 0.160 - 0.214: 3 0.214 - 0.267: 2 Chirality restraints: 2259 Sorted by residual: chirality pdb=" CA UNK E 1 " pdb=" N UNK E 1 " pdb=" C UNK E 1 " pdb=" CB UNK E 1 " both_signs ideal model delta sigma weight residual False 2.52 2.25 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA UNK F 1 " pdb=" N UNK F 1 " pdb=" C UNK F 1 " pdb=" CB UNK F 1 " both_signs ideal model delta sigma weight residual False 2.52 2.26 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" C2B FAD A 701 " pdb=" C1B FAD A 701 " pdb=" C3B FAD A 701 " pdb=" O2B FAD A 701 " both_signs ideal model delta sigma weight residual False -2.53 -2.71 0.18 2.00e-01 2.50e+01 8.08e-01 ... (remaining 2256 not shown) Planarity restraints: 2662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 105 " -0.036 5.00e-02 4.00e+02 5.38e-02 4.62e+00 pdb=" N PRO D 106 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 106 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 106 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 338 " 0.029 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO B 339 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 339 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 339 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 138 " 0.011 2.00e-02 2.50e+03 1.03e-02 2.66e+00 pdb=" CG TRP B 138 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP B 138 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP B 138 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 138 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 138 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 138 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 138 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 138 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 138 " -0.006 2.00e-02 2.50e+03 ... (remaining 2659 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 275 2.62 - 3.19: 15570 3.19 - 3.76: 22308 3.76 - 4.33: 31504 4.33 - 4.90: 48238 Nonbonded interactions: 117895 Sorted by model distance: nonbonded pdb=" O ASN B 235 " pdb=" OG SER B 243 " model vdw 2.049 3.040 nonbonded pdb=" OG1 THR B 244 " pdb=" O2A FAD B 701 " model vdw 2.070 3.040 nonbonded pdb=" O ARG C 111 " pdb=" OG1 THR C 114 " model vdw 2.077 3.040 nonbonded pdb=" OG SER A 31 " pdb=" O MET A 175 " model vdw 2.093 3.040 nonbonded pdb=" O THR D 149 " pdb=" OH TYR D 296 " model vdw 2.093 3.040 ... (remaining 117890 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 177 or resid 181 through 401 or resid 415 throug \ h 475 or resid 701)) selection = (chain 'B' and (resid 5 through 177 or resid 181 through 475 or resid 701)) selection = (chain 'C' and (resid 5 through 401 or resid 415 through 475 or resid 701)) selection = (chain 'D' and (resid 5 through 177 or resid 181 through 401 or resid 415 throug \ h 475 or resid 701)) } ncs_group { reference = chain 'E' selection = chain 'F' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 39.300 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.060 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 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 : 0.006 0.118 15711 Z= 0.386 Angle : 0.751 15.867 21401 Z= 0.394 Chirality : 0.046 0.267 2259 Planarity : 0.004 0.054 2662 Dihedral : 15.126 173.047 5771 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 29.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 0.06 % Allowed : 5.34 % Favored : 94.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -4.73 (0.17), residues: 1820 helix: -3.44 (0.12), residues: 767 sheet: -3.49 (0.37), residues: 122 loop : -2.79 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 138 HIS 0.008 0.001 HIS B 102 PHE 0.025 0.002 PHE C 306 TYR 0.018 0.002 TYR A 47 ARG 0.003 0.000 ARG A 266 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 167 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 429 TYR cc_start: 0.8818 (t80) cc_final: 0.8469 (t80) REVERT: A 14 ASP cc_start: 0.7562 (p0) cc_final: 0.6821 (p0) REVERT: A 57 LYS cc_start: 0.9270 (tppp) cc_final: 0.8876 (tptm) REVERT: A 220 LEU cc_start: 0.9213 (tp) cc_final: 0.8913 (tt) REVERT: A 345 MET cc_start: 0.9263 (mmm) cc_final: 0.9062 (mmt) REVERT: D 56 MET cc_start: 0.8555 (mtt) cc_final: 0.8354 (mtm) REVERT: D 134 LEU cc_start: 0.8894 (mt) cc_final: 0.8661 (mp) REVERT: D 347 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7895 (tm-30) REVERT: D 426 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7889 (tp30) outliers start: 1 outliers final: 1 residues processed: 168 average time/residue: 0.2861 time to fit residues: 69.7481 Evaluate side-chains 112 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 30.0000 chunk 138 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 143 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 166 optimal weight: 6.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 HIS C 196 ASN C 242 ASN C 252 HIS C 260 HIS C 466 ASN ** B 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 HIS B 419 GLN A 28 HIS D 196 ASN D 216 ASN D 252 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 15711 Z= 0.300 Angle : 0.691 7.999 21401 Z= 0.350 Chirality : 0.046 0.158 2259 Planarity : 0.005 0.048 2662 Dihedral : 11.513 162.817 2193 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 1.13 % Allowed : 11.74 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.18), residues: 1820 helix: -1.73 (0.16), residues: 847 sheet: -2.87 (0.38), residues: 125 loop : -2.44 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 172 HIS 0.005 0.001 HIS B 308 PHE 0.036 0.002 PHE C 306 TYR 0.021 0.002 TYR C 135 ARG 0.006 0.001 ARG D 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 146 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 161 MET cc_start: 0.8980 (tpp) cc_final: 0.8733 (tpp) REVERT: C 227 LYS cc_start: 0.9184 (mmmm) cc_final: 0.8888 (mmmm) REVERT: C 244 THR cc_start: 0.8972 (OUTLIER) cc_final: 0.8717 (m) REVERT: C 378 MET cc_start: 0.8018 (ttt) cc_final: 0.7745 (mtm) REVERT: C 429 TYR cc_start: 0.8608 (t80) cc_final: 0.8330 (t80) REVERT: B 132 ASP cc_start: 0.7433 (t0) cc_final: 0.7217 (t0) REVERT: B 133 LEU cc_start: 0.9278 (mp) cc_final: 0.8887 (mt) REVERT: B 172 TRP cc_start: 0.6983 (t60) cc_final: 0.6679 (t60) REVERT: B 354 MET cc_start: 0.8995 (mtp) cc_final: 0.8733 (mtp) REVERT: A 14 ASP cc_start: 0.7651 (p0) cc_final: 0.6902 (p0) REVERT: A 220 LEU cc_start: 0.9229 (tp) cc_final: 0.8905 (tt) REVERT: A 221 LEU cc_start: 0.9215 (tp) cc_final: 0.8922 (tp) REVERT: A 345 MET cc_start: 0.8935 (mmm) cc_final: 0.8652 (mmt) REVERT: A 445 ILE cc_start: 0.8908 (tt) cc_final: 0.8662 (tp) REVERT: D 167 MET cc_start: 0.7564 (ttm) cc_final: 0.7363 (ttm) REVERT: D 312 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8280 (mm) REVERT: D 347 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7791 (tm-30) REVERT: D 426 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7878 (tp30) REVERT: D 429 TYR cc_start: 0.9049 (t80) cc_final: 0.8793 (t80) outliers start: 18 outliers final: 9 residues processed: 159 average time/residue: 0.2650 time to fit residues: 63.4349 Evaluate side-chains 133 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 122 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 361 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 138 optimal weight: 9.9990 chunk 113 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 166 optimal weight: 0.9980 chunk 179 optimal weight: 7.9990 chunk 148 optimal weight: 9.9990 chunk 165 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 133 optimal weight: 0.6980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 466 ASN ** B 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 GLN A 419 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15711 Z= 0.179 Angle : 0.597 11.574 21401 Z= 0.298 Chirality : 0.043 0.149 2259 Planarity : 0.004 0.046 2662 Dihedral : 10.737 157.607 2191 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 1.88 % Allowed : 13.56 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.57 (0.19), residues: 1820 helix: -1.06 (0.17), residues: 855 sheet: -2.39 (0.40), residues: 125 loop : -2.23 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 172 HIS 0.005 0.001 HIS B 113 PHE 0.028 0.001 PHE C 306 TYR 0.019 0.001 TYR C 154 ARG 0.004 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 146 time to evaluate : 1.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 161 MET cc_start: 0.8895 (tpp) cc_final: 0.8669 (tpp) REVERT: C 227 LYS cc_start: 0.9211 (mmmm) cc_final: 0.8650 (mmmm) REVERT: C 244 THR cc_start: 0.8911 (OUTLIER) cc_final: 0.8637 (m) REVERT: C 429 TYR cc_start: 0.8554 (t80) cc_final: 0.8274 (t80) REVERT: B 132 ASP cc_start: 0.7527 (t0) cc_final: 0.7315 (t0) REVERT: B 133 LEU cc_start: 0.9285 (mp) cc_final: 0.8677 (mt) REVERT: B 172 TRP cc_start: 0.7074 (t60) cc_final: 0.6426 (t60) REVERT: B 354 MET cc_start: 0.8914 (mtp) cc_final: 0.8537 (mtp) REVERT: A 14 ASP cc_start: 0.7606 (p0) cc_final: 0.6954 (p0) REVERT: D 312 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8185 (mm) REVERT: D 346 ARG cc_start: 0.8459 (mtp85) cc_final: 0.8220 (mtp85) REVERT: D 347 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7743 (tm-30) REVERT: D 426 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7853 (tp30) REVERT: D 429 TYR cc_start: 0.9049 (t80) cc_final: 0.8804 (t80) outliers start: 30 outliers final: 17 residues processed: 167 average time/residue: 0.2900 time to fit residues: 74.3774 Evaluate side-chains 137 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 381 PHE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 187 CYS Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 312 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 164 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 167 optimal weight: 0.0060 chunk 176 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 158 optimal weight: 0.7980 chunk 47 optimal weight: 10.0000 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 HIS C 466 ASN ** B 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 GLN A 419 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15711 Z= 0.135 Angle : 0.564 11.221 21401 Z= 0.277 Chirality : 0.042 0.144 2259 Planarity : 0.003 0.043 2662 Dihedral : 10.161 149.078 2191 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.82 % Allowed : 14.38 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.20), residues: 1820 helix: -0.55 (0.18), residues: 844 sheet: -2.01 (0.41), residues: 125 loop : -1.87 (0.22), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 321 HIS 0.004 0.001 HIS B 113 PHE 0.026 0.001 PHE C 306 TYR 0.014 0.001 TYR C 154 ARG 0.003 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3640 Ramachandran restraints generated. 1820 Oldfield, 0 Emsley, 1820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 146 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 161 MET cc_start: 0.8853 (tpp) cc_final: 0.8618 (tpp) REVERT: C 244 THR cc_start: 0.8883 (OUTLIER) cc_final: 0.8639 (m) REVERT: C 321 TRP cc_start: 0.6018 (OUTLIER) cc_final: 0.3779 (m-90) REVERT: C 426 GLU cc_start: 0.7402 (tp30) cc_final: 0.7148 (tm-30) REVERT: C 429 TYR cc_start: 0.8413 (t80) cc_final: 0.8014 (t80) REVERT: B 132 ASP cc_start: 0.7614 (t0) cc_final: 0.7381 (t0) REVERT: B 133 LEU cc_start: 0.9220 (mp) cc_final: 0.8653 (mt) REVERT: B 172 TRP cc_start: 0.7057 (t60) cc_final: 0.6564 (t60) REVERT: A 14 ASP cc_start: 0.7410 (p0) cc_final: 0.6962 (p0) REVERT: A 242 ASN cc_start: 0.7891 (p0) cc_final: 0.7648 (p0) REVERT: D 14 ASP cc_start: 0.7922 (p0) cc_final: 0.7596 (p0) REVERT: D 267 MET cc_start: 0.6372 (ptt) cc_final: 0.5743 (ptp) REVERT: D 312 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8311 (mm) REVERT: D 346 ARG cc_start: 0.8387 (mtp85) cc_final: 0.8047 (mtp85) REVERT: D 347 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7566 (tm-30) REVERT: D 426 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7830 (tp30) REVERT: D 429 TYR cc_start: 0.8955 (t80) cc_final: 0.8726 (t80) outliers start: 45 outliers final: 22 residues processed: 181 average time/residue: 0.2491 time to fit residues: 69.0252 Evaluate side-chains 150 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 125 time to evaluate : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 321 TRP Chi-restraints excluded: chain C residue 381 PHE Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 127 GLN Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 419 GLN Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.7055 > 50: distance: 28 - 29: 4.430 distance: 28 - 31: 4.483 distance: 29 - 30: 18.040 distance: 29 - 33: 3.514 distance: 33 - 34: 3.486 distance: 34 - 35: 12.720 distance: 34 - 37: 10.084 distance: 35 - 36: 4.683 distance: 35 - 43: 10.888 distance: 37 - 38: 9.241 distance: 38 - 39: 11.988 distance: 38 - 40: 10.506 distance: 39 - 41: 5.774 distance: 40 - 42: 12.330 distance: 41 - 42: 15.038 distance: 43 - 44: 3.148 distance: 44 - 45: 7.279 distance: 44 - 47: 6.623 distance: 45 - 46: 10.337 distance: 45 - 51: 7.908 distance: 47 - 48: 3.963 distance: 48 - 49: 12.686 distance: 48 - 50: 23.430 distance: 52 - 55: 3.168 distance: 53 - 54: 8.357 distance: 53 - 62: 5.812 distance: 55 - 56: 3.891 distance: 56 - 57: 8.568 distance: 59 - 60: 3.564 distance: 62 - 63: 6.035 distance: 63 - 64: 5.099 distance: 63 - 66: 4.925 distance: 64 - 65: 11.574 distance: 66 - 67: 3.340 distance: 67 - 68: 5.451 distance: 68 - 70: 4.463 distance: 69 - 71: 5.775 distance: 71 - 72: 4.536 distance: 73 - 74: 8.042 distance: 74 - 75: 8.948 distance: 74 - 77: 8.734 distance: 75 - 76: 14.486 distance: 75 - 84: 12.555 distance: 77 - 78: 4.302 distance: 78 - 79: 10.126 distance: 78 - 80: 6.866 distance: 80 - 82: 5.750 distance: 81 - 83: 10.678 distance: 82 - 83: 7.751 distance: 84 - 85: 4.567 distance: 84 - 90: 4.162 distance: 85 - 86: 8.061 distance: 85 - 88: 5.054 distance: 86 - 87: 21.403 distance: 86 - 91: 16.124 distance: 88 - 89: 11.614 distance: 89 - 90: 9.029 distance: 91 - 92: 7.551 distance: 92 - 93: 13.273 distance: 92 - 95: 14.709 distance: 93 - 94: 26.854 distance: 93 - 105: 4.967 distance: 95 - 96: 8.139 distance: 96 - 97: 9.346 distance: 96 - 98: 14.738 distance: 97 - 99: 10.958 distance: 98 - 100: 13.115 distance: 98 - 101: 4.574 distance: 99 - 100: 6.694 distance: 100 - 102: 11.118 distance: 101 - 103: 12.037 distance: 102 - 104: 4.041 distance: 103 - 104: 8.494 distance: 106 - 107: 4.505 distance: 106 - 109: 4.117 distance: 107 - 108: 4.604 distance: 107 - 113: 3.292 distance: 109 - 110: 10.951 distance: 110 - 111: 8.538 distance: 110 - 112: 9.564 distance: 113 - 114: 5.900 distance: 114 - 115: 4.144 distance: 114 - 117: 6.527 distance: 115 - 118: 4.214