Starting phenix.real_space_refine on Wed Mar 4 14:41:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ukj_26582/03_2026/7ukj_26582.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ukj_26582/03_2026/7ukj_26582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ukj_26582/03_2026/7ukj_26582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ukj_26582/03_2026/7ukj_26582.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ukj_26582/03_2026/7ukj_26582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ukj_26582/03_2026/7ukj_26582.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 8916 2.51 5 N 2420 2.21 5 O 2794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14196 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4717 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 621, 4701 Classifications: {'peptide': 621} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 595} Conformer: "B" Number of residues, atoms: 621, 4701 Classifications: {'peptide': 621} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 595} bond proxies already assigned to first conformer: 4777 Chain: "B" Number of atoms: 4724 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 619, 4685 Classifications: {'peptide': 619} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 593} Conformer: "B" Number of residues, atoms: 619, 4685 Classifications: {'peptide': 619} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 593} bond proxies already assigned to first conformer: 4738 Chain: "C" Number of atoms: 4755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 622, 4701 Classifications: {'peptide': 622} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 25, 'TRANS': 596} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 622, 4701 Classifications: {'peptide': 622} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 25, 'TRANS': 596} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 4738 Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N AGLY A 235 " occ=0.43 ... (6 atoms not shown) pdb=" O BGLY A 235 " occ=0.57 residue: pdb=" N ASER B 234 " occ=0.68 ... (10 atoms not shown) pdb=" OG BSER B 234 " occ=0.32 residue: pdb=" N AGLY B 235 " occ=0.68 ... (6 atoms not shown) pdb=" O BGLY B 235 " occ=0.32 residue: pdb=" N ASER C 234 " occ=0.49 ... (10 atoms not shown) pdb=" OG BSER C 234 " occ=0.51 residue: pdb=" N AGLY C 235 " occ=0.49 ... (6 atoms not shown) pdb=" O BGLY C 235 " occ=0.51 Time building chain proxies: 5.79, per 1000 atoms: 0.41 Number of scatterers: 14196 At special positions: 0 Unit cell: (90.882, 86.394, 184.008, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 2794 8.00 N 2420 7.00 C 8916 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 - 3.00 Amino acid : True - 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: 1.04 Conformation dependent library (CDL) restraints added in 1.1 seconds 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3422 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 39 sheets defined 7.7% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 105 through 110 Processing helix chain 'A' and resid 114 through 123 Processing helix chain 'A' and resid 154 through 160 removed outlier: 3.774A pdb=" N ASN A 157 " --> pdb=" O HIS A 154 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LYS A 158 " --> pdb=" O ASP A 155 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A 159 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA A 160 " --> pdb=" O ASN A 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 154 through 160' Processing helix chain 'A' and resid 162 through 167 removed outlier: 3.502A pdb=" N ASP A 165 " --> pdb=" O SER A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 189 Processing helix chain 'B' and resid 110 through 123 Proline residue: B 116 - end of helix Processing helix chain 'B' and resid 125 through 129 Processing helix chain 'B' and resid 153 through 160 removed outlier: 4.498A pdb=" N ALA B 160 " --> pdb=" O LYS B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 167 Processing helix chain 'B' and resid 176 through 190 removed outlier: 3.692A pdb=" N LEU B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 46 Processing helix chain 'C' and resid 115 through 124 removed outlier: 3.841A pdb=" N ILE C 119 " --> pdb=" O GLY C 115 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLU C 120 " --> pdb=" O PRO C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 Processing helix chain 'C' and resid 134 through 138 Processing helix chain 'C' and resid 153 through 158 removed outlier: 3.754A pdb=" N LYS C 158 " --> pdb=" O HIS C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 167 removed outlier: 3.810A pdb=" N GLY C 167 " --> pdb=" O LEU C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 9 removed outlier: 4.082A pdb=" N VAL A 8 " --> pdb=" O THR C 84 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LYS C 81 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N VAL C 49 " --> pdb=" O VAL C 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 79 removed outlier: 3.604A pdb=" N GLN A 78 " --> pdb=" O TYR A 75 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR A 75 " --> pdb=" O GLN A 78 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL A 66 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 61 removed outlier: 4.634A pdb=" N VAL A 49 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS A 81 " --> pdb=" O GLU A 52 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL B 8 " --> pdb=" O THR A 84 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 141 Processing sheet with id=AA5, first strand: chain 'A' and resid 194 through 198 removed outlier: 5.779A pdb=" N TYR A 253 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG A 252 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ASP A 288 " --> pdb=" O ARG A 252 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU A 254 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N SER A 307 " --> pdb=" O SER A 331 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU A 392 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE A 370 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N MET A 394 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY A 415 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER A 417 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE A 416 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N SER A 451 " --> pdb=" O PHE A 416 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N PHE A 418 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LYS A 448 " --> pdb=" O PHE A 479 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N SER A 481 " --> pdb=" O LYS A 448 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL A 450 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A 502 " --> pdb=" O VAL A 478 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER A 521 " --> pdb=" O VAL A 501 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 207 through 209 removed outlier: 6.011A pdb=" N LEU A 230 " --> pdb=" O THR A 260 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 213 through 215 removed outlier: 5.947A pdb=" N LEU A 241 " --> pdb=" O ASP A 269 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU A 300 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N THR A 270 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N GLN A 302 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N TYR A 299 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU A 324 " --> pdb=" O TYR A 299 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N MET A 301 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLU A 296 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU A 321 " --> pdb=" O GLU A 296 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 213 through 215 removed outlier: 5.947A pdb=" N LEU A 241 " --> pdb=" O ASP A 269 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU A 300 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N THR A 270 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N GLN A 302 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N TYR A 299 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU A 324 " --> pdb=" O TYR A 299 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N MET A 301 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N GLY A 349 " --> pdb=" O CYS A 317 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL A 319 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ARG A 351 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU A 321 " --> pdb=" O ARG A 351 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N GLN A 353 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N PHE A 323 " --> pdb=" O GLN A 353 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 470 " --> pdb=" O ILE A 436 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 337 through 338 removed outlier: 3.552A pdb=" N ILE A 378 " --> pdb=" O PHE A 337 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N CYS A 377 " --> pdb=" O ASP A 400 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 355 through 357 removed outlier: 3.529A pdb=" N GLN A 355 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR A 357 " --> pdb=" O GLU A 362 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU A 362 " --> pdb=" O TYR A 357 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 421 through 423 removed outlier: 6.128A pdb=" N SER A 421 " --> pdb=" O HIS A 454 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 484 through 485 Processing sheet with id=AB4, first strand: chain 'A' and resid 555 through 558 Processing sheet with id=AB5, first strand: chain 'B' and resid 73 through 74 removed outlier: 3.555A pdb=" N VAL B 74 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL B 66 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY B 34 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE B 101 " --> pdb=" O VAL B 92 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 59 through 61 removed outlier: 4.168A pdb=" N VAL B 49 " --> pdb=" O VAL B 61 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 140 through 141 Processing sheet with id=AB8, first strand: chain 'B' and resid 196 through 198 removed outlier: 5.716A pdb=" N LEU B 196 " --> pdb=" O ARG B 222 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 207 through 209 removed outlier: 3.540A pdb=" N THR B 260 " --> pdb=" O LEU B 230 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 213 through 214 removed outlier: 5.759A pdb=" N LEU B 213 " --> pdb=" O ARG B 242 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLY B 267 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU B 241 " --> pdb=" O GLY B 267 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ALA B 298 " --> pdb=" O ASN B 266 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 322 through 323 removed outlier: 6.687A pdb=" N ALA B 383 " --> pdb=" O PHE B 348 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE B 352 " --> pdb=" O TYR B 385 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.801A pdb=" N ALA B 368 " --> pdb=" O VAL B 328 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 335 through 338 removed outlier: 6.023A pdb=" N CYS B 335 " --> pdb=" O MET B 376 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE B 378 " --> pdb=" O CYS B 335 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N PHE B 337 " --> pdb=" O ILE B 378 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TRP B 422 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ILE B 423 " --> pdb=" O ASN B 456 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N CYS B 483 " --> pdb=" O ILE B 507 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N CYS B 506 " --> pdb=" O TYR B 526 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 390 through 392 removed outlier: 3.860A pdb=" N ASP B 391 " --> pdb=" O ASN B 413 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLY B 415 " --> pdb=" O ASP B 391 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 554 through 555 Processing sheet with id=AC7, first strand: chain 'B' and resid 558 through 559 Processing sheet with id=AC8, first strand: chain 'C' and resid 30 through 31 removed outlier: 4.611A pdb=" N VAL C 66 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 140 through 141 Processing sheet with id=AD1, first strand: chain 'C' and resid 207 through 209 removed outlier: 3.739A pdb=" N THR C 260 " --> pdb=" O LEU C 230 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 213 through 215 removed outlier: 7.329A pdb=" N ASN C 266 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU C 300 " --> pdb=" O ASN C 266 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE C 268 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLU C 296 " --> pdb=" O CYS C 317 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N LEU C 321 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N LEU C 300 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N PHE C 323 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLY C 349 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ALA C 383 " --> pdb=" O PHE C 348 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N VAL C 408 " --> pdb=" O ASN C 382 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL C 384 " --> pdb=" O VAL C 408 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 221 through 222 removed outlier: 6.479A pdb=" N LEU C 254 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR C 283 " --> pdb=" O HIS C 306 " (cutoff:3.500A) removed outlier: 9.368A pdb=" N LYS C 308 " --> pdb=" O TYR C 283 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N TRP C 285 " --> pdb=" O LYS C 308 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ILE C 310 " --> pdb=" O TRP C 285 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N PHE C 287 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL C 330 " --> pdb=" O HIS C 306 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LYS C 308 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL C 332 " --> pdb=" O LYS C 308 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ILE C 310 " --> pdb=" O VAL C 332 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 312 through 314 removed outlier: 7.825A pdb=" N CYS C 312 " --> pdb=" O HIS C 336 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N SER C 338 " --> pdb=" O CYS C 312 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA C 314 " --> pdb=" O SER C 338 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N CYS C 335 " --> pdb=" O MET C 376 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ILE C 378 " --> pdb=" O CYS C 335 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N PHE C 337 " --> pdb=" O ILE C 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'C' and resid 355 through 356 removed outlier: 3.903A pdb=" N GLN C 355 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 389 through 390 removed outlier: 6.304A pdb=" N CYS C 389 " --> pdb=" O ASN C 413 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 416 through 418 removed outlier: 6.514A pdb=" N PHE C 416 " --> pdb=" O ILE C 449 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LYS C 448 " --> pdb=" O PHE C 479 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'C' and resid 495 through 497 removed outlier: 6.436A pdb=" N ARG C 516 " --> pdb=" O VAL C 495 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE C 497 " --> pdb=" O ARG C 516 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 512 through 514 removed outlier: 5.842A pdb=" N LEU C 512 " --> pdb=" O THR C 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 521 through 523 removed outlier: 6.641A pdb=" N VAL C 522 " --> pdb=" O ARG C 544 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 568 through 570 Processing sheet with id=AE3, first strand: chain 'C' and resid 583 through 584 removed outlier: 4.210A pdb=" N MET C 617 " --> pdb=" O LEU C 584 " (cutoff:3.500A) 241 hydrogen bonds defined for protein. 588 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: 2.44 Time building geometry restraints manager: 1.44 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: 4768 1.34 - 1.46: 3270 1.46 - 1.58: 6346 1.58 - 1.70: 0 1.70 - 1.82: 93 Bond restraints: 14477 Sorted by residual: bond pdb=" CA THR B 430 " pdb=" CB THR B 430 " ideal model delta sigma weight residual 1.528 1.562 -0.034 2.61e-02 1.47e+03 1.69e+00 bond pdb=" C VAL C 549 " pdb=" N PRO C 550 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.18e+00 bond pdb=" CG MET A 291 " pdb=" SD MET A 291 " ideal model delta sigma weight residual 1.803 1.776 0.027 2.50e-02 1.60e+03 1.17e+00 bond pdb=" N GLU A 532 " pdb=" CA GLU A 532 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.13e+00 bond pdb=" CB VAL B 74 " pdb=" CG2 VAL B 74 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.11e+00 ... (remaining 14472 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 19339 1.85 - 3.70: 328 3.70 - 5.55: 34 5.55 - 7.40: 12 7.40 - 9.25: 1 Bond angle restraints: 19714 Sorted by residual: angle pdb=" CA GLY C 554 " pdb=" C GLY C 554 " pdb=" N ILE C 555 " ideal model delta sigma weight residual 114.58 117.93 -3.35 8.60e-01 1.35e+00 1.51e+01 angle pdb=" CA MET A 394 " pdb=" CB MET A 394 " pdb=" CG MET A 394 " ideal model delta sigma weight residual 114.10 120.97 -6.87 2.00e+00 2.50e-01 1.18e+01 angle pdb=" CB MET A 617 " pdb=" CG MET A 617 " pdb=" SD MET A 617 " ideal model delta sigma weight residual 112.70 121.95 -9.25 3.00e+00 1.11e-01 9.50e+00 angle pdb=" N GLU B 85 " pdb=" CA GLU B 85 " pdb=" CB GLU B 85 " ideal model delta sigma weight residual 113.65 109.15 4.50 1.47e+00 4.63e-01 9.38e+00 angle pdb=" CA MET A 617 " pdb=" CB MET A 617 " pdb=" CG MET A 617 " ideal model delta sigma weight residual 114.10 119.78 -5.68 2.00e+00 2.50e-01 8.08e+00 ... (remaining 19709 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 7806 17.83 - 35.65: 624 35.65 - 53.48: 114 53.48 - 71.30: 40 71.30 - 89.13: 17 Dihedral angle restraints: 8601 sinusoidal: 3234 harmonic: 5367 Sorted by residual: dihedral pdb=" CA VAL A 282 " pdb=" C VAL A 282 " pdb=" N TYR A 283 " pdb=" CA TYR A 283 " ideal model delta harmonic sigma weight residual -180.00 -152.75 -27.25 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA ASP C 372 " pdb=" C ASP C 372 " pdb=" N SER C 373 " pdb=" CA SER C 373 " ideal model delta harmonic sigma weight residual 180.00 158.64 21.36 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA LEU C 321 " pdb=" C LEU C 321 " pdb=" N HIS C 322 " pdb=" CA HIS C 322 " ideal model delta harmonic sigma weight residual -180.00 -158.87 -21.13 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 8598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1496 0.039 - 0.079: 466 0.079 - 0.118: 253 0.118 - 0.157: 38 0.157 - 0.197: 3 Chirality restraints: 2256 Sorted by residual: chirality pdb=" CG LEU C 512 " pdb=" CB LEU C 512 " pdb=" CD1 LEU C 512 " pdb=" CD2 LEU C 512 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.67e-01 chirality pdb=" CB ILE C 476 " pdb=" CA ILE C 476 " pdb=" CG1 ILE C 476 " pdb=" CG2 ILE C 476 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 7.22e-01 chirality pdb=" CB THR A 249 " pdb=" CA THR A 249 " pdb=" OG1 THR A 249 " pdb=" CG2 THR A 249 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.09e-01 ... (remaining 2253 not shown) Planarity restraints: 2592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 440 " -0.044 5.00e-02 4.00e+02 6.73e-02 7.24e+00 pdb=" N PRO C 441 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 441 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 441 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 115 " -0.043 5.00e-02 4.00e+02 6.57e-02 6.91e+00 pdb=" N PRO C 116 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO C 116 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 116 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 145 " -0.039 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO A 146 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " -0.033 5.00e-02 4.00e+02 ... (remaining 2589 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 919 2.73 - 3.27: 15089 3.27 - 3.81: 23416 3.81 - 4.36: 28027 4.36 - 4.90: 48418 Nonbonded interactions: 115869 Sorted by model distance: nonbonded pdb=" NH2 ARG C 339 " pdb=" O SER C 343 " model vdw 2.183 3.120 nonbonded pdb=" NH1 ARG B 365 " pdb=" OD1 ASP B 388 " model vdw 2.242 3.120 nonbonded pdb=" OG ASER B 419 " pdb=" OD1 ASN B 420 " model vdw 2.244 3.040 nonbonded pdb=" OG BSER B 419 " pdb=" OD1 ASN B 420 " model vdw 2.251 3.040 nonbonded pdb=" O PRO A 550 " pdb=" ND2 ASN A 573 " model vdw 2.269 3.120 ... (remaining 115864 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 113 or (resid 114 through 115 and (name N or nam \ e CA or name C or name O )) or resid 116 through 157 or resid 159 through 233 or \ resid 236 through 337 or resid 339 through 344 or resid 346 through 418 or resi \ d 420 through 430 or resid 432 through 438 or resid 440 through 459 or resid 461 \ through 508 or resid 510 through 520 or resid 522 through 555 or resid 557 thro \ ugh 581 or resid 583 through 590 or resid 592 through 603 or resid 605 through 6 \ 20 or resid 622 through 623)) selection = (chain 'B' and (resid 5 through 113 or (resid 114 through 115 and (name N or nam \ e CA or name C or name O )) or resid 116 through 157 or resid 159 through 233 or \ resid 236 through 337 or resid 339 through 344 or resid 346 through 418 or resi \ d 420 through 430 or resid 432 through 438 or resid 440 through 459 or resid 461 \ through 508 or resid 510 through 520 or resid 522 through 555 or resid 557 thro \ ugh 581 or resid 583 through 590 or resid 592 through 603 or resid 605 through 6 \ 20 or resid 622 through 623)) selection = (chain 'C' and (resid 5 through 157 or resid 159 through 233 or resid 236 throug \ h 337 or resid 339 through 344 or resid 346 through 418 or resid 420 through 430 \ or resid 432 through 438 or resid 440 through 459 or resid 461 through 508 or r \ esid 510 through 520 or resid 522 through 555 or resid 557 through 581 or resid \ 583 through 590 or resid 592 through 603 or resid 605 through 620 or resid 622 t \ hrough 623)) } 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=0.00 max=1.00 mean=0.99 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: 9.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.380 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 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 : 0.003 0.035 14477 Z= 0.155 Angle : 0.609 9.245 19714 Z= 0.326 Chirality : 0.048 0.197 2256 Planarity : 0.005 0.067 2592 Dihedral : 14.529 89.126 5179 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.77 % Favored : 87.23 % Rotamer: Outliers : 1.78 % Allowed : 1.14 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.80 (0.19), residues: 1867 helix: 0.35 (0.58), residues: 91 sheet: -2.00 (0.26), residues: 447 loop : -2.09 (0.16), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 339 TYR 0.030 0.001 TYR A 283 PHE 0.030 0.001 PHE C 477 TRP 0.029 0.002 TRP A 490 HIS 0.014 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00342 (14477) covalent geometry : angle 0.60854 (19714) hydrogen bonds : bond 0.20360 ( 239) hydrogen bonds : angle 7.05703 ( 588) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.516 Fit side-chains revert: symmetry clash REVERT: C 291 MET cc_start: 0.7538 (mtp) cc_final: 0.7325 (mtm) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0911 time to fit residues: 7.8067 Evaluate side-chains 39 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 40.0000 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 40.0000 chunk 149 optimal weight: 50.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN C 293 ASN ** C 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.074836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.050429 restraints weight = 289294.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.053874 restraints weight = 65890.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.054864 restraints weight = 27019.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.055266 restraints weight = 17072.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.055627 restraints weight = 16738.646| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 43 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.0640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14477 Z= 0.138 Angle : 0.580 7.212 19714 Z= 0.311 Chirality : 0.048 0.218 2256 Planarity : 0.005 0.063 2592 Dihedral : 4.846 43.889 2014 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.23 % Favored : 87.77 % Rotamer: Outliers : 2.16 % Allowed : 4.20 % Favored : 93.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.19), residues: 1867 helix: 0.64 (0.60), residues: 90 sheet: -1.95 (0.26), residues: 455 loop : -2.07 (0.16), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 339 TYR 0.026 0.001 TYR A 283 PHE 0.010 0.001 PHE C 323 TRP 0.016 0.001 TRP A 490 HIS 0.009 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00317 (14477) covalent geometry : angle 0.57984 (19714) hydrogen bonds : bond 0.03711 ( 239) hydrogen bonds : angle 6.15622 ( 588) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.489 Fit side-chains REVERT: C 376 MET cc_start: 0.7347 (ptt) cc_final: 0.7032 (ptt) outliers start: 3 outliers final: 2 residues processed: 48 average time/residue: 0.0907 time to fit residues: 7.8199 Evaluate side-chains 41 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain B residue 405 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 26 optimal weight: 40.0000 chunk 149 optimal weight: 2.9990 chunk 42 optimal weight: 30.0000 chunk 162 optimal weight: 30.0000 chunk 179 optimal weight: 50.0000 chunk 23 optimal weight: 20.0000 chunk 107 optimal weight: 50.0000 chunk 141 optimal weight: 7.9990 chunk 109 optimal weight: 30.0000 chunk 28 optimal weight: 20.0000 chunk 108 optimal weight: 9.9990 overall best weight: 12.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN C 573 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.072880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.048500 restraints weight = 269481.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.051381 restraints weight = 62698.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.052630 restraints weight = 30201.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.053734 restraints weight = 17196.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.053817 restraints weight = 14580.920| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3093 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 46 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| r_final: 0.3092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 14477 Z= 0.252 Angle : 0.639 8.150 19714 Z= 0.344 Chirality : 0.049 0.182 2256 Planarity : 0.005 0.066 2592 Dihedral : 5.233 46.889 2014 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.42 % Favored : 86.58 % Rotamer: Outliers : 2.35 % Allowed : 6.04 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.18), residues: 1867 helix: 0.29 (0.58), residues: 90 sheet: -2.07 (0.26), residues: 441 loop : -2.19 (0.16), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 339 TYR 0.020 0.002 TYR A 283 PHE 0.015 0.002 PHE A 418 TRP 0.010 0.002 TRP C 490 HIS 0.013 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00580 (14477) covalent geometry : angle 0.63875 (19714) hydrogen bonds : bond 0.04291 ( 239) hydrogen bonds : angle 6.17082 ( 588) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.475 Fit side-chains REVERT: A 138 MET cc_start: 0.8926 (mtm) cc_final: 0.8713 (ptp) REVERT: C 376 MET cc_start: 0.7645 (ptt) cc_final: 0.7273 (ptt) REVERT: C 392 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8594 (tt) outliers start: 5 outliers final: 3 residues processed: 42 average time/residue: 0.0835 time to fit residues: 6.4876 Evaluate side-chains 43 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain C residue 389 CYS Chi-restraints excluded: chain C residue 392 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 72 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 170 optimal weight: 40.0000 chunk 6 optimal weight: 5.9990 chunk 100 optimal weight: 30.0000 chunk 26 optimal weight: 50.0000 chunk 138 optimal weight: 20.0000 chunk 175 optimal weight: 20.0000 chunk 94 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN C 182 ASN C 573 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.074246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.050177 restraints weight = 284514.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.053907 restraints weight = 65364.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.054456 restraints weight = 27164.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.054706 restraints weight = 18540.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.054925 restraints weight = 17870.667| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 55 | |-----------------------------------------------------------------------------| r_final: 0.3122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14477 Z= 0.133 Angle : 0.558 7.529 19714 Z= 0.300 Chirality : 0.048 0.171 2256 Planarity : 0.005 0.064 2592 Dihedral : 4.919 46.631 2014 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.58 % Favored : 88.42 % Rotamer: Outliers : 2.48 % Allowed : 7.37 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.19), residues: 1867 helix: 0.61 (0.60), residues: 90 sheet: -2.03 (0.26), residues: 449 loop : -2.12 (0.16), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 339 TYR 0.022 0.001 TYR A 283 PHE 0.010 0.001 PHE C 323 TRP 0.011 0.001 TRP C 490 HIS 0.010 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00306 (14477) covalent geometry : angle 0.55804 (19714) hydrogen bonds : bond 0.03318 ( 239) hydrogen bonds : angle 5.88124 ( 588) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.586 Fit side-chains REVERT: A 19 MET cc_start: 0.9486 (mmm) cc_final: 0.9043 (mmm) REVERT: C 376 MET cc_start: 0.7720 (ptt) cc_final: 0.7264 (ptt) REVERT: C 392 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8737 (tt) outliers start: 6 outliers final: 4 residues processed: 50 average time/residue: 0.0942 time to fit residues: 8.1584 Evaluate side-chains 45 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 549 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 103 optimal weight: 20.0000 chunk 81 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 167 optimal weight: 20.0000 chunk 1 optimal weight: 0.7980 chunk 72 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 chunk 175 optimal weight: 5.9990 chunk 177 optimal weight: 30.0000 chunk 15 optimal weight: 10.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.074451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.049995 restraints weight = 309303.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.053483 restraints weight = 67466.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.054422 restraints weight = 28344.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.055070 restraints weight = 16906.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.055294 restraints weight = 16004.538| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 55 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 55 | |-----------------------------------------------------------------------------| r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14477 Z= 0.130 Angle : 0.548 7.748 19714 Z= 0.294 Chirality : 0.047 0.194 2256 Planarity : 0.004 0.062 2592 Dihedral : 4.778 45.168 2014 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.12 % Favored : 87.88 % Rotamer: Outliers : 2.67 % Allowed : 8.39 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.19), residues: 1867 helix: 0.65 (0.60), residues: 90 sheet: -2.00 (0.26), residues: 450 loop : -2.08 (0.16), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 339 TYR 0.018 0.001 TYR A 283 PHE 0.009 0.001 PHE C 323 TRP 0.010 0.001 TRP C 490 HIS 0.009 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00299 (14477) covalent geometry : angle 0.54836 (19714) hydrogen bonds : bond 0.03150 ( 239) hydrogen bonds : angle 5.70177 ( 588) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.502 Fit side-chains REVERT: A 19 MET cc_start: 0.9486 (mmm) cc_final: 0.9003 (mmm) REVERT: C 376 MET cc_start: 0.7694 (ptt) cc_final: 0.7245 (ptt) REVERT: C 392 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8695 (tt) outliers start: 9 outliers final: 5 residues processed: 49 average time/residue: 0.0828 time to fit residues: 7.3306 Evaluate side-chains 46 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain C residue 389 CYS Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 549 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 40 optimal weight: 50.0000 chunk 80 optimal weight: 7.9990 chunk 14 optimal weight: 0.0970 chunk 118 optimal weight: 30.0000 chunk 140 optimal weight: 5.9990 chunk 169 optimal weight: 50.0000 chunk 86 optimal weight: 40.0000 chunk 155 optimal weight: 20.0000 chunk 161 optimal weight: 40.0000 chunk 101 optimal weight: 30.0000 chunk 181 optimal weight: 0.0060 overall best weight: 6.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.074115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.049999 restraints weight = 316984.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.053186 restraints weight = 72976.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.054245 restraints weight = 27885.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.054437 restraints weight = 18684.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.054650 restraints weight = 18076.404| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 55 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 55 | |-----------------------------------------------------------------------------| r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14477 Z= 0.154 Angle : 0.556 7.953 19714 Z= 0.299 Chirality : 0.047 0.179 2256 Planarity : 0.004 0.063 2592 Dihedral : 4.817 45.377 2014 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.12 % Favored : 87.88 % Rotamer: Outliers : 2.67 % Allowed : 9.35 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.19), residues: 1867 helix: 0.64 (0.60), residues: 90 sheet: -2.04 (0.25), residues: 462 loop : -2.08 (0.16), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 339 TYR 0.022 0.001 TYR A 514 PHE 0.009 0.001 PHE B 503 TRP 0.010 0.001 TRP C 490 HIS 0.011 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00355 (14477) covalent geometry : angle 0.55593 (19714) hydrogen bonds : bond 0.03280 ( 239) hydrogen bonds : angle 5.66006 ( 588) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.507 Fit side-chains REVERT: A 19 MET cc_start: 0.9501 (mmm) cc_final: 0.8953 (mmm) REVERT: B 376 MET cc_start: 0.6511 (ptt) cc_final: 0.6282 (ptt) REVERT: C 376 MET cc_start: 0.7719 (ptt) cc_final: 0.7248 (ptt) REVERT: C 392 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8679 (tt) outliers start: 9 outliers final: 8 residues processed: 50 average time/residue: 0.0782 time to fit residues: 7.1820 Evaluate side-chains 50 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 389 CYS Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 595 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 116 optimal weight: 0.1980 chunk 151 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 140 optimal weight: 40.0000 chunk 146 optimal weight: 0.0170 chunk 173 optimal weight: 30.0000 chunk 81 optimal weight: 7.9990 chunk 145 optimal weight: 20.0000 chunk 6 optimal weight: 7.9990 chunk 114 optimal weight: 30.0000 chunk 115 optimal weight: 20.0000 overall best weight: 3.8424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.074989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.051008 restraints weight = 271732.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.054428 restraints weight = 64952.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.055126 restraints weight = 26270.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.055139 restraints weight = 20521.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.055398 restraints weight = 19440.552| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 55 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14477 Z= 0.108 Angle : 0.527 8.451 19714 Z= 0.282 Chirality : 0.047 0.171 2256 Planarity : 0.004 0.062 2592 Dihedral : 4.636 44.360 2014 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 2.67 % Allowed : 10.04 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.19), residues: 1867 helix: 0.61 (0.57), residues: 96 sheet: -1.95 (0.25), residues: 456 loop : -2.06 (0.16), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 339 TYR 0.017 0.001 TYR A 283 PHE 0.010 0.001 PHE C 323 TRP 0.011 0.001 TRP C 490 HIS 0.009 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00248 (14477) covalent geometry : angle 0.52710 (19714) hydrogen bonds : bond 0.02872 ( 239) hydrogen bonds : angle 5.49726 ( 588) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.520 Fit side-chains REVERT: A 19 MET cc_start: 0.9465 (mmm) cc_final: 0.9217 (mmm) REVERT: C 376 MET cc_start: 0.7808 (ptt) cc_final: 0.7370 (ptt) REVERT: C 392 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8704 (tt) outliers start: 9 outliers final: 8 residues processed: 50 average time/residue: 0.0852 time to fit residues: 7.7483 Evaluate side-chains 49 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 389 CYS Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 549 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 30.0000 chunk 9 optimal weight: 10.0000 chunk 159 optimal weight: 30.0000 chunk 127 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 180 optimal weight: 30.0000 chunk 26 optimal weight: 30.0000 chunk 101 optimal weight: 7.9990 chunk 171 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 108 optimal weight: 40.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.073693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.049925 restraints weight = 264213.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.053429 restraints weight = 68579.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.053835 restraints weight = 27142.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.053862 restraints weight = 21826.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.054097 restraints weight = 20492.117| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 55 | |-----------------------------------------------------------------------------| r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14477 Z= 0.186 Angle : 0.572 8.273 19714 Z= 0.308 Chirality : 0.048 0.166 2256 Planarity : 0.005 0.063 2592 Dihedral : 4.882 46.032 2014 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.15 % Favored : 86.85 % Rotamer: Outliers : 2.80 % Allowed : 10.30 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.78 (0.19), residues: 1867 helix: 0.58 (0.59), residues: 90 sheet: -2.02 (0.25), residues: 457 loop : -2.08 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 339 TYR 0.023 0.001 TYR A 514 PHE 0.010 0.001 PHE B 503 TRP 0.010 0.001 TRP C 490 HIS 0.009 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00428 (14477) covalent geometry : angle 0.57231 (19714) hydrogen bonds : bond 0.03450 ( 239) hydrogen bonds : angle 5.63568 ( 588) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.504 Fit side-chains REVERT: A 19 MET cc_start: 0.9485 (mmm) cc_final: 0.9095 (mmm) REVERT: C 376 MET cc_start: 0.7884 (ptt) cc_final: 0.7434 (ptt) REVERT: C 392 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8667 (tt) outliers start: 11 outliers final: 10 residues processed: 53 average time/residue: 0.0801 time to fit residues: 7.7302 Evaluate side-chains 54 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 389 CYS Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 595 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 122 optimal weight: 50.0000 chunk 156 optimal weight: 30.0000 chunk 176 optimal weight: 0.9980 chunk 104 optimal weight: 8.9990 chunk 109 optimal weight: 20.0000 chunk 50 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 143 optimal weight: 20.0000 chunk 93 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 111 optimal weight: 8.9990 overall best weight: 6.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.074075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.049168 restraints weight = 250595.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.051952 restraints weight = 56344.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.053693 restraints weight = 26550.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.054777 restraints weight = 16787.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.055499 restraints weight = 12608.578| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 55 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14477 Z= 0.151 Angle : 0.560 8.573 19714 Z= 0.300 Chirality : 0.047 0.156 2256 Planarity : 0.004 0.064 2592 Dihedral : 4.847 46.582 2014 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.58 % Favored : 88.42 % Rotamer: Outliers : 2.80 % Allowed : 10.36 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.75 (0.19), residues: 1867 helix: 0.60 (0.59), residues: 90 sheet: -2.05 (0.25), residues: 451 loop : -2.04 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 339 TYR 0.015 0.001 TYR A 283 PHE 0.009 0.001 PHE C 323 TRP 0.011 0.001 TRP C 490 HIS 0.009 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00348 (14477) covalent geometry : angle 0.55980 (19714) hydrogen bonds : bond 0.03242 ( 239) hydrogen bonds : angle 5.58695 ( 588) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.428 Fit side-chains REVERT: A 19 MET cc_start: 0.9474 (mmm) cc_final: 0.9122 (mmm) REVERT: C 376 MET cc_start: 0.7923 (ptt) cc_final: 0.7475 (ptt) REVERT: C 392 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8614 (tt) outliers start: 11 outliers final: 10 residues processed: 52 average time/residue: 0.0854 time to fit residues: 8.0613 Evaluate side-chains 53 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 389 CYS Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 595 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 104 optimal weight: 7.9990 chunk 18 optimal weight: 20.0000 chunk 179 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 180 optimal weight: 0.0050 chunk 123 optimal weight: 8.9990 chunk 145 optimal weight: 30.0000 chunk 174 optimal weight: 50.0000 chunk 9 optimal weight: 7.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 229 GLN ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 GLN ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.083582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.057517 restraints weight = 286385.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.060649 restraints weight = 61279.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.062686 restraints weight = 28819.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.064002 restraints weight = 18178.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.064839 restraints weight = 13549.930| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14477 Z= 0.090 Angle : 0.525 8.720 19714 Z= 0.278 Chirality : 0.047 0.144 2256 Planarity : 0.004 0.061 2592 Dihedral : 4.396 41.506 2014 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 2.61 % Allowed : 10.62 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.19), residues: 1867 helix: 0.66 (0.58), residues: 96 sheet: -1.79 (0.26), residues: 436 loop : -1.99 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 516 TYR 0.021 0.001 TYR A 514 PHE 0.010 0.001 PHE C 323 TRP 0.011 0.001 TRP C 490 HIS 0.006 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00195 (14477) covalent geometry : angle 0.52482 (19714) hydrogen bonds : bond 0.02399 ( 239) hydrogen bonds : angle 5.26502 ( 588) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3734 Ramachandran restraints generated. 1867 Oldfield, 0 Emsley, 1867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.518 Fit side-chains REVERT: A 437 TYR cc_start: 0.7734 (t80) cc_final: 0.7484 (t80) REVERT: C 376 MET cc_start: 0.7582 (ptt) cc_final: 0.7121 (ptt) outliers start: 8 outliers final: 7 residues processed: 60 average time/residue: 0.0824 time to fit residues: 8.9021 Evaluate side-chains 51 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 389 CYS Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 595 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 160 optimal weight: 30.0000 chunk 173 optimal weight: 6.9990 chunk 47 optimal weight: 50.0000 chunk 60 optimal weight: 40.0000 chunk 181 optimal weight: 20.0000 chunk 15 optimal weight: 0.8980 chunk 37 optimal weight: 40.0000 chunk 50 optimal weight: 7.9990 chunk 18 optimal weight: 20.0000 chunk 51 optimal weight: 30.0000 chunk 2 optimal weight: 0.0040 overall best weight: 7.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.074405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.050317 restraints weight = 276309.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.053855 restraints weight = 65378.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.054482 restraints weight = 28458.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.054581 restraints weight = 19800.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.054890 restraints weight = 17888.941| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 56 | |-----------------------------------------------------------------------------| r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 14477 Z= 0.161 Angle : 0.592 19.658 19714 Z= 0.310 Chirality : 0.047 0.175 2256 Planarity : 0.004 0.061 2592 Dihedral : 4.629 43.108 2014 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.88 % Favored : 89.12 % Rotamer: Outliers : 2.67 % Allowed : 11.06 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.19), residues: 1867 helix: 0.62 (0.57), residues: 96 sheet: -1.94 (0.25), residues: 463 loop : -2.00 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 339 TYR 0.013 0.001 TYR A 283 PHE 0.010 0.001 PHE B 287 TRP 0.009 0.001 TRP C 285 HIS 0.010 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00367 (14477) covalent geometry : angle 0.59217 (19714) hydrogen bonds : bond 0.03276 ( 239) hydrogen bonds : angle 5.39479 ( 588) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2739.63 seconds wall clock time: 48 minutes 9.96 seconds (2889.96 seconds total)