Starting phenix.real_space_refine on Fri Feb 16 06:00:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euc_28611/02_2024/8euc_28611_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euc_28611/02_2024/8euc_28611.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euc_28611/02_2024/8euc_28611_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euc_28611/02_2024/8euc_28611_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euc_28611/02_2024/8euc_28611_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euc_28611/02_2024/8euc_28611.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euc_28611/02_2024/8euc_28611.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euc_28611/02_2024/8euc_28611_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8euc_28611/02_2024/8euc_28611_neut_updated.pdb" } resolution = 3.61 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.077 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 66 5.16 5 C 9491 2.51 5 N 2369 2.21 5 O 2630 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 170": "NH1" <-> "NH2" Residue "A TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A ASP 207": "OD1" <-> "OD2" Residue "A ARG 221": "NH1" <-> "NH2" Residue "A PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 235": "OD1" <-> "OD2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 252": "OD1" <-> "OD2" Residue "A PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 377": "OE1" <-> "OE2" Residue "A ARG 410": "NH1" <-> "NH2" Residue "A GLU 412": "OE1" <-> "OE2" Residue "A ASP 418": "OD1" <-> "OD2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 432": "OD1" <-> "OD2" Residue "A ARG 439": "NH1" <-> "NH2" Residue "A ASP 442": "OD1" <-> "OD2" Residue "A GLU 455": "OE1" <-> "OE2" Residue "A ASP 462": "OD1" <-> "OD2" Residue "A ARG 481": "NH1" <-> "NH2" Residue "A ASP 485": "OD1" <-> "OD2" Residue "A ARG 499": "NH1" <-> "NH2" Residue "A PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 549": "OE1" <-> "OE2" Residue "A ARG 569": "NH1" <-> "NH2" Residue "A GLU 593": "OE1" <-> "OE2" Residue "A ARG 603": "NH1" <-> "NH2" Residue "B TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 170": "NH1" <-> "NH2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 207": "OD1" <-> "OD2" Residue "B ASP 211": "OD1" <-> "OD2" Residue "B ARG 221": "NH1" <-> "NH2" Residue "B ASP 235": "OD1" <-> "OD2" Residue "B ARG 238": "NH1" <-> "NH2" Residue "B PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 347": "NH1" <-> "NH2" Residue "B ASP 384": "OD1" <-> "OD2" Residue "B ARG 410": "NH1" <-> "NH2" Residue "B GLU 412": "OE1" <-> "OE2" Residue "B ASP 418": "OD1" <-> "OD2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 434": "OE1" <-> "OE2" Residue "B ARG 439": "NH1" <-> "NH2" Residue "B GLU 453": "OE1" <-> "OE2" Residue "B GLU 455": "OE1" <-> "OE2" Residue "B ASP 475": "OD1" <-> "OD2" Residue "B ARG 481": "NH1" <-> "NH2" Residue "B ARG 499": "NH1" <-> "NH2" Residue "B PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 524": "OE1" <-> "OE2" Residue "B ASP 532": "OD1" <-> "OD2" Residue "B ASP 533": "OD1" <-> "OD2" Residue "B ASP 543": "OD1" <-> "OD2" Residue "B PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 563": "NH1" <-> "NH2" Residue "B ARG 569": "NH1" <-> "NH2" Residue "B TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 162": "OD1" <-> "OD2" Residue "C TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 170": "NH1" <-> "NH2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 217": "OD1" <-> "OD2" Residue "C ARG 221": "NH1" <-> "NH2" Residue "C PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 228": "OE1" <-> "OE2" Residue "C ASP 235": "OD1" <-> "OD2" Residue "C ARG 238": "NH1" <-> "NH2" Residue "C PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 289": "OD1" <-> "OD2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "C PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 344": "OE1" <-> "OE2" Residue "C ARG 347": "NH1" <-> "NH2" Residue "C ARG 410": "NH1" <-> "NH2" Residue "C PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 434": "OE1" <-> "OE2" Residue "C ARG 439": "NH1" <-> "NH2" Residue "C ASP 452": "OD1" <-> "OD2" Residue "C GLU 453": "OE1" <-> "OE2" Residue "C ASP 462": "OD1" <-> "OD2" Residue "C PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 493": "OE1" <-> "OE2" Residue "C ARG 499": "NH1" <-> "NH2" Residue "C ASP 507": "OD1" <-> "OD2" Residue "C TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 514": "OD1" <-> "OD2" Residue "C PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 543": "OD1" <-> "OD2" Residue "C TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 563": "NH1" <-> "NH2" Residue "C ARG 569": "NH1" <-> "NH2" Residue "C TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 575": "OD1" <-> "OD2" Residue "C ASP 583": "OD1" <-> "OD2" Residue "C GLU 586": "OE1" <-> "OE2" Residue "C ARG 603": "NH1" <-> "NH2" Residue "C ASP 609": "OD1" <-> "OD2" Residue "D ASP 211": "OD1" <-> "OD2" Residue "D TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 274": "NH1" <-> "NH2" Residue "D ARG 279": "NH1" <-> "NH2" Residue "D GLU 289": "OE1" <-> "OE2" Residue "D ARG 291": "NH1" <-> "NH2" Residue "D ARG 295": "NH1" <-> "NH2" Residue "D PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 352": "NH1" <-> "NH2" Residue "D ARG 355": "NH1" <-> "NH2" Residue "D PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 384": "NH1" <-> "NH2" Residue "D ARG 396": "NH1" <-> "NH2" Residue "D GLU 413": "OE1" <-> "OE2" Residue "D PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 456": "NH1" <-> "NH2" Residue "D TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 480": "NH1" <-> "NH2" Residue "D GLU 484": "OE1" <-> "OE2" Residue "D ARG 491": "NH1" <-> "NH2" Residue "D ASP 523": "OD1" <-> "OD2" Residue "D PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 539": "NH1" <-> "NH2" Residue "D PHE 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 568": "OE1" <-> "OE2" Residue "D PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 603": "NH1" <-> "NH2" Residue "D ARG 636": "NH1" <-> "NH2" Residue "D ARG 643": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14560 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3634 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 444, 3623 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 14, 'TRANS': 429} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 444, 3623 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 14, 'TRANS': 429} Chain breaks: 1 bond proxies already assigned to first conformer: 3692 Chain: "B" Number of atoms: 3555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3555 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 14, 'TRANS': 419} Chain breaks: 2 Chain: "C" Number of atoms: 3681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3681 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 14, 'TRANS': 437} Chain: "D" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3556 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 12, 'TRANS': 421} Chain breaks: 1 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE A 392 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 392 " occ=0.50 Time building chain proxies: 9.50, per 1000 atoms: 0.65 Number of scatterers: 14560 At special positions: 0 Unit cell: (132.25, 108.974, 104.742, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 P 4 15.00 O 2630 8.00 N 2369 7.00 C 9491 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 801 " - " ASN A 339 " " NAG B 801 " - " ASN B 339 " " NAG C 801 " - " ASN C 339 " Time building additional restraints: 5.91 Conformation dependent library (CDL) restraints added in 3.2 seconds 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3350 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 74 helices and 9 sheets defined 60.4% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.69 Creating SS restraints... Processing helix chain 'A' and resid 167 through 191 Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 193 through 198 Processing helix chain 'A' and resid 201 through 223 removed outlier: 4.115A pdb=" N ARG A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 244 Processing helix chain 'A' and resid 247 through 254 Processing helix chain 'A' and resid 271 through 279 removed outlier: 3.508A pdb=" N ARG A 274 " --> pdb=" O PRO A 271 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE A 275 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ASN A 276 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 294 Processing helix chain 'A' and resid 298 through 328 Processing helix chain 'A' and resid 348 through 363 Processing helix chain 'A' and resid 375 through 406 removed outlier: 3.825A pdb=" N ALA A 393 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY A 397 " --> pdb=" O ALA A 393 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN A 398 " --> pdb=" O THR A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 426 Processing helix chain 'A' and resid 431 through 447 Processing helix chain 'A' and resid 453 through 456 No H-bonds generated for 'chain 'A' and resid 453 through 456' Processing helix chain 'A' and resid 462 through 472 Processing helix chain 'A' and resid 474 through 477 No H-bonds generated for 'chain 'A' and resid 474 through 477' Processing helix chain 'A' and resid 488 through 497 Processing helix chain 'A' and resid 550 through 553 No H-bonds generated for 'chain 'A' and resid 550 through 553' Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 593 through 608 Processing helix chain 'B' and resid 167 through 192 Proline residue: B 178 - end of helix removed outlier: 3.780A pdb=" N TYR B 184 " --> pdb=" O PHE B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 198 No H-bonds generated for 'chain 'B' and resid 195 through 198' Processing helix chain 'B' and resid 200 through 222 Processing helix chain 'B' and resid 236 through 244 Processing helix chain 'B' and resid 247 through 255 Processing helix chain 'B' and resid 271 through 273 No H-bonds generated for 'chain 'B' and resid 271 through 273' Processing helix chain 'B' and resid 275 through 279 removed outlier: 3.825A pdb=" N LEU B 278 " --> pdb=" O PHE B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 294 Processing helix chain 'B' and resid 298 through 328 Processing helix chain 'B' and resid 348 through 363 Processing helix chain 'B' and resid 375 through 427 removed outlier: 5.617A pdb=" N SER B 409 " --> pdb=" O ASN B 405 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ARG B 410 " --> pdb=" O MET B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 447 Processing helix chain 'B' and resid 453 through 459 removed outlier: 4.014A pdb=" N LYS B 458 " --> pdb=" O LYS B 454 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N SER B 459 " --> pdb=" O GLU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 477 removed outlier: 3.811A pdb=" N ILE B 468 " --> pdb=" O LEU B 464 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 469 " --> pdb=" O LYS B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 497 Processing helix chain 'B' and resid 581 through 587 Processing helix chain 'B' and resid 592 through 609 Processing helix chain 'C' and resid 166 through 192 Proline residue: C 178 - end of helix Processing helix chain 'C' and resid 195 through 198 No H-bonds generated for 'chain 'C' and resid 195 through 198' Processing helix chain 'C' and resid 200 through 221 Processing helix chain 'C' and resid 236 through 244 Processing helix chain 'C' and resid 247 through 255 Processing helix chain 'C' and resid 260 through 266 Processing helix chain 'C' and resid 272 through 274 No H-bonds generated for 'chain 'C' and resid 272 through 274' Processing helix chain 'C' and resid 277 through 279 No H-bonds generated for 'chain 'C' and resid 277 through 279' Processing helix chain 'C' and resid 281 through 294 Processing helix chain 'C' and resid 298 through 328 Processing helix chain 'C' and resid 348 through 363 Processing helix chain 'C' and resid 375 through 426 removed outlier: 3.503A pdb=" N ASN C 407 " --> pdb=" O ILE C 403 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N SER C 409 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ARG C 410 " --> pdb=" O MET C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 446 Processing helix chain 'C' and resid 453 through 457 Processing helix chain 'C' and resid 462 through 477 removed outlier: 5.532A pdb=" N ASP C 475 " --> pdb=" O ASN C 471 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N THR C 476 " --> pdb=" O VAL C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 497 Processing helix chain 'C' and resid 550 through 552 No H-bonds generated for 'chain 'C' and resid 550 through 552' Processing helix chain 'C' and resid 581 through 587 Processing helix chain 'C' and resid 593 through 608 Processing helix chain 'D' and resid 216 through 241 Proline residue: D 237 - end of helix Processing helix chain 'D' and resid 250 through 269 Processing helix chain 'D' and resid 272 through 274 No H-bonds generated for 'chain 'D' and resid 272 through 274' Processing helix chain 'D' and resid 287 through 295 Processing helix chain 'D' and resid 298 through 306 Processing helix chain 'D' and resid 310 through 313 Processing helix chain 'D' and resid 323 through 328 removed outlier: 4.435A pdb=" N ASN D 326 " --> pdb=" O PHE D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 344 Processing helix chain 'D' and resid 348 through 378 Processing helix chain 'D' and resid 393 through 405 Processing helix chain 'D' and resid 417 through 468 removed outlier: 3.900A pdb=" N PHE D 432 " --> pdb=" O PHE D 428 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ASN D 451 " --> pdb=" O ALA D 447 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N GLN D 452 " --> pdb=" O ALA D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 489 Processing helix chain 'D' and resid 495 through 499 Processing helix chain 'D' and resid 504 through 521 removed outlier: 5.589A pdb=" N SER D 517 " --> pdb=" O ASP D 513 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ILE D 518 " --> pdb=" O VAL D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 525 No H-bonds generated for 'chain 'D' and resid 523 through 525' Processing helix chain 'D' and resid 530 through 538 Processing helix chain 'D' and resid 593 through 595 No H-bonds generated for 'chain 'D' and resid 593 through 595' Processing helix chain 'D' and resid 621 through 630 removed outlier: 4.915A pdb=" N HIS D 630 " --> pdb=" O GLU D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 642 Processing sheet with id= A, first strand: chain 'A' and resid 499 through 503 Processing sheet with id= B, first strand: chain 'A' and resid 527 through 530 removed outlier: 3.913A pdb=" N ASN A 567 " --> pdb=" O VAL A 530 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 499 through 503 removed outlier: 3.565A pdb=" N ARG B 499 " --> pdb=" O CYS B 578 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 527 through 529 Processing sheet with id= E, first strand: chain 'C' and resid 499 through 502 removed outlier: 3.612A pdb=" N ARG C 499 " --> pdb=" O CYS C 578 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 527 through 530 removed outlier: 3.569A pdb=" N ASN C 567 " --> pdb=" O VAL C 530 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 277 through 279 removed outlier: 4.263A pdb=" N PHE D 277 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP D 282 " --> pdb=" O ARG D 279 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 560 through 564 Processing sheet with id= I, first strand: chain 'D' and resid 569 through 571 786 hydrogen bonds defined for protein. 2325 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: 4.32 Time building geometry restraints manager: 6.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2298 1.32 - 1.44: 4199 1.44 - 1.57: 8306 1.57 - 1.70: 2 1.70 - 1.82: 105 Bond restraints: 14910 Sorted by residual: bond pdb=" C2' PCG B 802 " pdb=" C3' PCG B 802 " ideal model delta sigma weight residual 1.200 1.569 -0.369 2.00e-02 2.50e+03 3.41e+02 bond pdb=" C2' PCG A 802 " pdb=" C3' PCG A 802 " ideal model delta sigma weight residual 1.200 1.569 -0.369 2.00e-02 2.50e+03 3.40e+02 bond pdb=" C2' PCG C 802 " pdb=" C3' PCG C 802 " ideal model delta sigma weight residual 1.200 1.569 -0.369 2.00e-02 2.50e+03 3.40e+02 bond pdb=" C2' PCG D 901 " pdb=" C3' PCG D 901 " ideal model delta sigma weight residual 1.200 1.568 -0.368 2.00e-02 2.50e+03 3.39e+02 bond pdb=" C3' PCG D 901 " pdb=" C4' PCG D 901 " ideal model delta sigma weight residual 1.808 1.532 0.276 2.00e-02 2.50e+03 1.90e+02 ... (remaining 14905 not shown) Histogram of bond angle deviations from ideal: 97.51 - 105.58: 265 105.58 - 113.66: 8318 113.66 - 121.73: 8765 121.73 - 129.81: 2790 129.81 - 137.88: 103 Bond angle restraints: 20241 Sorted by residual: angle pdb=" N GLY A 397 " pdb=" CA GLY A 397 " pdb=" C GLY A 397 " ideal model delta sigma weight residual 112.77 103.87 8.90 1.28e+00 6.10e-01 4.83e+01 angle pdb=" N THR B 565 " pdb=" CA THR B 565 " pdb=" C THR B 565 " ideal model delta sigma weight residual 111.37 121.98 -10.61 1.64e+00 3.72e-01 4.19e+01 angle pdb=" N ILE A 391 " pdb=" CA ILE A 391 " pdb=" C ILE A 391 " ideal model delta sigma weight residual 110.36 116.77 -6.41 1.05e+00 9.07e-01 3.72e+01 angle pdb=" N ALA C 566 " pdb=" CA ALA C 566 " pdb=" C ALA C 566 " ideal model delta sigma weight residual 108.38 115.84 -7.46 1.35e+00 5.49e-01 3.05e+01 angle pdb=" C3' PCG C 802 " pdb=" C4' PCG C 802 " pdb=" C5' PCG C 802 " ideal model delta sigma weight residual 112.23 128.11 -15.88 3.00e+00 1.11e-01 2.80e+01 ... (remaining 20236 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 7776 17.75 - 35.50: 875 35.50 - 53.25: 156 53.25 - 71.00: 24 71.00 - 88.75: 9 Dihedral angle restraints: 8840 sinusoidal: 3630 harmonic: 5210 Sorted by residual: dihedral pdb=" N ILE A 395 " pdb=" C ILE A 395 " pdb=" CA ILE A 395 " pdb=" CB ILE A 395 " ideal model delta harmonic sigma weight residual 123.40 136.70 -13.30 0 2.50e+00 1.60e-01 2.83e+01 dihedral pdb=" C ILE A 395 " pdb=" N ILE A 395 " pdb=" CA ILE A 395 " pdb=" CB ILE A 395 " ideal model delta harmonic sigma weight residual -122.00 -134.32 12.32 0 2.50e+00 1.60e-01 2.43e+01 dihedral pdb=" CA ASP D 286 " pdb=" C ASP D 286 " pdb=" N SER D 287 " pdb=" CA SER D 287 " ideal model delta harmonic sigma weight residual -180.00 -157.92 -22.08 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 8837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.336: 2288 0.336 - 0.671: 7 0.671 - 1.007: 2 1.007 - 1.342: 0 1.342 - 1.678: 4 Chirality restraints: 2301 Sorted by residual: chirality pdb=" C4' PCG A 802 " pdb=" C3' PCG A 802 " pdb=" C5' PCG A 802 " pdb=" O4' PCG A 802 " both_signs ideal model delta sigma weight residual False -2.40 -0.72 -1.68 2.00e-01 2.50e+01 7.04e+01 chirality pdb=" C4' PCG B 802 " pdb=" C3' PCG B 802 " pdb=" C5' PCG B 802 " pdb=" O4' PCG B 802 " both_signs ideal model delta sigma weight residual False -2.40 -0.72 -1.68 2.00e-01 2.50e+01 7.03e+01 chirality pdb=" C4' PCG C 802 " pdb=" C3' PCG C 802 " pdb=" C5' PCG C 802 " pdb=" O4' PCG C 802 " both_signs ideal model delta sigma weight residual False -2.40 -0.72 -1.68 2.00e-01 2.50e+01 7.02e+01 ... (remaining 2298 not shown) Planarity restraints: 2490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 272 " 0.052 5.00e-02 4.00e+02 7.84e-02 9.84e+00 pdb=" N PRO D 273 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO D 273 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 273 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 499 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO B 500 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 500 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 500 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 187 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.73e+00 pdb=" C ILE B 187 " -0.041 2.00e-02 2.50e+03 pdb=" O ILE B 187 " 0.015 2.00e-02 2.50e+03 pdb=" N CYS B 188 " 0.014 2.00e-02 2.50e+03 ... (remaining 2487 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1723 2.75 - 3.29: 14214 3.29 - 3.82: 25021 3.82 - 4.36: 27487 4.36 - 4.90: 47423 Nonbonded interactions: 115868 Sorted by model distance: nonbonded pdb=" N THR D 605 " pdb=" O1A PCG D 901 " model vdw 2.211 2.520 nonbonded pdb=" O PHE D 516 " pdb=" OG SER D 520 " model vdw 2.284 2.440 nonbonded pdb=" OH TYR B 243 " pdb=" OD2 ASP B 252 " model vdw 2.285 2.440 nonbonded pdb=" OG1 THR B 565 " pdb=" N2 PCG B 802 " model vdw 2.286 2.520 nonbonded pdb=" O ARG A 603 " pdb=" CG LEU A 606 " model vdw 2.306 3.470 ... (remaining 115863 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 159 through 258 or resid 270 through 391 or resid 393 thro \ ugh 554 or resid 562 through 609 or resid 801 through 802)) selection = (chain 'B' and (resid 159 through 391 or resid 393 through 609 or resid 801 thro \ ugh 802)) selection = (chain 'C' and (resid 159 through 258 or resid 270 through 391 or resid 393 thro \ ugh 554 or resid 562 through 609 or resid 801 through 802)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 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: 0.010 Extract box with map and model: 6.090 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 41.790 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 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 : 0.013 0.369 14910 Z= 0.923 Angle : 1.066 15.876 20241 Z= 0.539 Chirality : 0.100 1.678 2301 Planarity : 0.007 0.078 2487 Dihedral : 14.898 88.753 5490 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.32 % Allowed : 8.25 % Favored : 91.43 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.03 (0.15), residues: 1751 helix: -2.41 (0.10), residues: 1160 sheet: -2.80 (0.45), residues: 94 loop : -2.74 (0.23), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 171 HIS 0.005 0.001 HIS D 293 PHE 0.023 0.002 PHE A 483 TYR 0.017 0.002 TYR A 352 ARG 0.008 0.001 ARG D 603 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 281 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 MET cc_start: 0.6758 (mmm) cc_final: 0.6290 (mpp) REVERT: A 297 TYR cc_start: 0.6889 (m-80) cc_final: 0.6668 (m-80) REVERT: A 389 VAL cc_start: 0.8328 (OUTLIER) cc_final: 0.8114 (p) REVERT: A 498 LEU cc_start: 0.8704 (mt) cc_final: 0.8485 (mt) REVERT: B 201 MET cc_start: 0.6987 (ppp) cc_final: 0.6664 (ppp) REVERT: B 425 GLN cc_start: 0.7710 (mt0) cc_final: 0.7471 (mt0) REVERT: B 434 GLU cc_start: 0.7235 (tp30) cc_final: 0.6430 (tp30) REVERT: B 497 LYS cc_start: 0.7442 (mtmm) cc_final: 0.7200 (mmmt) REVERT: B 524 GLU cc_start: 0.7415 (tt0) cc_final: 0.7209 (tt0) REVERT: B 547 PHE cc_start: 0.8751 (p90) cc_final: 0.8400 (p90) REVERT: C 353 ILE cc_start: 0.8968 (mm) cc_final: 0.8676 (mt) REVERT: D 316 PHE cc_start: 0.8225 (m-80) cc_final: 0.7778 (m-10) REVERT: D 619 LEU cc_start: 0.7295 (tp) cc_final: 0.7090 (tp) outliers start: 4 outliers final: 1 residues processed: 285 average time/residue: 0.2788 time to fit residues: 113.7809 Evaluate side-chains 187 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 185 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain C residue 563 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 137 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 102 optimal weight: 0.5980 chunk 158 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN A 299 ASN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 HIS A 405 ASN A 471 ASN ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 GLN B 407 ASN B 414 GLN B 425 GLN C 317 ASN C 407 ASN C 414 GLN ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 GLN D 340 HIS D 365 HIS D 367 ASN D 426 ASN D 507 GLN D 566 HIS D 570 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14910 Z= 0.182 Angle : 0.559 10.734 20241 Z= 0.289 Chirality : 0.040 0.159 2301 Planarity : 0.005 0.062 2487 Dihedral : 5.198 49.935 2056 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.45 % Allowed : 14.87 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.19), residues: 1751 helix: -0.28 (0.14), residues: 1155 sheet: -1.68 (0.53), residues: 78 loop : -2.15 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 440 HIS 0.003 0.001 HIS B 473 PHE 0.013 0.001 PHE B 413 TYR 0.019 0.001 TYR A 443 ARG 0.006 0.000 ARG A 410 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 205 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 TYR cc_start: 0.8053 (p90) cc_final: 0.7841 (p90) REVERT: B 201 MET cc_start: 0.7092 (ppp) cc_final: 0.6550 (ppp) REVERT: C 217 ASP cc_start: 0.7375 (t70) cc_final: 0.6915 (t70) REVERT: C 241 GLN cc_start: 0.8288 (pt0) cc_final: 0.8069 (pp30) REVERT: C 311 LEU cc_start: 0.8821 (tp) cc_final: 0.8533 (tt) REVERT: D 210 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8694 (mt) REVERT: D 316 PHE cc_start: 0.8210 (m-80) cc_final: 0.7772 (m-10) REVERT: D 561 MET cc_start: 0.7203 (tpp) cc_final: 0.6942 (tpp) outliers start: 22 outliers final: 10 residues processed: 221 average time/residue: 0.2405 time to fit residues: 80.4490 Evaluate side-chains 185 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 174 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 303 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 chunk 108 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 159 optimal weight: 0.8980 chunk 171 optimal weight: 9.9990 chunk 141 optimal weight: 0.9990 chunk 157 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 127 optimal weight: 30.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14910 Z= 0.178 Angle : 0.527 8.856 20241 Z= 0.272 Chirality : 0.039 0.157 2301 Planarity : 0.004 0.077 2487 Dihedral : 4.774 51.238 2051 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.21 % Allowed : 16.26 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.20), residues: 1751 helix: 0.50 (0.15), residues: 1158 sheet: -1.31 (0.59), residues: 70 loop : -1.95 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 440 HIS 0.005 0.001 HIS C 242 PHE 0.017 0.001 PHE B 413 TYR 0.015 0.001 TYR C 573 ARG 0.007 0.000 ARG B 221 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 187 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 TYR cc_start: 0.8129 (p90) cc_final: 0.7913 (p90) REVERT: B 524 GLU cc_start: 0.7446 (tt0) cc_final: 0.7063 (tt0) REVERT: C 217 ASP cc_start: 0.7322 (t70) cc_final: 0.6867 (t70) REVERT: C 311 LEU cc_start: 0.8829 (tp) cc_final: 0.8550 (tt) REVERT: D 210 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8715 (mt) REVERT: D 316 PHE cc_start: 0.8225 (m-80) cc_final: 0.7799 (m-10) REVERT: D 561 MET cc_start: 0.7335 (tpp) cc_final: 0.7120 (tpp) outliers start: 34 outliers final: 21 residues processed: 212 average time/residue: 0.2195 time to fit residues: 72.7077 Evaluate side-chains 197 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 175 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 260 CYS Chi-restraints excluded: chain D residue 303 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 82 optimal weight: 6.9990 chunk 17 optimal weight: 0.0270 chunk 75 optimal weight: 0.0170 chunk 106 optimal weight: 2.9990 chunk 159 optimal weight: 0.5980 chunk 169 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 554 ASN A 562 ASN C 447 ASN ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN D 507 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 14910 Z= 0.146 Angle : 0.497 8.512 20241 Z= 0.255 Chirality : 0.038 0.163 2301 Planarity : 0.004 0.068 2487 Dihedral : 4.443 43.828 2051 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.39 % Allowed : 17.58 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.20), residues: 1751 helix: 0.99 (0.15), residues: 1152 sheet: -0.84 (0.58), residues: 76 loop : -1.73 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 440 HIS 0.004 0.001 HIS C 242 PHE 0.019 0.001 PHE B 413 TYR 0.016 0.001 TYR B 423 ARG 0.010 0.000 ARG A 427 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 198 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 LEU cc_start: 0.8908 (mp) cc_final: 0.8474 (mt) REVERT: B 241 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.6693 (mt0) REVERT: B 524 GLU cc_start: 0.7264 (tt0) cc_final: 0.6888 (tt0) REVERT: B 547 PHE cc_start: 0.8557 (p90) cc_final: 0.8305 (p90) REVERT: C 217 ASP cc_start: 0.7265 (t70) cc_final: 0.6782 (t70) REVERT: C 311 LEU cc_start: 0.8791 (tp) cc_final: 0.8545 (tt) REVERT: C 447 ASN cc_start: 0.8202 (OUTLIER) cc_final: 0.7987 (m-40) REVERT: C 519 MET cc_start: 0.7438 (tpt) cc_final: 0.6992 (tpt) REVERT: D 210 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8703 (mt) REVERT: D 316 PHE cc_start: 0.8223 (m-80) cc_final: 0.7801 (m-10) REVERT: D 426 ASN cc_start: 0.8836 (OUTLIER) cc_final: 0.8540 (t0) outliers start: 37 outliers final: 22 residues processed: 228 average time/residue: 0.2236 time to fit residues: 78.6547 Evaluate side-chains 208 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 182 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 447 ASN Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 260 CYS Chi-restraints excluded: chain D residue 426 ASN Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 chunk 116 optimal weight: 0.0670 chunk 0 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 chunk 151 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 ASN A 562 ASN C 248 GLN ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14910 Z= 0.236 Angle : 0.546 7.119 20241 Z= 0.280 Chirality : 0.040 0.147 2301 Planarity : 0.004 0.055 2487 Dihedral : 4.350 33.252 2051 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.90 % Allowed : 18.90 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.20), residues: 1751 helix: 1.03 (0.15), residues: 1155 sheet: -0.83 (0.65), residues: 59 loop : -1.65 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP C 440 HIS 0.004 0.001 HIS C 242 PHE 0.017 0.001 PHE B 413 TYR 0.015 0.001 TYR C 573 ARG 0.007 0.000 ARG B 221 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 178 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 241 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.6762 (mp10) REVERT: B 413 PHE cc_start: 0.7925 (t80) cc_final: 0.7656 (t80) REVERT: B 524 GLU cc_start: 0.7483 (tt0) cc_final: 0.7105 (tt0) REVERT: B 547 PHE cc_start: 0.8675 (p90) cc_final: 0.8473 (p90) REVERT: C 217 ASP cc_start: 0.7389 (t70) cc_final: 0.6968 (t70) REVERT: C 311 LEU cc_start: 0.8855 (tp) cc_final: 0.8578 (tt) REVERT: C 442 ASP cc_start: 0.7541 (t70) cc_final: 0.7097 (t0) REVERT: C 519 MET cc_start: 0.7659 (tpt) cc_final: 0.7284 (tpt) REVERT: C 608 LYS cc_start: 0.4751 (pttt) cc_final: 0.4441 (mmtm) REVERT: D 316 PHE cc_start: 0.8238 (m-80) cc_final: 0.7821 (m-10) REVERT: D 426 ASN cc_start: 0.8835 (OUTLIER) cc_final: 0.8557 (t0) REVERT: D 530 THR cc_start: 0.7703 (p) cc_final: 0.7392 (t) REVERT: D 639 MET cc_start: 0.5567 (tmm) cc_final: 0.5333 (tmm) outliers start: 45 outliers final: 31 residues processed: 212 average time/residue: 0.2162 time to fit residues: 72.8894 Evaluate side-chains 206 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 173 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 424 MET Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain D residue 260 CYS Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 426 ASN Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 4.9990 chunk 152 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 169 optimal weight: 0.0770 chunk 140 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 chunk 14 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 overall best weight: 1.1540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 562 ASN ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14910 Z= 0.206 Angle : 0.526 7.101 20241 Z= 0.269 Chirality : 0.039 0.145 2301 Planarity : 0.004 0.054 2487 Dihedral : 4.246 32.430 2051 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.84 % Allowed : 19.79 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.20), residues: 1751 helix: 1.10 (0.15), residues: 1157 sheet: -0.81 (0.66), residues: 58 loop : -1.55 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 440 HIS 0.004 0.001 HIS C 242 PHE 0.014 0.001 PHE A 483 TYR 0.012 0.001 TYR D 372 ARG 0.005 0.000 ARG B 221 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 184 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 241 GLN cc_start: 0.7440 (OUTLIER) cc_final: 0.6756 (mp10) REVERT: B 413 PHE cc_start: 0.8036 (t80) cc_final: 0.7830 (t80) REVERT: B 524 GLU cc_start: 0.7465 (tt0) cc_final: 0.7094 (tt0) REVERT: C 309 TYR cc_start: 0.8174 (m-10) cc_final: 0.7838 (m-80) REVERT: C 311 LEU cc_start: 0.8831 (tp) cc_final: 0.8570 (tt) REVERT: C 442 ASP cc_start: 0.7559 (t70) cc_final: 0.7128 (t0) REVERT: C 519 MET cc_start: 0.7719 (tpt) cc_final: 0.7344 (tpt) REVERT: C 608 LYS cc_start: 0.5208 (pttt) cc_final: 0.4864 (mmtm) REVERT: D 316 PHE cc_start: 0.8249 (m-80) cc_final: 0.7829 (m-10) REVERT: D 426 ASN cc_start: 0.8821 (OUTLIER) cc_final: 0.8532 (t0) REVERT: D 530 THR cc_start: 0.7772 (p) cc_final: 0.7410 (t) outliers start: 44 outliers final: 30 residues processed: 221 average time/residue: 0.2201 time to fit residues: 76.2724 Evaluate side-chains 209 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 177 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain D residue 260 CYS Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 426 ASN Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 123 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 142 optimal weight: 0.0020 chunk 94 optimal weight: 5.9990 chunk 168 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 562 ASN ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14910 Z= 0.156 Angle : 0.499 6.368 20241 Z= 0.255 Chirality : 0.038 0.157 2301 Planarity : 0.004 0.051 2487 Dihedral : 4.088 33.554 2051 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.39 % Allowed : 20.48 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.21), residues: 1751 helix: 1.26 (0.16), residues: 1152 sheet: -0.71 (0.66), residues: 58 loop : -1.34 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 440 HIS 0.004 0.001 HIS B 473 PHE 0.013 0.001 PHE A 483 TYR 0.011 0.001 TYR C 573 ARG 0.004 0.000 ARG B 221 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 193 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 234 SER cc_start: 0.8801 (m) cc_final: 0.8597 (t) REVERT: B 241 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.6711 (mp10) REVERT: B 524 GLU cc_start: 0.7301 (tt0) cc_final: 0.6970 (tt0) REVERT: C 217 ASP cc_start: 0.7355 (t70) cc_final: 0.6938 (t70) REVERT: C 311 LEU cc_start: 0.8865 (tp) cc_final: 0.8604 (tt) REVERT: C 442 ASP cc_start: 0.7533 (t70) cc_final: 0.7117 (t0) REVERT: C 519 MET cc_start: 0.7682 (tpt) cc_final: 0.7318 (tpt) REVERT: C 608 LYS cc_start: 0.5714 (pttt) cc_final: 0.5329 (mmtm) REVERT: D 316 PHE cc_start: 0.8276 (m-80) cc_final: 0.7857 (m-10) REVERT: D 426 ASN cc_start: 0.8752 (OUTLIER) cc_final: 0.8517 (t0) REVERT: D 530 THR cc_start: 0.7469 (p) cc_final: 0.7112 (t) REVERT: D 566 HIS cc_start: 0.8152 (t70) cc_final: 0.7873 (t70) outliers start: 37 outliers final: 31 residues processed: 223 average time/residue: 0.2244 time to fit residues: 77.9484 Evaluate side-chains 216 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 183 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain D residue 260 CYS Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 426 ASN Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 0.9990 chunk 100 optimal weight: 0.0470 chunk 50 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 107 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 overall best weight: 1.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN A 562 ASN ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14910 Z= 0.206 Angle : 0.526 7.455 20241 Z= 0.269 Chirality : 0.039 0.142 2301 Planarity : 0.004 0.052 2487 Dihedral : 4.089 34.187 2051 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.77 % Allowed : 21.49 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.21), residues: 1751 helix: 1.25 (0.15), residues: 1153 sheet: -0.65 (0.66), residues: 58 loop : -1.39 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP C 440 HIS 0.004 0.001 HIS C 242 PHE 0.022 0.001 PHE B 413 TYR 0.014 0.001 TYR C 573 ARG 0.008 0.000 ARG A 563 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 190 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 234 SER cc_start: 0.8817 (m) cc_final: 0.8608 (t) REVERT: B 241 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.6740 (mp10) REVERT: B 524 GLU cc_start: 0.7450 (tt0) cc_final: 0.7137 (tt0) REVERT: B 603 ARG cc_start: 0.6192 (tpp80) cc_final: 0.5358 (mmt180) REVERT: C 217 ASP cc_start: 0.7399 (t70) cc_final: 0.6987 (t70) REVERT: C 311 LEU cc_start: 0.8854 (tp) cc_final: 0.8625 (tt) REVERT: C 442 ASP cc_start: 0.7574 (t70) cc_final: 0.7150 (t0) REVERT: C 519 MET cc_start: 0.7794 (tpt) cc_final: 0.7421 (tpt) REVERT: C 608 LYS cc_start: 0.6099 (pttt) cc_final: 0.5677 (mmtm) REVERT: D 316 PHE cc_start: 0.8285 (m-80) cc_final: 0.7868 (m-10) REVERT: D 426 ASN cc_start: 0.8779 (OUTLIER) cc_final: 0.8501 (t0) REVERT: D 530 THR cc_start: 0.7501 (p) cc_final: 0.7101 (t) REVERT: D 566 HIS cc_start: 0.8186 (t70) cc_final: 0.7910 (t70) outliers start: 43 outliers final: 34 residues processed: 222 average time/residue: 0.2230 time to fit residues: 77.2903 Evaluate side-chains 223 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 187 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain D residue 260 CYS Chi-restraints excluded: chain D residue 367 ASN Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 426 ASN Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 157 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN A 562 ASN ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 423 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14910 Z= 0.219 Angle : 0.535 8.118 20241 Z= 0.274 Chirality : 0.040 0.145 2301 Planarity : 0.004 0.051 2487 Dihedral : 4.115 35.069 2051 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.77 % Allowed : 21.36 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.21), residues: 1751 helix: 1.23 (0.15), residues: 1154 sheet: -0.59 (0.65), residues: 58 loop : -1.33 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP C 440 HIS 0.004 0.001 HIS C 242 PHE 0.015 0.001 PHE A 483 TYR 0.013 0.001 TYR C 573 ARG 0.005 0.000 ARG B 221 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 187 time to evaluate : 1.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 234 SER cc_start: 0.8845 (m) cc_final: 0.8620 (t) REVERT: B 241 GLN cc_start: 0.7486 (OUTLIER) cc_final: 0.6778 (mp10) REVERT: B 300 MET cc_start: 0.7632 (tpp) cc_final: 0.7265 (tmm) REVERT: B 413 PHE cc_start: 0.7779 (t80) cc_final: 0.7573 (t80) REVERT: B 524 GLU cc_start: 0.7475 (tt0) cc_final: 0.7239 (tt0) REVERT: B 603 ARG cc_start: 0.6204 (tpp80) cc_final: 0.5380 (mmt180) REVERT: C 217 ASP cc_start: 0.7368 (t70) cc_final: 0.6992 (t70) REVERT: C 232 MET cc_start: 0.7056 (tpt) cc_final: 0.6789 (tpt) REVERT: C 311 LEU cc_start: 0.8867 (tp) cc_final: 0.8648 (tt) REVERT: C 442 ASP cc_start: 0.7632 (t70) cc_final: 0.7216 (t0) REVERT: C 519 MET cc_start: 0.7812 (tpt) cc_final: 0.7430 (tpt) REVERT: C 608 LYS cc_start: 0.6176 (pttt) cc_final: 0.5812 (mmtm) REVERT: D 316 PHE cc_start: 0.8293 (m-80) cc_final: 0.7873 (m-10) REVERT: D 426 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.8500 (t0) REVERT: D 566 HIS cc_start: 0.8195 (t70) cc_final: 0.7929 (t70) outliers start: 43 outliers final: 36 residues processed: 220 average time/residue: 0.2242 time to fit residues: 77.1280 Evaluate side-chains 220 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 182 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 333 ASP Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain D residue 260 CYS Chi-restraints excluded: chain D residue 367 ASN Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 426 ASN Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 582 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 78 optimal weight: 0.0870 chunk 115 optimal weight: 0.7980 chunk 174 optimal weight: 0.9990 chunk 160 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 110 optimal weight: 0.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN A 562 ASN ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 531 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14910 Z= 0.166 Angle : 0.511 7.468 20241 Z= 0.264 Chirality : 0.039 0.140 2301 Planarity : 0.004 0.051 2487 Dihedral : 4.068 35.642 2051 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.52 % Allowed : 21.68 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.21), residues: 1751 helix: 1.38 (0.16), residues: 1144 sheet: -0.49 (0.66), residues: 58 loop : -1.23 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP C 440 HIS 0.004 0.001 HIS C 242 PHE 0.013 0.001 PHE A 483 TYR 0.017 0.001 TYR A 546 ARG 0.005 0.000 ARG C 499 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 189 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 234 SER cc_start: 0.8840 (m) cc_final: 0.8611 (t) REVERT: B 241 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.6783 (mp10) REVERT: B 300 MET cc_start: 0.7564 (tpp) cc_final: 0.7362 (tmm) REVERT: B 413 PHE cc_start: 0.7905 (t80) cc_final: 0.7698 (t80) REVERT: B 508 TYR cc_start: 0.7865 (m-80) cc_final: 0.7643 (m-80) REVERT: B 524 GLU cc_start: 0.7436 (tt0) cc_final: 0.7126 (tt0) REVERT: B 603 ARG cc_start: 0.6152 (tpp80) cc_final: 0.5438 (mmt180) REVERT: C 217 ASP cc_start: 0.7321 (t70) cc_final: 0.6934 (t70) REVERT: C 442 ASP cc_start: 0.7645 (t70) cc_final: 0.7249 (t0) REVERT: C 519 MET cc_start: 0.7755 (tpt) cc_final: 0.7380 (tpt) REVERT: C 608 LYS cc_start: 0.6154 (pttt) cc_final: 0.5817 (mmtm) REVERT: D 426 ASN cc_start: 0.8770 (OUTLIER) cc_final: 0.8478 (t0) REVERT: D 530 THR cc_start: 0.7504 (p) cc_final: 0.7115 (t) outliers start: 39 outliers final: 36 residues processed: 221 average time/residue: 0.2462 time to fit residues: 85.6193 Evaluate side-chains 223 residues out of total 1585 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 185 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 492 VAL Chi-restraints excluded: chain B residue 535 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 333 ASP Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 535 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain D residue 260 CYS Chi-restraints excluded: chain D residue 367 ASN Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 426 ASN Chi-restraints excluded: chain D residue 569 VAL Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 608 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 128 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 139 optimal weight: 0.0470 chunk 58 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 562 ASN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 607 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.151519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.115143 restraints weight = 36228.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.116029 restraints weight = 34389.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.117839 restraints weight = 22684.793| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14910 Z= 0.148 Angle : 0.513 12.513 20241 Z= 0.260 Chirality : 0.038 0.137 2301 Planarity : 0.003 0.049 2487 Dihedral : 3.941 35.486 2051 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.46 % Allowed : 21.99 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.21), residues: 1751 helix: 1.49 (0.16), residues: 1144 sheet: -0.46 (0.66), residues: 58 loop : -1.13 (0.28), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP C 440 HIS 0.004 0.001 HIS C 242 PHE 0.012 0.001 PHE A 483 TYR 0.013 0.001 TYR C 573 ARG 0.005 0.000 ARG C 499 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2777.88 seconds wall clock time: 51 minutes 47.56 seconds (3107.56 seconds total)