Starting phenix.real_space_refine on Thu Mar 21 05:12:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0y_32929/03_2024/7x0y_32929_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0y_32929/03_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_32929/03_2024/7x0y_32929.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0y_32929/03_2024/7x0y_32929.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0y_32929/03_2024/7x0y_32929_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x0y_32929/03_2024/7x0y_32929_trim_updated.pdb" } 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-5265/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: 8.11, per 1000 atoms: 0.53 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: 5.91 Conformation dependent library (CDL) restraints added in 2.3 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... running ksdssp... Secondary structure from input PDB file: 93 helices and 5 sheets defined 47.6% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.94 Creating SS restraints... Processing helix chain 'C' and resid 24 through 27 No H-bonds generated for 'chain 'C' and resid 24 through 27' Processing helix chain 'C' and resid 50 through 70 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) removed outlier: 4.426A pdb=" N ALA C 69 " --> pdb=" O GLN C 65 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU C 70 " --> pdb=" O SER C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 93 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 106 through 122 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 151 through 160 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 198 through 203 Proline residue: C 201 - end of helix No H-bonds generated for 'chain 'C' and resid 198 through 203' Processing helix chain 'C' and resid 205 through 208 Processing helix chain 'C' and resid 214 through 227 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 229 through 235 removed outlier: 4.351A pdb=" N ALA C 233 " --> pdb=" O ILE C 230 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN C 235 " --> pdb=" O TYR C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 252 Processing helix chain 'C' and resid 258 through 274 Processing helix chain 'C' and resid 278 through 303 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 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 326 through 333 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) removed outlier: 3.906A pdb=" N GLN C 333 " --> pdb=" O LYS C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 351 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 356 through 368 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 374 through 384 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 390 through 400 removed outlier: 4.699A pdb=" N LEU C 395 " --> pdb=" O GLU C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 433 Processing helix chain 'C' and resid 435 through 437 No H-bonds generated for 'chain 'C' and resid 435 through 437' Processing helix chain 'C' and resid 448 through 450 No H-bonds generated for 'chain 'C' and resid 448 through 450' Processing helix chain 'C' and resid 453 through 457 removed outlier: 4.491A pdb=" N LYS C 457 " --> pdb=" O THR C 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 27 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) Processing helix chain 'B' and resid 50 through 69 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) Processing helix chain 'B' and resid 82 through 92 removed outlier: 4.001A pdb=" N ARG B 91 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL B 92 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 120 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 151 through 160 removed outlier: 4.520A pdb=" N ASP B 160 " --> pdb=" O LYS B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 184 No H-bonds generated for 'chain 'B' and resid 182 through 184' Processing helix chain 'B' and resid 197 through 208 Proline residue: B 201 - end of helix removed outlier: 4.122A pdb=" N LEU B 205 " --> pdb=" O PRO B 201 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LEU B 206 " --> pdb=" O SER B 202 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N THR B 207 " --> pdb=" O ASN B 203 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ARG B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 225 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 229 through 234 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 248 through 252 Processing helix chain 'B' and resid 258 through 263 Processing helix chain 'B' and resid 267 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 278 through 284 Processing helix chain 'B' and resid 288 through 301 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 326 through 331 Processing helix chain 'B' and resid 341 through 351 removed outlier: 3.809A pdb=" N GLU B 347 " --> pdb=" O ALA B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 368 removed outlier: 4.294A pdb=" N SER B 363 " --> pdb=" O ARG B 359 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER B 364 " --> pdb=" O VAL B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 384 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 391 through 400 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) removed outlier: 4.443A pdb=" N ILE B 400 " --> pdb=" O GLY B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 4.143A pdb=" N LYS B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 433 No H-bonds generated for 'chain 'B' and resid 430 through 433' Processing helix chain 'B' and resid 435 through 437 No H-bonds generated for 'chain 'B' and resid 435 through 437' Processing helix chain 'B' and resid 442 through 445 No H-bonds generated for 'chain 'B' and resid 442 through 445' Processing helix chain 'B' and resid 448 through 450 No H-bonds generated for 'chain 'B' and resid 448 through 450' Processing helix chain 'B' and resid 453 through 458 removed outlier: 3.522A pdb=" N LYS B 457 " --> pdb=" O LEU B 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 29 removed outlier: 3.901A pdb=" N ALA A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 50 through 70 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) removed outlier: 4.191A pdb=" N LEU A 70 " --> pdb=" O SER A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 92 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 108 through 122 removed outlier: 3.720A pdb=" N GLU A 117 " --> pdb=" O HIS A 113 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N GLU A 121 " --> pdb=" O GLU A 117 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ARG A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 159 removed outlier: 3.907A pdb=" N LYS A 156 " --> pdb=" O ASN A 152 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LYS A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 208 removed outlier: 3.665A pdb=" N ALA A 204 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N LEU A 205 " --> pdb=" O PRO A 201 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LEU A 206 " --> pdb=" O SER A 202 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N THR A 207 " --> pdb=" O ASN A 203 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ARG A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 200 through 208' Processing helix chain 'A' and resid 214 through 235 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) removed outlier: 6.750A pdb=" N ILE A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ASP A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ALA A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LYS A 234 " --> pdb=" O ILE A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 253 Processing helix chain 'A' and resid 258 through 275 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 278 through 303 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 306 through 309 Processing helix chain 'A' and resid 325 through 331 Processing helix chain 'A' and resid 339 through 351 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 356 through 365 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) Processing helix chain 'A' and resid 374 through 384 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 391 through 399 removed outlier: 3.631A pdb=" N LEU A 395 " --> pdb=" O GLU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 423 removed outlier: 4.938A pdb=" N ALA A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 433 removed outlier: 3.621A pdb=" N TRP A 433 " --> pdb=" O TYR A 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 429 through 433' Processing helix chain 'A' and resid 442 through 450 removed outlier: 4.517A pdb=" N HIS A 446 " --> pdb=" O THR A 442 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N HIS A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Proline residue: A 448 - end of helix No H-bonds generated for 'chain 'A' and resid 442 through 450' Processing helix chain 'A' and resid 453 through 456 No H-bonds generated for 'chain 'A' and resid 453 through 456' Processing helix chain 'D' and resid 23 through 29 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) No H-bonds generated for 'chain 'D' and resid 23 through 29' Processing helix chain 'D' and resid 52 through 67 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) Processing helix chain 'D' and resid 82 through 93 Processing helix chain 'D' and resid 109 through 117 removed outlier: 3.576A pdb=" N HIS D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 122 No H-bonds generated for 'chain 'D' and resid 120 through 122' Processing helix chain 'D' and resid 151 through 160 Processing helix chain 'D' and resid 197 through 199 No H-bonds generated for 'chain 'D' and resid 197 through 199' Processing helix chain 'D' and resid 205 through 207 No H-bonds generated for 'chain 'D' and resid 205 through 207' Processing helix chain 'D' and resid 214 through 228 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 248 through 253 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) No H-bonds generated for 'chain 'D' and resid 248 through 253' Processing helix chain 'D' and resid 258 through 261 No H-bonds generated for 'chain 'D' and resid 258 through 261' Processing helix chain 'D' and resid 263 through 275 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 278 through 303 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 306 through 309 Processing helix chain 'D' and resid 326 through 333 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) Processing helix chain 'D' and resid 339 through 351 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 356 through 368 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 374 through 384 removed outlier: 3.734A pdb=" N TYR D 380 " --> pdb=" O TRP D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 399 removed outlier: 3.639A pdb=" N GLN D 398 " --> pdb=" O ILE D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 423 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 430 through 433 No H-bonds generated for 'chain 'D' and resid 430 through 433' Processing helix chain 'D' and resid 435 through 437 No H-bonds generated for 'chain 'D' and resid 435 through 437' Processing helix chain 'D' and resid 453 through 458 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 5 No H-bonds generated for 'chain 'E' and resid 2 through 5' Processing helix chain 'F' and resid 2 through 5 No H-bonds generated for 'chain 'F' and resid 2 through 5' Processing sheet with id= A, first strand: chain 'C' and resid 98 through 101 removed outlier: 4.292A pdb=" N GLN C 127 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE C 100 " --> pdb=" O GLN C 127 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 36 through 38 Processing sheet with id= C, 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: 7.332A pdb=" N LYS A 97 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N SER A 125 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 9.067A pdb=" N PHE A 100 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N GLN A 127 " --> pdb=" O PHE A 100 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 35 through 38 removed outlier: 6.718A pdb=" N THR A 75 " --> pdb=" O PHE A 36 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N TRP A 38 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE A 77 " --> pdb=" O TRP A 38 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'D' and resid 97 through 99 removed outlier: 4.144A pdb=" N LYS D 97 " --> pdb=" O LYS D 6 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N SER D 31 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N VAL D 9 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE D 33 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N PHE D 11 " --> pdb=" O PHE D 33 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL D 35 " --> pdb=" O PHE D 11 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR D 75 " --> pdb=" O PHE D 36 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N TRP D 38 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE D 77 " --> pdb=" O TRP D 38 " (cutoff:3.500A) 347 hydrogen bonds defined for protein. 1020 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: 3.51 Time building geometry restraints manager: 6.36 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: 285 2.62 - 3.19: 15652 3.19 - 3.76: 22442 3.76 - 4.33: 31727 4.33 - 4.90: 48281 Nonbonded interactions: 118387 Sorted by model distance: nonbonded pdb=" O ASN B 235 " pdb=" OG SER B 243 " model vdw 2.049 2.440 nonbonded pdb=" OG1 THR B 244 " pdb=" O2A FAD B 701 " model vdw 2.070 2.440 nonbonded pdb=" O ARG C 111 " pdb=" OG1 THR C 114 " model vdw 2.077 2.440 nonbonded pdb=" OG SER A 31 " pdb=" O MET A 175 " model vdw 2.093 2.440 nonbonded pdb=" O THR D 149 " pdb=" OH TYR D 296 " model vdw 2.093 2.440 ... (remaining 118382 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' 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.010 Extract box with map and model: 3.690 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 39.840 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.910 ------------------------------------------------------------------------------- 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= 0.392 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 : 1.835 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: 0.2971 time to fit residues: 72.3547 Evaluate side-chains 112 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 1.827 ------------------------------------------------------------------------------- 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: 6.9990 chunk 76 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 74 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 166 optimal weight: 7.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 B 446 HIS A 62 HIS A 252 HIS D 196 ASN D 216 ASN D 252 HIS D 446 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 15711 Z= 0.388 Angle : 0.727 10.251 21401 Z= 0.365 Chirality : 0.047 0.160 2259 Planarity : 0.005 0.057 2662 Dihedral : 11.657 161.261 2193 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.56 % Favored : 90.38 % Rotamer: Outliers : 1.44 % Allowed : 12.49 % Favored : 86.06 % 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: -3.65 (0.18), residues: 1820 helix: -2.08 (0.15), residues: 846 sheet: -3.15 (0.38), residues: 129 loop : -2.60 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 172 HIS 0.006 0.002 HIS B 308 PHE 0.024 0.002 PHE C 306 TYR 0.024 0.002 TYR A 47 ARG 0.007 0.001 ARG C 266 *********************** 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 160 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 137 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 161 MET cc_start: 0.9089 (tpp) cc_final: 0.8810 (tpp) REVERT: C 221 LEU cc_start: 0.9430 (tp) cc_final: 0.9212 (tp) REVERT: C 429 TYR cc_start: 0.8693 (t80) cc_final: 0.8429 (t80) REVERT: B 37 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8751 (tt) REVERT: B 132 ASP cc_start: 0.7316 (t0) cc_final: 0.7008 (t0) REVERT: B 172 TRP cc_start: 0.6973 (t60) cc_final: 0.6584 (t60) REVERT: B 354 MET cc_start: 0.9014 (mtp) cc_final: 0.8743 (mtp) REVERT: A 14 ASP cc_start: 0.7824 (p0) cc_final: 0.7055 (p0) REVERT: A 345 MET cc_start: 0.9022 (mmm) cc_final: 0.8798 (mmt) REVERT: D 56 MET cc_start: 0.8443 (mtt) cc_final: 0.8207 (mtm) REVERT: D 312 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8148 (mm) REVERT: D 346 ARG cc_start: 0.8475 (mtp85) cc_final: 0.8247 (mtp180) REVERT: D 426 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7986 (tp30) outliers start: 23 outliers final: 11 residues processed: 155 average time/residue: 0.2774 time to fit residues: 66.5595 Evaluate side-chains 127 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain D residue 23 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 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: 0.5980 chunk 51 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 166 optimal weight: 5.9990 chunk 179 optimal weight: 0.8980 chunk 148 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 133 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 HIS C 432 GLN C 466 ASN ** B 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 GLN A 419 GLN D 101 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15711 Z= 0.149 Angle : 0.571 12.304 21401 Z= 0.282 Chirality : 0.042 0.136 2259 Planarity : 0.004 0.044 2662 Dihedral : 10.673 156.566 2193 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.32 % Allowed : 15.13 % Favored : 83.55 % 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: -0.98 (0.18), residues: 840 sheet: -2.56 (0.40), residues: 125 loop : -2.29 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 172 HIS 0.004 0.001 HIS B 260 PHE 0.017 0.001 PHE C 306 TYR 0.015 0.001 TYR C 135 ARG 0.005 0.000 ARG C 266 *********************** 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: 21 poor density : 155 time to evaluate : 1.763 Fit side-chains revert: symmetry clash REVERT: C 161 MET cc_start: 0.9048 (tpp) cc_final: 0.8632 (tpp) REVERT: C 227 LYS cc_start: 0.9166 (mmmm) cc_final: 0.8589 (mmmm) REVERT: C 244 THR cc_start: 0.8913 (OUTLIER) cc_final: 0.8584 (m) REVERT: C 429 TYR cc_start: 0.8655 (t80) cc_final: 0.8376 (t80) REVERT: B 172 TRP cc_start: 0.7101 (t60) cc_final: 0.6401 (t60) REVERT: B 354 MET cc_start: 0.8852 (mtp) cc_final: 0.8524 (mtp) REVERT: A 14 ASP cc_start: 0.7551 (p0) cc_final: 0.6754 (p0) REVERT: D 89 CYS cc_start: 0.6362 (m) cc_final: 0.5876 (m) REVERT: D 312 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8236 (mm) REVERT: D 346 ARG cc_start: 0.8219 (mtp85) cc_final: 0.8015 (mtp180) REVERT: D 426 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7990 (tp30) REVERT: D 429 TYR cc_start: 0.9041 (t80) cc_final: 0.8829 (t80) outliers start: 21 outliers final: 9 residues processed: 172 average time/residue: 0.2417 time to fit residues: 64.6823 Evaluate side-chains 137 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 126 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 187 CYS Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 336 THR 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: 9.9990 chunk 125 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 167 optimal weight: 6.9990 chunk 176 optimal weight: 0.3980 chunk 87 optimal weight: 0.9980 chunk 158 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 15711 Z= 0.281 Angle : 0.619 10.070 21401 Z= 0.308 Chirality : 0.044 0.149 2259 Planarity : 0.004 0.037 2662 Dihedral : 10.356 143.332 2193 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 3.01 % Allowed : 16.38 % Favored : 80.60 % 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: -2.38 (0.19), residues: 1820 helix: -0.81 (0.17), residues: 863 sheet: -2.45 (0.40), residues: 125 loop : -2.24 (0.22), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 138 HIS 0.004 0.001 HIS B 113 PHE 0.017 0.001 PHE C 306 TYR 0.018 0.002 TYR C 154 ARG 0.003 0.000 ARG C 91 *********************** 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 174 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 126 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 161 MET cc_start: 0.9072 (tpp) cc_final: 0.8689 (tpp) REVERT: C 244 THR cc_start: 0.8988 (OUTLIER) cc_final: 0.8692 (m) REVERT: C 321 TRP cc_start: 0.6157 (OUTLIER) cc_final: 0.3986 (m-90) REVERT: B 172 TRP cc_start: 0.7091 (t60) cc_final: 0.6590 (t60) REVERT: B 208 ARG cc_start: 0.8967 (mtp-110) cc_final: 0.8746 (ptp-110) REVERT: A 14 ASP cc_start: 0.7708 (p0) cc_final: 0.6918 (p0) REVERT: A 345 MET cc_start: 0.8926 (mmm) cc_final: 0.8541 (mmt) REVERT: D 141 TYR cc_start: 0.7284 (OUTLIER) cc_final: 0.6878 (m-10) REVERT: D 167 MET cc_start: 0.7200 (ttt) cc_final: 0.6988 (tpp) REVERT: D 312 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8262 (mm) REVERT: D 426 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7978 (tp30) outliers start: 48 outliers final: 21 residues processed: 166 average time/residue: 0.2435 time to fit residues: 62.7206 Evaluate side-chains 145 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 120 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 17 ILE 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 321 TRP Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 336 THR 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 141 TYR 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 Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 147 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 131 optimal weight: 0.0770 chunk 72 optimal weight: 9.9990 chunk 150 optimal weight: 0.8980 chunk 122 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 90 optimal weight: 0.9990 chunk 158 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 overall best weight: 2.5944 ------------------------------------------------------------------------------- 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** ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 15711 Z= 0.226 Angle : 0.589 10.235 21401 Z= 0.291 Chirality : 0.043 0.146 2259 Planarity : 0.004 0.040 2662 Dihedral : 10.019 141.651 2193 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 3.20 % Allowed : 17.70 % Favored : 79.10 % 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: -2.05 (0.20), residues: 1820 helix: -0.49 (0.18), residues: 854 sheet: -2.25 (0.42), residues: 125 loop : -2.12 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 321 HIS 0.003 0.001 HIS B 308 PHE 0.015 0.001 PHE C 306 TYR 0.017 0.001 TYR C 154 ARG 0.008 0.000 ARG B 173 *********************** REFINEMENT MACRO_CYCLE 5 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 178 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 127 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 161 MET cc_start: 0.9076 (tpp) cc_final: 0.8658 (tpp) REVERT: C 244 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8674 (m) REVERT: C 267 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.7008 (ptt) REVERT: C 321 TRP cc_start: 0.6125 (OUTLIER) cc_final: 0.3871 (m-90) REVERT: B 172 TRP cc_start: 0.7204 (t60) cc_final: 0.6738 (t60) REVERT: B 208 ARG cc_start: 0.8949 (mtp-110) cc_final: 0.8726 (ptp-110) REVERT: B 345 MET cc_start: 0.7633 (mmm) cc_final: 0.7343 (mmm) REVERT: A 14 ASP cc_start: 0.7705 (p0) cc_final: 0.6887 (p0) REVERT: A 47 TYR cc_start: 0.9017 (OUTLIER) cc_final: 0.7644 (t80) REVERT: D 141 TYR cc_start: 0.7260 (OUTLIER) cc_final: 0.6790 (m-10) REVERT: D 167 MET cc_start: 0.7343 (ttt) cc_final: 0.6998 (tpp) REVERT: D 312 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8251 (mm) REVERT: D 346 ARG cc_start: 0.8268 (mtp180) cc_final: 0.8013 (mtp85) REVERT: D 426 GLU cc_start: 0.8252 (mm-30) cc_final: 0.8031 (tp30) outliers start: 51 outliers final: 30 residues processed: 164 average time/residue: 0.2465 time to fit residues: 62.4835 Evaluate side-chains 156 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 120 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 321 TRP 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 110 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 336 THR 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 73 ASP Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 141 TYR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 59 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 177 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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** ** A 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15711 Z= 0.240 Angle : 0.594 10.603 21401 Z= 0.292 Chirality : 0.043 0.149 2259 Planarity : 0.004 0.038 2662 Dihedral : 9.935 140.078 2193 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 3.33 % Allowed : 18.77 % Favored : 77.90 % 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: -1.84 (0.20), residues: 1820 helix: -0.34 (0.18), residues: 857 sheet: -2.07 (0.43), residues: 125 loop : -2.01 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 172 HIS 0.003 0.001 HIS B 308 PHE 0.014 0.001 PHE C 306 TYR 0.015 0.002 TYR A 299 ARG 0.005 0.000 ARG B 173 *********************** REFINEMENT MACRO_CYCLE 6 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 180 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 127 time to evaluate : 1.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 161 MET cc_start: 0.9042 (tpp) cc_final: 0.8742 (tpp) REVERT: C 244 THR cc_start: 0.8979 (OUTLIER) cc_final: 0.8699 (m) REVERT: C 321 TRP cc_start: 0.6084 (OUTLIER) cc_final: 0.3997 (m-90) REVERT: B 133 LEU cc_start: 0.9383 (mp) cc_final: 0.8776 (mt) REVERT: B 172 TRP cc_start: 0.7104 (t60) cc_final: 0.6564 (t60) REVERT: A 14 ASP cc_start: 0.7705 (p0) cc_final: 0.6892 (p0) REVERT: A 47 TYR cc_start: 0.9017 (OUTLIER) cc_final: 0.7686 (t80) REVERT: A 453 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.9007 (mm) REVERT: D 82 THR cc_start: 0.8498 (OUTLIER) cc_final: 0.8274 (t) REVERT: D 141 TYR cc_start: 0.7191 (OUTLIER) cc_final: 0.6856 (m-10) REVERT: D 167 MET cc_start: 0.7432 (ttt) cc_final: 0.7097 (tpp) REVERT: D 312 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8312 (mm) REVERT: D 426 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7975 (tp30) outliers start: 53 outliers final: 34 residues processed: 168 average time/residue: 0.2448 time to fit residues: 63.4583 Evaluate side-chains 160 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 119 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 321 TRP Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 466 ASN Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 336 THR 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 A residue 453 LEU Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 141 TYR Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 170 optimal weight: 10.0000 chunk 19 optimal weight: 0.2980 chunk 100 optimal weight: 0.9980 chunk 129 optimal weight: 0.6980 chunk 149 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 176 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15711 Z= 0.165 Angle : 0.565 11.033 21401 Z= 0.275 Chirality : 0.042 0.157 2259 Planarity : 0.003 0.039 2662 Dihedral : 9.666 138.615 2193 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.14 % Allowed : 19.59 % Favored : 77.28 % 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: -1.48 (0.20), residues: 1820 helix: -0.02 (0.19), residues: 852 sheet: -1.85 (0.44), residues: 125 loop : -1.85 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 172 HIS 0.003 0.001 HIS B 315 PHE 0.012 0.001 PHE C 306 TYR 0.015 0.001 TYR C 154 ARG 0.003 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 7 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 177 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 127 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 161 MET cc_start: 0.9068 (tpp) cc_final: 0.8767 (tpp) REVERT: C 244 THR cc_start: 0.8984 (OUTLIER) cc_final: 0.8708 (m) REVERT: C 321 TRP cc_start: 0.5921 (OUTLIER) cc_final: 0.3822 (m-90) REVERT: C 345 MET cc_start: 0.7738 (mmp) cc_final: 0.7366 (mmm) REVERT: B 133 LEU cc_start: 0.9313 (mp) cc_final: 0.8689 (mt) REVERT: B 172 TRP cc_start: 0.7069 (t60) cc_final: 0.6649 (t60) REVERT: B 387 ASP cc_start: 0.7584 (p0) cc_final: 0.7369 (p0) REVERT: A 14 ASP cc_start: 0.7618 (p0) cc_final: 0.6883 (p0) REVERT: D 141 TYR cc_start: 0.7163 (OUTLIER) cc_final: 0.6963 (m-10) REVERT: D 167 MET cc_start: 0.7377 (ttt) cc_final: 0.7017 (tpp) REVERT: D 312 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8337 (mm) REVERT: D 346 ARG cc_start: 0.8227 (mtp180) cc_final: 0.7903 (mtp85) REVERT: D 364 SER cc_start: 0.9335 (t) cc_final: 0.9079 (p) REVERT: D 426 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7976 (tp30) outliers start: 50 outliers final: 34 residues processed: 167 average time/residue: 0.2621 time to fit residues: 68.2275 Evaluate side-chains 158 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 120 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 28 HIS Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 321 TRP Chi-restraints excluded: chain C residue 466 ASN Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 315 HIS Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 141 TYR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 70 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 168 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 315 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15711 Z= 0.128 Angle : 0.551 11.940 21401 Z= 0.263 Chirality : 0.041 0.162 2259 Planarity : 0.003 0.034 2662 Dihedral : 9.373 135.864 2193 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 2.70 % Allowed : 19.96 % Favored : 77.34 % 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: -1.11 (0.21), residues: 1820 helix: 0.25 (0.19), residues: 855 sheet: -1.53 (0.43), residues: 139 loop : -1.64 (0.23), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 172 HIS 0.002 0.000 HIS B 315 PHE 0.010 0.001 PHE C 100 TYR 0.017 0.001 TYR C 467 ARG 0.006 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 8 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 185 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 142 time to evaluate : 2.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 161 MET cc_start: 0.9008 (tpp) cc_final: 0.8799 (tpp) REVERT: C 244 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8634 (m) REVERT: C 321 TRP cc_start: 0.5952 (OUTLIER) cc_final: 0.3657 (m-90) REVERT: C 345 MET cc_start: 0.7663 (mmp) cc_final: 0.7439 (mmp) REVERT: C 429 TYR cc_start: 0.8193 (t80) cc_final: 0.7982 (t80) REVERT: B 172 TRP cc_start: 0.7087 (t60) cc_final: 0.6613 (t60) REVERT: B 387 ASP cc_start: 0.7592 (p0) cc_final: 0.7350 (p0) REVERT: A 14 ASP cc_start: 0.7640 (p0) cc_final: 0.7067 (p0) REVERT: A 47 TYR cc_start: 0.8930 (OUTLIER) cc_final: 0.7472 (t80) REVERT: A 229 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8053 (tt) REVERT: A 453 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8977 (mm) REVERT: D 14 ASP cc_start: 0.7957 (p0) cc_final: 0.7688 (p0) REVERT: D 267 MET cc_start: 0.5941 (ptt) cc_final: 0.5527 (ptp) REVERT: D 364 SER cc_start: 0.9275 (t) cc_final: 0.9047 (p) REVERT: D 426 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7997 (tp30) outliers start: 43 outliers final: 20 residues processed: 176 average time/residue: 0.2397 time to fit residues: 65.7451 Evaluate side-chains 149 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 124 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 321 TRP Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 308 HIS Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 172 TRP Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 336 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 7.9990 chunk 164 optimal weight: 10.0000 chunk 168 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 50 optimal weight: 0.6980 chunk 148 optimal weight: 0.9990 chunk 155 optimal weight: 8.9990 chunk 163 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 ASN ** B 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15711 Z= 0.175 Angle : 0.582 12.024 21401 Z= 0.279 Chirality : 0.042 0.198 2259 Planarity : 0.003 0.051 2662 Dihedral : 9.344 136.119 2191 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.32 % Allowed : 21.16 % Favored : 76.52 % 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: -1.12 (0.21), residues: 1820 helix: 0.24 (0.19), residues: 862 sheet: -1.41 (0.43), residues: 139 loop : -1.68 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 172 HIS 0.002 0.001 HIS B 315 PHE 0.011 0.001 PHE C 253 TYR 0.014 0.001 TYR C 154 ARG 0.005 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 9 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 166 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 129 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 161 MET cc_start: 0.9019 (tpp) cc_final: 0.8818 (tpp) REVERT: C 244 THR cc_start: 0.8968 (OUTLIER) cc_final: 0.8706 (m) REVERT: C 321 TRP cc_start: 0.5911 (OUTLIER) cc_final: 0.3647 (m-90) REVERT: C 345 MET cc_start: 0.7778 (mmp) cc_final: 0.7347 (mmm) REVERT: B 132 ASP cc_start: 0.7365 (t0) cc_final: 0.7160 (t0) REVERT: B 133 LEU cc_start: 0.9345 (mp) cc_final: 0.8724 (mt) REVERT: B 172 TRP cc_start: 0.7078 (t60) cc_final: 0.6741 (t60) REVERT: B 387 ASP cc_start: 0.7577 (p0) cc_final: 0.7323 (p0) REVERT: A 14 ASP cc_start: 0.7687 (p0) cc_final: 0.7068 (p0) REVERT: A 47 TYR cc_start: 0.8943 (OUTLIER) cc_final: 0.7569 (t80) REVERT: A 453 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8994 (mm) REVERT: D 14 ASP cc_start: 0.7902 (p0) cc_final: 0.7641 (p0) REVERT: D 267 MET cc_start: 0.5946 (ptt) cc_final: 0.5511 (ptp) REVERT: D 312 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8339 (mm) REVERT: D 364 SER cc_start: 0.9281 (t) cc_final: 0.9075 (p) REVERT: D 426 GLU cc_start: 0.8289 (mm-30) cc_final: 0.8021 (tp30) outliers start: 37 outliers final: 25 residues processed: 157 average time/residue: 0.2294 time to fit residues: 56.7104 Evaluate side-chains 158 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 128 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 321 TRP Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 308 HIS Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 173 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 182 optimal weight: 9.9990 chunk 167 optimal weight: 7.9990 chunk 145 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 ASN ** B 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15711 Z= 0.188 Angle : 0.596 12.130 21401 Z= 0.285 Chirality : 0.042 0.167 2259 Planarity : 0.003 0.052 2662 Dihedral : 9.382 137.222 2191 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 2.57 % Allowed : 21.09 % Favored : 76.33 % 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: -1.05 (0.21), residues: 1820 helix: 0.32 (0.19), residues: 851 sheet: -1.43 (0.43), residues: 139 loop : -1.63 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 172 HIS 0.003 0.001 HIS C 252 PHE 0.010 0.001 PHE C 306 TYR 0.015 0.001 TYR C 154 ARG 0.004 0.000 ARG C 13 ********************** REFINEMENT MACRO_CYCLE 10 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 170 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 129 time to evaluate : 1.870 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 244 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8711 (m) REVERT: C 267 MET cc_start: 0.6718 (ptt) cc_final: 0.6418 (ptp) REVERT: C 321 TRP cc_start: 0.5866 (OUTLIER) cc_final: 0.3598 (m-90) REVERT: C 345 MET cc_start: 0.7809 (mmp) cc_final: 0.7384 (mmm) REVERT: B 73 ASP cc_start: 0.8002 (m-30) cc_final: 0.7667 (m-30) REVERT: B 133 LEU cc_start: 0.9350 (mp) cc_final: 0.8741 (mt) REVERT: B 172 TRP cc_start: 0.7085 (t60) cc_final: 0.6715 (t60) REVERT: B 387 ASP cc_start: 0.7561 (p0) cc_final: 0.7302 (p0) REVERT: A 14 ASP cc_start: 0.7641 (p0) cc_final: 0.7002 (p0) REVERT: A 47 TYR cc_start: 0.8877 (OUTLIER) cc_final: 0.7561 (t80) REVERT: A 453 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8995 (mm) REVERT: D 14 ASP cc_start: 0.7763 (p0) cc_final: 0.7485 (p0) REVERT: D 267 MET cc_start: 0.5964 (ptt) cc_final: 0.5496 (ptp) REVERT: D 312 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8342 (mm) REVERT: D 364 SER cc_start: 0.9277 (t) cc_final: 0.9071 (p) REVERT: D 378 MET cc_start: 0.8366 (tpp) cc_final: 0.7971 (tpp) REVERT: D 426 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8001 (tp30) outliers start: 41 outliers final: 31 residues processed: 161 average time/residue: 0.2265 time to fit residues: 56.9047 Evaluate side-chains 159 residues out of total 1593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 123 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 304 PHE Chi-restraints excluded: chain C residue 321 TRP Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 466 ASN Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 308 HIS Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 133 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 145 optimal weight: 0.9980 chunk 60 optimal weight: 8.9990 chunk 149 optimal weight: 7.9990 chunk 18 optimal weight: 0.0980 chunk 26 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 ASN ** B 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.090967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.075206 restraints weight = 50908.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.077739 restraints weight = 27329.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.079378 restraints weight = 17861.561| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15711 Z= 0.246 Angle : 0.640 11.857 21401 Z= 0.308 Chirality : 0.044 0.200 2259 Planarity : 0.004 0.048 2662 Dihedral : 9.585 138.770 2191 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 2.57 % Allowed : 21.16 % Favored : 76.27 % 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: -1.10 (0.21), residues: 1820 helix: 0.29 (0.19), residues: 848 sheet: -1.58 (0.45), residues: 123 loop : -1.64 (0.23), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 172 HIS 0.003 0.001 HIS C 252 PHE 0.012 0.001 PHE C 306 TYR 0.017 0.002 TYR C 104 ARG 0.003 0.000 ARG B 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2453.09 seconds wall clock time: 45 minutes 44.11 seconds (2744.11 seconds total)