Starting phenix.real_space_refine on Fri Feb 16 02:46:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ugd_20761/02_2024/6ugd_20761_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ugd_20761/02_2024/6ugd_20761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ugd_20761/02_2024/6ugd_20761.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ugd_20761/02_2024/6ugd_20761.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ugd_20761/02_2024/6ugd_20761_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ugd_20761/02_2024/6ugd_20761_neut_updated.pdb" } resolution = 3.5 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= 0.000 sd= 1.000 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 186 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: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 5 5.21 5 S 63 5.16 5 C 8800 2.51 5 N 2438 2.21 5 O 2604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 217": "OE1" <-> "OE2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 261": "OD1" <-> "OD2" Residue "A PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 292": "OD1" <-> "OD2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A ARG 406": "NH1" <-> "NH2" Residue "A ARG 414": "NH1" <-> "NH2" Residue "A TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 244": "NH1" <-> "NH2" Residue "B ARG 275": "NH1" <-> "NH2" Residue "B ASP 322": "OD1" <-> "OD2" Residue "B ARG 351": "NH1" <-> "NH2" Residue "B PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 367": "NH1" <-> "NH2" Residue "B GLU 372": "OE1" <-> "OE2" Residue "B PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 431": "OE1" <-> "OE2" Residue "C ARG 244": "NH1" <-> "NH2" Residue "C PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 295": "OD1" <-> "OD2" Residue "C GLU 344": "OE1" <-> "OE2" Residue "C PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 431": "OE1" <-> "OE2" Residue "C ASP 442": "OD1" <-> "OD2" Residue "C PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 194": "OD1" <-> "OD2" Residue "D PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 261": "OD1" <-> "OD2" Residue "D ARG 267": "NH1" <-> "NH2" Residue "D GLU 271": "OE1" <-> "OE2" Residue "D ASP 292": "OD1" <-> "OD2" Residue "D ARG 311": "NH1" <-> "NH2" Residue "D ARG 312": "NH1" <-> "NH2" Residue "D ARG 332": "NH1" <-> "NH2" Residue "D ARG 406": "NH1" <-> "NH2" Residue "D ARG 414": "NH1" <-> "NH2" Residue "D TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 431": "OE1" <-> "OE2" Residue "D PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 194": "OD1" <-> "OD2" Residue "E GLU 249": "OE1" <-> "OE2" Residue "E PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 312": "NH1" <-> "NH2" Residue "E PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 351": "NH1" <-> "NH2" Residue "E ASP 442": "OD1" <-> "OD2" Residue "E GLU 464": "OE1" <-> "OE2" Residue "E PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 312": "NH1" <-> "NH2" Residue "F ARG 352": "NH1" <-> "NH2" Residue "F PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 431": "OE1" <-> "OE2" Residue "G GLU 9": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13928 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2239 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 13, 'TRANS': 291} Chain breaks: 2 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ASN:plan1': 1, 'ARG:plan': 4, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 90 Chain: "B" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2273 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 13, 'TRANS': 291} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 72 Chain: "C" Number of atoms: 2297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2297 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 13, 'TRANS': 294} Chain breaks: 2 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 68 Chain: "D" Number of atoms: 2318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2318 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 13, 'TRANS': 296} Chain breaks: 2 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 61 Chain: "E" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2306 Classifications: {'peptide': 312} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 13, 'TRANS': 298} Chain breaks: 1 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 12, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 86 Chain: "F" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2186 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 13, 'TRANS': 297} Chain breaks: 2 Unresolved non-hydrogen bonds: 230 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 13, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 151 Chain: "G" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 118 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.12, per 1000 atoms: 0.51 Number of scatterers: 13928 At special positions: 0 Unit cell: (132.84, 139.32, 118.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 P 18 15.00 Mg 5 11.99 O 2604 8.00 N 2438 7.00 C 8800 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: 5.12 Conformation dependent library (CDL) restraints added in 2.5 seconds 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3492 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 88 helices and 8 sheets defined 39.6% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.54 Creating SS restraints... Processing helix chain 'A' and resid 174 through 181 removed outlier: 4.167A pdb=" N GLY A 180 " --> pdb=" O GLN A 176 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N THR A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 208 Processing helix chain 'A' and resid 211 through 214 No H-bonds generated for 'chain 'A' and resid 211 through 214' Processing helix chain 'A' and resid 239 through 249 removed outlier: 3.819A pdb=" N ALA A 243 " --> pdb=" O LYS A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 284 Processing helix chain 'A' and resid 294 through 297 No H-bonds generated for 'chain 'A' and resid 294 through 297' Processing helix chain 'A' and resid 309 through 319 removed outlier: 3.824A pdb=" N VAL A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 352 No H-bonds generated for 'chain 'A' and resid 349 through 352' Processing helix chain 'A' and resid 364 through 374 removed outlier: 4.053A pdb=" N LYS A 368 " --> pdb=" O ILE A 364 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 391 Processing helix chain 'A' and resid 398 through 414 removed outlier: 3.997A pdb=" N VAL A 402 " --> pdb=" O GLY A 398 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 409 " --> pdb=" O CYS A 405 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 435 Processing helix chain 'A' and resid 440 through 449 removed outlier: 3.709A pdb=" N ALA A 449 " --> pdb=" O ALA A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 468 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 172 through 180 removed outlier: 3.528A pdb=" N GLN B 176 " --> pdb=" O ALA B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'B' and resid 199 through 209 Processing helix chain 'B' and resid 211 through 214 No H-bonds generated for 'chain 'B' and resid 211 through 214' Processing helix chain 'B' and resid 242 through 248 Processing helix chain 'B' and resid 270 through 281 Processing helix chain 'B' and resid 310 through 320 Processing helix chain 'B' and resid 342 through 344 No H-bonds generated for 'chain 'B' and resid 342 through 344' Processing helix chain 'B' and resid 348 through 352 Processing helix chain 'B' and resid 366 through 374 Processing helix chain 'B' and resid 386 through 392 Processing helix chain 'B' and resid 401 through 414 Processing helix chain 'B' and resid 441 through 447 removed outlier: 3.647A pdb=" N ALA B 445 " --> pdb=" O ILE B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 469 Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'C' and resid 174 through 181 Processing helix chain 'C' and resid 199 through 206 Processing helix chain 'C' and resid 211 through 214 No H-bonds generated for 'chain 'C' and resid 211 through 214' Processing helix chain 'C' and resid 221 through 223 No H-bonds generated for 'chain 'C' and resid 221 through 223' Processing helix chain 'C' and resid 241 through 248 Processing helix chain 'C' and resid 272 through 284 Processing helix chain 'C' and resid 309 through 320 removed outlier: 3.958A pdb=" N LYS C 314 " --> pdb=" O SER C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 375 Processing helix chain 'C' and resid 386 through 391 Processing helix chain 'C' and resid 399 through 410 Processing helix chain 'C' and resid 426 through 433 removed outlier: 4.082A pdb=" N GLU C 431 " --> pdb=" O THR C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 447 Processing helix chain 'C' and resid 457 through 468 Processing helix chain 'D' and resid 160 through 162 No H-bonds generated for 'chain 'D' and resid 160 through 162' Processing helix chain 'D' and resid 172 through 181 removed outlier: 3.545A pdb=" N ALA D 177 " --> pdb=" O TYR D 173 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 194 No H-bonds generated for 'chain 'D' and resid 192 through 194' Processing helix chain 'D' and resid 199 through 209 Processing helix chain 'D' and resid 211 through 214 No H-bonds generated for 'chain 'D' and resid 211 through 214' Processing helix chain 'D' and resid 239 through 249 removed outlier: 3.755A pdb=" N ALA D 243 " --> pdb=" O LYS D 239 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 294 through 297 No H-bonds generated for 'chain 'D' and resid 294 through 297' Processing helix chain 'D' and resid 308 through 320 removed outlier: 3.967A pdb=" N ARG D 312 " --> pdb=" O GLU D 308 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 344 No H-bonds generated for 'chain 'D' and resid 342 through 344' Processing helix chain 'D' and resid 349 through 352 No H-bonds generated for 'chain 'D' and resid 349 through 352' Processing helix chain 'D' and resid 367 through 374 Processing helix chain 'D' and resid 386 through 392 Processing helix chain 'D' and resid 398 through 414 removed outlier: 4.039A pdb=" N ALA D 409 " --> pdb=" O CYS D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 449 removed outlier: 4.635A pdb=" N GLN D 448 " --> pdb=" O GLU D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 465 Processing helix chain 'E' and resid 160 through 162 No H-bonds generated for 'chain 'E' and resid 160 through 162' Processing helix chain 'E' and resid 172 through 181 removed outlier: 4.394A pdb=" N THR E 181 " --> pdb=" O ALA E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 209 Processing helix chain 'E' and resid 221 through 223 No H-bonds generated for 'chain 'E' and resid 221 through 223' Processing helix chain 'E' and resid 241 through 248 Processing helix chain 'E' and resid 270 through 284 Processing helix chain 'E' and resid 294 through 296 No H-bonds generated for 'chain 'E' and resid 294 through 296' Processing helix chain 'E' and resid 310 through 321 Processing helix chain 'E' and resid 347 through 350 No H-bonds generated for 'chain 'E' and resid 347 through 350' Processing helix chain 'E' and resid 364 through 374 Processing helix chain 'E' and resid 386 through 392 Processing helix chain 'E' and resid 400 through 415 removed outlier: 4.356A pdb=" N VAL E 412 " --> pdb=" O ALA E 408 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LEU E 413 " --> pdb=" O ALA E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 435 removed outlier: 4.041A pdb=" N LYS E 434 " --> pdb=" O MET E 430 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ALA E 435 " --> pdb=" O GLU E 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 430 through 435' Processing helix chain 'E' and resid 440 through 448 Processing helix chain 'E' and resid 457 through 468 Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 174 through 181 removed outlier: 4.450A pdb=" N THR F 181 " --> pdb=" O ALA F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 208 Processing helix chain 'F' and resid 211 through 214 No H-bonds generated for 'chain 'F' and resid 211 through 214' Processing helix chain 'F' and resid 239 through 249 Processing helix chain 'F' and resid 271 through 283 Processing helix chain 'F' and resid 294 through 297 No H-bonds generated for 'chain 'F' and resid 294 through 297' Processing helix chain 'F' and resid 311 through 320 Processing helix chain 'F' and resid 364 through 374 removed outlier: 3.622A pdb=" N LYS F 369 " --> pdb=" O ASP F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 391 Processing helix chain 'F' and resid 400 through 411 Processing helix chain 'F' and resid 428 through 431 No H-bonds generated for 'chain 'F' and resid 428 through 431' Processing helix chain 'F' and resid 440 through 449 Processing helix chain 'F' and resid 456 through 466 removed outlier: 3.541A pdb=" N LEU F 460 " --> pdb=" O PRO F 456 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS F 461 " --> pdb=" O ASP F 457 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 288 through 292 removed outlier: 6.771A pdb=" N PHE A 334 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ILE A 291 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU A 336 " --> pdb=" O ILE A 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 230 through 233 Processing sheet with id= C, first strand: chain 'B' and resid 289 through 291 removed outlier: 3.684A pdb=" N ILE B 291 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 228 through 232 removed outlier: 6.379A pdb=" N VAL C 335 " --> pdb=" O MET C 229 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N LEU C 231 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA C 337 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE C 289 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N ALA C 338 " --> pdb=" O ILE C 289 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE C 291 " --> pdb=" O ALA C 338 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'D' and resid 228 through 232 removed outlier: 8.524A pdb=" N MET D 229 " --> pdb=" O VAL D 333 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL D 335 " --> pdb=" O MET D 229 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N LEU D 231 " --> pdb=" O VAL D 335 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA D 337 " --> pdb=" O LEU D 231 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N SER D 287 " --> pdb=" O PHE D 334 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N LEU D 336 " --> pdb=" O SER D 287 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILE D 289 " --> pdb=" O LEU D 336 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N ALA D 338 " --> pdb=" O ILE D 289 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE D 291 " --> pdb=" O ALA D 338 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 356 through 359 removed outlier: 8.299A pdb=" N ILE E 357 " --> pdb=" O ALA E 228 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL E 230 " --> pdb=" O ILE E 357 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N ILE E 359 " --> pdb=" O VAL E 230 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ALA E 232 " --> pdb=" O ILE E 359 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL E 335 " --> pdb=" O MET E 229 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LEU E 231 " --> pdb=" O VAL E 335 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA E 337 " --> pdb=" O LEU E 231 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N GLY E 233 " --> pdb=" O ALA E 337 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N THR E 339 " --> pdb=" O GLY E 233 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE E 289 " --> pdb=" O LEU E 336 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N ALA E 338 " --> pdb=" O ILE E 289 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE E 291 " --> pdb=" O ALA E 338 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 230 through 233 Processing sheet with id= H, first strand: chain 'F' and resid 254 through 257 removed outlier: 6.627A pdb=" N ILE F 288 " --> pdb=" O PHE F 255 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N VAL F 257 " --> pdb=" O ILE F 288 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N PHE F 290 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE F 291 " --> pdb=" O LEU F 336 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA F 338 " --> pdb=" O ILE F 291 " (cutoff:3.500A) 385 hydrogen bonds defined for protein. 1155 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: 3.43 Time building geometry restraints manager: 5.52 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: 4490 1.34 - 1.46: 2008 1.46 - 1.57: 7544 1.57 - 1.69: 30 1.69 - 1.81: 109 Bond restraints: 14181 Sorted by residual: bond pdb=" C4 ATP A 501 " pdb=" C5 ATP A 501 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.91e+01 bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.71e+01 bond pdb=" C4 ATP F 501 " pdb=" C5 ATP F 501 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.69e+01 bond pdb=" C4 ATP E 501 " pdb=" C5 ATP E 501 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.11e+01 bond pdb=" C4 ATP B 501 " pdb=" C5 ATP B 501 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.09e+01 ... (remaining 14176 not shown) Histogram of bond angle deviations from ideal: 98.97 - 106.54: 452 106.54 - 114.11: 8203 114.11 - 121.69: 7376 121.69 - 129.26: 3158 129.26 - 136.83: 86 Bond angle restraints: 19275 Sorted by residual: angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 117.00 22.87 1.00e+00 1.00e+00 5.23e+02 angle pdb=" PB ATP B 501 " pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 139.87 119.04 20.83 1.00e+00 1.00e+00 4.34e+02 angle pdb=" PA ATP C 501 " pdb=" O3A ATP C 501 " pdb=" PB ATP C 501 " ideal model delta sigma weight residual 136.83 116.23 20.60 1.00e+00 1.00e+00 4.24e+02 angle pdb=" PB ATP A 501 " pdb=" O3B ATP A 501 " pdb=" PG ATP A 501 " ideal model delta sigma weight residual 139.87 120.06 19.81 1.00e+00 1.00e+00 3.92e+02 angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 120.37 19.50 1.00e+00 1.00e+00 3.80e+02 ... (remaining 19270 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 7690 18.00 - 35.99: 774 35.99 - 53.99: 119 53.99 - 71.99: 32 71.99 - 89.98: 12 Dihedral angle restraints: 8627 sinusoidal: 3258 harmonic: 5369 Sorted by residual: dihedral pdb=" CA THR C 296 " pdb=" C THR C 296 " pdb=" N LEU C 297 " pdb=" CA LEU C 297 " ideal model delta harmonic sigma weight residual 180.00 -155.31 -24.69 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA TYR B 284 " pdb=" C TYR B 284 " pdb=" N ALA B 285 " pdb=" CA ALA B 285 " ideal model delta harmonic sigma weight residual -180.00 -155.85 -24.15 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA ASP C 295 " pdb=" C ASP C 295 " pdb=" N THR C 296 " pdb=" CA THR C 296 " ideal model delta harmonic sigma weight residual 180.00 157.88 22.12 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 8624 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1529 0.045 - 0.090: 534 0.090 - 0.135: 139 0.135 - 0.180: 29 0.180 - 0.225: 7 Chirality restraints: 2238 Sorted by residual: chirality pdb=" CB ILE F 441 " pdb=" CA ILE F 441 " pdb=" CG1 ILE F 441 " pdb=" CG2 ILE F 441 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB VAL B 401 " pdb=" CA VAL B 401 " pdb=" CG1 VAL B 401 " pdb=" CG2 VAL B 401 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CB ILE A 288 " pdb=" CA ILE A 288 " pdb=" CG1 ILE A 288 " pdb=" CG2 ILE A 288 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 2235 not shown) Planarity restraints: 2448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 211 " 0.053 5.00e-02 4.00e+02 8.01e-02 1.03e+01 pdb=" N PRO C 212 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO C 212 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 212 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 285 " -0.045 5.00e-02 4.00e+02 6.80e-02 7.40e+00 pdb=" N PRO A 286 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 286 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 286 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 211 " -0.044 5.00e-02 4.00e+02 6.57e-02 6.92e+00 pdb=" N PRO F 212 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO F 212 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO F 212 " -0.037 5.00e-02 4.00e+02 ... (remaining 2445 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 151 2.65 - 3.21: 11536 3.21 - 3.77: 19714 3.77 - 4.34: 25740 4.34 - 4.90: 43663 Nonbonded interactions: 100804 Sorted by model distance: nonbonded pdb=" O3B ATP C 501 " pdb="MG MG C 502 " model vdw 2.082 2.170 nonbonded pdb=" O3G ATP B 501 " pdb="MG MG B 502 " model vdw 2.117 2.170 nonbonded pdb=" OG1 THR C 240 " pdb="MG MG C 502 " model vdw 2.124 2.170 nonbonded pdb=" O2B ATP D 501 " pdb="MG MG D 502 " model vdw 2.126 2.170 nonbonded pdb=" O3G ATP D 501 " pdb="MG MG D 502 " model vdw 2.127 2.170 ... (remaining 100799 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 156 through 182 or (resid 188 through 191 and (name N or n \ ame CA or name C or name O or name CB )) or resid 192 or (resid 193 through 194 \ and (name N or name CA or name C or name O or name CB )) or resid 195 through 21 \ 6 or (resid 217 and (name N or name CA or name C or name O or name CB )) or resi \ d 218 through 219 or (resid 220 and (name N or name CA or name C or name O or na \ me CB )) or resid 221 through 243 or (resid 244 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 245 through 248 or (resid 249 and ( \ name N or name CA or name C or name O or name CB )) or resid 250 through 259 or \ (resid 260 and (name N or name CA or name C or name O or name CB )) or resid 261 \ through 294 or (resid 295 and (name N or name CA or name C or name O or name CB \ )) or resid 296 through 303 or (resid 304 and (name N or name CA or name C or n \ ame O or name CB )) or resid 305 through 322 or resid 332 through 343 or (resid \ 344 and (name N or name CA or name C or name O or name CB )) or resid 345 throug \ h 360 or (resid 361 and (name N or name CA or name C or name O or name CB )) or \ resid 362 or (resid 363 and (name N or name CA or name C or name O or name CB )) \ or resid 364 through 366 or (resid 367 and (name N or name CA or name C or name \ O or name CB )) or resid 368 or (resid 369 and (name N or name CA or name C or \ name O or name CB )) or resid 370 through 371 or (resid 372 through 373 and (nam \ e N or name CA or name C or name O or name CB )) or resid 374 or (resid 375 and \ (name N or name CA or name C or name O or name CB )) or resid 376 through 377 or \ (resid 378 and (name N or name CA or name C or name O or name CB )) or resid 37 \ 9 or (resid 380 and (name N or name CA or name C or name O or name CB )) or resi \ d 381 or (resid 382 through 385 and (name N or name CA or name C or name O or na \ me CB )) or resid 386 or (resid 387 through 394 and (name N or name CA or name C \ or name O or name CB )) or resid 395 through 399 or (resid 400 and (name N or n \ ame CA or name C or name O or name CB )) or resid 401 through 405 or (resid 406 \ and (name N or name CA or name C or name O or name CB )) or resid 407 through 41 \ 3 or (resid 414 and (name N or name CA or name C or name O or name CB )) or resi \ d 415 through 417 or (resid 418 through 419 and (name N or name CA or name C or \ name O or name CB )) or resid 420 or (resid 421 through 422 and (name N or name \ CA or name C or name O or name CB )) or resid 423 through 436 or (resid 437 and \ (name N or name CA or name C or name O or name CB )) or resid 438 or (resid 439 \ and (name N or name CA or name C or name O or name CB )) or resid 440 through 44 \ 3 or (resid 444 through 446 and (name N or name CA or name C or name O or name C \ B )) or resid 447 or (resid 448 through 449 and (name N or name CA or name C or \ name O or name CB )) or resid 450 through 457 or (resid 458 through 464 and (nam \ e N or name CA or name C or name O or name CB )) or resid 465 through 466 or (re \ sid 467 through 468 and (name N or name CA or name C or name O or name CB )) or \ resid 469 through 472 or resid 501)) selection = (chain 'B' and (resid 156 through 167 or (resid 168 through 169 and (name N or n \ ame CA or name C or name O or name CB )) or resid 170 through 175 or (resid 176 \ through 177 and (name N or name CA or name C or name O or name CB )) or resid 17 \ 8 through 182 or (resid 188 through 191 and (name N or name CA or name C or name \ O or name CB )) or resid 192 or (resid 193 through 194 and (name N or name CA o \ r name C or name O or name CB )) or resid 195 through 199 or (resid 200 and (nam \ e N or name CA or name C or name O or name CB )) or resid 201 through 216 or (re \ sid 217 and (name N or name CA or name C or name O or name CB )) or resid 218 th \ rough 222 or (resid 223 and (name N or name CA or name C or name O or name CB )) \ or resid 224 through 226 or (resid 227 through 228 and (name N or name CA or na \ me C or name O or name CB )) or resid 229 or (resid 230 and (name N or name CA o \ r name C or name O or name CB )) or resid 231 through 243 or (resid 244 and (nam \ e N or name CA or name C or name O or name CB or name CG )) or resid 245 through \ 248 or (resid 249 and (name N or name CA or name C or name O or name CB )) or r \ esid 250 or (resid 251 and (name N or name CA or name C or name O or name CB )) \ or resid 252 through 268 or (resid 269 and (name N or name CA or name C or name \ O or name CB )) or resid 270 or (resid 271 and (name N or name CA or name C or n \ ame O or name CB )) or resid 272 through 278 or (resid 279 and (name N or name C \ A or name C or name O or name CB )) or resid 280 through 294 or (resid 295 and ( \ name N or name CA or name C or name O or name CB )) or resid 296 through 303 or \ (resid 304 and (name N or name CA or name C or name O or name CB )) or resid 305 \ or (resid 306 and (name N or name CA or name C or name O or name CB )) or resid \ 307 or (resid 308 through 309 and (name N or name CA or name C or name O or nam \ e CB )) or resid 310 through 314 or (resid 315 through 316 and (name N or name C \ A or name C or name O or name CB )) or resid 317 through 318 or (resid 319 and ( \ name N or name CA or name C or name O or name CB )) or resid 320 through 322 or \ (resid 332 and (name N or name CA or name C or name O or name CB )) or resid 333 \ through 343 or (resid 344 and (name N or name CA or name C or name O or name CB \ )) or resid 345 or (resid 346 through 348 and (name N or name CA or name C or n \ ame O or name CB )) or resid 349 through 354 or (resid 355 through 356 and (name \ N or name CA or name C or name O or name CB )) or resid 357 through 360 or (res \ id 361 and (name N or name CA or name C or name O or name CB )) or resid 362 thr \ ough 366 or (resid 367 and (name N or name CA or name C or name O or name CB )) \ or resid 368 or (resid 369 and (name N or name CA or name C or name O or name CB \ )) or resid 370 through 371 or (resid 372 through 373 and (name N or name CA or \ name C or name O or name CB )) or resid 374 or (resid 375 and (name N or name C \ A or name C or name O or name CB )) or resid 376 through 377 or (resid 378 and ( \ name N or name CA or name C or name O or name CB )) or resid 379 through 387 or \ (resid 388 through 394 and (name N or name CA or name C or name O or name CB )) \ or resid 395 through 399 or (resid 400 and (name N or name CA or name C or name \ O or name CB )) or resid 401 through 405 or (resid 406 and (name N or name CA or \ name C or name O or name CB )) or resid 407 through 413 or (resid 414 and (name \ N or name CA or name C or name O or name CB )) or resid 415 through 417 or (res \ id 418 through 419 and (name N or name CA or name C or name O or name CB )) or r \ esid 420 or (resid 421 through 422 and (name N or name CA or name C or name O or \ name CB )) or resid 423 through 435 or (resid 436 through 437 and (name N or na \ me CA or name C or name O or name CB )) or resid 438 through 443 or (resid 444 t \ hrough 446 and (name N or name CA or name C or name O or name CB )) or resid 447 \ or (resid 448 through 449 and (name N or name CA or name C or name O or name CB \ )) or resid 450 through 452 or (resid 453 through 454 and (name N or name CA or \ name C or name O or name CB )) or resid 455 through 457 or (resid 458 through 4 \ 64 and (name N or name CA or name C or name O or name CB )) or resid 465 through \ 466 or (resid 467 through 468 and (name N or name CA or name C or name O or nam \ e CB )) or resid 469 through 471 or (resid 472 and (name N or name CA or name C \ or name O or name CB )) or resid 501)) selection = (chain 'C' and (resid 156 through 182 or (resid 188 through 191 and (name N or n \ ame CA or name C or name O or name CB )) or resid 192 through 193 or (resid 194 \ and (name N or name CA or name C or name O or name CB )) or resid 195 through 21 \ 9 or (resid 220 and (name N or name CA or name C or name O or name CB )) or resi \ d 221 through 222 or (resid 223 and (name N or name CA or name C or name O or na \ me CB )) or resid 224 through 229 or (resid 230 and (name N or name CA or name C \ or name O or name CB )) or resid 231 through 243 or (resid 244 and (name N or n \ ame CA or name C or name O or name CB or name CG )) or resid 245 through 248 or \ (resid 249 and (name N or name CA or name C or name O or name CB )) or resid 250 \ through 258 or (resid 259 through 260 and (name N or name CA or name C or name \ O or name CB )) or resid 261 through 268 or (resid 269 and (name N or name CA or \ name C or name O or name CB )) or resid 270 or (resid 271 and (name N or name C \ A or name C or name O or name CB )) or resid 272 through 278 or (resid 279 and ( \ name N or name CA or name C or name O or name CB )) or resid 280 through 294 or \ (resid 295 and (name N or name CA or name C or name O or name CB )) or resid 296 \ through 303 or (resid 304 and (name N or name CA or name C or name O or name CB \ )) or resid 305 or (resid 306 and (name N or name CA or name C or name O or nam \ e CB )) or resid 307 or (resid 308 through 309 and (name N or name CA or name C \ or name O or name CB )) or resid 310 through 314 or (resid 315 through 316 and ( \ name N or name CA or name C or name O or name CB )) or resid 317 through 318 or \ (resid 319 and (name N or name CA or name C or name O or name CB )) or resid 320 \ through 322 or (resid 332 and (name N or name CA or name C or name O or name CB \ )) or resid 333 through 343 or (resid 344 and (name N or name CA or name C or n \ ame O or name CB )) or resid 345 or (resid 346 through 348 and (name N or name C \ A or name C or name O or name CB )) or resid 349 through 354 or (resid 355 throu \ gh 356 and (name N or name CA or name C or name O or name CB )) or resid 357 thr \ ough 360 or (resid 361 and (name N or name CA or name C or name O or name CB )) \ or resid 362 through 366 or (resid 367 and (name N or name CA or name C or name \ O or name CB )) or resid 368 or (resid 369 and (name N or name CA or name C or n \ ame O or name CB )) or resid 370 through 371 or (resid 372 through 373 and (name \ N or name CA or name C or name O or name CB )) or resid 374 or (resid 375 and ( \ name N or name CA or name C or name O or name CB )) or resid 376 through 377 or \ (resid 378 and (name N or name CA or name C or name O or name CB )) or resid 379 \ or (resid 380 and (name N or name CA or name C or name O or name CB )) or resid \ 381 through 382 or (resid 383 through 385 and (name N or name CA or name C or n \ ame O or name CB )) or resid 386 through 387 or (resid 388 through 394 and (name \ N or name CA or name C or name O or name CB )) or resid 395 through 405 or (res \ id 406 and (name N or name CA or name C or name O or name CB )) or resid 407 thr \ ough 413 or (resid 414 and (name N or name CA or name C or name O or name CB )) \ or resid 415 through 420 or (resid 421 through 422 and (name N or name CA or nam \ e C or name O or name CB )) or resid 423 through 435 or (resid 436 through 437 a \ nd (name N or name CA or name C or name O or name CB )) or resid 438 or (resid 4 \ 39 and (name N or name CA or name C or name O or name CB )) or resid 440 through \ 443 or (resid 444 through 446 and (name N or name CA or name C or name O or nam \ e CB )) or resid 447 or (resid 448 through 449 and (name N or name CA or name C \ or name O or name CB )) or resid 450 through 452 or (resid 453 through 454 and ( \ name N or name CA or name C or name O or name CB )) or resid 455 through 456 or \ (resid 457 through 464 and (name N or name CA or name C or name O or name CB )) \ or resid 465 through 467 or (resid 468 and (name N or name CA or name C or name \ O or name CB )) or resid 469 through 472 or resid 501)) selection = (chain 'D' and (resid 156 through 175 or (resid 176 through 177 and (name N or n \ ame CA or name C or name O or name CB )) or resid 178 through 189 or (resid 190 \ through 191 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 2 or (resid 193 through 194 and (name N or name CA or name C or name O or name C \ B )) or resid 195 through 199 or (resid 200 and (name N or name CA or name C or \ name O or name CB )) or resid 201 through 219 or (resid 220 and (name N or name \ CA or name C or name O or name CB )) or resid 221 through 222 or (resid 223 and \ (name N or name CA or name C or name O or name CB )) or resid 224 through 229 or \ (resid 230 and (name N or name CA or name C or name O or name CB )) or resid 23 \ 1 through 243 or (resid 244 and (name N or name CA or name C or name O or name C \ B or name CG )) or resid 245 through 248 or (resid 249 and (name N or name CA or \ name C or name O or name CB )) or resid 250 or (resid 251 and (name N or name C \ A or name C or name O or name CB )) or resid 252 through 258 or (resid 259 throu \ gh 260 and (name N or name CA or name C or name O or name CB )) or resid 261 thr \ ough 268 or (resid 269 and (name N or name CA or name C or name O or name CB )) \ or resid 270 or (resid 271 and (name N or name CA or name C or name O or name CB \ )) or resid 272 through 278 or (resid 279 and (name N or name CA or name C or n \ ame O or name CB )) or resid 280 through 294 or (resid 295 and (name N or name C \ A or name C or name O or name CB )) or resid 296 through 303 or (resid 304 and ( \ name N or name CA or name C or name O or name CB )) or resid 305 or (resid 306 a \ nd (name N or name CA or name C or name O or name CB )) or resid 307 or (resid 3 \ 08 through 309 and (name N or name CA or name C or name O or name CB )) or resid \ 310 through 314 or (resid 315 through 316 and (name N or name CA or name C or n \ ame O or name CB )) or resid 317 through 318 or (resid 319 and (name N or name C \ A or name C or name O or name CB )) or resid 320 through 322 or (resid 332 and ( \ name N or name CA or name C or name O or name CB )) or resid 333 through 343 or \ (resid 344 and (name N or name CA or name C or name O or name CB )) or resid 345 \ through 346 or (resid 347 through 348 and (name N or name CA or name C or name \ O or name CB )) or resid 349 through 354 or (resid 355 through 356 and (name N o \ r name CA or name C or name O or name CB )) or resid 357 through 360 or (resid 3 \ 61 and (name N or name CA or name C or name O or name CB )) or resid 362 or (res \ id 363 and (name N or name CA or name C or name O or name CB )) or resid 364 thr \ ough 366 or (resid 367 and (name N or name CA or name C or name O or name CB )) \ or resid 368 or (resid 369 and (name N or name CA or name C or name O or name CB \ )) or resid 370 through 371 or (resid 372 through 373 and (name N or name CA or \ name C or name O or name CB )) or resid 374 or (resid 375 and (name N or name C \ A or name C or name O or name CB )) or resid 376 through 377 or (resid 378 and ( \ name N or name CA or name C or name O or name CB )) or resid 379 or (resid 380 a \ nd (name N or name CA or name C or name O or name CB )) or resid 381 or (resid 3 \ 82 through 385 and (name N or name CA or name C or name O or name CB )) or resid \ 386 or (resid 387 through 394 and (name N or name CA or name C or name O or nam \ e CB )) or resid 395 through 399 or (resid 400 and (name N or name CA or name C \ or name O or name CB )) or resid 401 through 405 or (resid 406 and (name N or na \ me CA or name C or name O or name CB )) or resid 407 through 413 or (resid 414 a \ nd (name N or name CA or name C or name O or name CB )) or resid 415 through 417 \ or (resid 418 through 419 and (name N or name CA or name C or name O or name CB \ )) or resid 420 or (resid 421 through 422 and (name N or name CA or name C or n \ ame O or name CB )) or resid 423 through 436 or (resid 437 and (name N or name C \ A or name C or name O or name CB )) or resid 438 or (resid 439 and (name N or na \ me CA or name C or name O or name CB )) or resid 440 through 447 or (resid 448 t \ hrough 449 and (name N or name CA or name C or name O or name CB )) or resid 450 \ through 457 or (resid 458 through 464 and (name N or name CA or name C or name \ O or name CB )) or resid 465 through 467 or (resid 468 and (name N or name CA or \ name C or name O or name CB )) or resid 469 through 472 or resid 501)) selection = (chain 'E' and (resid 156 through 182 or (resid 188 through 191 and (name N or n \ ame CA or name C or name O or name CB )) or resid 192 or (resid 193 through 194 \ and (name N or name CA or name C or name O or name CB )) or resid 195 through 19 \ 9 or (resid 200 and (name N or name CA or name C or name O or name CB )) or resi \ d 201 through 216 or (resid 217 and (name N or name CA or name C or name O or na \ me CB )) or resid 218 through 219 or (resid 220 and (name N or name CA or name C \ or name O or name CB )) or resid 221 through 222 or (resid 223 and (name N or n \ ame CA or name C or name O or name CB )) or resid 224 through 226 or (resid 227 \ through 228 and (name N or name CA or name C or name O or name CB )) or resid 22 \ 9 or (resid 230 and (name N or name CA or name C or name O or name CB )) or resi \ d 231 through 243 or (resid 244 and (name N or name CA or name C or name O or na \ me CB or name CG )) or resid 245 through 248 or (resid 249 and (name N or name C \ A or name C or name O or name CB )) or resid 250 or (resid 251 and (name N or na \ me CA or name C or name O or name CB )) or resid 252 through 258 or (resid 259 t \ hrough 260 and (name N or name CA or name C or name O or name CB )) or resid 261 \ through 268 or (resid 269 and (name N or name CA or name C or name O or name CB \ )) or resid 270 or (resid 271 and (name N or name CA or name C or name O or nam \ e CB )) or resid 272 through 278 or (resid 279 and (name N or name CA or name C \ or name O or name CB )) or resid 280 through 294 or (resid 295 and (name N or na \ me CA or name C or name O or name CB )) or resid 296 through 305 or (resid 306 a \ nd (name N or name CA or name C or name O or name CB )) or resid 307 through 314 \ or (resid 315 through 316 and (name N or name CA or name C or name O or name CB \ )) or resid 317 through 318 or (resid 319 and (name N or name CA or name C or n \ ame O or name CB )) or resid 320 through 322 or (resid 332 and (name N or name C \ A or name C or name O or name CB )) or resid 333 through 343 or (resid 344 and ( \ name N or name CA or name C or name O or name CB )) or resid 345 through 346 or \ (resid 347 through 348 and (name N or name CA or name C or name O or name CB )) \ or resid 349 through 354 or (resid 355 through 356 and (name N or name CA or nam \ e C or name O or name CB )) or resid 357 through 360 or (resid 361 and (name N o \ r name CA or name C or name O or name CB )) or resid 362 through 366 or (resid 3 \ 67 and (name N or name CA or name C or name O or name CB )) or resid 368 or (res \ id 369 and (name N or name CA or name C or name O or name CB )) or resid 370 thr \ ough 371 or (resid 372 through 373 and (name N or name CA or name C or name O or \ name CB )) or resid 374 or (resid 375 and (name N or name CA or name C or name \ O or name CB )) or resid 376 through 377 or (resid 378 and (name N or name CA or \ name C or name O or name CB )) or resid 379 through 383 or (resid 384 through 3 \ 85 and (name N or name CA or name C or name O or name CB )) or resid 386 through \ 388 or (resid 389 through 394 and (name N or name CA or name C or name O or nam \ e CB )) or resid 395 through 399 or (resid 400 and (name N or name CA or name C \ or name O or name CB )) or resid 401 through 405 or (resid 406 and (name N or na \ me CA or name C or name O or name CB )) or resid 407 through 413 or (resid 414 a \ nd (name N or name CA or name C or name O or name CB )) or resid 415 through 417 \ or (resid 418 through 419 and (name N or name CA or name C or name O or name CB \ )) or resid 420 through 436 or (resid 437 and (name N or name CA or name C or n \ ame O or name CB )) or resid 438 or (resid 439 and (name N or name CA or name C \ or name O or name CB )) or resid 440 through 452 or (resid 453 through 454 and ( \ name N or name CA or name C or name O or name CB )) or resid 455 through 457 or \ (resid 458 through 464 and (name N or name CA or name C or name O or name CB )) \ or resid 465 through 467 or (resid 468 and (name N or name CA or name C or name \ O or name CB )) or resid 469 through 472 or resid 501)) selection = (chain 'F' and (resid 156 through 170 or (resid 171 through 172 and (name N or n \ ame CA or name C or name O or name CB )) or resid 173 through 175 or (resid 176 \ through 177 and (name N or name CA or name C or name O or name CB )) or resid 17 \ 8 through 192 or (resid 193 through 194 and (name N or name CA or name C or name \ O or name CB )) or resid 195 through 219 or (resid 220 and (name N or name CA o \ r name C or name O or name CB )) or resid 221 through 222 or (resid 223 and (nam \ e N or name CA or name C or name O or name CB )) or resid 224 through 226 or (re \ sid 227 through 228 and (name N or name CA or name C or name O or name CB )) or \ resid 229 or (resid 230 and (name N or name CA or name C or name O or name CB )) \ or resid 231 through 258 or (resid 259 through 260 and (name N or name CA or na \ me C or name O or name CB )) or resid 261 through 270 or (resid 271 and (name N \ or name CA or name C or name O or name CB )) or resid 272 through 303 or (resid \ 304 and (name N or name CA or name C or name O or name CB )) or resid 305 throug \ h 314 or (resid 315 through 316 and (name N or name CA or name C or name O or na \ me CB )) or resid 317 through 318 or (resid 319 and (name N or name CA or name C \ or name O or name CB )) or resid 320 through 322 or resid 332 through 345 or (r \ esid 346 through 348 and (name N or name CA or name C or name O or name CB )) or \ resid 349 through 354 or (resid 355 through 356 and (name N or name CA or name \ C or name O or name CB )) or resid 357 through 399 or (resid 400 and (name N or \ name CA or name C or name O or name CB )) or resid 401 through 417 or (resid 418 \ through 419 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 20 or (resid 421 through 422 and (name N or name CA or name C or name O or name \ CB )) or resid 423 through 443 or (resid 444 through 446 and (name N or name CA \ or name C or name O or name CB )) or resid 447 or (resid 448 through 449 and (na \ me N or name CA or name C or name O or name CB )) or resid 450 through 452 or (r \ esid 453 through 454 and (name N or name CA or name C or name O or name CB )) or \ resid 455 through 472 or resid 501)) } 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: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 3.280 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 37.240 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.080 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 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 0.083 14181 Z= 0.371 Angle : 1.002 22.873 19275 Z= 0.710 Chirality : 0.050 0.225 2238 Planarity : 0.007 0.080 2448 Dihedral : 14.945 89.984 5135 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.44 % Favored : 92.51 % Rotamer: Outliers : 0.23 % Allowed : 7.96 % Favored : 91.81 % 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: -4.95 (0.14), residues: 1829 helix: -3.33 (0.11), residues: 802 sheet: -2.68 (0.38), residues: 170 loop : -3.32 (0.16), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 343 HIS 0.007 0.001 HIS D 206 PHE 0.017 0.002 PHE A 254 TYR 0.011 0.001 TYR C 173 ARG 0.007 0.000 ARG B 352 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 203 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 179 ARG cc_start: 0.6990 (ttt-90) cc_final: 0.6633 (ttm-80) REVERT: D 190 MET cc_start: 0.6256 (ptp) cc_final: 0.5993 (ptp) REVERT: E 194 ASP cc_start: 0.9055 (t0) cc_final: 0.8802 (t0) REVERT: E 227 LYS cc_start: 0.8457 (ptmt) cc_final: 0.7959 (pttm) REVERT: E 246 ILE cc_start: 0.8670 (tp) cc_final: 0.8338 (tp) REVERT: E 265 LYS cc_start: 0.7899 (tttt) cc_final: 0.7671 (tttm) REVERT: F 346 ASP cc_start: 0.8858 (t0) cc_final: 0.8625 (m-30) outliers start: 3 outliers final: 0 residues processed: 206 average time/residue: 0.2402 time to fit residues: 73.4703 Evaluate side-chains 147 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.7980 chunk 139 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 167 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN A 307 HIS A 340 ASN A 440 ASN B 300 GLN D 320 GLN E 220 GLN E 320 GLN E 411 ASN F 176 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14181 Z= 0.191 Angle : 0.498 9.831 19275 Z= 0.259 Chirality : 0.039 0.145 2238 Planarity : 0.004 0.051 2448 Dihedral : 8.930 81.372 2193 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.88 % Allowed : 14.80 % Favored : 83.32 % 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: -3.37 (0.17), residues: 1829 helix: -1.54 (0.17), residues: 796 sheet: -2.33 (0.38), residues: 185 loop : -2.90 (0.17), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 343 HIS 0.003 0.001 HIS F 206 PHE 0.023 0.001 PHE E 218 TYR 0.013 0.001 TYR B 173 ARG 0.003 0.000 ARG D 301 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 152 time to evaluate : 1.511 Fit side-chains TARDY: cannot create tardy model for: "SER B 259 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: B 179 ARG cc_start: 0.6981 (ttt-90) cc_final: 0.6633 (ttm-80) REVERT: D 430 MET cc_start: 0.6080 (mmm) cc_final: 0.5430 (mmm) REVERT: E 246 ILE cc_start: 0.8621 (tp) cc_final: 0.8330 (tp) REVERT: F 346 ASP cc_start: 0.8872 (t0) cc_final: 0.8562 (m-30) REVERT: G 11 GLU cc_start: 0.2733 (mt-10) cc_final: 0.2501 (mt-10) outliers start: 25 outliers final: 14 residues processed: 169 average time/residue: 0.2221 time to fit residues: 58.5975 Evaluate side-chains 156 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 142 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 340 ASN Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain E residue 443 PHE Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 466 CYS Chi-restraints excluded: chain G residue 4 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 139 optimal weight: 0.0670 chunk 113 optimal weight: 0.0570 chunk 46 optimal weight: 6.9990 chunk 167 optimal weight: 2.9990 chunk 180 optimal weight: 9.9990 chunk 149 optimal weight: 1.9990 chunk 165 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6644 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14181 Z= 0.119 Angle : 0.442 9.216 19275 Z= 0.226 Chirality : 0.038 0.137 2238 Planarity : 0.004 0.048 2448 Dihedral : 8.104 85.921 2193 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.88 % Allowed : 15.93 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.18), residues: 1829 helix: -0.64 (0.19), residues: 793 sheet: -1.95 (0.39), residues: 181 loop : -2.59 (0.18), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 343 HIS 0.002 0.000 HIS D 206 PHE 0.013 0.001 PHE B 353 TYR 0.013 0.001 TYR B 173 ARG 0.001 0.000 ARG D 352 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 164 time to evaluate : 1.607 Fit side-chains TARDY: cannot create tardy model for: "SER B 259 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 226 TRP cc_start: 0.5959 (m100) cc_final: 0.5642 (m100) REVERT: B 179 ARG cc_start: 0.6920 (ttt-90) cc_final: 0.6594 (ttm-80) REVERT: E 194 ASP cc_start: 0.8666 (t0) cc_final: 0.8350 (t0) REVERT: E 246 ILE cc_start: 0.8567 (tp) cc_final: 0.8299 (tp) REVERT: E 249 GLU cc_start: 0.8372 (tt0) cc_final: 0.8008 (tt0) REVERT: E 265 LYS cc_start: 0.7489 (OUTLIER) cc_final: 0.7123 (tttp) REVERT: F 292 ASP cc_start: 0.8117 (t70) cc_final: 0.6907 (p0) REVERT: F 293 GLN cc_start: 0.7810 (mm-40) cc_final: 0.7282 (mm-40) outliers start: 25 outliers final: 11 residues processed: 185 average time/residue: 0.2113 time to fit residues: 61.5890 Evaluate side-chains 157 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 145 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 340 ASN Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain E residue 265 LYS Chi-restraints excluded: chain E residue 357 ILE Chi-restraints excluded: chain E residue 443 PHE Chi-restraints excluded: chain F residue 466 CYS Chi-restraints excluded: chain G residue 4 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 112 optimal weight: 0.3980 chunk 167 optimal weight: 0.8980 chunk 177 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 159 optimal weight: 0.9990 chunk 47 optimal weight: 0.0010 overall best weight: 0.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN D 340 ASN D 440 ASN F 176 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14181 Z= 0.138 Angle : 0.442 8.486 19275 Z= 0.224 Chirality : 0.038 0.135 2238 Planarity : 0.003 0.047 2448 Dihedral : 7.787 86.528 2193 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.48 % Allowed : 16.68 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.19), residues: 1829 helix: -0.16 (0.19), residues: 783 sheet: -1.63 (0.39), residues: 185 loop : -2.37 (0.18), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP F 343 HIS 0.002 0.000 HIS D 206 PHE 0.012 0.001 PHE B 353 TYR 0.010 0.001 TYR B 173 ARG 0.002 0.000 ARG D 352 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 158 time to evaluate : 1.492 Fit side-chains TARDY: cannot create tardy model for: "SER B 259 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 226 TRP cc_start: 0.6126 (m100) cc_final: 0.5758 (m100) REVERT: B 179 ARG cc_start: 0.7030 (ttt-90) cc_final: 0.6649 (ttm-80) REVERT: C 430 MET cc_start: 0.6010 (mmp) cc_final: 0.5404 (mmp) REVERT: E 194 ASP cc_start: 0.8497 (t0) cc_final: 0.8240 (t0) REVERT: E 246 ILE cc_start: 0.8508 (tp) cc_final: 0.8255 (tp) REVERT: E 249 GLU cc_start: 0.8353 (tt0) cc_final: 0.7965 (tt0) REVERT: E 375 MET cc_start: 0.8703 (mmm) cc_final: 0.8493 (mmm) REVERT: F 292 ASP cc_start: 0.8052 (t70) cc_final: 0.6920 (p0) REVERT: F 293 GLN cc_start: 0.7796 (mm-40) cc_final: 0.7258 (mm-40) outliers start: 33 outliers final: 20 residues processed: 185 average time/residue: 0.2112 time to fit residues: 61.0794 Evaluate side-chains 167 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 147 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 340 ASN Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 357 ILE Chi-restraints excluded: chain E residue 443 PHE Chi-restraints excluded: chain F residue 466 CYS Chi-restraints excluded: chain G residue 2 GLU Chi-restraints excluded: chain G residue 4 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 chunk 159 optimal weight: 0.0870 chunk 44 optimal weight: 3.9990 overall best weight: 2.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 GLN B 448 GLN D 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14181 Z= 0.315 Angle : 0.538 8.303 19275 Z= 0.275 Chirality : 0.041 0.137 2238 Planarity : 0.004 0.052 2448 Dihedral : 8.416 80.561 2193 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 3.01 % Allowed : 17.43 % Favored : 79.56 % 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: -1.97 (0.19), residues: 1829 helix: -0.14 (0.19), residues: 774 sheet: -1.86 (0.38), residues: 199 loop : -2.29 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP F 343 HIS 0.004 0.001 HIS F 206 PHE 0.015 0.001 PHE B 353 TYR 0.016 0.001 TYR C 284 ARG 0.004 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 149 time to evaluate : 1.589 Fit side-chains revert: symmetry clash REVERT: A 173 TYR cc_start: 0.8113 (p90) cc_final: 0.7750 (p90) REVERT: A 196 ILE cc_start: 0.7087 (OUTLIER) cc_final: 0.6791 (pt) REVERT: A 226 TRP cc_start: 0.6212 (m100) cc_final: 0.5896 (m100) REVERT: A 451 SER cc_start: 0.7829 (t) cc_final: 0.7503 (t) REVERT: B 179 ARG cc_start: 0.7389 (ttt-90) cc_final: 0.7009 (ttp-170) REVERT: C 203 GLN cc_start: 0.6395 (tt0) cc_final: 0.6046 (tm-30) REVERT: E 246 ILE cc_start: 0.8600 (tp) cc_final: 0.8348 (tp) REVERT: E 249 GLU cc_start: 0.8377 (tt0) cc_final: 0.7748 (tt0) REVERT: F 292 ASP cc_start: 0.8114 (t70) cc_final: 0.7023 (p0) outliers start: 40 outliers final: 24 residues processed: 181 average time/residue: 0.2110 time to fit residues: 60.0958 Evaluate side-chains 167 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 142 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 340 ASN Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain E residue 265 LYS Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain E residue 357 ILE Chi-restraints excluded: chain F residue 339 THR Chi-restraints excluded: chain F residue 466 CYS Chi-restraints excluded: chain G residue 2 GLU Chi-restraints excluded: chain G residue 4 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 0.0970 chunk 160 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 178 optimal weight: 0.5980 chunk 147 optimal weight: 40.0000 chunk 82 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 HIS D 340 ASN D 411 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14181 Z= 0.126 Angle : 0.453 10.689 19275 Z= 0.228 Chirality : 0.038 0.165 2238 Planarity : 0.003 0.046 2448 Dihedral : 7.806 85.432 2193 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.25 % Allowed : 18.18 % Favored : 79.56 % 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: -1.61 (0.19), residues: 1829 helix: 0.18 (0.20), residues: 776 sheet: -1.54 (0.40), residues: 183 loop : -2.16 (0.19), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP F 343 HIS 0.002 0.000 HIS D 206 PHE 0.012 0.001 PHE B 353 TYR 0.009 0.001 TYR B 173 ARG 0.003 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 155 time to evaluate : 1.685 Fit side-chains TARDY: cannot create tardy model for: "SER B 259 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 173 TYR cc_start: 0.8000 (p90) cc_final: 0.7714 (p90) REVERT: A 196 ILE cc_start: 0.6505 (OUTLIER) cc_final: 0.6186 (pt) REVERT: A 226 TRP cc_start: 0.6307 (m100) cc_final: 0.5931 (m100) REVERT: B 179 ARG cc_start: 0.7211 (ttt-90) cc_final: 0.6821 (ttp-170) REVERT: C 430 MET cc_start: 0.5954 (mmp) cc_final: 0.5336 (mmp) REVERT: E 194 ASP cc_start: 0.8653 (t0) cc_final: 0.8450 (t0) REVERT: E 246 ILE cc_start: 0.8508 (tp) cc_final: 0.8259 (tp) REVERT: E 249 GLU cc_start: 0.8361 (tt0) cc_final: 0.7751 (tt0) REVERT: F 156 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6753 (mt) REVERT: F 292 ASP cc_start: 0.8112 (t70) cc_final: 0.7023 (p0) outliers start: 30 outliers final: 18 residues processed: 179 average time/residue: 0.2074 time to fit residues: 58.4848 Evaluate side-chains 164 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 144 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 443 PHE Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 340 ASN Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain E residue 357 ILE Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 466 CYS Chi-restraints excluded: chain G residue 2 GLU Chi-restraints excluded: chain G residue 4 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 0.0070 chunk 20 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 177 optimal weight: 0.0270 chunk 110 optimal weight: 1.9990 chunk 108 optimal weight: 0.0870 chunk 81 optimal weight: 10.0000 overall best weight: 0.6236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 340 ASN D 440 ASN F 448 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14181 Z= 0.123 Angle : 0.442 10.587 19275 Z= 0.221 Chirality : 0.038 0.134 2238 Planarity : 0.003 0.045 2448 Dihedral : 7.571 87.467 2193 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.48 % Allowed : 18.56 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.20), residues: 1829 helix: 0.44 (0.20), residues: 768 sheet: -1.37 (0.39), residues: 188 loop : -2.00 (0.19), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP F 343 HIS 0.002 0.000 HIS D 206 PHE 0.010 0.001 PHE B 353 TYR 0.008 0.001 TYR B 173 ARG 0.003 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 151 time to evaluate : 1.566 Fit side-chains TARDY: cannot create tardy model for: "SER B 259 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 173 TYR cc_start: 0.7981 (p90) cc_final: 0.7670 (p90) REVERT: A 226 TRP cc_start: 0.6324 (m100) cc_final: 0.5881 (m100) REVERT: B 179 ARG cc_start: 0.7186 (ttt-90) cc_final: 0.6767 (ttp-170) REVERT: C 203 GLN cc_start: 0.6410 (tt0) cc_final: 0.6148 (tm-30) REVERT: C 209 VAL cc_start: 0.7678 (t) cc_final: 0.7280 (m) REVERT: C 430 MET cc_start: 0.5952 (mmp) cc_final: 0.5309 (mmp) REVERT: E 194 ASP cc_start: 0.8766 (t0) cc_final: 0.8485 (t0) REVERT: E 246 ILE cc_start: 0.8583 (tp) cc_final: 0.8343 (tp) REVERT: E 249 GLU cc_start: 0.8376 (tt0) cc_final: 0.7790 (tt0) REVERT: F 292 ASP cc_start: 0.8116 (t70) cc_final: 0.7020 (p0) outliers start: 33 outliers final: 21 residues processed: 178 average time/residue: 0.2072 time to fit residues: 58.5603 Evaluate side-chains 166 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 145 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 443 PHE Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 340 ASN Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 357 ILE Chi-restraints excluded: chain F residue 466 CYS Chi-restraints excluded: chain G residue 4 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 161 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 340 ASN F 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 14181 Z= 0.297 Angle : 0.533 10.748 19275 Z= 0.271 Chirality : 0.041 0.136 2238 Planarity : 0.004 0.050 2448 Dihedral : 8.178 81.335 2193 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 2.55 % Allowed : 19.08 % Favored : 78.36 % 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: -1.50 (0.20), residues: 1829 helix: 0.28 (0.20), residues: 766 sheet: -1.60 (0.38), residues: 199 loop : -2.05 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP F 343 HIS 0.003 0.001 HIS C 206 PHE 0.016 0.001 PHE B 218 TYR 0.015 0.001 TYR C 284 ARG 0.004 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 145 time to evaluate : 1.500 Fit side-chains REVERT: A 173 TYR cc_start: 0.8073 (p90) cc_final: 0.7772 (p90) REVERT: B 179 ARG cc_start: 0.7317 (ttt-90) cc_final: 0.6968 (ttp-170) REVERT: C 203 GLN cc_start: 0.6498 (tt0) cc_final: 0.6171 (tm-30) REVERT: C 209 VAL cc_start: 0.8046 (t) cc_final: 0.7643 (m) REVERT: D 229 MET cc_start: 0.9207 (ttp) cc_final: 0.9005 (ttm) REVERT: E 246 ILE cc_start: 0.8636 (tp) cc_final: 0.8373 (tp) REVERT: E 249 GLU cc_start: 0.8363 (tt0) cc_final: 0.7788 (tt0) REVERT: F 156 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.6926 (mt) REVERT: F 292 ASP cc_start: 0.8185 (t70) cc_final: 0.7139 (p0) outliers start: 34 outliers final: 27 residues processed: 172 average time/residue: 0.2104 time to fit residues: 56.8029 Evaluate side-chains 168 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 140 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 443 PHE Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 340 ASN Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain E residue 320 GLN Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 357 ILE Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 339 THR Chi-restraints excluded: chain F residue 466 CYS Chi-restraints excluded: chain G residue 2 GLU Chi-restraints excluded: chain G residue 4 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 9.9990 chunk 155 optimal weight: 9.9990 chunk 165 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 50 optimal weight: 0.3980 chunk 149 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 chunk 164 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 220 GLN D 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14181 Z= 0.150 Angle : 0.466 10.513 19275 Z= 0.234 Chirality : 0.039 0.157 2238 Planarity : 0.003 0.047 2448 Dihedral : 7.776 84.802 2193 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.33 % Allowed : 19.61 % Favored : 78.06 % 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: -1.24 (0.20), residues: 1829 helix: 0.48 (0.20), residues: 766 sheet: -1.42 (0.40), residues: 188 loop : -1.90 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP F 343 HIS 0.003 0.000 HIS F 199 PHE 0.016 0.001 PHE B 218 TYR 0.007 0.001 TYR B 173 ARG 0.003 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 148 time to evaluate : 1.548 Fit side-chains TARDY: cannot create tardy model for: "SER B 259 " (corrupted residue). Skipping it. REVERT: A 173 TYR cc_start: 0.7974 (p90) cc_final: 0.7679 (p90) REVERT: B 179 ARG cc_start: 0.7224 (ttt-90) cc_final: 0.6812 (ttp-170) REVERT: C 203 GLN cc_start: 0.6517 (tt0) cc_final: 0.6148 (tm-30) REVERT: C 209 VAL cc_start: 0.7889 (t) cc_final: 0.7494 (m) REVERT: C 430 MET cc_start: 0.5943 (mmp) cc_final: 0.5296 (mmp) REVERT: D 229 MET cc_start: 0.9170 (ttp) cc_final: 0.8916 (ttm) REVERT: E 246 ILE cc_start: 0.8615 (tp) cc_final: 0.8353 (tp) REVERT: E 249 GLU cc_start: 0.8355 (tt0) cc_final: 0.7784 (tt0) REVERT: F 156 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6807 (mt) REVERT: F 292 ASP cc_start: 0.8195 (t70) cc_final: 0.7113 (p0) outliers start: 31 outliers final: 27 residues processed: 171 average time/residue: 0.2155 time to fit residues: 58.3967 Evaluate side-chains 172 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 144 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 443 PHE Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 340 ASN Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 357 ILE Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 339 THR Chi-restraints excluded: chain F residue 466 CYS Chi-restraints excluded: chain G residue 2 GLU Chi-restraints excluded: chain G residue 4 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 20.0000 chunk 106 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 chunk 183 optimal weight: 4.9990 chunk 168 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 411 ASN F 199 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 14181 Z= 0.490 Angle : 0.660 11.024 19275 Z= 0.335 Chirality : 0.045 0.182 2238 Planarity : 0.004 0.057 2448 Dihedral : 9.038 75.356 2193 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.47 % Favored : 91.47 % Rotamer: Outliers : 2.33 % Allowed : 19.68 % Favored : 77.99 % 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: -1.79 (0.19), residues: 1829 helix: -0.03 (0.19), residues: 763 sheet: -1.75 (0.38), residues: 200 loop : -2.14 (0.19), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP F 343 HIS 0.005 0.001 HIS C 206 PHE 0.018 0.002 PHE C 469 TYR 0.022 0.002 TYR C 284 ARG 0.004 0.001 ARG A 406 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3658 Ramachandran restraints generated. 1829 Oldfield, 0 Emsley, 1829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 136 time to evaluate : 1.623 Fit side-chains REVERT: B 179 ARG cc_start: 0.7380 (ttt-90) cc_final: 0.7028 (ttp-170) REVERT: C 203 GLN cc_start: 0.6509 (tt0) cc_final: 0.6158 (tm-30) REVERT: F 292 ASP cc_start: 0.8217 (t70) cc_final: 0.7165 (p0) outliers start: 31 outliers final: 28 residues processed: 160 average time/residue: 0.2090 time to fit residues: 52.8869 Evaluate side-chains 161 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 133 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 443 PHE Chi-restraints excluded: chain B residue 158 GLN Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 248 SER Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 340 ASN Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain D residue 319 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 357 ILE Chi-restraints excluded: chain F residue 339 THR Chi-restraints excluded: chain F residue 466 CYS Chi-restraints excluded: chain G residue 2 GLU Chi-restraints excluded: chain G residue 4 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 146 optimal weight: 8.9990 chunk 61 optimal weight: 0.3980 chunk 150 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 128 optimal weight: 0.7980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 411 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.126891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.094973 restraints weight = 21996.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.096905 restraints weight = 12941.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.099154 restraints weight = 8122.573| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14181 Z= 0.188 Angle : 0.499 10.535 19275 Z= 0.253 Chirality : 0.040 0.167 2238 Planarity : 0.003 0.049 2448 Dihedral : 8.265 78.640 2193 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.10 % Allowed : 20.14 % Favored : 77.76 % 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: -1.50 (0.20), residues: 1829 helix: 0.26 (0.20), residues: 760 sheet: -1.63 (0.39), residues: 197 loop : -2.00 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP F 343 HIS 0.002 0.000 HIS B 307 PHE 0.015 0.001 PHE B 218 TYR 0.025 0.001 TYR A 173 ARG 0.003 0.000 ARG A 406 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2421.13 seconds wall clock time: 44 minutes 58.07 seconds (2698.07 seconds total)