Starting phenix.real_space_refine on Wed Jan 14 00:57:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qu8_18657/01_2026/8qu8_18657.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qu8_18657/01_2026/8qu8_18657.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qu8_18657/01_2026/8qu8_18657.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qu8_18657/01_2026/8qu8_18657.map" model { file = "/net/cci-nas-00/data/ceres_data/8qu8_18657/01_2026/8qu8_18657.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qu8_18657/01_2026/8qu8_18657.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.028 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2 5.49 5 S 72 5.16 5 C 6866 2.51 5 N 1860 2.21 5 O 2044 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10846 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1136 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 125} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 814 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 8, 'TRANS': 94} Chain: "C" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 760 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "D" Number of atoms: 5974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5974 Classifications: {'peptide': 729} Link IDs: {'PTRANS': 18, 'TRANS': 710} Chain breaks: 1 Chain: "E" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 696 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 86} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 1364 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 170, 1356 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 165} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 170, 1356 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 165} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1368 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 72 Unusual residues: {'WYL': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8909 SG CYS E 42 65.339 55.288 117.949 1.00215.10 S ATOM 8928 SG CYS E 45 63.111 58.326 117.656 1.00206.97 S ATOM 9219 SG CYS E 83 62.797 55.470 115.079 1.00232.79 S ATOM 8995 SG CYS E 53 60.091 56.484 112.306 1.00228.24 S ATOM 9018 SG CYS E 56 58.819 57.359 108.780 1.00236.60 S ATOM 9098 SG CYS E 68 56.530 55.429 111.230 1.00220.30 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AILE F 142 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE F 142 " occ=0.50 residue: pdb=" O5' GDP F 201 " occ=0.00 ... (26 atoms not shown) pdb=" PB GDP F 201 " occ=0.00 Time building chain proxies: 2.74, per 1000 atoms: 0.25 Number of scatterers: 10846 At special positions: 0 Unit cell: (99.3333, 137.08, 174.827, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 72 16.00 P 2 15.00 O 2044 8.00 N 1860 7.00 C 6866 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 561.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 201 " pdb="ZN ZN E 201 " - pdb=" ND1 HIS E 80 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 42 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 45 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 83 " pdb=" ZN E 202 " pdb="ZN ZN E 202 " - pdb=" NE2 HIS E 82 " pdb="ZN ZN E 202 " - pdb=" SG CYS E 68 " pdb="ZN ZN E 202 " - pdb=" SG CYS E 56 " pdb="ZN ZN E 202 " - pdb=" SG CYS E 53 " Number of angles added : 6 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2548 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 6 sheets defined 52.5% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 157 through 170 removed outlier: 3.550A pdb=" N VAL A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 190 removed outlier: 3.795A pdb=" N ASP A 187 " --> pdb=" O SER A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 200 removed outlier: 3.599A pdb=" N ARG A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 36 removed outlier: 3.537A pdb=" N GLY B 33 " --> pdb=" O ARG B 29 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE B 34 " --> pdb=" O ILE B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 67 removed outlier: 3.928A pdb=" N THR B 66 " --> pdb=" O PHE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.602A pdb=" N LYS B 104 " --> pdb=" O ASP B 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 37 Processing helix chain 'C' and resid 39 through 47 Processing helix chain 'C' and resid 66 through 84 Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 99 through 111 Processing helix chain 'D' and resid 12 through 25 removed outlier: 3.644A pdb=" N THR D 19 " --> pdb=" O ASN D 15 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR D 20 " --> pdb=" O LYS D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 28 No H-bonds generated for 'chain 'D' and resid 26 through 28' Processing helix chain 'D' and resid 31 through 47 removed outlier: 4.016A pdb=" N PHE D 39 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER D 40 " --> pdb=" O ASN D 36 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP D 41 " --> pdb=" O ASP D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 79 removed outlier: 3.571A pdb=" N ARG D 75 " --> pdb=" O HIS D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 105 removed outlier: 3.565A pdb=" N GLU D 93 " --> pdb=" O ARG D 89 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP D 99 " --> pdb=" O SER D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 121 removed outlier: 3.589A pdb=" N GLN D 111 " --> pdb=" O TYR D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 134 removed outlier: 3.562A pdb=" N GLU D 134 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 153 removed outlier: 3.611A pdb=" N LEU D 150 " --> pdb=" O MET D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 168 Processing helix chain 'D' and resid 169 through 172 Processing helix chain 'D' and resid 177 through 191 removed outlier: 3.659A pdb=" N ILE D 181 " --> pdb=" O ASN D 177 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE D 188 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL D 189 " --> pdb=" O ILE D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 207 Processing helix chain 'D' and resid 207 through 228 removed outlier: 3.502A pdb=" N SER D 224 " --> pdb=" O LYS D 220 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU D 227 " --> pdb=" O ALA D 223 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN D 228 " --> pdb=" O SER D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 254 removed outlier: 3.796A pdb=" N MET D 236 " --> pdb=" O CYS D 232 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU D 237 " --> pdb=" O SER D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 257 No H-bonds generated for 'chain 'D' and resid 255 through 257' Processing helix chain 'D' and resid 258 through 271 removed outlier: 3.527A pdb=" N VAL D 262 " --> pdb=" O SER D 258 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE D 263 " --> pdb=" O TYR D 259 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG D 269 " --> pdb=" O GLU D 265 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET D 270 " --> pdb=" O CYS D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 281 removed outlier: 3.907A pdb=" N GLU D 281 " --> pdb=" O PHE D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 288 Processing helix chain 'D' and resid 290 through 304 removed outlier: 3.766A pdb=" N MET D 294 " --> pdb=" O LYS D 290 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASN D 296 " --> pdb=" O ASN D 292 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU D 300 " --> pdb=" O ASN D 296 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA D 303 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 329 removed outlier: 3.877A pdb=" N MET D 311 " --> pdb=" O GLY D 307 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN D 313 " --> pdb=" O PRO D 309 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU D 314 " --> pdb=" O HIS D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 357 removed outlier: 4.198A pdb=" N VAL D 340 " --> pdb=" O PRO D 336 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU D 341 " --> pdb=" O THR D 337 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLN D 352 " --> pdb=" O GLY D 348 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN D 355 " --> pdb=" O VAL D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 377 removed outlier: 3.915A pdb=" N ALA D 367 " --> pdb=" O HIS D 363 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU D 368 " --> pdb=" O PHE D 364 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N SER D 374 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL D 375 " --> pdb=" O ALA D 371 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASN D 377 " --> pdb=" O THR D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 396 removed outlier: 3.824A pdb=" N CYS D 395 " --> pdb=" O LEU D 391 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASP D 396 " --> pdb=" O ALA D 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 399 No H-bonds generated for 'chain 'D' and resid 397 through 399' Processing helix chain 'D' and resid 410 through 423 removed outlier: 3.785A pdb=" N ILE D 419 " --> pdb=" O LEU D 415 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N THR D 420 " --> pdb=" O THR D 416 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N VAL D 421 " --> pdb=" O SER D 417 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE D 422 " --> pdb=" O PHE D 418 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS D 423 " --> pdb=" O ILE D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 446 removed outlier: 3.713A pdb=" N ARG D 442 " --> pdb=" O MET D 438 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU D 443 " --> pdb=" O LEU D 439 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE D 444 " --> pdb=" O ALA D 440 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N HIS D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 465 removed outlier: 3.535A pdb=" N ILE D 458 " --> pdb=" O GLU D 454 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLN D 463 " --> pdb=" O ASN D 459 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA D 464 " --> pdb=" O LYS D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 495 removed outlier: 4.071A pdb=" N PHE D 469 " --> pdb=" O CYS D 465 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LYS D 472 " --> pdb=" O GLU D 468 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU D 473 " --> pdb=" O PHE D 469 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG D 475 " --> pdb=" O SER D 471 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET D 476 " --> pdb=" O LYS D 472 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR D 477 " --> pdb=" O LEU D 473 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR D 478 " --> pdb=" O HIS D 474 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET D 480 " --> pdb=" O MET D 476 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASP D 485 " --> pdb=" O SER D 481 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU D 486 " --> pdb=" O VAL D 482 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN D 487 " --> pdb=" O SER D 483 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ASN D 488 " --> pdb=" O ALA D 484 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS D 495 " --> pdb=" O ASN D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 549 removed outlier: 3.693A pdb=" N LYS D 535 " --> pdb=" O GLN D 531 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N SER D 536 " --> pdb=" O GLU D 532 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLN D 546 " --> pdb=" O LEU D 542 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N HIS D 547 " --> pdb=" O PHE D 543 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE D 548 " --> pdb=" O TYR D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 610 through 616 removed outlier: 3.735A pdb=" N SER D 616 " --> pdb=" O LYS D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 681 removed outlier: 4.133A pdb=" N GLN D 667 " --> pdb=" O GLN D 663 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR D 668 " --> pdb=" O GLU D 664 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 691 removed outlier: 4.192A pdb=" N ARG D 686 " --> pdb=" O ALA D 682 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE D 687 " --> pdb=" O ALA D 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 695 through 700 removed outlier: 4.015A pdb=" N ILE D 700 " --> pdb=" O HIS D 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 701 through 708 Processing helix chain 'D' and resid 714 through 727 removed outlier: 3.503A pdb=" N LYS D 719 " --> pdb=" O ILE D 715 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LYS D 720 " --> pdb=" O SER D 716 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU D 723 " --> pdb=" O LYS D 719 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL D 724 " --> pdb=" O LYS D 720 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASP D 727 " --> pdb=" O GLU D 723 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 42 Processing helix chain 'E' and resid 54 through 58 removed outlier: 3.738A pdb=" N GLN E 57 " --> pdb=" O ILE E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 91 removed outlier: 3.631A pdb=" N LEU E 88 " --> pdb=" O ILE E 84 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS E 89 " --> pdb=" O SER E 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 26 Processing helix chain 'F' and resid 65 through 74 Processing helix chain 'F' and resid 86 through 92 Processing helix chain 'F' and resid 92 through 105 removed outlier: 3.690A pdb=" N GLN F 99 " --> pdb=" O HIS F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 138 removed outlier: 3.545A pdb=" N ALA F 130 " --> pdb=" O ASP F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 169 removed outlier: 3.666A pdb=" N LYS F 169 " --> pdb=" O LYS F 165 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 106 through 110 removed outlier: 6.794A pdb=" N GLN A 73 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ALA A 149 " --> pdb=" O GLN A 73 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ILE A 75 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE A 151 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N CYS A 77 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 88 Processing sheet with id=AA3, first strand: chain 'B' and resid 43 through 45 removed outlier: 3.530A pdb=" N GLY B 76 " --> pdb=" O TYR B 45 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N PHE B 4 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N VAL B 75 " --> pdb=" O PHE B 4 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N MET B 6 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU B 77 " --> pdb=" O MET B 6 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ARG B 8 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR B 16 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N LYS C 32 " --> pdb=" O PHE B 15 " (cutoff:3.500A) removed outlier: 11.290A pdb=" N ASP B 17 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N VAL C 60 " --> pdb=" O TYR C 18 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LYS C 20 " --> pdb=" O VAL C 60 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 507 through 511 removed outlier: 3.798A pdb=" N GLN D 508 " --> pdb=" O TRP E 27 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA E 29 " --> pdb=" O GLN D 508 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA E 31 " --> pdb=" O TYR D 510 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 71 through 72 removed outlier: 4.143A pdb=" N ALA E 71 " --> pdb=" O PHE E 79 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE E 79 " --> pdb=" O ALA E 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'F' and resid 38 through 46 removed outlier: 6.452A pdb=" N TYR F 4 " --> pdb=" O ASP F 54 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LEU F 56 " --> pdb=" O TYR F 4 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU F 6 " --> pdb=" O LEU F 56 " (cutoff:3.500A) removed outlier: 8.916A pdb=" N GLY F 77 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LYS F 5 " --> pdb=" O GLY F 77 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N LEU F 79 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL F 7 " --> pdb=" O LEU F 79 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N VAL F 81 " --> pdb=" O VAL F 7 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL F 9 " --> pdb=" O VAL F 81 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ALA F 83 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE F 78 " --> pdb=" O VAL F 112 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL F 114 " --> pdb=" O PHE F 78 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N CYS F 80 " --> pdb=" O VAL F 114 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ASN F 116 " --> pdb=" O CYS F 80 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N PHE F 82 " --> pdb=" O ASN F 116 " (cutoff:3.500A) 429 hydrogen bonds defined for protein. 1251 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: 1.23 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1820 1.28 - 1.42: 2719 1.42 - 1.55: 6404 1.55 - 1.69: 11 1.69 - 1.82: 117 Bond restraints: 11071 Sorted by residual: bond pdb=" C21 WYL F 202 " pdb=" N19 WYL F 202 " ideal model delta sigma weight residual 1.461 1.503 -0.042 2.00e-02 2.50e+03 4.42e+00 bond pdb=" C26 WYL F 202 " pdb=" N25 WYL F 202 " ideal model delta sigma weight residual 1.352 1.394 -0.042 2.00e-02 2.50e+03 4.41e+00 bond pdb=" CA VAL E 70 " pdb=" CB VAL E 70 " ideal model delta sigma weight residual 1.530 1.552 -0.022 1.05e-02 9.07e+03 4.30e+00 bond pdb=" C17 WYL F 202 " pdb=" N19 WYL F 202 " ideal model delta sigma weight residual 1.463 1.503 -0.040 2.00e-02 2.50e+03 4.05e+00 bond pdb=" CB LYS D 650 " pdb=" CG LYS D 650 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.56e+00 ... (remaining 11066 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 14677 2.18 - 4.36: 233 4.36 - 6.54: 39 6.54 - 8.71: 11 8.71 - 10.89: 9 Bond angle restraints: 14969 Sorted by residual: angle pdb=" CA LYS D 650 " pdb=" CB LYS D 650 " pdb=" CG LYS D 650 " ideal model delta sigma weight residual 114.10 124.99 -10.89 2.00e+00 2.50e-01 2.97e+01 angle pdb=" CA GLN D 604 " pdb=" C GLN D 604 " pdb=" N MET D 605 " ideal model delta sigma weight residual 118.15 125.80 -7.65 1.80e+00 3.09e-01 1.81e+01 angle pdb=" CB LYS D 650 " pdb=" CG LYS D 650 " pdb=" CD LYS D 650 " ideal model delta sigma weight residual 111.30 120.38 -9.08 2.30e+00 1.89e-01 1.56e+01 angle pdb=" N2 WYL F 202 " pdb=" C1 WYL F 202 " pdb=" O13 WYL F 202 " ideal model delta sigma weight residual 119.51 129.65 -10.14 3.00e+00 1.11e-01 1.14e+01 angle pdb=" C VAL A 142 " pdb=" N ASP A 143 " pdb=" CA ASP A 143 " ideal model delta sigma weight residual 121.54 127.83 -6.29 1.91e+00 2.74e-01 1.08e+01 ... (remaining 14964 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.16: 6084 18.16 - 36.32: 552 36.32 - 54.49: 124 54.49 - 72.65: 18 72.65 - 90.81: 7 Dihedral angle restraints: 6785 sinusoidal: 2864 harmonic: 3921 Sorted by residual: dihedral pdb=" C5' GDP F 201 " pdb=" O5' GDP F 201 " pdb=" PA GDP F 201 " pdb=" O3A GDP F 201 " ideal model delta sinusoidal sigma weight residual 179.98 -89.21 -90.81 1 2.00e+01 2.50e-03 2.43e+01 dihedral pdb=" CA LYS D 386 " pdb=" C LYS D 386 " pdb=" N ALA D 387 " pdb=" CA ALA D 387 " ideal model delta harmonic sigma weight residual -180.00 -161.13 -18.87 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CB GLU D 153 " pdb=" CG GLU D 153 " pdb=" CD GLU D 153 " pdb=" OE1 GLU D 153 " ideal model delta sinusoidal sigma weight residual 0.00 90.42 -90.42 1 3.00e+01 1.11e-03 1.07e+01 ... (remaining 6782 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1165 0.038 - 0.075: 357 0.075 - 0.113: 110 0.113 - 0.150: 15 0.150 - 0.188: 4 Chirality restraints: 1651 Sorted by residual: chirality pdb=" C44 WYL F 202 " pdb=" C36 WYL F 202 " pdb=" C45 WYL F 202 " pdb=" C49 WYL F 202 " both_signs ideal model delta sigma weight residual False -2.75 -2.94 0.19 2.00e-01 2.50e+01 8.82e-01 chirality pdb=" CA ILE D 529 " pdb=" N ILE D 529 " pdb=" C ILE D 529 " pdb=" CB ILE D 529 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.15e-01 chirality pdb=" CB VAL B 31 " pdb=" CA VAL B 31 " pdb=" CG1 VAL B 31 " pdb=" CG2 VAL B 31 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.17e-01 ... (remaining 1648 not shown) Planarity restraints: 1917 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C50 WYL F 202 " 0.031 2.00e-02 2.50e+03 3.17e-02 1.26e+01 pdb=" C51 WYL F 202 " -0.016 2.00e-02 2.50e+03 pdb=" C60 WYL F 202 " 0.038 2.00e-02 2.50e+03 pdb=" N53 WYL F 202 " -0.048 2.00e-02 2.50e+03 pdb=" O54 WYL F 202 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 99 " 0.035 5.00e-02 4.00e+02 5.30e-02 4.50e+00 pdb=" N PRO B 100 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 100 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 100 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 650 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.89e+00 pdb=" C LYS D 650 " -0.034 2.00e-02 2.50e+03 pdb=" O LYS D 650 " 0.013 2.00e-02 2.50e+03 pdb=" N PHE D 651 " 0.011 2.00e-02 2.50e+03 ... (remaining 1914 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 140 2.66 - 3.22: 10559 3.22 - 3.78: 15900 3.78 - 4.34: 21237 4.34 - 4.90: 33584 Nonbonded interactions: 81420 Sorted by model distance: nonbonded pdb=" OG1 THR A 124 " pdb=" OD1 ASP A 126 " model vdw 2.100 3.040 nonbonded pdb=" OD1 ASN D 231 " pdb=" N CYS D 232 " model vdw 2.197 3.120 nonbonded pdb=" OE2 GLU F 62 " pdb=" OH TYR F 64 " model vdw 2.229 3.040 nonbonded pdb=" OH TYR D 219 " pdb=" OE1 GLU D 246 " model vdw 2.256 3.040 nonbonded pdb=" O MET D 665 " pdb=" OG1 THR D 668 " model vdw 2.284 3.040 ... (remaining 81415 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=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: 4.360 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: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.080 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11079 Z= 0.137 Angle : 0.684 10.892 14975 Z= 0.335 Chirality : 0.040 0.188 1651 Planarity : 0.004 0.053 1917 Dihedral : 14.540 90.812 4237 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.10 % Favored : 93.75 % Rotamer: Outliers : 0.17 % Allowed : 17.39 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.23), residues: 1314 helix: 0.91 (0.22), residues: 569 sheet: 0.65 (0.47), residues: 114 loop : -1.21 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 475 TYR 0.025 0.001 TYR C 76 PHE 0.027 0.001 PHE F 90 TRP 0.011 0.001 TRP E 35 HIS 0.016 0.001 HIS D 625 Details of bonding type rmsd covalent geometry : bond 0.00287 (11071) covalent geometry : angle 0.68362 (14969) hydrogen bonds : bond 0.27458 ( 429) hydrogen bonds : angle 7.36386 ( 1251) metal coordination : bond 0.01154 ( 8) metal coordination : angle 1.38681 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 226 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 GLN cc_start: 0.9121 (mt0) cc_final: 0.8735 (mp10) REVERT: C 76 TYR cc_start: 0.8097 (t80) cc_final: 0.7851 (t80) REVERT: D 451 MET cc_start: 0.8564 (tpp) cc_final: 0.8162 (tpp) REVERT: D 462 LYS cc_start: 0.8539 (tptp) cc_final: 0.8122 (tppt) REVERT: F 1 MET cc_start: 0.0711 (ptp) cc_final: 0.0318 (ptp) outliers start: 2 outliers final: 1 residues processed: 226 average time/residue: 0.1097 time to fit residues: 34.8383 Evaluate side-chains 227 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 226 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 33 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.2980 chunk 35 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN D 508 GLN D 735 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.149439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.116099 restraints weight = 30563.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.119977 restraints weight = 13997.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.122280 restraints weight = 8305.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.123834 restraints weight = 5901.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.124787 restraints weight = 4703.691| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3842 r_free = 0.3842 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3842 r_free = 0.3842 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.3842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11079 Z= 0.165 Angle : 0.638 8.581 14975 Z= 0.331 Chirality : 0.043 0.148 1651 Planarity : 0.004 0.053 1917 Dihedral : 6.186 90.808 1539 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.33 % Favored : 93.52 % Rotamer: Outliers : 2.34 % Allowed : 15.80 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.24), residues: 1314 helix: 1.23 (0.22), residues: 578 sheet: 0.49 (0.47), residues: 115 loop : -1.13 (0.26), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 102 TYR 0.026 0.001 TYR C 76 PHE 0.015 0.001 PHE F 90 TRP 0.006 0.001 TRP D 555 HIS 0.011 0.001 HIS D 625 Details of bonding type rmsd covalent geometry : bond 0.00348 (11071) covalent geometry : angle 0.63755 (14969) hydrogen bonds : bond 0.07094 ( 429) hydrogen bonds : angle 5.29289 ( 1251) metal coordination : bond 0.00797 ( 8) metal coordination : angle 0.77560 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 243 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.7070 (mt-10) cc_final: 0.6766 (mt-10) REVERT: A 195 GLN cc_start: 0.9158 (mt0) cc_final: 0.8922 (mp10) REVERT: B 82 ASP cc_start: 0.7021 (t0) cc_final: 0.6630 (t0) REVERT: C 102 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7375 (mm-30) REVERT: C 105 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.6280 (mpp) REVERT: D 370 LYS cc_start: 0.8748 (mptt) cc_final: 0.8518 (mttm) REVERT: D 372 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8945 (mp) REVERT: D 454 GLU cc_start: 0.7603 (pm20) cc_final: 0.7310 (pm20) REVERT: D 475 ARG cc_start: 0.8224 (mmm160) cc_final: 0.7128 (mmm160) REVERT: D 479 ASP cc_start: 0.8481 (m-30) cc_final: 0.7338 (m-30) REVERT: D 665 MET cc_start: 0.8546 (pmm) cc_final: 0.8130 (pmm) REVERT: F 1 MET cc_start: 0.0815 (ptp) cc_final: 0.0390 (ptp) REVERT: F 102 ARG cc_start: 0.6871 (ttp80) cc_final: 0.6547 (ttp80) outliers start: 28 outliers final: 16 residues processed: 252 average time/residue: 0.1117 time to fit residues: 39.1678 Evaluate side-chains 249 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 231 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 465 CYS Chi-restraints excluded: chain D residue 469 PHE Chi-restraints excluded: chain D residue 509 ILE Chi-restraints excluded: chain D residue 557 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 106 optimal weight: 0.2980 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 81 optimal weight: 0.2980 chunk 46 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 432 GLN D 681 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.147737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.111265 restraints weight = 57472.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.116460 restraints weight = 20749.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.119579 restraints weight = 10863.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.121513 restraints weight = 7022.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.122786 restraints weight = 5261.954| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3844 r_free = 0.3844 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3844 r_free = 0.3844 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11079 Z= 0.149 Angle : 0.618 8.338 14975 Z= 0.315 Chirality : 0.043 0.177 1651 Planarity : 0.004 0.061 1917 Dihedral : 6.172 88.336 1537 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.56 % Favored : 93.29 % Rotamer: Outliers : 2.51 % Allowed : 16.30 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.23), residues: 1314 helix: 1.18 (0.22), residues: 582 sheet: 0.31 (0.45), residues: 115 loop : -1.18 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 135 TYR 0.036 0.001 TYR C 76 PHE 0.013 0.001 PHE D 364 TRP 0.012 0.001 TRP D 517 HIS 0.007 0.001 HIS D 625 Details of bonding type rmsd covalent geometry : bond 0.00328 (11071) covalent geometry : angle 0.61761 (14969) hydrogen bonds : bond 0.05632 ( 429) hydrogen bonds : angle 4.83219 ( 1251) metal coordination : bond 0.00463 ( 8) metal coordination : angle 0.63848 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 246 time to evaluate : 0.432 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 160 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6897 (mt-10) REVERT: B 82 ASP cc_start: 0.6757 (t0) cc_final: 0.6244 (t0) REVERT: C 105 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.6277 (mpp) REVERT: D 37 ASP cc_start: 0.8197 (t0) cc_final: 0.7883 (t0) REVERT: D 454 GLU cc_start: 0.7722 (pm20) cc_final: 0.7462 (pm20) REVERT: D 475 ARG cc_start: 0.8362 (mmm160) cc_final: 0.7564 (mmm160) REVERT: D 513 GLN cc_start: 0.8107 (tp40) cc_final: 0.7490 (tp40) REVERT: D 548 PHE cc_start: 0.8254 (t80) cc_final: 0.7540 (m-10) REVERT: D 665 MET cc_start: 0.8498 (pmm) cc_final: 0.8075 (pmm) REVERT: D 669 ARG cc_start: 0.9184 (mtm-85) cc_final: 0.8948 (ptp-110) REVERT: D 717 MET cc_start: 0.7816 (ptt) cc_final: 0.7403 (ppp) REVERT: F 1 MET cc_start: 0.0903 (ptp) cc_final: 0.0455 (ptp) REVERT: F 102 ARG cc_start: 0.7096 (ttp80) cc_final: 0.6707 (ttp80) outliers start: 30 outliers final: 19 residues processed: 256 average time/residue: 0.1091 time to fit residues: 39.0441 Evaluate side-chains 259 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 239 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain D residue 282 CYS Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 377 ASN Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 465 CYS Chi-restraints excluded: chain D residue 469 PHE Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 557 HIS Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 52 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 71 optimal weight: 0.2980 chunk 58 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 114 optimal weight: 0.3980 chunk 7 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 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 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 432 GLN ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.144988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.109153 restraints weight = 49497.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.114025 restraints weight = 19177.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.116949 restraints weight = 10365.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.118754 restraints weight = 6862.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.119931 restraints weight = 5235.139| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3784 r_free = 0.3784 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3784 r_free = 0.3784 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11079 Z= 0.170 Angle : 0.636 8.492 14975 Z= 0.326 Chirality : 0.044 0.174 1651 Planarity : 0.004 0.062 1917 Dihedral : 6.404 86.762 1537 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.33 % Favored : 93.52 % Rotamer: Outliers : 3.43 % Allowed : 16.97 % Favored : 79.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.23), residues: 1314 helix: 1.19 (0.21), residues: 582 sheet: -0.01 (0.42), residues: 115 loop : -1.29 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 287 TYR 0.019 0.001 TYR D 203 PHE 0.023 0.002 PHE D 490 TRP 0.006 0.001 TRP A 117 HIS 0.005 0.001 HIS D 625 Details of bonding type rmsd covalent geometry : bond 0.00382 (11071) covalent geometry : angle 0.63569 (14969) hydrogen bonds : bond 0.05242 ( 429) hydrogen bonds : angle 4.58314 ( 1251) metal coordination : bond 0.00456 ( 8) metal coordination : angle 0.84897 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 253 time to evaluate : 0.419 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 160 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7137 (mt-10) REVERT: B 82 ASP cc_start: 0.7050 (t0) cc_final: 0.6346 (t0) REVERT: C 34 GLU cc_start: 0.8232 (tp30) cc_final: 0.8023 (tp30) REVERT: C 64 GLU cc_start: 0.7446 (tp30) cc_final: 0.7137 (mm-30) REVERT: C 105 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.6594 (mpp) REVERT: D 14 TRP cc_start: 0.8877 (t-100) cc_final: 0.8659 (t-100) REVERT: D 37 ASP cc_start: 0.8261 (t0) cc_final: 0.7940 (t0) REVERT: D 212 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.7157 (mp) REVERT: D 316 GLN cc_start: 0.7049 (tm-30) cc_final: 0.6729 (tm-30) REVERT: D 361 ASP cc_start: 0.7577 (t0) cc_final: 0.7282 (t0) REVERT: D 454 GLU cc_start: 0.7812 (pm20) cc_final: 0.7497 (pm20) REVERT: D 513 GLN cc_start: 0.8066 (tp40) cc_final: 0.7480 (tp40) REVERT: D 665 MET cc_start: 0.8450 (pmm) cc_final: 0.8154 (pmm) REVERT: D 667 GLN cc_start: 0.9140 (mp10) cc_final: 0.8726 (mp10) REVERT: D 743 TYR cc_start: 0.4806 (OUTLIER) cc_final: 0.4268 (p90) REVERT: F 1 MET cc_start: 0.0864 (ptp) cc_final: 0.0396 (ptp) outliers start: 41 outliers final: 26 residues processed: 264 average time/residue: 0.1110 time to fit residues: 40.6757 Evaluate side-chains 266 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 236 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 282 CYS Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 377 ASN Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 465 CYS Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 477 TYR Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 557 HIS Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 743 TYR Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 52 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 2 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 115 optimal weight: 0.0970 chunk 117 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN D 317 ASN D 432 GLN D 681 GLN F 25 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.144664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.108295 restraints weight = 56055.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.113427 restraints weight = 20777.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.116426 restraints weight = 10977.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.118291 restraints weight = 7188.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.119520 restraints weight = 5440.279| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3773 r_free = 0.3773 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3773 r_free = 0.3773 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11079 Z= 0.171 Angle : 0.657 8.915 14975 Z= 0.334 Chirality : 0.044 0.142 1651 Planarity : 0.004 0.057 1917 Dihedral : 6.371 86.471 1537 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.64 % Favored : 93.14 % Rotamer: Outliers : 3.93 % Allowed : 18.14 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.23), residues: 1314 helix: 1.14 (0.21), residues: 587 sheet: -0.20 (0.41), residues: 115 loop : -1.29 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 37 TYR 0.018 0.001 TYR D 203 PHE 0.023 0.001 PHE D 490 TRP 0.006 0.001 TRP A 117 HIS 0.005 0.001 HIS D 310 Details of bonding type rmsd covalent geometry : bond 0.00390 (11071) covalent geometry : angle 0.65715 (14969) hydrogen bonds : bond 0.05064 ( 429) hydrogen bonds : angle 4.49778 ( 1251) metal coordination : bond 0.00436 ( 8) metal coordination : angle 0.85940 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 246 time to evaluate : 0.415 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 88 TRP cc_start: 0.6416 (t60) cc_final: 0.5965 (t60) REVERT: A 160 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7121 (mt-10) REVERT: A 195 GLN cc_start: 0.8910 (mp10) cc_final: 0.8668 (mp10) REVERT: B 82 ASP cc_start: 0.7117 (t0) cc_final: 0.6605 (t0) REVERT: C 34 GLU cc_start: 0.8239 (tp30) cc_final: 0.8033 (tp30) REVERT: C 105 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.6562 (mpp) REVERT: D 14 TRP cc_start: 0.8905 (t-100) cc_final: 0.8668 (t-100) REVERT: D 37 ASP cc_start: 0.8239 (t0) cc_final: 0.7937 (t0) REVERT: D 134 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8367 (pm20) REVERT: D 212 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.7129 (mp) REVERT: D 316 GLN cc_start: 0.7121 (tm-30) cc_final: 0.6783 (tm-30) REVERT: D 370 LYS cc_start: 0.8751 (mtpt) cc_final: 0.8411 (mttm) REVERT: D 454 GLU cc_start: 0.7701 (pm20) cc_final: 0.7371 (pm20) REVERT: D 475 ARG cc_start: 0.8445 (mmm160) cc_final: 0.7305 (mmm160) REVERT: D 665 MET cc_start: 0.8475 (pmm) cc_final: 0.8159 (pmm) REVERT: D 667 GLN cc_start: 0.9133 (mp10) cc_final: 0.8724 (mp10) REVERT: D 743 TYR cc_start: 0.4776 (OUTLIER) cc_final: 0.4262 (p90) REVERT: E 20 LYS cc_start: 0.6986 (mmmt) cc_final: 0.6669 (mmtt) REVERT: F 1 MET cc_start: 0.0886 (ptp) cc_final: 0.0444 (ptp) REVERT: F 156 PHE cc_start: 0.8515 (m-80) cc_final: 0.8288 (m-10) outliers start: 47 outliers final: 25 residues processed: 265 average time/residue: 0.1033 time to fit residues: 38.5128 Evaluate side-chains 270 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 240 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 282 CYS Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 377 ASN Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 469 PHE Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 557 HIS Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 743 TYR Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 52 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 101 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 4 optimal weight: 0.2980 chunk 60 optimal weight: 0.4980 chunk 110 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 HIS D 221 GLN D 225 ASN D 317 ASN D 432 GLN D 681 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.144646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.109335 restraints weight = 46171.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.114063 restraints weight = 18493.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.116899 restraints weight = 10119.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.118708 restraints weight = 6757.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.119782 restraints weight = 5229.379| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3776 r_free = 0.3776 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3776 r_free = 0.3776 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11079 Z= 0.156 Angle : 0.663 9.672 14975 Z= 0.337 Chirality : 0.043 0.187 1651 Planarity : 0.004 0.057 1917 Dihedral : 6.341 81.249 1537 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.86 % Favored : 92.91 % Rotamer: Outliers : 3.26 % Allowed : 19.23 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.23), residues: 1314 helix: 1.17 (0.21), residues: 581 sheet: -0.39 (0.41), residues: 113 loop : -1.20 (0.26), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 135 TYR 0.015 0.001 TYR C 76 PHE 0.026 0.002 PHE D 490 TRP 0.015 0.001 TRP D 555 HIS 0.004 0.001 HIS D 310 Details of bonding type rmsd covalent geometry : bond 0.00358 (11071) covalent geometry : angle 0.66257 (14969) hydrogen bonds : bond 0.04799 ( 429) hydrogen bonds : angle 4.44546 ( 1251) metal coordination : bond 0.00398 ( 8) metal coordination : angle 0.84426 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 243 time to evaluate : 0.386 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 160 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7130 (mt-10) REVERT: A 195 GLN cc_start: 0.8880 (mp10) cc_final: 0.8166 (mp10) REVERT: B 82 ASP cc_start: 0.7147 (t0) cc_final: 0.6628 (t0) REVERT: C 64 GLU cc_start: 0.7379 (tp30) cc_final: 0.7086 (mm-30) REVERT: C 105 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.6471 (mpp) REVERT: D 14 TRP cc_start: 0.8900 (t-100) cc_final: 0.8634 (t-100) REVERT: D 37 ASP cc_start: 0.8279 (t0) cc_final: 0.7818 (t0) REVERT: D 134 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8369 (pm20) REVERT: D 212 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7229 (mp) REVERT: D 316 GLN cc_start: 0.7146 (tm-30) cc_final: 0.6785 (tm-30) REVERT: D 370 LYS cc_start: 0.8741 (mtpt) cc_final: 0.8379 (mttm) REVERT: D 454 GLU cc_start: 0.7757 (pm20) cc_final: 0.7338 (pm20) REVERT: D 475 ARG cc_start: 0.8452 (mmm160) cc_final: 0.7355 (mmm160) REVERT: D 642 MET cc_start: 0.6028 (ttp) cc_final: 0.4999 (tmm) REVERT: D 665 MET cc_start: 0.8416 (pmm) cc_final: 0.8116 (pmm) REVERT: D 667 GLN cc_start: 0.9129 (mp10) cc_final: 0.8686 (mp10) REVERT: D 717 MET cc_start: 0.7867 (ptt) cc_final: 0.7286 (ppp) REVERT: D 743 TYR cc_start: 0.4732 (OUTLIER) cc_final: 0.4140 (p90) REVERT: E 20 LYS cc_start: 0.7015 (mmmt) cc_final: 0.6715 (mmtt) REVERT: E 35 TRP cc_start: 0.6267 (m100) cc_final: 0.5986 (m100) REVERT: F 1 MET cc_start: 0.0926 (ptp) cc_final: 0.0507 (ptp) REVERT: F 156 PHE cc_start: 0.8509 (m-80) cc_final: 0.8237 (m-10) outliers start: 39 outliers final: 26 residues processed: 255 average time/residue: 0.1078 time to fit residues: 38.2733 Evaluate side-chains 268 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 237 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 282 CYS Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 377 ASN Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 477 TYR Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 557 HIS Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 743 TYR Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 52 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 77 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 94 optimal weight: 0.2980 chunk 99 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 ASN D 432 GLN ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.143503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.108378 restraints weight = 46472.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.113103 restraints weight = 18673.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.115968 restraints weight = 10258.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.117726 restraints weight = 6860.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.118936 restraints weight = 5262.560| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3765 r_free = 0.3765 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3765 r_free = 0.3765 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3765 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11079 Z= 0.173 Angle : 0.681 9.992 14975 Z= 0.345 Chirality : 0.044 0.164 1651 Planarity : 0.004 0.061 1917 Dihedral : 6.347 67.940 1537 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.94 % Favored : 92.83 % Rotamer: Outliers : 4.01 % Allowed : 19.31 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.23), residues: 1314 helix: 1.18 (0.21), residues: 577 sheet: -0.63 (0.40), residues: 113 loop : -1.21 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 135 TYR 0.017 0.001 TYR D 203 PHE 0.029 0.002 PHE D 490 TRP 0.011 0.001 TRP A 88 HIS 0.005 0.001 HIS D 310 Details of bonding type rmsd covalent geometry : bond 0.00397 (11071) covalent geometry : angle 0.68115 (14969) hydrogen bonds : bond 0.04866 ( 429) hydrogen bonds : angle 4.40528 ( 1251) metal coordination : bond 0.00413 ( 8) metal coordination : angle 0.92420 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 240 time to evaluate : 0.434 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: symmetry clash REVERT: A 160 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7146 (mt-10) REVERT: A 195 GLN cc_start: 0.8908 (mp10) cc_final: 0.8454 (mp10) REVERT: B 82 ASP cc_start: 0.6836 (t0) cc_final: 0.6324 (t0) REVERT: C 64 GLU cc_start: 0.7402 (tp30) cc_final: 0.7101 (mm-30) REVERT: C 105 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.6534 (mpp) REVERT: D 37 ASP cc_start: 0.8272 (t0) cc_final: 0.7839 (t0) REVERT: D 134 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8360 (pm20) REVERT: D 212 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7229 (mp) REVERT: D 316 GLN cc_start: 0.7145 (tm-30) cc_final: 0.6786 (tm-30) REVERT: D 370 LYS cc_start: 0.8777 (mtpt) cc_final: 0.8404 (mttm) REVERT: D 454 GLU cc_start: 0.7806 (pm20) cc_final: 0.7375 (pm20) REVERT: D 475 ARG cc_start: 0.8439 (mmm160) cc_final: 0.7193 (mmm160) REVERT: D 479 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.6953 (m-30) REVERT: D 665 MET cc_start: 0.8414 (pmm) cc_final: 0.8135 (pmm) REVERT: D 667 GLN cc_start: 0.9139 (mp10) cc_final: 0.8683 (mp10) REVERT: D 743 TYR cc_start: 0.4435 (OUTLIER) cc_final: 0.3702 (p90) REVERT: E 20 LYS cc_start: 0.7062 (mmmt) cc_final: 0.6791 (mmtt) REVERT: E 35 TRP cc_start: 0.6146 (m100) cc_final: 0.5921 (m100) REVERT: F 1 MET cc_start: 0.0982 (ptp) cc_final: 0.0600 (ptp) REVERT: F 156 PHE cc_start: 0.8481 (m-80) cc_final: 0.8235 (m-10) outliers start: 48 outliers final: 32 residues processed: 258 average time/residue: 0.1034 time to fit residues: 37.2858 Evaluate side-chains 272 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 234 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 282 CYS Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 377 ASN Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 469 PHE Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 477 TYR Chi-restraints excluded: chain D residue 479 ASP Chi-restraints excluded: chain D residue 489 LYS Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 557 HIS Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 743 TYR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 52 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 9 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 0.0770 chunk 84 optimal weight: 0.0370 chunk 89 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 95 optimal weight: 0.3980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN D 317 ASN D 432 GLN ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 131 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.145093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.110122 restraints weight = 45467.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.114869 restraints weight = 18277.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.117712 restraints weight = 10021.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.119546 restraints weight = 6690.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.120676 restraints weight = 5147.459| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3788 r_free = 0.3788 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3788 r_free = 0.3788 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11079 Z= 0.139 Angle : 0.688 10.373 14975 Z= 0.344 Chirality : 0.043 0.155 1651 Planarity : 0.004 0.058 1917 Dihedral : 5.950 61.493 1537 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.94 % Favored : 92.83 % Rotamer: Outliers : 2.93 % Allowed : 20.57 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.23), residues: 1314 helix: 1.23 (0.22), residues: 577 sheet: -0.60 (0.41), residues: 113 loop : -1.23 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 135 TYR 0.014 0.001 TYR C 76 PHE 0.020 0.001 PHE F 78 TRP 0.027 0.002 TRP D 555 HIS 0.004 0.001 HIS D 625 Details of bonding type rmsd covalent geometry : bond 0.00313 (11071) covalent geometry : angle 0.68815 (14969) hydrogen bonds : bond 0.04350 ( 429) hydrogen bonds : angle 4.30912 ( 1251) metal coordination : bond 0.00335 ( 8) metal coordination : angle 0.81672 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 241 time to evaluate : 0.391 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: symmetry clash REVERT: A 160 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7129 (mt-10) REVERT: A 195 GLN cc_start: 0.8904 (mp10) cc_final: 0.8436 (mp10) REVERT: B 82 ASP cc_start: 0.6916 (t0) cc_final: 0.6385 (t0) REVERT: C 64 GLU cc_start: 0.7244 (tp30) cc_final: 0.6958 (mm-30) REVERT: C 105 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.6332 (mpp) REVERT: D 37 ASP cc_start: 0.8206 (t0) cc_final: 0.7797 (t0) REVERT: D 134 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8345 (pm20) REVERT: D 137 MET cc_start: 0.6482 (mmm) cc_final: 0.6185 (mmm) REVERT: D 212 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7227 (mp) REVERT: D 316 GLN cc_start: 0.7119 (tm-30) cc_final: 0.6806 (tm-30) REVERT: D 370 LYS cc_start: 0.8725 (mtpt) cc_final: 0.8365 (mttm) REVERT: D 418 PHE cc_start: 0.9254 (OUTLIER) cc_final: 0.8874 (t80) REVERT: D 454 GLU cc_start: 0.7825 (pm20) cc_final: 0.7352 (pm20) REVERT: D 475 ARG cc_start: 0.8425 (mmm160) cc_final: 0.7079 (mmm160) REVERT: D 479 ASP cc_start: 0.8526 (OUTLIER) cc_final: 0.6850 (m-30) REVERT: D 665 MET cc_start: 0.8375 (pmm) cc_final: 0.8100 (pmm) REVERT: D 667 GLN cc_start: 0.9093 (mp10) cc_final: 0.8658 (mp10) REVERT: D 717 MET cc_start: 0.7691 (ptt) cc_final: 0.7282 (ppp) REVERT: D 743 TYR cc_start: 0.4358 (OUTLIER) cc_final: 0.3625 (p90) REVERT: E 20 LYS cc_start: 0.6976 (mmmt) cc_final: 0.6741 (mmtt) REVERT: E 35 TRP cc_start: 0.6004 (m100) cc_final: 0.5779 (m100) REVERT: F 1 MET cc_start: 0.0846 (ptp) cc_final: 0.0470 (ptp) outliers start: 35 outliers final: 21 residues processed: 253 average time/residue: 0.1101 time to fit residues: 38.8465 Evaluate side-chains 263 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 235 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 TRP Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 282 CYS Chi-restraints excluded: chain D residue 291 LYS Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 418 PHE Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 477 TYR Chi-restraints excluded: chain D residue 479 ASP Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 557 HIS Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 743 TYR Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 52 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 112 optimal weight: 8.9990 chunk 22 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 75 optimal weight: 0.0970 chunk 27 optimal weight: 0.8980 chunk 93 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 ASN ** D 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 95 HIS F 131 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.143575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.108478 restraints weight = 47301.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.113287 restraints weight = 18762.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.116185 restraints weight = 10243.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.118008 restraints weight = 6805.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.119111 restraints weight = 5191.150| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3771 r_free = 0.3771 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3771 r_free = 0.3771 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3771 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11079 Z= 0.165 Angle : 0.724 10.970 14975 Z= 0.358 Chirality : 0.045 0.315 1651 Planarity : 0.004 0.056 1917 Dihedral : 5.948 61.519 1537 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.86 % Favored : 92.91 % Rotamer: Outliers : 2.93 % Allowed : 21.32 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.23), residues: 1314 helix: 1.13 (0.21), residues: 586 sheet: -0.63 (0.40), residues: 121 loop : -1.29 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 551 TYR 0.016 0.001 TYR C 76 PHE 0.025 0.001 PHE D 490 TRP 0.023 0.001 TRP D 555 HIS 0.012 0.001 HIS F 95 Details of bonding type rmsd covalent geometry : bond 0.00379 (11071) covalent geometry : angle 0.72410 (14969) hydrogen bonds : bond 0.04692 ( 429) hydrogen bonds : angle 4.35862 ( 1251) metal coordination : bond 0.00409 ( 8) metal coordination : angle 0.95487 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 237 time to evaluate : 0.426 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: symmetry clash REVERT: A 160 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7137 (mt-10) REVERT: A 195 GLN cc_start: 0.8936 (mp10) cc_final: 0.8467 (mp10) REVERT: B 82 ASP cc_start: 0.6956 (t0) cc_final: 0.6473 (t0) REVERT: C 64 GLU cc_start: 0.7371 (tp30) cc_final: 0.7080 (mm-30) REVERT: C 105 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.6425 (mpp) REVERT: D 37 ASP cc_start: 0.8242 (t0) cc_final: 0.7829 (t0) REVERT: D 134 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8348 (pm20) REVERT: D 212 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7208 (mp) REVERT: D 316 GLN cc_start: 0.7207 (tm-30) cc_final: 0.6833 (tm-30) REVERT: D 370 LYS cc_start: 0.8780 (mtpt) cc_final: 0.8414 (mttp) REVERT: D 418 PHE cc_start: 0.9232 (OUTLIER) cc_final: 0.8851 (t80) REVERT: D 475 ARG cc_start: 0.8451 (mmm160) cc_final: 0.8217 (mmm160) REVERT: D 526 THR cc_start: 0.6206 (m) cc_final: 0.5925 (p) REVERT: D 665 MET cc_start: 0.8385 (pmm) cc_final: 0.8112 (pmm) REVERT: D 667 GLN cc_start: 0.9122 (mp10) cc_final: 0.8678 (mp10) REVERT: D 717 MET cc_start: 0.7716 (ptt) cc_final: 0.7261 (ppp) REVERT: D 743 TYR cc_start: 0.4437 (OUTLIER) cc_final: 0.3601 (p90) REVERT: E 20 LYS cc_start: 0.6980 (mmmt) cc_final: 0.6711 (mmtt) REVERT: F 1 MET cc_start: 0.0909 (ptp) cc_final: 0.0568 (ptp) outliers start: 35 outliers final: 22 residues processed: 253 average time/residue: 0.1082 time to fit residues: 38.4840 Evaluate side-chains 262 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 234 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 282 CYS Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 377 ASN Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 418 PHE Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 477 TYR Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 557 HIS Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 743 TYR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 52 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 116 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 109 optimal weight: 5.9990 chunk 69 optimal weight: 0.1980 chunk 7 optimal weight: 0.5980 chunk 87 optimal weight: 0.2980 chunk 89 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN D 317 ASN D 432 GLN D 606 ASN ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.144586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.111063 restraints weight = 35519.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.115256 restraints weight = 15630.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.117842 restraints weight = 9048.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.119407 restraints weight = 6241.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.120405 restraints weight = 4914.450| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3792 r_free = 0.3792 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3792 r_free = 0.3792 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11079 Z= 0.146 Angle : 0.732 11.182 14975 Z= 0.360 Chirality : 0.044 0.182 1651 Planarity : 0.004 0.059 1917 Dihedral : 5.860 61.762 1537 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.86 % Favored : 92.83 % Rotamer: Outliers : 2.76 % Allowed : 21.66 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.23), residues: 1314 helix: 1.04 (0.21), residues: 598 sheet: -0.61 (0.40), residues: 121 loop : -1.36 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 37 TYR 0.015 0.001 TYR C 76 PHE 0.029 0.001 PHE D 490 TRP 0.047 0.002 TRP D 517 HIS 0.004 0.001 HIS D 625 Details of bonding type rmsd covalent geometry : bond 0.00332 (11071) covalent geometry : angle 0.73216 (14969) hydrogen bonds : bond 0.04393 ( 429) hydrogen bonds : angle 4.33409 ( 1251) metal coordination : bond 0.00347 ( 8) metal coordination : angle 0.88499 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 236 time to evaluate : 0.451 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 160 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7124 (mt-10) REVERT: A 195 GLN cc_start: 0.8991 (mp10) cc_final: 0.8507 (mp10) REVERT: B 82 ASP cc_start: 0.6996 (t0) cc_final: 0.6485 (t0) REVERT: C 64 GLU cc_start: 0.7260 (tp30) cc_final: 0.6972 (mm-30) REVERT: C 105 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.6334 (mpp) REVERT: D 37 ASP cc_start: 0.8229 (t0) cc_final: 0.7823 (t0) REVERT: D 134 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8325 (pm20) REVERT: D 212 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7192 (mp) REVERT: D 316 GLN cc_start: 0.7160 (tm-30) cc_final: 0.6803 (tm-30) REVERT: D 370 LYS cc_start: 0.8748 (mtpt) cc_final: 0.8385 (mttp) REVERT: D 418 PHE cc_start: 0.9250 (OUTLIER) cc_final: 0.8872 (t80) REVERT: D 475 ARG cc_start: 0.8551 (mmm160) cc_final: 0.7726 (mmm160) REVERT: D 665 MET cc_start: 0.8389 (pmm) cc_final: 0.8101 (pmm) REVERT: D 667 GLN cc_start: 0.9095 (mp10) cc_final: 0.8657 (mp10) REVERT: D 717 MET cc_start: 0.7703 (ptt) cc_final: 0.7242 (ppp) REVERT: D 743 TYR cc_start: 0.4436 (OUTLIER) cc_final: 0.3494 (p90) REVERT: E 20 LYS cc_start: 0.7016 (mmmt) cc_final: 0.6749 (mmtt) REVERT: F 1 MET cc_start: 0.0939 (ptp) cc_final: 0.0593 (ptp) outliers start: 33 outliers final: 20 residues processed: 251 average time/residue: 0.1084 time to fit residues: 38.1048 Evaluate side-chains 257 residues out of total 1198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 231 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 160 GLU Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain C residue 105 MET Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 134 GLU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 282 CYS Chi-restraints excluded: chain D residue 377 ASN Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 418 PHE Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 479 ASP Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 557 HIS Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 743 TYR Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 52 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 93 optimal weight: 0.0040 chunk 114 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 27 optimal weight: 0.0060 chunk 26 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.4608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 ASN D 432 GLN ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.144194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.110698 restraints weight = 37636.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.115012 restraints weight = 16037.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.117607 restraints weight = 9075.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.119265 restraints weight = 6199.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.120160 restraints weight = 4846.799| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3783 r_free = 0.3783 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3783 r_free = 0.3783 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11079 Z= 0.145 Angle : 0.726 11.540 14975 Z= 0.356 Chirality : 0.043 0.164 1651 Planarity : 0.004 0.060 1917 Dihedral : 5.767 61.838 1537 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.79 % Favored : 92.91 % Rotamer: Outliers : 2.42 % Allowed : 22.58 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.23), residues: 1314 helix: 1.04 (0.21), residues: 597 sheet: -0.60 (0.40), residues: 123 loop : -1.38 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 135 TYR 0.018 0.001 TYR D 378 PHE 0.029 0.001 PHE D 490 TRP 0.033 0.002 TRP D 517 HIS 0.004 0.001 HIS D 310 Details of bonding type rmsd covalent geometry : bond 0.00332 (11071) covalent geometry : angle 0.72556 (14969) hydrogen bonds : bond 0.04283 ( 429) hydrogen bonds : angle 4.31444 ( 1251) metal coordination : bond 0.00367 ( 8) metal coordination : angle 0.90839 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2630.71 seconds wall clock time: 45 minutes 55.33 seconds (2755.33 seconds total)