Starting phenix.real_space_refine on Sun Aug 24 17:38:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jk2_22359/08_2025/7jk2_22359.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jk2_22359/08_2025/7jk2_22359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jk2_22359/08_2025/7jk2_22359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jk2_22359/08_2025/7jk2_22359.map" model { file = "/net/cci-nas-00/data/ceres_data/7jk2_22359/08_2025/7jk2_22359.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jk2_22359/08_2025/7jk2_22359.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 P 78 5.49 5 Mg 4 5.21 5 S 110 5.16 5 C 13528 2.51 5 N 3786 2.21 5 O 4113 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21619 Number of models: 1 Model: "" Number of chains: 13 Chain: "B" Number of atoms: 2290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2290 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 11, 'TRANS': 273} Chain breaks: 4 Chain: "C" Number of atoms: 4892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 4892 Classifications: {'peptide': 609} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 585} Chain breaks: 7 Chain: "D" Number of atoms: 3549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3549 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 11, 'TRANS': 429} Chain breaks: 2 Chain: "E" Number of atoms: 3161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3161 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 386} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 143 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "A" Number of atoms: 3129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3129 Classifications: {'peptide': 401} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 383} Chain: "G" Number of atoms: 2974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2974 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 13, 'TRANS': 358} Chain breaks: 2 Chain: "H" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 660 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "I" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 693 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.71, per 1000 atoms: 0.22 Number of scatterers: 21619 At special positions: 0 Unit cell: (127.449, 156.06, 121.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 110 16.00 P 78 15.00 Mg 4 11.99 O 4113 8.00 N 3786 7.00 C 13528 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 743.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4830 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 12 sheets defined 63.0% alpha, 6.9% beta 33 base pairs and 64 stacking pairs defined. Time for finding SS restraints: 2.65 Creating SS restraints... Processing helix chain 'B' and resid 280 through 285 Processing helix chain 'B' and resid 324 through 338 Processing helix chain 'B' and resid 339 through 349 removed outlier: 3.612A pdb=" N GLU B 349 " --> pdb=" O CYS B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 372 Processing helix chain 'B' and resid 389 through 401 removed outlier: 3.605A pdb=" N ILE B 401 " --> pdb=" O ILE B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 423 Processing helix chain 'B' and resid 444 through 456 removed outlier: 3.625A pdb=" N GLN B 448 " --> pdb=" O ASN B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 474 removed outlier: 3.559A pdb=" N LEU B 473 " --> pdb=" O ASN B 470 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 474 " --> pdb=" O THR B 471 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 470 through 474' Processing helix chain 'B' and resid 476 through 483 Processing helix chain 'B' and resid 496 through 501 removed outlier: 3.860A pdb=" N THR B 500 " --> pdb=" O TYR B 496 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA B 501 " --> pdb=" O THR B 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 496 through 501' Processing helix chain 'B' and resid 516 through 525 removed outlier: 3.973A pdb=" N SER B 525 " --> pdb=" O SER B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 544 Processing helix chain 'B' and resid 554 through 565 removed outlier: 3.643A pdb=" N LEU B 558 " --> pdb=" O PRO B 554 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 565 " --> pdb=" O SER B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 584 removed outlier: 3.963A pdb=" N LEU B 574 " --> pdb=" O SER B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 615 removed outlier: 3.731A pdb=" N GLN B 615 " --> pdb=" O PHE B 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 46 removed outlier: 3.653A pdb=" N VAL C 45 " --> pdb=" O GLY C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 88 removed outlier: 3.674A pdb=" N GLU C 51 " --> pdb=" O GLN C 47 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ARG C 74 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N THR C 75 " --> pdb=" O SER C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 108 No H-bonds generated for 'chain 'C' and resid 106 through 108' Processing helix chain 'C' and resid 109 through 122 removed outlier: 4.344A pdb=" N GLN C 113 " --> pdb=" O ASP C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 159 Processing helix chain 'C' and resid 184 through 197 removed outlier: 3.999A pdb=" N ASP C 197 " --> pdb=" O THR C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 230 Processing helix chain 'C' and resid 245 through 253 removed outlier: 4.028A pdb=" N VAL C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 259 Processing helix chain 'C' and resid 270 through 282 Processing helix chain 'C' and resid 293 through 307 Processing helix chain 'C' and resid 310 through 327 Processing helix chain 'C' and resid 328 through 335 removed outlier: 5.853A pdb=" N ALA C 331 " --> pdb=" O GLY C 328 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 334 " --> pdb=" O ALA C 331 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS C 335 " --> pdb=" O PHE C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 349 through 358 removed outlier: 4.033A pdb=" N MET C 353 " --> pdb=" O THR C 349 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG C 358 " --> pdb=" O GLU C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 368 Processing helix chain 'C' and resid 383 through 416 Proline residue: C 390 - end of helix removed outlier: 4.247A pdb=" N ASP C 416 " --> pdb=" O GLU C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 436 removed outlier: 3.873A pdb=" N LEU C 429 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ARG C 436 " --> pdb=" O ASN C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 453 removed outlier: 3.748A pdb=" N LYS C 445 " --> pdb=" O THR C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 477 removed outlier: 3.829A pdb=" N PHE C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 508 Proline residue: C 493 - end of helix Processing helix chain 'C' and resid 563 through 576 Processing helix chain 'C' and resid 599 through 607 removed outlier: 3.516A pdb=" N ILE C 607 " --> pdb=" O ARG C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 620 removed outlier: 3.574A pdb=" N ALA C 613 " --> pdb=" O ALA C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 626 Processing helix chain 'C' and resid 643 through 654 removed outlier: 3.760A pdb=" N GLU C 654 " --> pdb=" O LYS C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 672 removed outlier: 3.780A pdb=" N TRP C 664 " --> pdb=" O ASN C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 703 Processing helix chain 'D' and resid 3 through 21 removed outlier: 3.885A pdb=" N LEU D 8 " --> pdb=" O ALA D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 45 Processing helix chain 'D' and resid 61 through 74 Processing helix chain 'D' and resid 75 through 77 No H-bonds generated for 'chain 'D' and resid 75 through 77' Processing helix chain 'D' and resid 95 through 107 Processing helix chain 'D' and resid 120 through 135 removed outlier: 3.505A pdb=" N GLY D 135 " --> pdb=" O CYS D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 154 removed outlier: 3.545A pdb=" N PHE D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 157 No H-bonds generated for 'chain 'D' and resid 155 through 157' Processing helix chain 'D' and resid 158 through 165 Processing helix chain 'D' and resid 185 through 189 removed outlier: 3.526A pdb=" N GLU D 188 " --> pdb=" O ASP D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 198 Processing helix chain 'D' and resid 211 through 224 removed outlier: 3.551A pdb=" N TYR D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU D 223 " --> pdb=" O CYS D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 244 removed outlier: 3.964A pdb=" N ILE D 244 " --> pdb=" O ASN D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 254 removed outlier: 3.782A pdb=" N ARG D 253 " --> pdb=" O TYR D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 280 Processing helix chain 'D' and resid 282 through 295 Processing helix chain 'D' and resid 297 through 310 removed outlier: 3.820A pdb=" N LEU D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 333 removed outlier: 3.770A pdb=" N GLY D 333 " --> pdb=" O SER D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 341 Processing helix chain 'D' and resid 344 through 362 Processing helix chain 'D' and resid 367 through 380 removed outlier: 3.511A pdb=" N ILE D 371 " --> pdb=" O ASN D 367 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE D 378 " --> pdb=" O ARG D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 403 removed outlier: 3.847A pdb=" N VAL D 393 " --> pdb=" O GLU D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 443 removed outlier: 3.570A pdb=" N ILE D 436 " --> pdb=" O THR D 432 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN D 441 " --> pdb=" O HIS D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 454 Processing helix chain 'E' and resid 2 through 9 Processing helix chain 'E' and resid 15 through 27 Processing helix chain 'E' and resid 47 through 62 removed outlier: 3.711A pdb=" N THR E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 89 removed outlier: 3.882A pdb=" N MET E 80 " --> pdb=" O THR E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 96 removed outlier: 3.550A pdb=" N ALA E 95 " --> pdb=" O GLN E 92 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU E 96 " --> pdb=" O GLY E 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 92 through 96' Processing helix chain 'E' and resid 100 through 110 Processing helix chain 'E' and resid 128 through 134 removed outlier: 3.622A pdb=" N ARG E 132 " --> pdb=" O GLU E 129 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET E 134 " --> pdb=" O LEU E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 143 removed outlier: 3.580A pdb=" N VAL E 141 " --> pdb=" O ASN E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 150 Processing helix chain 'E' and resid 162 through 166 Processing helix chain 'E' and resid 184 through 194 Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.575A pdb=" N GLN E 206 " --> pdb=" O GLN E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 218 Processing helix chain 'E' and resid 222 through 238 removed outlier: 4.052A pdb=" N VAL E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR E 238 " --> pdb=" O LEU E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 259 removed outlier: 4.080A pdb=" N LYS E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 265 Processing helix chain 'E' and resid 275 through 287 removed outlier: 3.535A pdb=" N ILE E 279 " --> pdb=" O LEU E 275 " (cutoff:3.500A) Proline residue: E 282 - end of helix Processing helix chain 'E' and resid 322 through 338 Processing helix chain 'E' and resid 339 through 341 No H-bonds generated for 'chain 'E' and resid 339 through 341' Processing helix chain 'E' and resid 342 through 347 removed outlier: 3.975A pdb=" N PHE E 347 " --> pdb=" O ASP E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 394 removed outlier: 3.966A pdb=" N GLU E 394 " --> pdb=" O TYR E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 413 removed outlier: 4.065A pdb=" N LEU E 404 " --> pdb=" O THR E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 449 removed outlier: 3.704A pdb=" N VAL E 441 " --> pdb=" O GLY E 437 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 238 Processing helix chain 'A' and resid 520 through 529 Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 571 through 588 Processing helix chain 'A' and resid 603 through 621 removed outlier: 3.515A pdb=" N GLN A 621 " --> pdb=" O ARG A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 652 removed outlier: 3.982A pdb=" N VAL A 645 " --> pdb=" O ARG A 641 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 652 " --> pdb=" O TYR A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 671 Processing helix chain 'A' and resid 686 through 689 Processing helix chain 'A' and resid 695 through 703 Processing helix chain 'A' and resid 704 through 706 No H-bonds generated for 'chain 'A' and resid 704 through 706' Processing helix chain 'A' and resid 721 through 726 Processing helix chain 'A' and resid 728 through 736 removed outlier: 3.914A pdb=" N GLY A 736 " --> pdb=" O THR A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 759 Processing helix chain 'A' and resid 765 through 778 removed outlier: 3.692A pdb=" N VAL A 769 " --> pdb=" O LYS A 765 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN A 770 " --> pdb=" O GLY A 766 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 778 " --> pdb=" O ARG A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 800 removed outlier: 4.051A pdb=" N ALA A 786 " --> pdb=" O ASP A 782 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR A 799 " --> pdb=" O GLU A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 818 removed outlier: 3.508A pdb=" N VAL A 810 " --> pdb=" O THR A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 828 removed outlier: 3.830A pdb=" N ILE A 826 " --> pdb=" O LYS A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 848 removed outlier: 3.524A pdb=" N ALA A 841 " --> pdb=" O LEU A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 869 Processing helix chain 'A' and resid 874 through 888 removed outlier: 3.740A pdb=" N ARG A 880 " --> pdb=" O GLY A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 919 removed outlier: 3.627A pdb=" N ILE A 913 " --> pdb=" O SER A 909 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG A 918 " --> pdb=" O HIS A 914 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 260 removed outlier: 4.174A pdb=" N ASN G 260 " --> pdb=" O ARG G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 287 removed outlier: 3.668A pdb=" N GLN G 275 " --> pdb=" O GLU G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 311 Processing helix chain 'G' and resid 312 through 317 removed outlier: 6.204A pdb=" N ASP G 315 " --> pdb=" O ARG G 312 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 345 Processing helix chain 'G' and resid 352 through 366 removed outlier: 3.644A pdb=" N LYS G 365 " --> pdb=" O GLN G 361 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR G 366 " --> pdb=" O ARG G 362 " (cutoff:3.500A) Processing helix chain 'G' and resid 378 through 382 Processing helix chain 'G' and resid 386 through 393 Processing helix chain 'G' and resid 394 through 398 Processing helix chain 'G' and resid 413 through 418 Processing helix chain 'G' and resid 419 through 425 removed outlier: 3.566A pdb=" N LEU G 422 " --> pdb=" O LEU G 419 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG G 425 " --> pdb=" O LEU G 422 " (cutoff:3.500A) Processing helix chain 'G' and resid 439 through 453 removed outlier: 3.600A pdb=" N ILE G 443 " --> pdb=" O SER G 439 " (cutoff:3.500A) Processing helix chain 'G' and resid 461 through 476 removed outlier: 3.680A pdb=" N LEU G 465 " --> pdb=" O PRO G 461 " (cutoff:3.500A) Processing helix chain 'G' and resid 478 through 498 removed outlier: 3.534A pdb=" N ALA G 482 " --> pdb=" O ASP G 478 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL G 490 " --> pdb=" O GLY G 486 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN G 495 " --> pdb=" O GLU G 491 " (cutoff:3.500A) Processing helix chain 'G' and resid 530 through 542 removed outlier: 3.730A pdb=" N VAL G 534 " --> pdb=" O GLN G 530 " (cutoff:3.500A) Processing helix chain 'G' and resid 557 through 573 Processing helix chain 'G' and resid 581 through 595 removed outlier: 3.541A pdb=" N VAL G 587 " --> pdb=" O ARG G 583 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG G 590 " --> pdb=" O GLU G 586 " (cutoff:3.500A) Processing helix chain 'G' and resid 601 through 614 removed outlier: 3.838A pdb=" N GLY G 607 " --> pdb=" O ALA G 603 " (cutoff:3.500A) Processing helix chain 'G' and resid 625 through 628 Processing helix chain 'G' and resid 636 through 645 Processing helix chain 'G' and resid 646 through 654 removed outlier: 3.989A pdb=" N SER G 652 " --> pdb=" O GLN G 648 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 485 through 488 removed outlier: 6.284A pdb=" N ASN B 352 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N TRP B 488 " --> pdb=" O ASN B 352 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU B 354 " --> pdb=" O TRP B 488 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL B 378 " --> pdb=" O TYR C 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 588 through 590 Processing sheet with id=AA3, first strand: chain 'C' and resid 127 through 131 removed outlier: 5.997A pdb=" N MET C 128 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ILE C 208 " --> pdb=" O MET C 128 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS C 130 " --> pdb=" O ILE C 208 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU C 101 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N PHE C 266 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA C 100 " --> pdb=" O PHE C 266 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 658 through 659 Processing sheet with id=AA5, first strand: chain 'D' and resid 83 through 89 removed outlier: 6.565A pdb=" N ASN D 50 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N GLY D 179 " --> pdb=" O ASN D 50 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU D 52 " --> pdb=" O GLY D 179 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 406 through 408 Processing sheet with id=AA7, first strand: chain 'E' and resid 64 through 70 removed outlier: 6.717A pdb=" N PHE E 121 " --> pdb=" O CYS E 154 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ILE E 156 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE E 123 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N LEU E 158 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL E 125 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE E 37 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N SER E 159 " --> pdb=" O ILE E 37 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU E 39 " --> pdb=" O SER E 159 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ALA E 36 " --> pdb=" O VAL E 176 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N LEU E 178 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR E 38 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N LEU E 180 " --> pdb=" O TYR E 38 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N PHE E 40 " --> pdb=" O LEU E 180 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 380 through 381 removed outlier: 6.808A pdb=" N GLN E 433 " --> pdb=" O PHE E 418 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N PHE E 418 " --> pdb=" O GLN E 433 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 627 through 633 removed outlier: 6.500A pdb=" N GLU A 628 " --> pdb=" O VAL A 680 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N LEU A 682 " --> pdb=" O GLU A 628 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU A 630 " --> pdb=" O LEU A 682 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ASP A 684 " --> pdb=" O LEU A 630 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE A 632 " --> pdb=" O ASP A 684 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLY A 592 " --> pdb=" O VAL A 713 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N THR A 715 " --> pdb=" O GLY A 592 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N MET A 594 " --> pdb=" O THR A 715 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ALA A 717 " --> pdb=" O MET A 594 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL A 596 " --> pdb=" O ALA A 717 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 852 through 853 Processing sheet with id=AB2, first strand: chain 'G' and resid 320 through 326 removed outlier: 6.170A pdb=" N GLN G 321 " --> pdb=" O LEU G 372 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N VAL G 374 " --> pdb=" O GLN G 321 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL G 323 " --> pdb=" O VAL G 374 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ASP G 376 " --> pdb=" O VAL G 323 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE G 325 " --> pdb=" O ASP G 376 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLY G 291 " --> pdb=" O LEU G 405 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N GLY G 407 " --> pdb=" O GLY G 291 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU G 293 " --> pdb=" O GLY G 407 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ALA G 409 " --> pdb=" O LEU G 293 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL G 295 " --> pdb=" O ALA G 409 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 579 through 580 removed outlier: 4.592A pdb=" N ILE G 579 " --> pdb=" O VAL G 631 " (cutoff:3.500A) 1053 hydrogen bonds defined for protein. 3075 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 66 hydrogen bonds 132 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 64 stacking parallelities Total time for adding SS restraints: 4.26 Time building geometry restraints manager: 2.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5140 1.33 - 1.45: 4406 1.45 - 1.57: 12271 1.57 - 1.69: 150 1.69 - 1.81: 162 Bond restraints: 22129 Sorted by residual: bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.07e+01 bond pdb=" C4 ATP E 901 " pdb=" C5 ATP E 901 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.92e+01 bond pdb=" C4 ATP G 901 " pdb=" C5 ATP G 901 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.87e+01 bond pdb=" C4 ATP A1001 " pdb=" C5 ATP A1001 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.69e+01 bond pdb=" C5 ATP E 901 " pdb=" C6 ATP E 901 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.62e+01 ... (remaining 22124 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.72: 29970 3.72 - 7.45: 187 7.45 - 11.17: 33 11.17 - 14.89: 4 14.89 - 18.62: 6 Bond angle restraints: 30200 Sorted by residual: angle pdb=" PB ATP G 901 " pdb=" O3B ATP G 901 " pdb=" PG ATP G 901 " ideal model delta sigma weight residual 139.87 121.25 18.62 1.00e+00 1.00e+00 3.47e+02 angle pdb=" PB ATP D 901 " pdb=" O3B ATP D 901 " pdb=" PG ATP D 901 " ideal model delta sigma weight residual 139.87 121.27 18.60 1.00e+00 1.00e+00 3.46e+02 angle pdb=" PB ATP E 901 " pdb=" O3B ATP E 901 " pdb=" PG ATP E 901 " ideal model delta sigma weight residual 139.87 121.96 17.91 1.00e+00 1.00e+00 3.21e+02 angle pdb=" PA ATP G 901 " pdb=" O3A ATP G 901 " pdb=" PB ATP G 901 " ideal model delta sigma weight residual 136.83 120.10 16.73 1.00e+00 1.00e+00 2.80e+02 angle pdb=" PB ATP A1001 " pdb=" O3B ATP A1001 " pdb=" PG ATP A1001 " ideal model delta sigma weight residual 139.87 123.68 16.19 1.00e+00 1.00e+00 2.62e+02 ... (remaining 30195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 11488 17.90 - 35.80: 1351 35.80 - 53.71: 478 53.71 - 71.61: 106 71.61 - 89.51: 25 Dihedral angle restraints: 13448 sinusoidal: 6051 harmonic: 7397 Sorted by residual: dihedral pdb=" CA LYS C 712 " pdb=" C LYS C 712 " pdb=" N THR C 713 " pdb=" CA THR C 713 " ideal model delta harmonic sigma weight residual -180.00 -152.09 -27.91 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA LEU G 259 " pdb=" C LEU G 259 " pdb=" N ASN G 260 " pdb=" CA ASN G 260 " ideal model delta harmonic sigma weight residual 180.00 153.34 26.66 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA ASN E 338 " pdb=" C ASN E 338 " pdb=" N ALA E 339 " pdb=" CA ALA E 339 " ideal model delta harmonic sigma weight residual 180.00 153.76 26.24 0 5.00e+00 4.00e-02 2.75e+01 ... (remaining 13445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 3041 0.070 - 0.140: 409 0.140 - 0.210: 33 0.210 - 0.280: 2 0.280 - 0.350: 2 Chirality restraints: 3487 Sorted by residual: chirality pdb=" CG LEU A 750 " pdb=" CB LEU A 750 " pdb=" CD1 LEU A 750 " pdb=" CD2 LEU A 750 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" CB ILE C 5 " pdb=" CA ILE C 5 " pdb=" CG1 ILE C 5 " pdb=" CG2 ILE C 5 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA THR B 471 " pdb=" N THR B 471 " pdb=" C THR B 471 " pdb=" CB THR B 471 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 3484 not shown) Planarity restraints: 3594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 664 " -0.030 2.00e-02 2.50e+03 2.13e-02 1.13e+01 pdb=" CG TRP C 664 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP C 664 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP C 664 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 664 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 664 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 664 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 664 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 664 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 664 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU E 9 " -0.054 5.00e-02 4.00e+02 8.04e-02 1.04e+01 pdb=" N PRO E 10 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO E 10 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO E 10 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 872 " 0.053 5.00e-02 4.00e+02 7.96e-02 1.01e+01 pdb=" N PRO A 873 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO A 873 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 873 " 0.043 5.00e-02 4.00e+02 ... (remaining 3591 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 265 2.65 - 3.22: 18050 3.22 - 3.78: 33969 3.78 - 4.34: 47038 4.34 - 4.90: 75830 Nonbonded interactions: 175152 Sorted by model distance: nonbonded pdb=" OG1 THR D 63 " pdb="MG MG D 902 " model vdw 2.092 2.170 nonbonded pdb=" O2B ATP E 901 " pdb="MG MG E 902 " model vdw 2.112 2.170 nonbonded pdb=" OG1 THR A 605 " pdb="MG MG A1002 " model vdw 2.113 2.170 nonbonded pdb=" O2B ATP D 901 " pdb="MG MG D 902 " model vdw 2.121 2.170 nonbonded pdb=" OG1 THR E 48 " pdb="MG MG E 902 " model vdw 2.121 2.170 ... (remaining 175147 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.780 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: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 21.310 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 22129 Z= 0.299 Angle : 0.916 18.617 30200 Z= 0.568 Chirality : 0.048 0.350 3487 Planarity : 0.007 0.080 3594 Dihedral : 17.904 89.509 8618 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.23 % Allowed : 8.00 % Favored : 91.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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 aren not related in a simple way. whole: -3.50 (0.13), residues: 2471 helix: -2.34 (0.10), residues: 1449 sheet: -1.53 (0.31), residues: 225 loop : -2.07 (0.18), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 785 TYR 0.018 0.002 TYR G 588 PHE 0.021 0.002 PHE D 304 TRP 0.056 0.002 TRP C 664 HIS 0.006 0.001 HIS B 468 Details of bonding type rmsd covalent geometry : bond 0.00553 (22129) covalent geometry : angle 0.91626 (30200) hydrogen bonds : bond 0.13575 ( 1119) hydrogen bonds : angle 6.50355 ( 3207) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 290 time to evaluate : 0.707 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: symmetry clash REVERT: B 333 MET cc_start: 0.9140 (tpp) cc_final: 0.8713 (mmm) REVERT: B 555 PHE cc_start: 0.7807 (t80) cc_final: 0.7509 (t80) REVERT: C 326 PHE cc_start: 0.8955 (m-10) cc_final: 0.8543 (m-10) REVERT: C 378 VAL cc_start: 0.8436 (t) cc_final: 0.8018 (m) REVERT: C 417 LEU cc_start: 0.8562 (tp) cc_final: 0.8287 (tp) REVERT: C 573 GLU cc_start: 0.8444 (tt0) cc_final: 0.8206 (tm-30) REVERT: C 658 MET cc_start: 0.7999 (tpt) cc_final: 0.7477 (mmm) REVERT: D 347 GLU cc_start: 0.8750 (mp0) cc_final: 0.8383 (mp0) REVERT: E 82 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8300 (mt-10) REVERT: E 394 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7656 (pp20) REVERT: A 618 MET cc_start: 0.8689 (mtp) cc_final: 0.8478 (mtt) REVERT: A 666 GLU cc_start: 0.8629 (tp30) cc_final: 0.8350 (tp30) outliers start: 5 outliers final: 4 residues processed: 294 average time/residue: 0.1897 time to fit residues: 80.9157 Evaluate side-chains 184 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 180 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 750 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 247 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 348 ASN B 366 GLN B 544 ASN C 16 ASN C 78 GLN C 449 GLN C 464 ASN ** C 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 ASN D 157 ASN D 202 GLN E 218 GLN ** E 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 GLN E 454 GLN A 650 GLN A 749 GLN A 838 GLN G 254 ASN G 356 HIS G 533 GLN G 648 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.091230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.063653 restraints weight = 55416.580| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.28 r_work: 0.2847 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22129 Z= 0.171 Angle : 0.583 9.625 30200 Z= 0.311 Chirality : 0.039 0.171 3487 Planarity : 0.005 0.061 3594 Dihedral : 16.975 68.735 3666 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.17 % Allowed : 11.03 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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 aren not related in a simple way. whole: -1.01 (0.16), residues: 2471 helix: -0.07 (0.13), residues: 1462 sheet: -1.14 (0.33), residues: 231 loop : -1.46 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 575 TYR 0.013 0.001 TYR C 365 PHE 0.017 0.001 PHE C 459 TRP 0.029 0.001 TRP C 664 HIS 0.005 0.001 HIS C 580 Details of bonding type rmsd covalent geometry : bond 0.00383 (22129) covalent geometry : angle 0.58279 (30200) hydrogen bonds : bond 0.03824 ( 1119) hydrogen bonds : angle 4.24851 ( 3207) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 1.052 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: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9188 (tpp) cc_final: 0.8811 (mmm) REVERT: B 413 GLU cc_start: 0.9329 (tt0) cc_final: 0.9066 (tp30) REVERT: C 72 TYR cc_start: 0.8375 (t80) cc_final: 0.8134 (t80) REVERT: C 384 TYR cc_start: 0.8357 (t80) cc_final: 0.7918 (t80) REVERT: C 586 ASP cc_start: 0.7758 (m-30) cc_final: 0.7082 (p0) REVERT: C 598 ASP cc_start: 0.7888 (t0) cc_final: 0.7629 (t0) REVERT: D 347 GLU cc_start: 0.9208 (mp0) cc_final: 0.8900 (mp0) REVERT: D 362 ASP cc_start: 0.9102 (t0) cc_final: 0.8854 (t0) REVERT: D 423 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8689 (mp0) REVERT: E 254 CYS cc_start: 0.8364 (m) cc_final: 0.8133 (t) REVERT: A 666 GLU cc_start: 0.9073 (tp30) cc_final: 0.8513 (tp30) REVERT: A 788 ASP cc_start: 0.9145 (m-30) cc_final: 0.8710 (t0) REVERT: A 915 TYR cc_start: 0.9381 (t80) cc_final: 0.9117 (t80) outliers start: 26 outliers final: 16 residues processed: 212 average time/residue: 0.1502 time to fit residues: 49.5913 Evaluate side-chains 178 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 350 HIS Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain G residue 352 THR Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 456 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 195 optimal weight: 5.9990 chunk 213 optimal weight: 9.9990 chunk 124 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 235 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 102 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 325 HIS B 435 HIS C 325 HIS ** C 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.092034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.064541 restraints weight = 55513.672| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.33 r_work: 0.2869 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22129 Z= 0.116 Angle : 0.515 8.795 30200 Z= 0.275 Chirality : 0.037 0.165 3487 Planarity : 0.004 0.051 3594 Dihedral : 17.028 73.612 3665 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.72 % Allowed : 11.84 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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 aren not related in a simple way. whole: 0.22 (0.17), residues: 2471 helix: 0.99 (0.14), residues: 1466 sheet: -1.05 (0.32), residues: 250 loop : -0.97 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 370 TYR 0.013 0.001 TYR B 283 PHE 0.017 0.001 PHE C 459 TRP 0.019 0.001 TRP C 664 HIS 0.003 0.001 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00255 (22129) covalent geometry : angle 0.51483 (30200) hydrogen bonds : bond 0.03276 ( 1119) hydrogen bonds : angle 3.85511 ( 3207) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 180 time to evaluate : 0.836 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: symmetry clash REVERT: B 344 MET cc_start: 0.9322 (mmm) cc_final: 0.9093 (tpt) REVERT: C 323 MET cc_start: 0.9317 (ttp) cc_final: 0.9056 (ttp) REVERT: C 384 TYR cc_start: 0.8280 (t80) cc_final: 0.7854 (t80) REVERT: C 586 ASP cc_start: 0.7817 (m-30) cc_final: 0.7181 (p0) REVERT: C 598 ASP cc_start: 0.7937 (t0) cc_final: 0.7551 (t0) REVERT: D 347 GLU cc_start: 0.9210 (mp0) cc_final: 0.8968 (mp0) REVERT: D 362 ASP cc_start: 0.9124 (t0) cc_final: 0.8860 (t0) REVERT: D 423 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8600 (mp0) REVERT: D 426 MET cc_start: 0.8880 (mmp) cc_final: 0.8572 (mmm) REVERT: E 254 CYS cc_start: 0.8430 (m) cc_final: 0.8199 (t) REVERT: E 276 TRP cc_start: 0.8094 (t-100) cc_final: 0.7850 (t-100) REVERT: A 666 GLU cc_start: 0.9043 (tp30) cc_final: 0.8510 (tp30) REVERT: A 788 ASP cc_start: 0.9123 (m-30) cc_final: 0.8652 (t0) REVERT: A 807 MET cc_start: 0.8685 (ttm) cc_final: 0.8342 (tpp) outliers start: 38 outliers final: 17 residues processed: 209 average time/residue: 0.1422 time to fit residues: 47.2940 Evaluate side-chains 176 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 350 HIS Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain G residue 352 THR Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 456 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 46 optimal weight: 0.8980 chunk 142 optimal weight: 0.9990 chunk 206 optimal weight: 0.0770 chunk 60 optimal weight: 6.9990 chunk 185 optimal weight: 2.9990 chunk 254 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 222 optimal weight: 4.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.091436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.063582 restraints weight = 55756.479| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.33 r_work: 0.2853 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22129 Z= 0.133 Angle : 0.513 9.305 30200 Z= 0.272 Chirality : 0.037 0.153 3487 Planarity : 0.003 0.046 3594 Dihedral : 16.901 80.354 3663 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.72 % Allowed : 12.70 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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 aren not related in a simple way. whole: 0.82 (0.17), residues: 2471 helix: 1.49 (0.14), residues: 1466 sheet: -0.82 (0.32), residues: 250 loop : -0.75 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 617 TYR 0.022 0.001 TYR C 72 PHE 0.018 0.001 PHE C 459 TRP 0.015 0.001 TRP C 664 HIS 0.003 0.001 HIS G 284 Details of bonding type rmsd covalent geometry : bond 0.00298 (22129) covalent geometry : angle 0.51292 (30200) hydrogen bonds : bond 0.03223 ( 1119) hydrogen bonds : angle 3.70457 ( 3207) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9289 (mmm) cc_final: 0.8891 (mmm) REVERT: B 413 GLU cc_start: 0.9300 (tt0) cc_final: 0.9027 (tp30) REVERT: C 128 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8408 (mtp) REVERT: C 323 MET cc_start: 0.9337 (ttp) cc_final: 0.9075 (ttp) REVERT: C 326 PHE cc_start: 0.9056 (m-10) cc_final: 0.8600 (m-80) REVERT: C 384 TYR cc_start: 0.8261 (t80) cc_final: 0.7858 (t80) REVERT: C 449 GLN cc_start: 0.8717 (mm-40) cc_final: 0.8463 (mt0) REVERT: C 586 ASP cc_start: 0.7881 (m-30) cc_final: 0.7376 (p0) REVERT: C 598 ASP cc_start: 0.8018 (t0) cc_final: 0.7655 (t0) REVERT: C 710 LYS cc_start: 0.9237 (mmtt) cc_final: 0.8905 (tttt) REVERT: D 45 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8202 (mp0) REVERT: D 362 ASP cc_start: 0.9128 (t0) cc_final: 0.8880 (t0) REVERT: D 423 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8639 (mp0) REVERT: D 426 MET cc_start: 0.8903 (mmp) cc_final: 0.8615 (mmm) REVERT: E 254 CYS cc_start: 0.8450 (m) cc_final: 0.8217 (t) REVERT: E 446 LYS cc_start: 0.9222 (tmmt) cc_final: 0.8810 (ptpp) REVERT: A 666 GLU cc_start: 0.9035 (tp30) cc_final: 0.8514 (tp30) REVERT: A 788 ASP cc_start: 0.9132 (m-30) cc_final: 0.8685 (t0) outliers start: 38 outliers final: 28 residues processed: 195 average time/residue: 0.1376 time to fit residues: 42.6770 Evaluate side-chains 183 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 350 HIS Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain G residue 306 CYS Chi-restraints excluded: chain G residue 352 THR Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 426 CYS Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 570 MET Chi-restraints excluded: chain G residue 659 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 46 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 234 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 166 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 184 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 470 ASN ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.092479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.064942 restraints weight = 55347.368| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.29 r_work: 0.2881 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22129 Z= 0.103 Angle : 0.495 9.400 30200 Z= 0.262 Chirality : 0.037 0.152 3487 Planarity : 0.003 0.045 3594 Dihedral : 16.772 86.191 3663 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.76 % Allowed : 12.97 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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 aren not related in a simple way. whole: 1.24 (0.18), residues: 2471 helix: 1.76 (0.14), residues: 1468 sheet: -0.61 (0.33), residues: 239 loop : -0.46 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 575 TYR 0.035 0.001 TYR C 72 PHE 0.018 0.001 PHE C 459 TRP 0.021 0.001 TRP E 276 HIS 0.007 0.001 HIS C 580 Details of bonding type rmsd covalent geometry : bond 0.00227 (22129) covalent geometry : angle 0.49515 (30200) hydrogen bonds : bond 0.02892 ( 1119) hydrogen bonds : angle 3.55811 ( 3207) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 163 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9282 (mmm) cc_final: 0.8889 (mmm) REVERT: B 476 ASP cc_start: 0.8926 (p0) cc_final: 0.8608 (p0) REVERT: C 128 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8371 (mtp) REVERT: C 277 GLU cc_start: 0.9211 (tt0) cc_final: 0.8679 (tm-30) REVERT: C 323 MET cc_start: 0.9344 (ttp) cc_final: 0.9063 (ttp) REVERT: C 384 TYR cc_start: 0.8208 (t80) cc_final: 0.7803 (t80) REVERT: C 449 GLN cc_start: 0.8709 (mm-40) cc_final: 0.8473 (mt0) REVERT: C 586 ASP cc_start: 0.7976 (m-30) cc_final: 0.7549 (p0) REVERT: C 598 ASP cc_start: 0.8098 (t0) cc_final: 0.7779 (t0) REVERT: C 710 LYS cc_start: 0.9200 (mmtt) cc_final: 0.8828 (ptmt) REVERT: D 362 ASP cc_start: 0.9157 (t0) cc_final: 0.8936 (t0) REVERT: D 423 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8548 (mp0) REVERT: D 426 MET cc_start: 0.8866 (mmp) cc_final: 0.8590 (mmm) REVERT: E 446 LYS cc_start: 0.9205 (tmmt) cc_final: 0.8784 (ptpp) REVERT: F 232 MET cc_start: 0.8476 (ttm) cc_final: 0.8217 (ttp) REVERT: A 666 GLU cc_start: 0.8992 (tp30) cc_final: 0.8656 (tp30) outliers start: 39 outliers final: 26 residues processed: 192 average time/residue: 0.1411 time to fit residues: 43.1181 Evaluate side-chains 180 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 350 HIS Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain G residue 352 THR Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 426 CYS Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 570 MET Chi-restraints excluded: chain G residue 659 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 214 optimal weight: 2.9990 chunk 81 optimal weight: 30.0000 chunk 163 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 224 optimal weight: 8.9990 chunk 228 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.089884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.062570 restraints weight = 55605.575| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.25 r_work: 0.2831 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22129 Z= 0.189 Angle : 0.543 9.978 30200 Z= 0.283 Chirality : 0.039 0.162 3487 Planarity : 0.003 0.045 3594 Dihedral : 16.819 86.507 3663 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.99 % Allowed : 13.42 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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 aren not related in a simple way. whole: 1.35 (0.18), residues: 2471 helix: 1.85 (0.14), residues: 1470 sheet: -0.52 (0.33), residues: 239 loop : -0.46 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 575 TYR 0.033 0.001 TYR C 72 PHE 0.017 0.001 PHE C 459 TRP 0.017 0.001 TRP E 276 HIS 0.005 0.001 HIS C 580 Details of bonding type rmsd covalent geometry : bond 0.00431 (22129) covalent geometry : angle 0.54336 (30200) hydrogen bonds : bond 0.03407 ( 1119) hydrogen bonds : angle 3.62454 ( 3207) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 148 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 425 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.8978 (tp) REVERT: B 476 ASP cc_start: 0.8913 (p0) cc_final: 0.8617 (p0) REVERT: C 128 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8547 (mtp) REVERT: C 277 GLU cc_start: 0.9209 (tt0) cc_final: 0.8672 (tm-30) REVERT: C 323 MET cc_start: 0.9335 (ttp) cc_final: 0.9058 (ttp) REVERT: C 384 TYR cc_start: 0.8245 (t80) cc_final: 0.7792 (t80) REVERT: C 449 GLN cc_start: 0.8711 (mm-40) cc_final: 0.8482 (mt0) REVERT: C 450 MET cc_start: 0.7052 (ptp) cc_final: 0.6794 (ptm) REVERT: C 586 ASP cc_start: 0.8081 (m-30) cc_final: 0.7579 (p0) REVERT: C 598 ASP cc_start: 0.8090 (t0) cc_final: 0.7786 (t0) REVERT: C 710 LYS cc_start: 0.9199 (mmtt) cc_final: 0.8810 (ptmt) REVERT: D 45 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8289 (mp0) REVERT: D 362 ASP cc_start: 0.9171 (t0) cc_final: 0.8938 (t0) REVERT: D 423 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8569 (mp0) REVERT: D 426 MET cc_start: 0.8858 (mmp) cc_final: 0.8579 (mmm) REVERT: E 446 LYS cc_start: 0.9246 (tmmt) cc_final: 0.8831 (ptpp) REVERT: A 666 GLU cc_start: 0.9032 (tp30) cc_final: 0.8523 (tp30) REVERT: A 788 ASP cc_start: 0.9156 (m-30) cc_final: 0.8828 (t0) outliers start: 44 outliers final: 34 residues processed: 182 average time/residue: 0.1381 time to fit residues: 39.8266 Evaluate side-chains 180 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 350 HIS Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain G residue 295 VAL Chi-restraints excluded: chain G residue 306 CYS Chi-restraints excluded: chain G residue 352 THR Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 426 CYS Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 570 MET Chi-restraints excluded: chain G residue 659 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 86 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 chunk 152 optimal weight: 6.9990 chunk 229 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 237 optimal weight: 2.9990 chunk 226 optimal weight: 0.0670 chunk 217 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 150 ASN ** E 406 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 = 0.3588 r_free = 0.3588 target = 0.090796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.063307 restraints weight = 55291.027| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.28 r_work: 0.2853 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22129 Z= 0.129 Angle : 0.513 10.938 30200 Z= 0.268 Chirality : 0.037 0.148 3487 Planarity : 0.003 0.045 3594 Dihedral : 16.782 83.014 3663 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.12 % Allowed : 13.96 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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 aren not related in a simple way. whole: 1.49 (0.18), residues: 2471 helix: 1.96 (0.14), residues: 1469 sheet: -0.44 (0.34), residues: 239 loop : -0.38 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 575 TYR 0.027 0.001 TYR C 72 PHE 0.019 0.001 PHE C 459 TRP 0.014 0.001 TRP E 276 HIS 0.004 0.001 HIS E 278 Details of bonding type rmsd covalent geometry : bond 0.00292 (22129) covalent geometry : angle 0.51305 (30200) hydrogen bonds : bond 0.03070 ( 1119) hydrogen bonds : angle 3.54692 ( 3207) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 160 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9261 (mmm) cc_final: 0.8879 (mmm) REVERT: B 395 ASP cc_start: 0.8596 (p0) cc_final: 0.8255 (p0) REVERT: B 425 ILE cc_start: 0.9353 (OUTLIER) cc_final: 0.8982 (tp) REVERT: B 476 ASP cc_start: 0.8882 (p0) cc_final: 0.8568 (p0) REVERT: C 145 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8816 (mt-10) REVERT: C 277 GLU cc_start: 0.9191 (tt0) cc_final: 0.8682 (tm-30) REVERT: C 323 MET cc_start: 0.9356 (ttp) cc_final: 0.9093 (ttp) REVERT: C 384 TYR cc_start: 0.8188 (t80) cc_final: 0.7717 (t80) REVERT: C 449 GLN cc_start: 0.8697 (mm-40) cc_final: 0.8470 (mt0) REVERT: C 586 ASP cc_start: 0.8137 (m-30) cc_final: 0.7598 (p0) REVERT: C 598 ASP cc_start: 0.8095 (t0) cc_final: 0.7805 (t0) REVERT: C 710 LYS cc_start: 0.9188 (mmtt) cc_final: 0.8802 (ptmt) REVERT: D 45 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8197 (mp0) REVERT: D 362 ASP cc_start: 0.9189 (t0) cc_final: 0.8972 (t0) REVERT: D 423 GLU cc_start: 0.9159 (mt-10) cc_final: 0.8709 (mp0) REVERT: D 426 MET cc_start: 0.8865 (mmp) cc_final: 0.8548 (mmm) REVERT: F 232 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8195 (ttm) REVERT: A 666 GLU cc_start: 0.9032 (tp30) cc_final: 0.8492 (tp30) REVERT: A 788 ASP cc_start: 0.9141 (m-30) cc_final: 0.8780 (t0) REVERT: G 484 ASP cc_start: 0.9148 (t0) cc_final: 0.8766 (t0) outliers start: 47 outliers final: 32 residues processed: 196 average time/residue: 0.1189 time to fit residues: 37.3320 Evaluate side-chains 186 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 350 HIS Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 385 LEU Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 232 MET Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 596 VAL Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain G residue 306 CYS Chi-restraints excluded: chain G residue 352 THR Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 426 CYS Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 570 MET Chi-restraints excluded: chain G residue 659 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 107 optimal weight: 0.9980 chunk 191 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 chunk 175 optimal weight: 0.9990 chunk 152 optimal weight: 6.9990 chunk 201 optimal weight: 0.9980 chunk 200 optimal weight: 5.9990 chunk 19 optimal weight: 0.0070 chunk 63 optimal weight: 0.8980 chunk 212 optimal weight: 0.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.091934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.064587 restraints weight = 55342.894| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 3.28 r_work: 0.2884 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 22129 Z= 0.100 Angle : 0.505 12.179 30200 Z= 0.263 Chirality : 0.037 0.151 3487 Planarity : 0.003 0.044 3594 Dihedral : 16.640 79.784 3663 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.67 % Allowed : 14.78 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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 aren not related in a simple way. whole: 1.66 (0.18), residues: 2471 helix: 2.06 (0.14), residues: 1468 sheet: -0.37 (0.33), residues: 244 loop : -0.24 (0.23), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 575 TYR 0.038 0.001 TYR C 72 PHE 0.021 0.001 PHE C 459 TRP 0.012 0.001 TRP C 191 HIS 0.006 0.001 HIS E 278 Details of bonding type rmsd covalent geometry : bond 0.00218 (22129) covalent geometry : angle 0.50494 (30200) hydrogen bonds : bond 0.02809 ( 1119) hydrogen bonds : angle 3.44790 ( 3207) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9268 (mmm) cc_final: 0.8923 (mmm) REVERT: B 425 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.9002 (tp) REVERT: B 476 ASP cc_start: 0.8824 (p0) cc_final: 0.8523 (p0) REVERT: C 145 GLU cc_start: 0.9053 (mt-10) cc_final: 0.8811 (mt-10) REVERT: C 277 GLU cc_start: 0.9182 (tt0) cc_final: 0.8692 (tm-30) REVERT: C 323 MET cc_start: 0.9370 (ttp) cc_final: 0.9108 (ttp) REVERT: C 384 TYR cc_start: 0.8192 (t80) cc_final: 0.7840 (t80) REVERT: C 449 GLN cc_start: 0.8715 (mm-40) cc_final: 0.8500 (mt0) REVERT: C 586 ASP cc_start: 0.8140 (m-30) cc_final: 0.7648 (p0) REVERT: C 598 ASP cc_start: 0.8133 (t0) cc_final: 0.7862 (t0) REVERT: C 637 LEU cc_start: 0.6856 (OUTLIER) cc_final: 0.6632 (mm) REVERT: C 658 MET cc_start: 0.7969 (tpt) cc_final: 0.7563 (mmm) REVERT: D 45 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8146 (mp0) REVERT: D 148 GLU cc_start: 0.9198 (mp0) cc_final: 0.8929 (mp0) REVERT: D 423 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8681 (mp0) REVERT: D 426 MET cc_start: 0.8864 (mmp) cc_final: 0.8553 (mmm) REVERT: A 666 GLU cc_start: 0.8991 (tp30) cc_final: 0.8648 (tp30) REVERT: A 788 ASP cc_start: 0.9122 (m-30) cc_final: 0.8657 (t0) REVERT: G 484 ASP cc_start: 0.9126 (t0) cc_final: 0.8753 (t0) outliers start: 37 outliers final: 25 residues processed: 189 average time/residue: 0.1321 time to fit residues: 39.3733 Evaluate side-chains 180 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain G residue 306 CYS Chi-restraints excluded: chain G residue 352 THR Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 570 MET Chi-restraints excluded: chain G residue 659 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 236 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 212 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 159 optimal weight: 0.2980 chunk 36 optimal weight: 0.1980 chunk 172 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.093203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.065309 restraints weight = 55493.358| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 3.37 r_work: 0.2892 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22129 Z= 0.100 Angle : 0.523 12.621 30200 Z= 0.267 Chirality : 0.037 0.146 3487 Planarity : 0.003 0.044 3594 Dihedral : 16.537 82.303 3663 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.22 % Allowed : 15.23 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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 aren not related in a simple way. whole: 1.72 (0.18), residues: 2471 helix: 2.10 (0.14), residues: 1469 sheet: -0.31 (0.33), residues: 244 loop : -0.24 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 575 TYR 0.032 0.001 TYR C 72 PHE 0.018 0.001 PHE C 459 TRP 0.014 0.001 TRP F 228 HIS 0.007 0.001 HIS C 580 Details of bonding type rmsd covalent geometry : bond 0.00217 (22129) covalent geometry : angle 0.52341 (30200) hydrogen bonds : bond 0.02807 ( 1119) hydrogen bonds : angle 3.41924 ( 3207) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9269 (mmm) cc_final: 0.8926 (mmm) REVERT: B 425 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.9007 (tp) REVERT: B 476 ASP cc_start: 0.8828 (p0) cc_final: 0.8524 (p0) REVERT: B 535 MET cc_start: 0.7800 (tmm) cc_final: 0.6882 (tpp) REVERT: C 1 MET cc_start: 0.5559 (mtt) cc_final: 0.5270 (ttm) REVERT: C 145 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8853 (mt-10) REVERT: C 277 GLU cc_start: 0.9211 (tt0) cc_final: 0.8702 (tm-30) REVERT: C 323 MET cc_start: 0.9406 (ttp) cc_final: 0.9143 (ttp) REVERT: C 384 TYR cc_start: 0.8242 (t80) cc_final: 0.7825 (t80) REVERT: C 586 ASP cc_start: 0.8138 (m-30) cc_final: 0.7648 (p0) REVERT: C 598 ASP cc_start: 0.8133 (t0) cc_final: 0.7865 (t0) REVERT: C 637 LEU cc_start: 0.6773 (OUTLIER) cc_final: 0.6555 (mm) REVERT: C 658 MET cc_start: 0.7983 (tpt) cc_final: 0.7568 (mmm) REVERT: C 710 LYS cc_start: 0.9138 (mmtt) cc_final: 0.8794 (ptmt) REVERT: D 6 ARG cc_start: 0.8665 (mpt180) cc_final: 0.8415 (mpt180) REVERT: D 45 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8098 (mp0) REVERT: D 148 GLU cc_start: 0.9198 (mp0) cc_final: 0.8902 (mp0) REVERT: D 423 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8696 (mp0) REVERT: D 426 MET cc_start: 0.8853 (mmp) cc_final: 0.8546 (mmm) REVERT: E 426 MET cc_start: 0.7603 (mmt) cc_final: 0.7309 (mmm) REVERT: F 232 MET cc_start: 0.8560 (ttm) cc_final: 0.8187 (ttm) REVERT: A 666 GLU cc_start: 0.9021 (tp30) cc_final: 0.8658 (tp30) REVERT: A 788 ASP cc_start: 0.9168 (m-30) cc_final: 0.8664 (t0) REVERT: G 484 ASP cc_start: 0.9151 (t0) cc_final: 0.8777 (t0) REVERT: G 527 LYS cc_start: 0.8759 (mmmt) cc_final: 0.8506 (tppt) outliers start: 27 outliers final: 22 residues processed: 184 average time/residue: 0.1268 time to fit residues: 36.9822 Evaluate side-chains 178 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain G residue 306 CYS Chi-restraints excluded: chain G residue 352 THR Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 659 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 104 optimal weight: 0.6980 chunk 119 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 244 optimal weight: 7.9990 chunk 212 optimal weight: 0.9980 chunk 160 optimal weight: 0.0040 chunk 69 optimal weight: 10.0000 overall best weight: 2.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 ASN C 449 GLN ** E 406 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 = 0.3594 r_free = 0.3594 target = 0.091199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.063004 restraints weight = 55865.356| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 3.35 r_work: 0.2836 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22129 Z= 0.167 Angle : 0.562 10.361 30200 Z= 0.287 Chirality : 0.038 0.159 3487 Planarity : 0.004 0.082 3594 Dihedral : 16.589 79.670 3663 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.31 % Allowed : 15.27 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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 aren not related in a simple way. whole: 1.69 (0.18), residues: 2471 helix: 2.09 (0.14), residues: 1469 sheet: -0.28 (0.34), residues: 239 loop : -0.27 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B 575 TYR 0.032 0.001 TYR C 72 PHE 0.021 0.001 PHE C 459 TRP 0.019 0.001 TRP E 276 HIS 0.006 0.001 HIS E 278 Details of bonding type rmsd covalent geometry : bond 0.00383 (22129) covalent geometry : angle 0.56201 (30200) hydrogen bonds : bond 0.03319 ( 1119) hydrogen bonds : angle 3.51436 ( 3207) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4942 Ramachandran restraints generated. 2471 Oldfield, 0 Emsley, 2471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 425 ILE cc_start: 0.9340 (OUTLIER) cc_final: 0.8983 (tp) REVERT: B 476 ASP cc_start: 0.8882 (p0) cc_final: 0.8555 (p0) REVERT: B 535 MET cc_start: 0.7794 (tmm) cc_final: 0.6869 (tpp) REVERT: B 575 ARG cc_start: 0.7201 (mtt90) cc_final: 0.6951 (mtt90) REVERT: C 145 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8864 (mt-10) REVERT: C 277 GLU cc_start: 0.9212 (tt0) cc_final: 0.8660 (tm-30) REVERT: C 323 MET cc_start: 0.9421 (ttp) cc_final: 0.9172 (ttp) REVERT: C 384 TYR cc_start: 0.8274 (t80) cc_final: 0.7805 (t80) REVERT: C 586 ASP cc_start: 0.8189 (m-30) cc_final: 0.7714 (p0) REVERT: C 598 ASP cc_start: 0.8176 (t0) cc_final: 0.7923 (t0) REVERT: C 637 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6478 (mm) REVERT: C 658 MET cc_start: 0.8016 (tpt) cc_final: 0.7607 (mmm) REVERT: C 710 LYS cc_start: 0.9152 (mmtt) cc_final: 0.8778 (ptmt) REVERT: D 45 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8235 (mp0) REVERT: D 423 GLU cc_start: 0.9196 (mt-10) cc_final: 0.8755 (mp0) REVERT: D 426 MET cc_start: 0.8849 (mmp) cc_final: 0.8537 (mmm) REVERT: E 426 MET cc_start: 0.7674 (mmt) cc_final: 0.7326 (mmm) REVERT: A 579 TYR cc_start: 0.9020 (t80) cc_final: 0.8761 (t80) REVERT: A 666 GLU cc_start: 0.9060 (tp30) cc_final: 0.8703 (tp30) REVERT: A 788 ASP cc_start: 0.9192 (m-30) cc_final: 0.8782 (t0) REVERT: G 484 ASP cc_start: 0.9168 (t0) cc_final: 0.8790 (t0) REVERT: G 527 LYS cc_start: 0.8704 (mmmt) cc_final: 0.8473 (tppt) outliers start: 29 outliers final: 24 residues processed: 174 average time/residue: 0.1232 time to fit residues: 33.7963 Evaluate side-chains 176 residues out of total 2214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 637 LEU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 337 HIS Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain G residue 306 CYS Chi-restraints excluded: chain G residue 352 THR Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 456 VAL Chi-restraints excluded: chain G residue 570 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 246 optimal weight: 8.9990 chunk 197 optimal weight: 0.7980 chunk 179 optimal weight: 1.9990 chunk 251 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 205 optimal weight: 0.8980 chunk 232 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 240 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.092585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.065007 restraints weight = 55246.639| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.34 r_work: 0.2880 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22129 Z= 0.106 Angle : 0.547 16.857 30200 Z= 0.276 Chirality : 0.037 0.170 3487 Planarity : 0.003 0.069 3594 Dihedral : 16.509 81.334 3663 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.17 % Allowed : 15.50 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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 aren not related in a simple way. whole: 1.81 (0.18), residues: 2471 helix: 2.19 (0.14), residues: 1460 sheet: -0.24 (0.34), residues: 244 loop : -0.20 (0.24), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 575 TYR 0.031 0.001 TYR C 72 PHE 0.020 0.001 PHE C 459 TRP 0.019 0.001 TRP E 276 HIS 0.005 0.001 HIS E 278 Details of bonding type rmsd covalent geometry : bond 0.00231 (22129) covalent geometry : angle 0.54726 (30200) hydrogen bonds : bond 0.02804 ( 1119) hydrogen bonds : angle 3.43839 ( 3207) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4719.15 seconds wall clock time: 81 minutes 41.87 seconds (4901.87 seconds total)