Starting phenix.real_space_refine on Fri Mar 6 14:06:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vbv_21145/03_2026/6vbv_21145.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vbv_21145/03_2026/6vbv_21145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vbv_21145/03_2026/6vbv_21145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vbv_21145/03_2026/6vbv_21145.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vbv_21145/03_2026/6vbv_21145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vbv_21145/03_2026/6vbv_21145.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 Ca 2 9.91 5 P 3 5.49 5 S 155 5.16 5 C 20179 2.51 5 N 5414 2.21 5 O 5923 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 251 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31676 Number of models: 1 Model: "" Number of chains: 11 Chain: "0" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 421 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "1" Number of atoms: 3767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3767 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 29, 'TRANS': 456} Chain breaks: 3 Chain: "2" Number of atoms: 5145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5145 Classifications: {'peptide': 659} Link IDs: {'PTRANS': 22, 'TRANS': 636} Chain breaks: 4 Chain: "4" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3156 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 10, 'TRANS': 380} Chain breaks: 1 Chain: "5" Number of atoms: 2411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2411 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 9, 'TRANS': 290} Chain breaks: 2 Chain: "7" Number of atoms: 5575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 706, 5575 Classifications: {'peptide': 706} Link IDs: {'PTRANS': 26, 'TRANS': 679} Chain breaks: 2 Chain: "8" Number of atoms: 3797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3797 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 20, 'TRANS': 454} Chain breaks: 2 Chain: "9" Number of atoms: 6034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 6034 Classifications: {'peptide': 764} Link IDs: {'PTRANS': 31, 'TRANS': 732} Chain breaks: 5 Chain: "3" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1336 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 5, 'TRANS': 161} Chain: "2" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "3" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.46, per 1000 atoms: 0.20 Number of scatterers: 31676 At special positions: 0 Unit cell: (153.7, 182.32, 187.62, 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) Ca 2 19.99 S 155 16.00 P 3 15.00 O 5923 8.00 N 5414 7.00 C 20179 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: 2.37 Conformation dependent library (CDL) restraints added in 1.5 seconds 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7536 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 50 sheets defined 35.7% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain '0' and resid 38 through 58 removed outlier: 3.670A pdb=" N GLU 0 42 " --> pdb=" O SER 0 38 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA 0 51 " --> pdb=" O MET 0 47 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN 0 52 " --> pdb=" O GLN 0 48 " (cutoff:3.500A) Processing helix chain '1' and resid 431 through 444 removed outlier: 3.543A pdb=" N VAL 1 435 " --> pdb=" O THR 1 431 " (cutoff:3.500A) Processing helix chain '1' and resid 444 through 474 removed outlier: 3.557A pdb=" N MET 1 448 " --> pdb=" O ALA 1 444 " (cutoff:3.500A) Processing helix chain '2' and resid 36 through 38 No H-bonds generated for 'chain '2' and resid 36 through 38' Processing helix chain '2' and resid 339 through 359 removed outlier: 3.553A pdb=" N GLN 2 343 " --> pdb=" O ARG 2 339 " (cutoff:3.500A) Processing helix chain '2' and resid 490 through 494 Processing helix chain '2' and resid 506 through 517 Processing helix chain '2' and resid 560 through 575 removed outlier: 3.729A pdb=" N ALA 2 564 " --> pdb=" O ASP 2 560 " (cutoff:3.500A) Processing helix chain '2' and resid 586 through 635 removed outlier: 3.685A pdb=" N GLU 2 592 " --> pdb=" O VAL 2 588 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASP 2 601 " --> pdb=" O LEU 2 597 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU 2 602 " --> pdb=" O VAL 2 598 " (cutoff:3.500A) Processing helix chain '2' and resid 636 through 685 Processing helix chain '2' and resid 688 through 703 removed outlier: 3.846A pdb=" N ASN 2 692 " --> pdb=" O GLY 2 688 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL 2 694 " --> pdb=" O PRO 2 690 " (cutoff:3.500A) Processing helix chain '2' and resid 706 through 716 Processing helix chain '4' and resid 35 through 45 Processing helix chain '4' and resid 49 through 63 Processing helix chain '4' and resid 68 through 80 removed outlier: 3.551A pdb=" N VAL 4 72 " --> pdb=" O TYR 4 68 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN 4 73 " --> pdb=" O ALA 4 69 " (cutoff:3.500A) Processing helix chain '4' and resid 84 through 97 Processing helix chain '4' and resid 100 through 114 removed outlier: 3.540A pdb=" N LEU 4 114 " --> pdb=" O SER 4 110 " (cutoff:3.500A) Processing helix chain '4' and resid 117 through 129 removed outlier: 3.751A pdb=" N GLU 4 126 " --> pdb=" O GLU 4 122 " (cutoff:3.500A) Processing helix chain '4' and resid 134 through 148 removed outlier: 4.273A pdb=" N CYS 4 138 " --> pdb=" O ASP 4 134 " (cutoff:3.500A) Processing helix chain '4' and resid 150 through 165 Processing helix chain '4' and resid 167 through 182 Processing helix chain '4' and resid 183 through 197 removed outlier: 3.767A pdb=" N ALA 4 187 " --> pdb=" O ASP 4 183 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLU 4 189 " --> pdb=" O ASP 4 185 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE 4 190 " --> pdb=" O LYS 4 186 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE 4 197 " --> pdb=" O LYS 4 193 " (cutoff:3.500A) Processing helix chain '4' and resid 201 through 215 Processing helix chain '4' and resid 218 through 232 removed outlier: 3.664A pdb=" N TYR 4 231 " --> pdb=" O ASN 4 227 " (cutoff:3.500A) Processing helix chain '4' and resid 235 through 249 removed outlier: 3.980A pdb=" N ALA 4 241 " --> pdb=" O LYS 4 237 " (cutoff:3.500A) Processing helix chain '4' and resid 251 through 263 removed outlier: 3.790A pdb=" N ALA 4 255 " --> pdb=" O ASP 4 251 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL 4 262 " --> pdb=" O LYS 4 258 " (cutoff:3.500A) Processing helix chain '4' and resid 269 through 283 Processing helix chain '4' and resid 286 through 299 removed outlier: 3.903A pdb=" N CYS 4 292 " --> pdb=" O ALA 4 288 " (cutoff:3.500A) Processing helix chain '4' and resid 303 through 317 Processing helix chain '4' and resid 321 through 334 removed outlier: 3.739A pdb=" N HIS 4 325 " --> pdb=" O ALA 4 321 " (cutoff:3.500A) Processing helix chain '4' and resid 338 through 350 removed outlier: 3.756A pdb=" N ASN 4 350 " --> pdb=" O VAL 4 346 " (cutoff:3.500A) Processing helix chain '4' and resid 353 through 368 removed outlier: 3.573A pdb=" N ALA 4 357 " --> pdb=" O ASP 4 353 " (cutoff:3.500A) Processing helix chain '4' and resid 371 through 385 removed outlier: 4.363A pdb=" N ASN 4 375 " --> pdb=" O ASN 4 371 " (cutoff:3.500A) Processing helix chain '4' and resid 389 through 402 removed outlier: 3.745A pdb=" N ALA 4 393 " --> pdb=" O ARG 4 389 " (cutoff:3.500A) Processing helix chain '4' and resid 412 through 423 removed outlier: 3.787A pdb=" N GLU 4 416 " --> pdb=" O GLU 4 412 " (cutoff:3.500A) Processing helix chain '5' and resid 119 through 133 removed outlier: 3.806A pdb=" N SER 5 123 " --> pdb=" O ARG 5 119 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE 5 125 " --> pdb=" O TYR 5 121 " (cutoff:3.500A) Processing helix chain '5' and resid 239 through 260 removed outlier: 4.225A pdb=" N LEU 5 243 " --> pdb=" O PRO 5 239 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASN 5 260 " --> pdb=" O VAL 5 256 " (cutoff:3.500A) Processing helix chain '5' and resid 298 through 302 Processing helix chain '5' and resid 332 through 337 Processing helix chain '7' and resid 336 through 368 removed outlier: 4.179A pdb=" N GLN 7 368 " --> pdb=" O GLN 7 364 " (cutoff:3.500A) Processing helix chain '7' and resid 516 through 528 Processing helix chain '7' and resid 569 through 588 removed outlier: 3.759A pdb=" N ILE 7 573 " --> pdb=" O ASN 7 569 " (cutoff:3.500A) Processing helix chain '7' and resid 600 through 634 Proline residue: 7 611 - end of helix removed outlier: 3.868A pdb=" N LEU 7 625 " --> pdb=" O LYS 7 621 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ASP 7 627 " --> pdb=" O VAL 7 623 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ALA 7 628 " --> pdb=" O GLN 7 624 " (cutoff:3.500A) Processing helix chain '7' and resid 635 through 639 removed outlier: 3.916A pdb=" N ASN 7 638 " --> pdb=" O HIS 7 635 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR 7 639 " --> pdb=" O GLU 7 636 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 635 through 639' Processing helix chain '7' and resid 643 through 661 removed outlier: 3.813A pdb=" N ILE 7 649 " --> pdb=" O GLU 7 645 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU 7 651 " --> pdb=" O ARG 7 647 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU 7 652 " --> pdb=" O CYS 7 648 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ASP 7 654 " --> pdb=" O LEU 7 650 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N HIS 7 655 " --> pdb=" O GLU 7 651 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS 7 661 " --> pdb=" O GLN 7 657 " (cutoff:3.500A) Processing helix chain '7' and resid 662 through 684 removed outlier: 3.616A pdb=" N HIS 7 666 " --> pdb=" O LYS 7 662 " (cutoff:3.500A) Processing helix chain '7' and resid 692 through 703 Processing helix chain '7' and resid 704 through 715 Processing helix chain '8' and resid 2 through 13 Processing helix chain '8' and resid 17 through 30 Processing helix chain '8' and resid 33 through 48 removed outlier: 3.607A pdb=" N TRP 8 37 " --> pdb=" O ASP 8 33 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL 8 48 " --> pdb=" O LEU 8 44 " (cutoff:3.500A) Processing helix chain '8' and resid 51 through 55 removed outlier: 3.604A pdb=" N ASP 8 54 " --> pdb=" O ASP 8 51 " (cutoff:3.500A) Processing helix chain '8' and resid 60 through 65 removed outlier: 3.877A pdb=" N ILE 8 64 " --> pdb=" O ILE 8 60 " (cutoff:3.500A) Processing helix chain '8' and resid 120 through 126 Processing helix chain '8' and resid 167 through 172 removed outlier: 3.504A pdb=" N TYR 8 171 " --> pdb=" O ASN 8 167 " (cutoff:3.500A) Processing helix chain '8' and resid 174 through 188 removed outlier: 4.263A pdb=" N ALA 8 180 " --> pdb=" O LYS 8 176 " (cutoff:3.500A) Processing helix chain '8' and resid 191 through 206 Processing helix chain '8' and resid 210 through 225 removed outlier: 3.650A pdb=" N LYS 8 214 " --> pdb=" O ASP 8 210 " (cutoff:3.500A) Processing helix chain '8' and resid 227 through 241 removed outlier: 3.928A pdb=" N GLN 8 233 " --> pdb=" O GLU 8 229 " (cutoff:3.500A) Processing helix chain '8' and resid 243 through 257 Processing helix chain '8' and resid 259 through 274 Processing helix chain '8' and resid 277 through 291 removed outlier: 3.544A pdb=" N LEU 8 281 " --> pdb=" O GLU 8 277 " (cutoff:3.500A) Processing helix chain '8' and resid 293 through 308 removed outlier: 3.649A pdb=" N ALA 8 297 " --> pdb=" O ASN 8 293 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLU 8 299 " --> pdb=" O SER 8 295 " (cutoff:3.500A) Processing helix chain '8' and resid 311 through 325 Processing helix chain '8' and resid 327 through 341 removed outlier: 3.690A pdb=" N LEU 8 338 " --> pdb=" O PHE 8 334 " (cutoff:3.500A) Processing helix chain '8' and resid 345 through 359 removed outlier: 3.970A pdb=" N PHE 8 349 " --> pdb=" O ASN 8 345 " (cutoff:3.500A) Processing helix chain '8' and resid 365 through 376 removed outlier: 3.501A pdb=" N PHE 8 369 " --> pdb=" O THR 8 365 " (cutoff:3.500A) Processing helix chain '8' and resid 379 through 397 Processing helix chain '8' and resid 398 through 413 removed outlier: 3.746A pdb=" N ALA 8 402 " --> pdb=" O ASP 8 398 " (cutoff:3.500A) Processing helix chain '8' and resid 416 through 431 Processing helix chain '8' and resid 432 through 447 Processing helix chain '8' and resid 451 through 465 Processing helix chain '8' and resid 466 through 481 removed outlier: 3.734A pdb=" N LYS 8 476 " --> pdb=" O ALA 8 472 " (cutoff:3.500A) Processing helix chain '8' and resid 485 through 498 Processing helix chain '9' and resid 64 through 66 No H-bonds generated for 'chain '9' and resid 64 through 66' Processing helix chain '9' and resid 207 through 213 Processing helix chain '9' and resid 377 through 396 removed outlier: 3.524A pdb=" N ASN 9 396 " --> pdb=" O ILE 9 392 " (cutoff:3.500A) Processing helix chain '9' and resid 530 through 533 Processing helix chain '9' and resid 558 through 563 Processing helix chain '9' and resid 605 through 627 removed outlier: 3.682A pdb=" N LEU 9 609 " --> pdb=" O GLN 9 605 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TRP 9 610 " --> pdb=" O PHE 9 606 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU 9 611 " --> pdb=" O GLU 9 607 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE 9 612 " --> pdb=" O ASP 9 608 " (cutoff:3.500A) Processing helix chain '9' and resid 645 through 686 removed outlier: 3.537A pdb=" N ILE 9 649 " --> pdb=" O TYR 9 645 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU 9 668 " --> pdb=" O GLU 9 664 " (cutoff:3.500A) Processing helix chain '9' and resid 694 through 742 Processing helix chain '9' and resid 745 through 757 Processing helix chain '9' and resid 767 through 783 Processing helix chain '9' and resid 787 through 794 Processing helix chain '9' and resid 805 through 821 Processing helix chain '3' and resid 29 through 36 Processing helix chain '3' and resid 73 through 85 removed outlier: 4.891A pdb=" N ASN 3 78 " --> pdb=" O ARG 3 75 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LEU 3 79 " --> pdb=" O TYR 3 76 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR 3 83 " --> pdb=" O TRP 3 80 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LYS 3 85 " --> pdb=" O HIS 3 82 " (cutoff:3.500A) Processing helix chain '3' and resid 101 through 114 Processing helix chain '3' and resid 139 through 148 Processing helix chain '3' and resid 169 through 183 removed outlier: 3.665A pdb=" N SER 3 183 " --> pdb=" O ASP 3 179 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 3 through 9 removed outlier: 4.948A pdb=" N ASP 1 5 " --> pdb=" O ILE 1 401 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ILE 1 401 " --> pdb=" O ASP 1 5 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LEU 1 397 " --> pdb=" O MET 1 390 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N MET 1 390 " --> pdb=" O LEU 1 397 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE 1 399 " --> pdb=" O LEU 1 388 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU 1 388 " --> pdb=" O ILE 1 399 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER 1 375 " --> pdb=" O THR 1 391 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '1' and resid 21 through 25 removed outlier: 3.959A pdb=" N SER 1 58 " --> pdb=" O VAL 1 50 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LYS 1 52 " --> pdb=" O LEU 1 56 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU 1 56 " --> pdb=" O LYS 1 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1' and resid 66 through 72 removed outlier: 4.068A pdb=" N ALA 1 68 " --> pdb=" O ALA 1 87 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL 1 70 " --> pdb=" O ALA 1 85 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '1' and resid 200 through 207 removed outlier: 3.707A pdb=" N THR 1 202 " --> pdb=" O GLY 1 222 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU 1 219 " --> pdb=" O LEU 1 231 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU 1 227 " --> pdb=" O THR 1 223 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU 1 228 " --> pdb=" O LYS 1 241 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LYS 1 241 " --> pdb=" O LEU 1 228 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL 1 230 " --> pdb=" O LEU 1 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '1' and resid 248 through 256 removed outlier: 6.553A pdb=" N ALA 1 266 " --> pdb=" O ALA 1 249 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU 1 251 " --> pdb=" O ALA 1 264 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA 1 264 " --> pdb=" O LEU 1 251 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA 1 253 " --> pdb=" O ARG 1 262 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ARG 1 262 " --> pdb=" O ALA 1 253 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY 1 255 " --> pdb=" O GLU 1 260 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLU 1 260 " --> pdb=" O GLY 1 255 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER 1 271 " --> pdb=" O CYS 1 267 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '1' and resid 292 through 297 removed outlier: 6.488A pdb=" N GLY 1 305 " --> pdb=" O VAL 1 293 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LEU 1 295 " --> pdb=" O VAL 1 303 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N VAL 1 303 " --> pdb=" O LEU 1 295 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N GLY 1 297 " --> pdb=" O VAL 1 301 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL 1 301 " --> pdb=" O GLY 1 297 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER 1 310 " --> pdb=" O SER 1 306 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N THR 1 315 " --> pdb=" O ARG 1 320 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ARG 1 320 " --> pdb=" O THR 1 315 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '1' and resid 330 through 332 removed outlier: 6.725A pdb=" N ALA 1 349 " --> pdb=" O LEU 1 331 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU 1 354 " --> pdb=" O LEU 1 350 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE 1 357 " --> pdb=" O ASN 1 365 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASN 1 365 " --> pdb=" O ILE 1 357 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '1' and resid 335 through 338 Processing sheet with id=AA9, first strand: chain '1' and resid 487 through 493 Processing sheet with id=AB1, first strand: chain '1' and resid 534 through 536 Processing sheet with id=AB2, first strand: chain '2' and resid 6 through 9 removed outlier: 4.767A pdb=" N GLU 2 313 " --> pdb=" O SER 2 309 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '2' and resid 19 through 22 removed outlier: 3.889A pdb=" N LYS 2 39 " --> pdb=" O THR 2 35 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '2' and resid 75 through 81 removed outlier: 3.988A pdb=" N PHE 2 112 " --> pdb=" O ALA 2 102 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASP 2 104 " --> pdb=" O ASP 2 110 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ASP 2 110 " --> pdb=" O ASP 2 104 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '2' and resid 138 through 139 removed outlier: 3.961A pdb=" N PHE 2 155 " --> pdb=" O GLY 2 146 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '2' and resid 163 through 169 removed outlier: 3.925A pdb=" N SER 2 165 " --> pdb=" O GLY 2 182 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP 2 187 " --> pdb=" O SER 2 183 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE 2 188 " --> pdb=" O GLU 2 199 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLU 2 199 " --> pdb=" O ILE 2 188 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL 2 190 " --> pdb=" O VAL 2 197 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '2' and resid 208 through 211 removed outlier: 3.943A pdb=" N SER 2 208 " --> pdb=" O ALA 2 220 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TRP 2 236 " --> pdb=" O VAL 2 228 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '2' and resid 246 through 250 removed outlier: 3.553A pdb=" N SER 2 246 " --> pdb=" O GLY 2 263 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '2' and resid 269 through 271 Processing sheet with id=AC1, first strand: chain '2' and resid 377 through 378 removed outlier: 3.805A pdb=" N ILE 2 377 " --> pdb=" O SER 7 374 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '2' and resid 383 through 390 Processing sheet with id=AC3, first strand: chain '2' and resid 427 through 430 removed outlier: 4.422A pdb=" N ILE 2 417 " --> pdb=" O HIS 2 428 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL 2 415 " --> pdb=" O VAL 2 430 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE 2 412 " --> pdb=" O GLY 2 462 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLY 2 462 " --> pdb=" O ILE 2 412 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA 2 414 " --> pdb=" O PHE 2 460 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS 2 458 " --> pdb=" O LEU 2 416 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N THR 7 480 " --> pdb=" O PRO 7 474 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N THR 7 467 " --> pdb=" O SER 7 411 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N SER 7 411 " --> pdb=" O THR 7 467 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLN 7 469 " --> pdb=" O ILE 7 409 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE 7 409 " --> pdb=" O GLN 7 469 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N TYR 7 471 " --> pdb=" O VAL 7 407 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL 7 407 " --> pdb=" O TYR 7 471 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N THR 7 473 " --> pdb=" O ASP 7 405 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE 7 409 " --> pdb=" O ALA 7 443 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '2' and resid 485 through 487 removed outlier: 3.596A pdb=" N ALA 2 485 " --> pdb=" O THR 2 536 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N CYS 2 534 " --> pdb=" O THR 2 487 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '5' and resid 13 through 15 removed outlier: 3.521A pdb=" N ASP 5 32 " --> pdb=" O VAL 5 52 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '5' and resid 37 through 40 removed outlier: 6.234A pdb=" N ALA 5 94 " --> pdb=" O THR 5 81 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N THR 5 81 " --> pdb=" O ALA 5 94 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR 5 96 " --> pdb=" O ILE 5 79 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE 5 79 " --> pdb=" O TYR 5 96 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU 5 98 " --> pdb=" O LEU 5 77 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '5' and resid 141 through 142 removed outlier: 3.728A pdb=" N LYS 5 141 " --> pdb=" O SER 5 200 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARG 5 186 " --> pdb=" O THR 5 183 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLY 5 178 " --> pdb=" O ASN 5 165 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ASN 5 165 " --> pdb=" O GLY 5 178 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N PHE 5 180 " --> pdb=" O LYS 5 163 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LYS 5 163 " --> pdb=" O PHE 5 180 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE 5 182 " --> pdb=" O TYR 5 161 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '5' and resid 206 through 210 removed outlier: 6.886A pdb=" N GLU 5 223 " --> pdb=" O ARG 5 207 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL 5 209 " --> pdb=" O VAL 5 221 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL 5 221 " --> pdb=" O VAL 5 209 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '5' and resid 314 through 316 Processing sheet with id=AD1, first strand: chain '7' and resid 6 through 12 removed outlier: 4.968A pdb=" N ILE 7 314 " --> pdb=" O TYR 7 10 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TRP 7 313 " --> pdb=" O THR 7 309 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL 7 306 " --> pdb=" O ILE 7 292 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILE 7 292 " --> pdb=" O VAL 7 306 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N SER 7 308 " --> pdb=" O THR 7 290 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '7' and resid 21 through 24 removed outlier: 3.797A pdb=" N LYS 7 34 " --> pdb=" O LEU 7 24 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '7' and resid 69 through 72 removed outlier: 3.652A pdb=" N LEU 7 101 " --> pdb=" O GLY 7 92 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '7' and resid 114 through 117 removed outlier: 6.264A pdb=" N CYS 7 133 " --> pdb=" O ASP 7 137 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ASP 7 137 " --> pdb=" O CYS 7 133 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '7' and resid 147 through 152 removed outlier: 4.116A pdb=" N ASP 7 149 " --> pdb=" O ALA 7 166 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL 7 171 " --> pdb=" O CYS 7 167 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR 7 182 " --> pdb=" O VAL 7 174 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N GLN 7 176 " --> pdb=" O VAL 7 180 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N VAL 7 180 " --> pdb=" O GLN 7 176 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '7' and resid 190 through 193 Processing sheet with id=AD7, first strand: chain '7' and resid 220 through 221 Processing sheet with id=AD8, first strand: chain '7' and resid 244 through 247 removed outlier: 6.348A pdb=" N VAL 7 266 " --> pdb=" O ASP 7 282 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP 7 282 " --> pdb=" O VAL 7 266 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL 7 268 " --> pdb=" O ARG 7 280 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '7' and resid 325 through 326 removed outlier: 6.508A pdb=" N ILE 3 125 " --> pdb=" O HIS 3 158 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N CYS 3 160 " --> pdb=" O ILE 3 125 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N PHE 3 127 " --> pdb=" O CYS 3 160 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N SER 3 162 " --> pdb=" O PHE 3 127 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ALA 3 129 " --> pdb=" O SER 3 162 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain '7' and resid 384 through 387 removed outlier: 4.261A pdb=" N THR 7 386 " --> pdb=" O SER 7 395 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain '7' and resid 540 through 543 removed outlier: 3.777A pdb=" N GLU 7 562 " --> pdb=" O ARG 7 559 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU 7 509 " --> pdb=" O PHE 7 565 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain '9' and resid 6 through 13 removed outlier: 4.979A pdb=" N ASP 9 8 " --> pdb=" O TYR 9 358 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N TYR 9 358 " --> pdb=" O ASP 9 8 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N TRP 9 10 " --> pdb=" O CYS 9 356 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEU 9 348 " --> pdb=" O ALA 9 332 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ALA 9 332 " --> pdb=" O LEU 9 348 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain '9' and resid 26 through 28 removed outlier: 3.575A pdb=" N ALA 9 28 " --> pdb=" O LYS 9 39 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain '9' and resid 79 through 84 removed outlier: 4.765A pdb=" N GLN 9 80 " --> pdb=" O LEU 9 98 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU 9 98 " --> pdb=" O GLN 9 80 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU 9 95 " --> pdb=" O TYR 9 106 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR 9 127 " --> pdb=" O VAL 9 105 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain '9' and resid 108 through 111 Processing sheet with id=AE7, first strand: chain '9' and resid 138 through 141 Processing sheet with id=AE8, first strand: chain '9' and resid 185 through 187 Processing sheet with id=AE9, first strand: chain '9' and resid 245 through 251 removed outlier: 7.193A pdb=" N LEU 9 263 " --> pdb=" O ILE 9 246 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ILE 9 248 " --> pdb=" O PHE 9 261 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N PHE 9 261 " --> pdb=" O ILE 9 248 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ILE 9 250 " --> pdb=" O SER 9 259 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N SER 9 259 " --> pdb=" O ILE 9 250 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain '9' and resid 287 through 291 removed outlier: 3.766A pdb=" N CYS 9 289 " --> pdb=" O GLY 9 306 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N MET 9 311 " --> pdb=" O ASN 9 307 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU 9 312 " --> pdb=" O ALA 9 323 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ALA 9 323 " --> pdb=" O LEU 9 312 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE 9 314 " --> pdb=" O LYS 9 321 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR 9 319 " --> pdb=" O GLN 9 316 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain '9' and resid 411 through 417 Processing sheet with id=AF3, first strand: chain '9' and resid 471 through 474 removed outlier: 5.573A pdb=" N LYS 9 454 " --> pdb=" O SER 9 509 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER 9 509 " --> pdb=" O LYS 9 454 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain '9' and resid 535 through 537 Processing sheet with id=AF5, first strand: chain '3' and resid 18 through 19 1505 hydrogen bonds defined for protein. 4317 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.88 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5289 1.31 - 1.43: 8270 1.43 - 1.56: 18493 1.56 - 1.69: 5 1.69 - 1.82: 232 Bond restraints: 32289 Sorted by residual: bond pdb=" CA SER 7 428 " pdb=" CB SER 7 428 " ideal model delta sigma weight residual 1.527 1.451 0.076 7.60e-03 1.73e+04 1.00e+02 bond pdb=" C ALA 8 20 " pdb=" O ALA 8 20 " ideal model delta sigma weight residual 1.237 1.177 0.059 1.17e-02 7.31e+03 2.58e+01 bond pdb=" CA SER 2 254 " pdb=" CB SER 2 254 " ideal model delta sigma weight residual 1.530 1.465 0.065 1.50e-02 4.44e+03 1.87e+01 bond pdb=" CA SER 7 430 " pdb=" CB SER 7 430 " ideal model delta sigma weight residual 1.529 1.458 0.071 1.70e-02 3.46e+03 1.75e+01 bond pdb=" N VAL 1 373 " pdb=" CA VAL 1 373 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.20e-02 6.94e+03 1.34e+01 ... (remaining 32284 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 42682 2.01 - 4.01: 840 4.01 - 6.02: 135 6.02 - 8.03: 31 8.03 - 10.03: 12 Bond angle restraints: 43700 Sorted by residual: angle pdb=" C ASP 2 172 " pdb=" CA ASP 2 172 " pdb=" CB ASP 2 172 " ideal model delta sigma weight residual 109.83 118.15 -8.32 9.90e-01 1.02e+00 7.06e+01 angle pdb=" C ASP 2 251 " pdb=" CA ASP 2 251 " pdb=" CB ASP 2 251 " ideal model delta sigma weight residual 111.70 103.13 8.57 1.48e+00 4.57e-01 3.35e+01 angle pdb=" N ALA 8 20 " pdb=" CA ALA 8 20 " pdb=" C ALA 8 20 " ideal model delta sigma weight residual 111.28 105.16 6.12 1.09e+00 8.42e-01 3.15e+01 angle pdb=" C ASP 9 362 " pdb=" CA ASP 9 362 " pdb=" CB ASP 9 362 " ideal model delta sigma weight residual 110.71 102.25 8.46 1.53e+00 4.27e-01 3.05e+01 angle pdb=" N GLN 8 25 " pdb=" CA GLN 8 25 " pdb=" C GLN 8 25 " ideal model delta sigma weight residual 110.97 104.95 6.02 1.09e+00 8.42e-01 3.05e+01 ... (remaining 43695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.20: 18924 31.20 - 62.39: 542 62.39 - 93.59: 55 93.59 - 124.78: 3 124.78 - 155.98: 2 Dihedral angle restraints: 19526 sinusoidal: 7873 harmonic: 11653 Sorted by residual: dihedral pdb=" C8 GTP 3 201 " pdb=" C1' GTP 3 201 " pdb=" N9 GTP 3 201 " pdb=" O4' GTP 3 201 " ideal model delta sinusoidal sigma weight residual 104.59 -51.39 155.98 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" C5' GTP 3 201 " pdb=" O5' GTP 3 201 " pdb=" PA GTP 3 201 " pdb=" O3A GTP 3 201 " ideal model delta sinusoidal sigma weight residual 69.27 -150.42 -140.31 1 2.00e+01 2.50e-03 4.25e+01 dihedral pdb=" O3B GTP 3 201 " pdb=" O3A GTP 3 201 " pdb=" PB GTP 3 201 " pdb=" PA GTP 3 201 " ideal model delta sinusoidal sigma weight residual -68.92 55.24 -124.16 1 2.00e+01 2.50e-03 3.75e+01 ... (remaining 19523 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 4658 0.096 - 0.192: 275 0.192 - 0.288: 28 0.288 - 0.384: 10 0.384 - 0.480: 3 Chirality restraints: 4974 Sorted by residual: chirality pdb=" CA ASP 2 172 " pdb=" N ASP 2 172 " pdb=" C ASP 2 172 " pdb=" CB ASP 2 172 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.75e+00 chirality pdb=" CA PHE 2 171 " pdb=" N PHE 2 171 " pdb=" C PHE 2 171 " pdb=" CB PHE 2 171 " both_signs ideal model delta sigma weight residual False 2.51 2.98 -0.47 2.00e-01 2.50e+01 5.55e+00 chirality pdb=" CA GLU 2 259 " pdb=" N GLU 2 259 " pdb=" C GLU 2 259 " pdb=" CB GLU 2 259 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.86e+00 ... (remaining 4971 not shown) Planarity restraints: 5596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL 7 427 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C VAL 7 427 " 0.062 2.00e-02 2.50e+03 pdb=" O VAL 7 427 " -0.024 2.00e-02 2.50e+03 pdb=" N SER 7 428 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE 8 16 " -0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C PHE 8 16 " 0.058 2.00e-02 2.50e+03 pdb=" O PHE 8 16 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN 8 17 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE 2 250 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C PHE 2 250 " -0.055 2.00e-02 2.50e+03 pdb=" O PHE 2 250 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP 2 251 " 0.018 2.00e-02 2.50e+03 ... (remaining 5593 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 459 2.64 - 3.20: 28793 3.20 - 3.77: 48076 3.77 - 4.33: 67536 4.33 - 4.90: 112377 Nonbonded interactions: 257241 Sorted by model distance: nonbonded pdb=" O SER 7 428 " pdb=" OG SER 7 428 " model vdw 2.070 3.040 nonbonded pdb=" OD2 ASP 7 433 " pdb=" OG SER 7 436 " model vdw 2.200 3.040 nonbonded pdb=" O HIS 7 323 " pdb=" OG SER 3 140 " model vdw 2.201 3.040 nonbonded pdb=" OG1 THR 5 83 " pdb=" OE1 GLU 5 93 " model vdw 2.208 3.040 nonbonded pdb=" ND2 ASN 7 148 " pdb=" O PRO 7 190 " model vdw 2.212 3.120 ... (remaining 257236 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.920 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: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 28.070 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 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 : 0.004 0.076 32289 Z= 0.236 Angle : 0.714 10.033 43700 Z= 0.424 Chirality : 0.052 0.480 4974 Planarity : 0.004 0.050 5596 Dihedral : 15.128 155.981 11990 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.20 % Favored : 92.72 % Rotamer: Outliers : 0.72 % Allowed : 6.87 % Favored : 92.42 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.09 (0.12), residues: 3944 helix: -0.62 (0.12), residues: 1352 sheet: -2.24 (0.15), residues: 991 loop : -3.14 (0.13), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 8 12 TYR 0.015 0.001 TYR 7 445 PHE 0.020 0.002 PHE 7 58 TRP 0.016 0.001 TRP 9 237 HIS 0.006 0.001 HIS 5 190 Details of bonding type rmsd covalent geometry : bond 0.00415 (32289) covalent geometry : angle 0.71442 (43700) hydrogen bonds : bond 0.13214 ( 1505) hydrogen bonds : angle 6.28776 ( 4317) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 799 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 17 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7720 (mm-40) REVERT: 1 11 MET cc_start: 0.8010 (mmp) cc_final: 0.7121 (ptt) REVERT: 1 274 ILE cc_start: 0.7286 (pt) cc_final: 0.6956 (mp) REVERT: 1 426 ASN cc_start: 0.6927 (t0) cc_final: 0.6688 (t0) REVERT: 1 479 SER cc_start: 0.7642 (m) cc_final: 0.7292 (t) REVERT: 2 152 ASN cc_start: 0.7962 (m-40) cc_final: 0.7620 (t0) REVERT: 2 171 PHE cc_start: 0.5888 (OUTLIER) cc_final: 0.4603 (m-80) REVERT: 2 287 SER cc_start: 0.8364 (t) cc_final: 0.7875 (p) REVERT: 2 384 HIS cc_start: 0.6726 (p-80) cc_final: 0.6525 (p-80) REVERT: 2 714 MET cc_start: 0.8351 (mtm) cc_final: 0.8032 (mtm) REVERT: 4 134 ASP cc_start: 0.5591 (p0) cc_final: 0.4771 (p0) REVERT: 4 137 ILE cc_start: 0.8087 (mt) cc_final: 0.7758 (mp) REVERT: 5 93 GLU cc_start: 0.5964 (mm-30) cc_final: 0.5143 (mp0) REVERT: 5 98 LEU cc_start: 0.7819 (tp) cc_final: 0.7496 (tp) REVERT: 5 232 VAL cc_start: 0.8973 (p) cc_final: 0.8676 (m) REVERT: 5 233 LEU cc_start: 0.8843 (mm) cc_final: 0.8355 (mp) REVERT: 7 325 GLU cc_start: 0.6990 (pp20) cc_final: 0.5807 (pm20) REVERT: 7 389 LYS cc_start: 0.7599 (tptt) cc_final: 0.7126 (ttpt) REVERT: 7 390 ASP cc_start: 0.6805 (p0) cc_final: 0.6222 (p0) REVERT: 7 671 TYR cc_start: 0.7909 (m-10) cc_final: 0.7381 (m-10) REVERT: 7 700 LEU cc_start: 0.7079 (mm) cc_final: 0.6479 (mm) REVERT: 8 10 TYR cc_start: 0.8180 (m-10) cc_final: 0.7629 (m-80) REVERT: 8 22 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7140 (tt) REVERT: 8 171 TYR cc_start: 0.7730 (m-80) cc_final: 0.6957 (m-10) REVERT: 8 293 ASN cc_start: 0.8362 (p0) cc_final: 0.7982 (p0) REVERT: 8 496 GLN cc_start: 0.8321 (tt0) cc_final: 0.8109 (mt0) REVERT: 9 127 TYR cc_start: 0.6468 (p90) cc_final: 0.6115 (p90) REVERT: 9 309 ASN cc_start: 0.6892 (t0) cc_final: 0.6526 (t0) REVERT: 9 367 GLN cc_start: 0.6703 (tt0) cc_final: 0.6271 (mt0) REVERT: 3 47 ILE cc_start: 0.5058 (mm) cc_final: 0.4454 (mm) REVERT: 3 142 LYS cc_start: 0.7805 (mmtt) cc_final: 0.7578 (mmmt) outliers start: 25 outliers final: 10 residues processed: 814 average time/residue: 0.2031 time to fit residues: 262.2473 Evaluate side-chains 437 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 424 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 17 GLN Chi-restraints excluded: chain 1 residue 376 LEU Chi-restraints excluded: chain 1 residue 392 THR Chi-restraints excluded: chain 2 residue 171 PHE Chi-restraints excluded: chain 2 residue 252 LEU Chi-restraints excluded: chain 4 residue 409 SER Chi-restraints excluded: chain 4 residue 411 LEU Chi-restraints excluded: chain 4 residue 413 PHE Chi-restraints excluded: chain 5 residue 299 PHE Chi-restraints excluded: chain 8 residue 19 CYS Chi-restraints excluded: chain 8 residue 22 LEU Chi-restraints excluded: chain 9 residue 361 THR Chi-restraints excluded: chain 9 residue 364 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 0.0970 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.4980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 15 HIS 1 45 GLN 1 54 HIS 1 291 GLN 1 365 ASN 1 449 HIS 1 545 ASN 2 28 HIS 2 36 GLN 2 223 ASN 2 343 GLN ** 2 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 358 ASN 2 384 HIS ** 2 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 516 GLN 2 532 GLN 2 540 ASN 2 543 GLN 2 569 GLN 2 656 ASN 2 684 HIS 4 35 GLN 4 40 HIS 4 58 GLN 4 91 GLN 4 224 HIS 4 377 ASN 5 44 ASN 5 176 ASN 5 190 HIS 5 205 GLN 5 334 GLN 7 6 ASN 7 99 GLN ** 7 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 228 HIS 7 477 GLN ** 7 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 502 HIS 7 610 HIS 7 624 GLN ** 7 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 216 GLN 8 233 GLN 8 307 GLN 8 322 HIS 8 350 ASN 8 351 ASN 8 360 GLN 8 388 ASN ** 8 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 454 HIS 8 456 ASN 8 496 GLN 9 22 GLN 9 201 GLN 9 276 GLN 9 652 HIS 9 693 GLN 3 27 ASN ** 3 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 43 GLN 3 120 HIS Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.164455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.141994 restraints weight = 48467.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.142016 restraints weight = 57967.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.143051 restraints weight = 52569.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.143325 restraints weight = 35547.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.143513 restraints weight = 34106.025| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 32289 Z= 0.145 Angle : 0.631 9.971 43700 Z= 0.323 Chirality : 0.044 0.184 4974 Planarity : 0.004 0.061 5596 Dihedral : 6.925 159.737 4331 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.26 % Allowed : 13.42 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.13), residues: 3944 helix: 0.73 (0.14), residues: 1382 sheet: -1.69 (0.16), residues: 1005 loop : -2.57 (0.14), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 8 469 TYR 0.026 0.001 TYR 7 660 PHE 0.025 0.002 PHE 4 413 TRP 0.014 0.001 TRP 3 157 HIS 0.012 0.001 HIS 7 196 Details of bonding type rmsd covalent geometry : bond 0.00331 (32289) covalent geometry : angle 0.63055 (43700) hydrogen bonds : bond 0.04302 ( 1505) hydrogen bonds : angle 4.93444 ( 4317) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 469 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 11 MET cc_start: 0.7687 (mmp) cc_final: 0.7211 (ptt) REVERT: 1 274 ILE cc_start: 0.7376 (pt) cc_final: 0.6987 (mp) REVERT: 1 479 SER cc_start: 0.7513 (m) cc_final: 0.7289 (t) REVERT: 2 287 SER cc_start: 0.8471 (t) cc_final: 0.8110 (p) REVERT: 4 134 ASP cc_start: 0.5905 (p0) cc_final: 0.4902 (p0) REVERT: 4 137 ILE cc_start: 0.8085 (mt) cc_final: 0.7672 (mp) REVERT: 4 178 PHE cc_start: 0.7961 (m-10) cc_final: 0.7728 (m-10) REVERT: 4 411 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7424 (mt) REVERT: 5 93 GLU cc_start: 0.6275 (mm-30) cc_final: 0.5533 (mm-30) REVERT: 5 233 LEU cc_start: 0.8393 (mm) cc_final: 0.7947 (mp) REVERT: 7 325 GLU cc_start: 0.6941 (pp20) cc_final: 0.5943 (pm20) REVERT: 7 389 LYS cc_start: 0.7682 (tptt) cc_final: 0.7245 (ttpt) REVERT: 7 461 ILE cc_start: 0.7523 (OUTLIER) cc_final: 0.6790 (mp) REVERT: 7 671 TYR cc_start: 0.7846 (m-10) cc_final: 0.7611 (m-10) REVERT: 7 700 LEU cc_start: 0.6977 (mm) cc_final: 0.6460 (mm) REVERT: 8 10 TYR cc_start: 0.7916 (m-10) cc_final: 0.7490 (m-80) REVERT: 8 171 TYR cc_start: 0.7632 (m-80) cc_final: 0.6949 (m-80) REVERT: 8 293 ASN cc_start: 0.8299 (p0) cc_final: 0.7945 (p0) REVERT: 9 480 GLU cc_start: 0.6416 (mm-30) cc_final: 0.5597 (tm-30) REVERT: 3 171 GLN cc_start: 0.7274 (mm-40) cc_final: 0.6970 (mm-40) outliers start: 79 outliers final: 37 residues processed: 517 average time/residue: 0.1876 time to fit residues: 158.1886 Evaluate side-chains 429 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 390 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 11 VAL Chi-restraints excluded: chain 0 residue 12 LEU Chi-restraints excluded: chain 1 residue 198 THR Chi-restraints excluded: chain 1 residue 261 PHE Chi-restraints excluded: chain 1 residue 376 LEU Chi-restraints excluded: chain 1 residue 392 THR Chi-restraints excluded: chain 1 residue 502 THR Chi-restraints excluded: chain 1 residue 514 ILE Chi-restraints excluded: chain 1 residue 552 VAL Chi-restraints excluded: chain 2 residue 123 ILE Chi-restraints excluded: chain 2 residue 441 VAL Chi-restraints excluded: chain 2 residue 546 ILE Chi-restraints excluded: chain 2 residue 708 ASN Chi-restraints excluded: chain 4 residue 177 ILE Chi-restraints excluded: chain 4 residue 409 SER Chi-restraints excluded: chain 4 residue 411 LEU Chi-restraints excluded: chain 5 residue 17 VAL Chi-restraints excluded: chain 5 residue 57 ILE Chi-restraints excluded: chain 5 residue 201 ILE Chi-restraints excluded: chain 5 residue 241 GLU Chi-restraints excluded: chain 7 residue 11 LEU Chi-restraints excluded: chain 7 residue 155 VAL Chi-restraints excluded: chain 7 residue 296 CYS Chi-restraints excluded: chain 7 residue 461 ILE Chi-restraints excluded: chain 7 residue 673 MET Chi-restraints excluded: chain 7 residue 709 ILE Chi-restraints excluded: chain 8 residue 354 LEU Chi-restraints excluded: chain 8 residue 399 THR Chi-restraints excluded: chain 9 residue 29 ASP Chi-restraints excluded: chain 9 residue 319 THR Chi-restraints excluded: chain 9 residue 361 THR Chi-restraints excluded: chain 9 residue 364 SER Chi-restraints excluded: chain 9 residue 505 VAL Chi-restraints excluded: chain 9 residue 546 HIS Chi-restraints excluded: chain 9 residue 552 THR Chi-restraints excluded: chain 9 residue 688 THR Chi-restraints excluded: chain 3 residue 70 MET Chi-restraints excluded: chain 3 residue 141 VAL Chi-restraints excluded: chain 3 residue 170 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 260 optimal weight: 4.9990 chunk 171 optimal weight: 0.6980 chunk 166 optimal weight: 4.9990 chunk 313 optimal weight: 0.9990 chunk 152 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 360 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 268 optimal weight: 0.9980 chunk 182 optimal weight: 20.0000 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 308 GLN 1 545 ASN 2 36 GLN ** 2 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 436 HIS 2 569 GLN ** 2 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 45 GLN 4 91 GLN 4 140 ASN 7 99 GLN ** 7 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 635 HIS 8 422 ASN 9 53 ASN 9 309 ASN 9 367 GLN 9 694 HIS ** 9 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 811 HIS 3 27 ASN 3 120 HIS 3 158 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.164733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.142115 restraints weight = 48616.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.141917 restraints weight = 54368.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.142998 restraints weight = 51733.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.143181 restraints weight = 35309.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.143433 restraints weight = 33774.755| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32289 Z= 0.125 Angle : 0.578 9.136 43700 Z= 0.297 Chirality : 0.043 0.186 4974 Planarity : 0.004 0.049 5596 Dihedral : 6.301 157.706 4317 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.80 % Allowed : 15.71 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.13), residues: 3944 helix: 1.36 (0.14), residues: 1369 sheet: -1.38 (0.16), residues: 982 loop : -2.28 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 5 129 TYR 0.018 0.001 TYR 7 132 PHE 0.023 0.002 PHE 4 413 TRP 0.013 0.001 TRP 9 237 HIS 0.008 0.001 HIS 3 115 Details of bonding type rmsd covalent geometry : bond 0.00283 (32289) covalent geometry : angle 0.57799 (43700) hydrogen bonds : bond 0.03860 ( 1505) hydrogen bonds : angle 4.64128 ( 4317) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 452 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 11 MET cc_start: 0.7762 (mmp) cc_final: 0.7200 (ptm) REVERT: 1 274 ILE cc_start: 0.7364 (pt) cc_final: 0.6995 (mp) REVERT: 1 426 ASN cc_start: 0.6570 (t0) cc_final: 0.6253 (t0) REVERT: 1 479 SER cc_start: 0.7713 (m) cc_final: 0.7422 (t) REVERT: 4 134 ASP cc_start: 0.5918 (p0) cc_final: 0.4957 (p0) REVERT: 4 137 ILE cc_start: 0.8167 (mt) cc_final: 0.7743 (mp) REVERT: 4 411 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7342 (mt) REVERT: 4 412 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6524 (tp30) REVERT: 5 93 GLU cc_start: 0.6255 (mm-30) cc_final: 0.5433 (mm-30) REVERT: 5 154 LEU cc_start: 0.8263 (mt) cc_final: 0.7935 (mt) REVERT: 5 233 LEU cc_start: 0.8390 (mm) cc_final: 0.7952 (mp) REVERT: 7 21 MET cc_start: 0.7317 (ttp) cc_final: 0.7020 (ttp) REVERT: 7 325 GLU cc_start: 0.7118 (pp20) cc_final: 0.6128 (pm20) REVERT: 7 506 MET cc_start: 0.7192 (tpp) cc_final: 0.6884 (tpp) REVERT: 7 671 TYR cc_start: 0.7868 (m-10) cc_final: 0.7624 (m-10) REVERT: 7 700 LEU cc_start: 0.7323 (mm) cc_final: 0.6804 (mt) REVERT: 8 10 TYR cc_start: 0.7985 (m-10) cc_final: 0.7560 (m-10) REVERT: 8 171 TYR cc_start: 0.7597 (m-80) cc_final: 0.6939 (m-80) REVERT: 8 293 ASN cc_start: 0.8291 (p0) cc_final: 0.7926 (p0) REVERT: 9 480 GLU cc_start: 0.6414 (mm-30) cc_final: 0.5633 (tm-30) REVERT: 9 686 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7393 (t70) REVERT: 3 73 GLN cc_start: 0.7757 (mm-40) cc_final: 0.7515 (mm-40) REVERT: 3 78 ASN cc_start: 0.6294 (m110) cc_final: 0.5561 (m110) outliers start: 98 outliers final: 49 residues processed: 515 average time/residue: 0.1891 time to fit residues: 160.3464 Evaluate side-chains 438 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 386 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 11 VAL Chi-restraints excluded: chain 0 residue 12 LEU Chi-restraints excluded: chain 1 residue 376 LEU Chi-restraints excluded: chain 1 residue 392 THR Chi-restraints excluded: chain 1 residue 488 LEU Chi-restraints excluded: chain 1 residue 552 VAL Chi-restraints excluded: chain 1 residue 583 ASN Chi-restraints excluded: chain 2 residue 123 ILE Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 2 residue 228 VAL Chi-restraints excluded: chain 2 residue 252 LEU Chi-restraints excluded: chain 2 residue 341 LEU Chi-restraints excluded: chain 2 residue 404 ILE Chi-restraints excluded: chain 2 residue 546 ILE Chi-restraints excluded: chain 2 residue 708 ASN Chi-restraints excluded: chain 4 residue 177 ILE Chi-restraints excluded: chain 4 residue 411 LEU Chi-restraints excluded: chain 4 residue 412 GLU Chi-restraints excluded: chain 5 residue 57 ILE Chi-restraints excluded: chain 5 residue 80 THR Chi-restraints excluded: chain 5 residue 97 VAL Chi-restraints excluded: chain 5 residue 201 ILE Chi-restraints excluded: chain 5 residue 241 GLU Chi-restraints excluded: chain 7 residue 11 LEU Chi-restraints excluded: chain 7 residue 193 LEU Chi-restraints excluded: chain 7 residue 296 CYS Chi-restraints excluded: chain 7 residue 349 LEU Chi-restraints excluded: chain 7 residue 381 VAL Chi-restraints excluded: chain 7 residue 390 ASP Chi-restraints excluded: chain 7 residue 650 LEU Chi-restraints excluded: chain 7 residue 709 ILE Chi-restraints excluded: chain 8 residue 12 ARG Chi-restraints excluded: chain 8 residue 39 LEU Chi-restraints excluded: chain 8 residue 354 LEU Chi-restraints excluded: chain 8 residue 399 THR Chi-restraints excluded: chain 9 residue 134 THR Chi-restraints excluded: chain 9 residue 319 THR Chi-restraints excluded: chain 9 residue 361 THR Chi-restraints excluded: chain 9 residue 364 SER Chi-restraints excluded: chain 9 residue 413 VAL Chi-restraints excluded: chain 9 residue 460 TYR Chi-restraints excluded: chain 9 residue 461 VAL Chi-restraints excluded: chain 9 residue 505 VAL Chi-restraints excluded: chain 9 residue 546 HIS Chi-restraints excluded: chain 9 residue 642 LEU Chi-restraints excluded: chain 9 residue 686 ASP Chi-restraints excluded: chain 9 residue 688 THR Chi-restraints excluded: chain 9 residue 747 ASP Chi-restraints excluded: chain 3 residue 70 MET Chi-restraints excluded: chain 3 residue 132 MET Chi-restraints excluded: chain 3 residue 141 VAL Chi-restraints excluded: chain 3 residue 170 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 329 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 388 optimal weight: 7.9990 chunk 64 optimal weight: 0.7980 chunk 343 optimal weight: 3.9990 chunk 391 optimal weight: 10.0000 chunk 394 optimal weight: 9.9990 chunk 202 optimal weight: 2.9990 chunk 324 optimal weight: 10.0000 chunk 209 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 17 GLN 1 308 GLN 1 359 HIS 1 545 ASN 2 36 GLN 2 343 GLN ** 2 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 91 GLN 4 103 ASN 5 60 HIS 5 102 ASN 7 76 ASN ** 7 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 188 HIS 8 269 GLN 9 37 GLN 9 73 HIS 3 158 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.159579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.136946 restraints weight = 48763.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.136189 restraints weight = 62853.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.137023 restraints weight = 56726.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.138249 restraints weight = 40710.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.138384 restraints weight = 36074.693| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 32289 Z= 0.198 Angle : 0.636 8.382 43700 Z= 0.324 Chirality : 0.045 0.187 4974 Planarity : 0.004 0.055 5596 Dihedral : 6.151 152.403 4316 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 3.35 % Allowed : 16.94 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.14), residues: 3944 helix: 1.41 (0.14), residues: 1368 sheet: -1.29 (0.16), residues: 1011 loop : -2.18 (0.15), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 5 129 TYR 0.020 0.002 TYR 2 229 PHE 0.029 0.002 PHE 4 413 TRP 0.018 0.001 TRP 9 237 HIS 0.006 0.001 HIS 3 115 Details of bonding type rmsd covalent geometry : bond 0.00472 (32289) covalent geometry : angle 0.63555 (43700) hydrogen bonds : bond 0.04201 ( 1505) hydrogen bonds : angle 4.71455 ( 4317) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 422 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 274 ILE cc_start: 0.7498 (pt) cc_final: 0.7123 (mp) REVERT: 1 426 ASN cc_start: 0.6843 (t0) cc_final: 0.6567 (t0) REVERT: 1 479 SER cc_start: 0.7794 (m) cc_final: 0.7375 (t) REVERT: 2 206 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8408 (mm) REVERT: 4 134 ASP cc_start: 0.6314 (p0) cc_final: 0.5387 (t70) REVERT: 4 411 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7319 (mt) REVERT: 5 93 GLU cc_start: 0.6204 (mm-30) cc_final: 0.5567 (mm-30) REVERT: 5 324 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.8022 (tt) REVERT: 7 21 MET cc_start: 0.7691 (ttp) cc_final: 0.7309 (ttp) REVERT: 7 309 THR cc_start: 0.8681 (m) cc_final: 0.8065 (m) REVERT: 7 325 GLU cc_start: 0.7266 (pp20) cc_final: 0.6334 (pm20) REVERT: 7 671 TYR cc_start: 0.8085 (m-10) cc_final: 0.7737 (m-80) REVERT: 7 700 LEU cc_start: 0.7683 (mm) cc_final: 0.7312 (mt) REVERT: 8 10 TYR cc_start: 0.8032 (m-10) cc_final: 0.7618 (m-10) REVERT: 8 103 ARG cc_start: 0.6347 (mmt90) cc_final: 0.6131 (mmm160) REVERT: 8 171 TYR cc_start: 0.7663 (m-80) cc_final: 0.6898 (m-10) REVERT: 8 293 ASN cc_start: 0.8367 (p0) cc_final: 0.7890 (p0) REVERT: 9 480 GLU cc_start: 0.6549 (mm-30) cc_final: 0.5920 (tm-30) REVERT: 9 686 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.7250 (t70) REVERT: 3 73 GLN cc_start: 0.7772 (mm-40) cc_final: 0.7461 (mm-40) REVERT: 3 78 ASN cc_start: 0.6589 (m110) cc_final: 0.5945 (m110) outliers start: 117 outliers final: 74 residues processed: 507 average time/residue: 0.1924 time to fit residues: 159.8816 Evaluate side-chains 449 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 371 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 11 VAL Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 33 LEU Chi-restraints excluded: chain 1 residue 198 THR Chi-restraints excluded: chain 1 residue 261 PHE Chi-restraints excluded: chain 1 residue 362 VAL Chi-restraints excluded: chain 1 residue 392 THR Chi-restraints excluded: chain 1 residue 488 LEU Chi-restraints excluded: chain 1 residue 502 THR Chi-restraints excluded: chain 1 residue 505 LEU Chi-restraints excluded: chain 1 residue 514 ILE Chi-restraints excluded: chain 1 residue 550 THR Chi-restraints excluded: chain 1 residue 552 VAL Chi-restraints excluded: chain 2 residue 123 ILE Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 2 residue 206 ILE Chi-restraints excluded: chain 2 residue 212 MET Chi-restraints excluded: chain 2 residue 213 TYR Chi-restraints excluded: chain 2 residue 228 VAL Chi-restraints excluded: chain 2 residue 341 LEU Chi-restraints excluded: chain 2 residue 441 VAL Chi-restraints excluded: chain 2 residue 546 ILE Chi-restraints excluded: chain 2 residue 708 ASN Chi-restraints excluded: chain 4 residue 177 ILE Chi-restraints excluded: chain 4 residue 190 ILE Chi-restraints excluded: chain 4 residue 373 LEU Chi-restraints excluded: chain 4 residue 411 LEU Chi-restraints excluded: chain 5 residue 17 VAL Chi-restraints excluded: chain 5 residue 57 ILE Chi-restraints excluded: chain 5 residue 97 VAL Chi-restraints excluded: chain 5 residue 120 LEU Chi-restraints excluded: chain 5 residue 201 ILE Chi-restraints excluded: chain 5 residue 232 VAL Chi-restraints excluded: chain 5 residue 241 GLU Chi-restraints excluded: chain 5 residue 324 ILE Chi-restraints excluded: chain 7 residue 11 LEU Chi-restraints excluded: chain 7 residue 15 VAL Chi-restraints excluded: chain 7 residue 133 CYS Chi-restraints excluded: chain 7 residue 155 VAL Chi-restraints excluded: chain 7 residue 174 VAL Chi-restraints excluded: chain 7 residue 180 VAL Chi-restraints excluded: chain 7 residue 192 VAL Chi-restraints excluded: chain 7 residue 193 LEU Chi-restraints excluded: chain 7 residue 291 SER Chi-restraints excluded: chain 7 residue 381 VAL Chi-restraints excluded: chain 7 residue 390 ASP Chi-restraints excluded: chain 7 residue 420 VAL Chi-restraints excluded: chain 7 residue 461 ILE Chi-restraints excluded: chain 7 residue 508 THR Chi-restraints excluded: chain 8 residue 12 ARG Chi-restraints excluded: chain 8 residue 39 LEU Chi-restraints excluded: chain 8 residue 133 THR Chi-restraints excluded: chain 8 residue 354 LEU Chi-restraints excluded: chain 8 residue 399 THR Chi-restraints excluded: chain 9 residue 9 TRP Chi-restraints excluded: chain 9 residue 134 THR Chi-restraints excluded: chain 9 residue 189 ARG Chi-restraints excluded: chain 9 residue 205 TYR Chi-restraints excluded: chain 9 residue 319 THR Chi-restraints excluded: chain 9 residue 361 THR Chi-restraints excluded: chain 9 residue 364 SER Chi-restraints excluded: chain 9 residue 395 VAL Chi-restraints excluded: chain 9 residue 413 VAL Chi-restraints excluded: chain 9 residue 460 TYR Chi-restraints excluded: chain 9 residue 461 VAL Chi-restraints excluded: chain 9 residue 488 SER Chi-restraints excluded: chain 9 residue 505 VAL Chi-restraints excluded: chain 9 residue 546 HIS Chi-restraints excluded: chain 9 residue 552 THR Chi-restraints excluded: chain 9 residue 642 LEU Chi-restraints excluded: chain 9 residue 686 ASP Chi-restraints excluded: chain 9 residue 688 THR Chi-restraints excluded: chain 9 residue 747 ASP Chi-restraints excluded: chain 3 residue 70 MET Chi-restraints excluded: chain 3 residue 111 THR Chi-restraints excluded: chain 3 residue 128 PHE Chi-restraints excluded: chain 3 residue 132 MET Chi-restraints excluded: chain 3 residue 141 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 290 optimal weight: 0.9990 chunk 187 optimal weight: 5.9990 chunk 353 optimal weight: 8.9990 chunk 198 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 278 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 364 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 355 optimal weight: 10.0000 chunk 390 optimal weight: 7.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 308 GLN 1 545 ASN ** 1 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 36 GLN ** 2 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 343 GLN ** 2 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 91 GLN 5 102 ASN ** 3 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 158 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.159542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.136937 restraints weight = 48750.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.136313 restraints weight = 61012.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.137486 restraints weight = 54893.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.137596 restraints weight = 39739.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.137967 restraints weight = 38238.709| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 32289 Z= 0.193 Angle : 0.631 8.712 43700 Z= 0.321 Chirality : 0.045 0.182 4974 Planarity : 0.004 0.054 5596 Dihedral : 5.920 144.488 4314 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 3.95 % Allowed : 18.14 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.14), residues: 3944 helix: 1.48 (0.14), residues: 1370 sheet: -1.18 (0.17), residues: 989 loop : -2.09 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 2 339 TYR 0.033 0.002 TYR 7 660 PHE 0.025 0.002 PHE 4 413 TRP 0.017 0.001 TRP 9 9 HIS 0.006 0.001 HIS 1 54 Details of bonding type rmsd covalent geometry : bond 0.00460 (32289) covalent geometry : angle 0.63102 (43700) hydrogen bonds : bond 0.04118 ( 1505) hydrogen bonds : angle 4.70004 ( 4317) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 393 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 11 MET cc_start: 0.7712 (mmp) cc_final: 0.7125 (ptm) REVERT: 1 274 ILE cc_start: 0.7598 (pt) cc_final: 0.7113 (mp) REVERT: 1 426 ASN cc_start: 0.6887 (t0) cc_final: 0.6627 (t0) REVERT: 1 479 SER cc_start: 0.7829 (m) cc_final: 0.7434 (t) REVERT: 2 206 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8425 (mm) REVERT: 4 411 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7258 (mt) REVERT: 5 93 GLU cc_start: 0.6245 (mm-30) cc_final: 0.5641 (mm-30) REVERT: 5 324 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.8004 (tt) REVERT: 7 21 MET cc_start: 0.7656 (ttp) cc_final: 0.7252 (ttp) REVERT: 7 309 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8300 (m) REVERT: 7 389 LYS cc_start: 0.7855 (tptt) cc_final: 0.7170 (tttt) REVERT: 7 671 TYR cc_start: 0.8055 (m-10) cc_final: 0.7512 (m-80) REVERT: 7 700 LEU cc_start: 0.7395 (mm) cc_final: 0.7006 (mt) REVERT: 8 10 TYR cc_start: 0.8067 (m-10) cc_final: 0.7670 (m-80) REVERT: 8 171 TYR cc_start: 0.7695 (m-80) cc_final: 0.6872 (m-10) REVERT: 8 293 ASN cc_start: 0.8290 (p0) cc_final: 0.7879 (p0) REVERT: 9 480 GLU cc_start: 0.6593 (mm-30) cc_final: 0.6068 (tm-30) REVERT: 9 686 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.7156 (t70) REVERT: 3 78 ASN cc_start: 0.6737 (m110) cc_final: 0.6134 (m110) REVERT: 3 158 HIS cc_start: 0.6872 (t-90) cc_final: 0.6623 (t70) REVERT: 3 171 GLN cc_start: 0.7187 (mm-40) cc_final: 0.6926 (mm-40) outliers start: 138 outliers final: 92 residues processed: 497 average time/residue: 0.1904 time to fit residues: 155.7769 Evaluate side-chains 461 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 364 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 11 VAL Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 33 LEU Chi-restraints excluded: chain 1 residue 10 SER Chi-restraints excluded: chain 1 residue 50 VAL Chi-restraints excluded: chain 1 residue 105 SER Chi-restraints excluded: chain 1 residue 202 THR Chi-restraints excluded: chain 1 residue 220 VAL Chi-restraints excluded: chain 1 residue 246 SER Chi-restraints excluded: chain 1 residue 362 VAL Chi-restraints excluded: chain 1 residue 369 THR Chi-restraints excluded: chain 1 residue 376 LEU Chi-restraints excluded: chain 1 residue 392 THR Chi-restraints excluded: chain 1 residue 488 LEU Chi-restraints excluded: chain 1 residue 502 THR Chi-restraints excluded: chain 1 residue 514 ILE Chi-restraints excluded: chain 1 residue 545 ASN Chi-restraints excluded: chain 1 residue 552 VAL Chi-restraints excluded: chain 1 residue 582 ILE Chi-restraints excluded: chain 2 residue 123 ILE Chi-restraints excluded: chain 2 residue 124 VAL Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 2 residue 206 ILE Chi-restraints excluded: chain 2 residue 212 MET Chi-restraints excluded: chain 2 residue 228 VAL Chi-restraints excluded: chain 2 residue 341 LEU Chi-restraints excluded: chain 2 residue 441 VAL Chi-restraints excluded: chain 2 residue 526 ILE Chi-restraints excluded: chain 2 residue 546 ILE Chi-restraints excluded: chain 2 residue 548 ILE Chi-restraints excluded: chain 2 residue 610 LEU Chi-restraints excluded: chain 2 residue 634 MET Chi-restraints excluded: chain 2 residue 708 ASN Chi-restraints excluded: chain 4 residue 177 ILE Chi-restraints excluded: chain 4 residue 190 ILE Chi-restraints excluded: chain 4 residue 373 LEU Chi-restraints excluded: chain 4 residue 411 LEU Chi-restraints excluded: chain 5 residue 17 VAL Chi-restraints excluded: chain 5 residue 40 THR Chi-restraints excluded: chain 5 residue 57 ILE Chi-restraints excluded: chain 5 residue 79 ILE Chi-restraints excluded: chain 5 residue 97 VAL Chi-restraints excluded: chain 5 residue 120 LEU Chi-restraints excluded: chain 5 residue 201 ILE Chi-restraints excluded: chain 5 residue 232 VAL Chi-restraints excluded: chain 5 residue 241 GLU Chi-restraints excluded: chain 5 residue 324 ILE Chi-restraints excluded: chain 7 residue 11 LEU Chi-restraints excluded: chain 7 residue 77 THR Chi-restraints excluded: chain 7 residue 133 CYS Chi-restraints excluded: chain 7 residue 155 VAL Chi-restraints excluded: chain 7 residue 174 VAL Chi-restraints excluded: chain 7 residue 192 VAL Chi-restraints excluded: chain 7 residue 193 LEU Chi-restraints excluded: chain 7 residue 296 CYS Chi-restraints excluded: chain 7 residue 309 THR Chi-restraints excluded: chain 7 residue 381 VAL Chi-restraints excluded: chain 7 residue 390 ASP Chi-restraints excluded: chain 7 residue 420 VAL Chi-restraints excluded: chain 7 residue 461 ILE Chi-restraints excluded: chain 7 residue 508 THR Chi-restraints excluded: chain 7 residue 650 LEU Chi-restraints excluded: chain 7 residue 709 ILE Chi-restraints excluded: chain 8 residue 39 LEU Chi-restraints excluded: chain 8 residue 99 THR Chi-restraints excluded: chain 8 residue 133 THR Chi-restraints excluded: chain 8 residue 161 ILE Chi-restraints excluded: chain 8 residue 204 GLU Chi-restraints excluded: chain 8 residue 262 THR Chi-restraints excluded: chain 8 residue 354 LEU Chi-restraints excluded: chain 8 residue 399 THR Chi-restraints excluded: chain 9 residue 9 TRP Chi-restraints excluded: chain 9 residue 29 ASP Chi-restraints excluded: chain 9 residue 81 VAL Chi-restraints excluded: chain 9 residue 87 VAL Chi-restraints excluded: chain 9 residue 134 THR Chi-restraints excluded: chain 9 residue 157 VAL Chi-restraints excluded: chain 9 residue 189 ARG Chi-restraints excluded: chain 9 residue 205 TYR Chi-restraints excluded: chain 9 residue 319 THR Chi-restraints excluded: chain 9 residue 341 LEU Chi-restraints excluded: chain 9 residue 361 THR Chi-restraints excluded: chain 9 residue 364 SER Chi-restraints excluded: chain 9 residue 395 VAL Chi-restraints excluded: chain 9 residue 413 VAL Chi-restraints excluded: chain 9 residue 460 TYR Chi-restraints excluded: chain 9 residue 505 VAL Chi-restraints excluded: chain 9 residue 642 LEU Chi-restraints excluded: chain 9 residue 686 ASP Chi-restraints excluded: chain 9 residue 688 THR Chi-restraints excluded: chain 9 residue 747 ASP Chi-restraints excluded: chain 9 residue 763 THR Chi-restraints excluded: chain 3 residue 70 MET Chi-restraints excluded: chain 3 residue 111 THR Chi-restraints excluded: chain 3 residue 112 LEU Chi-restraints excluded: chain 3 residue 132 MET Chi-restraints excluded: chain 3 residue 141 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 243 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 267 optimal weight: 5.9990 chunk 359 optimal weight: 6.9990 chunk 191 optimal weight: 9.9990 chunk 374 optimal weight: 2.9990 chunk 225 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 36 GLN ** 2 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 343 GLN ** 2 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 91 GLN 4 224 HIS ** 7 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 27 ASN ** 3 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.158544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.136088 restraints weight = 48599.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.135795 restraints weight = 57926.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.136899 restraints weight = 54938.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.136945 restraints weight = 36319.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.137317 restraints weight = 36430.014| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 32289 Z= 0.204 Angle : 0.640 8.607 43700 Z= 0.326 Chirality : 0.045 0.179 4974 Planarity : 0.004 0.052 5596 Dihedral : 5.866 136.428 4314 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 3.69 % Allowed : 18.83 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.14), residues: 3944 helix: 1.46 (0.14), residues: 1367 sheet: -1.21 (0.17), residues: 998 loop : -2.00 (0.15), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 8 333 TYR 0.023 0.002 TYR 7 660 PHE 0.025 0.002 PHE 4 413 TRP 0.018 0.002 TRP 9 9 HIS 0.006 0.001 HIS 1 54 Details of bonding type rmsd covalent geometry : bond 0.00490 (32289) covalent geometry : angle 0.64011 (43700) hydrogen bonds : bond 0.04175 ( 1505) hydrogen bonds : angle 4.73035 ( 4317) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 396 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 274 ILE cc_start: 0.7709 (pt) cc_final: 0.7199 (mp) REVERT: 1 426 ASN cc_start: 0.6970 (t0) cc_final: 0.6577 (t0) REVERT: 1 479 SER cc_start: 0.7816 (m) cc_final: 0.7411 (t) REVERT: 2 128 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7928 (mp) REVERT: 2 469 PHE cc_start: 0.7393 (OUTLIER) cc_final: 0.6966 (p90) REVERT: 2 616 ASP cc_start: 0.7092 (m-30) cc_final: 0.6890 (m-30) REVERT: 4 411 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7126 (mt) REVERT: 5 93 GLU cc_start: 0.6391 (mm-30) cc_final: 0.5818 (mm-30) REVERT: 5 324 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7967 (tt) REVERT: 7 21 MET cc_start: 0.7750 (ttp) cc_final: 0.7245 (ttp) REVERT: 7 389 LYS cc_start: 0.7835 (tptt) cc_final: 0.7169 (tttt) REVERT: 7 671 TYR cc_start: 0.8140 (m-10) cc_final: 0.7593 (m-80) REVERT: 7 700 LEU cc_start: 0.7394 (mm) cc_final: 0.7049 (mt) REVERT: 8 10 TYR cc_start: 0.8054 (m-10) cc_final: 0.7713 (m-80) REVERT: 8 171 TYR cc_start: 0.7680 (m-80) cc_final: 0.6863 (m-10) REVERT: 8 258 ASP cc_start: 0.7700 (t70) cc_final: 0.7364 (t70) REVERT: 8 293 ASN cc_start: 0.8343 (p0) cc_final: 0.7962 (p0) REVERT: 9 480 GLU cc_start: 0.6672 (mm-30) cc_final: 0.6212 (tm-30) REVERT: 9 686 ASP cc_start: 0.7647 (OUTLIER) cc_final: 0.7173 (t70) REVERT: 3 78 ASN cc_start: 0.6665 (m110) cc_final: 0.6066 (m110) REVERT: 3 158 HIS cc_start: 0.6764 (t-90) cc_final: 0.6054 (t-90) REVERT: 3 171 GLN cc_start: 0.7166 (mm-40) cc_final: 0.6909 (mm-40) outliers start: 129 outliers final: 96 residues processed: 494 average time/residue: 0.1960 time to fit residues: 158.2415 Evaluate side-chains 465 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 364 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 11 VAL Chi-restraints excluded: chain 0 residue 12 LEU Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 33 LEU Chi-restraints excluded: chain 1 residue 50 VAL Chi-restraints excluded: chain 1 residue 198 THR Chi-restraints excluded: chain 1 residue 202 THR Chi-restraints excluded: chain 1 residue 246 SER Chi-restraints excluded: chain 1 residue 362 VAL Chi-restraints excluded: chain 1 residue 369 THR Chi-restraints excluded: chain 1 residue 488 LEU Chi-restraints excluded: chain 1 residue 502 THR Chi-restraints excluded: chain 1 residue 505 LEU Chi-restraints excluded: chain 1 residue 514 ILE Chi-restraints excluded: chain 1 residue 550 THR Chi-restraints excluded: chain 1 residue 552 VAL Chi-restraints excluded: chain 1 residue 582 ILE Chi-restraints excluded: chain 2 residue 123 ILE Chi-restraints excluded: chain 2 residue 124 VAL Chi-restraints excluded: chain 2 residue 128 LEU Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 2 residue 181 VAL Chi-restraints excluded: chain 2 residue 212 MET Chi-restraints excluded: chain 2 residue 228 VAL Chi-restraints excluded: chain 2 residue 341 LEU Chi-restraints excluded: chain 2 residue 441 VAL Chi-restraints excluded: chain 2 residue 469 PHE Chi-restraints excluded: chain 2 residue 499 VAL Chi-restraints excluded: chain 2 residue 526 ILE Chi-restraints excluded: chain 2 residue 546 ILE Chi-restraints excluded: chain 2 residue 548 ILE Chi-restraints excluded: chain 2 residue 610 LEU Chi-restraints excluded: chain 2 residue 708 ASN Chi-restraints excluded: chain 4 residue 79 LEU Chi-restraints excluded: chain 4 residue 177 ILE Chi-restraints excluded: chain 4 residue 190 ILE Chi-restraints excluded: chain 4 residue 373 LEU Chi-restraints excluded: chain 4 residue 411 LEU Chi-restraints excluded: chain 5 residue 17 VAL Chi-restraints excluded: chain 5 residue 40 THR Chi-restraints excluded: chain 5 residue 57 ILE Chi-restraints excluded: chain 5 residue 79 ILE Chi-restraints excluded: chain 5 residue 80 THR Chi-restraints excluded: chain 5 residue 92 THR Chi-restraints excluded: chain 5 residue 97 VAL Chi-restraints excluded: chain 5 residue 120 LEU Chi-restraints excluded: chain 5 residue 201 ILE Chi-restraints excluded: chain 5 residue 232 VAL Chi-restraints excluded: chain 5 residue 241 GLU Chi-restraints excluded: chain 5 residue 324 ILE Chi-restraints excluded: chain 7 residue 11 LEU Chi-restraints excluded: chain 7 residue 15 VAL Chi-restraints excluded: chain 7 residue 77 THR Chi-restraints excluded: chain 7 residue 155 VAL Chi-restraints excluded: chain 7 residue 174 VAL Chi-restraints excluded: chain 7 residue 180 VAL Chi-restraints excluded: chain 7 residue 192 VAL Chi-restraints excluded: chain 7 residue 296 CYS Chi-restraints excluded: chain 7 residue 381 VAL Chi-restraints excluded: chain 7 residue 420 VAL Chi-restraints excluded: chain 7 residue 461 ILE Chi-restraints excluded: chain 7 residue 508 THR Chi-restraints excluded: chain 7 residue 650 LEU Chi-restraints excluded: chain 8 residue 39 LEU Chi-restraints excluded: chain 8 residue 99 THR Chi-restraints excluded: chain 8 residue 133 THR Chi-restraints excluded: chain 8 residue 161 ILE Chi-restraints excluded: chain 8 residue 162 ASN Chi-restraints excluded: chain 8 residue 204 GLU Chi-restraints excluded: chain 8 residue 262 THR Chi-restraints excluded: chain 8 residue 354 LEU Chi-restraints excluded: chain 8 residue 399 THR Chi-restraints excluded: chain 9 residue 9 TRP Chi-restraints excluded: chain 9 residue 29 ASP Chi-restraints excluded: chain 9 residue 81 VAL Chi-restraints excluded: chain 9 residue 87 VAL Chi-restraints excluded: chain 9 residue 134 THR Chi-restraints excluded: chain 9 residue 157 VAL Chi-restraints excluded: chain 9 residue 189 ARG Chi-restraints excluded: chain 9 residue 205 TYR Chi-restraints excluded: chain 9 residue 303 THR Chi-restraints excluded: chain 9 residue 319 THR Chi-restraints excluded: chain 9 residue 361 THR Chi-restraints excluded: chain 9 residue 364 SER Chi-restraints excluded: chain 9 residue 395 VAL Chi-restraints excluded: chain 9 residue 413 VAL Chi-restraints excluded: chain 9 residue 460 TYR Chi-restraints excluded: chain 9 residue 488 SER Chi-restraints excluded: chain 9 residue 505 VAL Chi-restraints excluded: chain 9 residue 546 HIS Chi-restraints excluded: chain 9 residue 642 LEU Chi-restraints excluded: chain 9 residue 686 ASP Chi-restraints excluded: chain 9 residue 688 THR Chi-restraints excluded: chain 9 residue 747 ASP Chi-restraints excluded: chain 9 residue 763 THR Chi-restraints excluded: chain 3 residue 70 MET Chi-restraints excluded: chain 3 residue 111 THR Chi-restraints excluded: chain 3 residue 112 LEU Chi-restraints excluded: chain 3 residue 128 PHE Chi-restraints excluded: chain 3 residue 132 MET Chi-restraints excluded: chain 3 residue 141 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 205 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 chunk 3 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 343 optimal weight: 5.9990 chunk 284 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 245 optimal weight: 9.9990 chunk 276 optimal weight: 0.5980 chunk 279 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 36 GLN ** 2 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 343 GLN 2 706 ASN 4 91 GLN ** 7 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 353 HIS 3 27 ASN ** 3 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.162662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.139808 restraints weight = 48470.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.139776 restraints weight = 58417.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.140870 restraints weight = 49649.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.141062 restraints weight = 34488.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.141378 restraints weight = 33896.357| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32289 Z= 0.118 Angle : 0.581 8.604 43700 Z= 0.296 Chirality : 0.042 0.227 4974 Planarity : 0.004 0.051 5596 Dihedral : 5.555 132.082 4313 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.72 % Allowed : 20.31 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.14), residues: 3944 helix: 1.83 (0.14), residues: 1362 sheet: -0.97 (0.17), residues: 974 loop : -1.84 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 5 129 TYR 0.019 0.001 TYR 2 213 PHE 0.022 0.001 PHE 4 413 TRP 0.014 0.001 TRP 9 9 HIS 0.007 0.001 HIS 9 117 Details of bonding type rmsd covalent geometry : bond 0.00266 (32289) covalent geometry : angle 0.58079 (43700) hydrogen bonds : bond 0.03682 ( 1505) hydrogen bonds : angle 4.48126 ( 4317) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 398 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 11 MET cc_start: 0.7774 (mmp) cc_final: 0.7277 (ptm) REVERT: 1 274 ILE cc_start: 0.7650 (pt) cc_final: 0.7138 (mp) REVERT: 2 229 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.7895 (m-80) REVERT: 5 93 GLU cc_start: 0.6341 (mm-30) cc_final: 0.5745 (mm-30) REVERT: 5 324 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7923 (tt) REVERT: 7 21 MET cc_start: 0.7584 (ttp) cc_final: 0.7159 (ttp) REVERT: 7 39 ASP cc_start: 0.7267 (OUTLIER) cc_final: 0.7041 (t70) REVERT: 7 389 LYS cc_start: 0.7721 (tptt) cc_final: 0.7007 (tttt) REVERT: 7 671 TYR cc_start: 0.8079 (m-10) cc_final: 0.7547 (m-80) REVERT: 7 700 LEU cc_start: 0.7307 (mm) cc_final: 0.7042 (mt) REVERT: 8 10 TYR cc_start: 0.8011 (m-10) cc_final: 0.7703 (m-80) REVERT: 8 171 TYR cc_start: 0.7576 (m-80) cc_final: 0.6806 (m-10) REVERT: 8 258 ASP cc_start: 0.7761 (t70) cc_final: 0.7431 (t70) REVERT: 8 269 GLN cc_start: 0.8484 (tt0) cc_final: 0.8261 (tt0) REVERT: 8 293 ASN cc_start: 0.8302 (p0) cc_final: 0.7918 (p0) REVERT: 9 353 HIS cc_start: 0.7845 (OUTLIER) cc_final: 0.7508 (m90) REVERT: 9 480 GLU cc_start: 0.6614 (mm-30) cc_final: 0.6176 (tm-30) REVERT: 9 686 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.6958 (t70) REVERT: 9 794 ASN cc_start: 0.7888 (m110) cc_final: 0.7501 (m110) REVERT: 3 78 ASN cc_start: 0.6636 (m110) cc_final: 0.6048 (m110) REVERT: 3 171 GLN cc_start: 0.7152 (mm-40) cc_final: 0.6850 (mm-40) outliers start: 95 outliers final: 68 residues processed: 470 average time/residue: 0.1890 time to fit residues: 147.2118 Evaluate side-chains 440 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 367 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 11 VAL Chi-restraints excluded: chain 0 residue 12 LEU Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 33 LEU Chi-restraints excluded: chain 1 residue 10 SER Chi-restraints excluded: chain 1 residue 105 SER Chi-restraints excluded: chain 1 residue 202 THR Chi-restraints excluded: chain 1 residue 362 VAL Chi-restraints excluded: chain 1 residue 488 LEU Chi-restraints excluded: chain 1 residue 502 THR Chi-restraints excluded: chain 1 residue 505 LEU Chi-restraints excluded: chain 1 residue 552 VAL Chi-restraints excluded: chain 2 residue 123 ILE Chi-restraints excluded: chain 2 residue 124 VAL Chi-restraints excluded: chain 2 residue 181 VAL Chi-restraints excluded: chain 2 residue 212 MET Chi-restraints excluded: chain 2 residue 229 TYR Chi-restraints excluded: chain 2 residue 293 VAL Chi-restraints excluded: chain 2 residue 341 LEU Chi-restraints excluded: chain 2 residue 377 ILE Chi-restraints excluded: chain 2 residue 384 HIS Chi-restraints excluded: chain 2 residue 499 VAL Chi-restraints excluded: chain 2 residue 546 ILE Chi-restraints excluded: chain 2 residue 610 LEU Chi-restraints excluded: chain 2 residue 708 ASN Chi-restraints excluded: chain 4 residue 79 LEU Chi-restraints excluded: chain 4 residue 177 ILE Chi-restraints excluded: chain 4 residue 190 ILE Chi-restraints excluded: chain 5 residue 17 VAL Chi-restraints excluded: chain 5 residue 40 THR Chi-restraints excluded: chain 5 residue 57 ILE Chi-restraints excluded: chain 5 residue 97 VAL Chi-restraints excluded: chain 5 residue 120 LEU Chi-restraints excluded: chain 5 residue 201 ILE Chi-restraints excluded: chain 5 residue 232 VAL Chi-restraints excluded: chain 5 residue 241 GLU Chi-restraints excluded: chain 5 residue 324 ILE Chi-restraints excluded: chain 7 residue 39 ASP Chi-restraints excluded: chain 7 residue 77 THR Chi-restraints excluded: chain 7 residue 174 VAL Chi-restraints excluded: chain 7 residue 192 VAL Chi-restraints excluded: chain 7 residue 296 CYS Chi-restraints excluded: chain 7 residue 381 VAL Chi-restraints excluded: chain 7 residue 390 ASP Chi-restraints excluded: chain 7 residue 508 THR Chi-restraints excluded: chain 7 residue 609 ILE Chi-restraints excluded: chain 7 residue 650 LEU Chi-restraints excluded: chain 8 residue 39 LEU Chi-restraints excluded: chain 8 residue 99 THR Chi-restraints excluded: chain 8 residue 133 THR Chi-restraints excluded: chain 8 residue 262 THR Chi-restraints excluded: chain 9 residue 9 TRP Chi-restraints excluded: chain 9 residue 134 THR Chi-restraints excluded: chain 9 residue 157 VAL Chi-restraints excluded: chain 9 residue 189 ARG Chi-restraints excluded: chain 9 residue 194 ILE Chi-restraints excluded: chain 9 residue 205 TYR Chi-restraints excluded: chain 9 residue 353 HIS Chi-restraints excluded: chain 9 residue 361 THR Chi-restraints excluded: chain 9 residue 395 VAL Chi-restraints excluded: chain 9 residue 460 TYR Chi-restraints excluded: chain 9 residue 461 VAL Chi-restraints excluded: chain 9 residue 488 SER Chi-restraints excluded: chain 9 residue 505 VAL Chi-restraints excluded: chain 9 residue 546 HIS Chi-restraints excluded: chain 9 residue 552 THR Chi-restraints excluded: chain 9 residue 575 VAL Chi-restraints excluded: chain 9 residue 642 LEU Chi-restraints excluded: chain 9 residue 686 ASP Chi-restraints excluded: chain 9 residue 688 THR Chi-restraints excluded: chain 9 residue 747 ASP Chi-restraints excluded: chain 3 residue 132 MET Chi-restraints excluded: chain 3 residue 141 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 394 optimal weight: 9.9990 chunk 222 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 363 optimal weight: 8.9990 chunk 320 optimal weight: 4.9990 chunk 165 optimal weight: 9.9990 chunk 110 optimal weight: 0.3980 chunk 158 optimal weight: 9.9990 chunk 285 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 426 ASN ** 1 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 36 GLN 2 343 GLN ** 2 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 249 HIS ** 7 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 265 ASN 9 309 ASN 9 353 HIS 3 27 ASN 3 114 ASN ** 3 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.159296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.136293 restraints weight = 48813.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.135940 restraints weight = 60128.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.137057 restraints weight = 54696.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.137227 restraints weight = 37125.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.137504 restraints weight = 37477.977| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 32289 Z= 0.189 Angle : 0.625 8.158 43700 Z= 0.319 Chirality : 0.044 0.216 4974 Planarity : 0.004 0.055 5596 Dihedral : 5.647 134.554 4310 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 2.83 % Allowed : 20.43 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.14), residues: 3944 helix: 1.67 (0.14), residues: 1371 sheet: -0.99 (0.17), residues: 978 loop : -1.90 (0.15), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 5 129 TYR 0.019 0.002 TYR 7 660 PHE 0.024 0.002 PHE 4 413 TRP 0.019 0.002 TRP 3 176 HIS 0.016 0.001 HIS 3 115 Details of bonding type rmsd covalent geometry : bond 0.00452 (32289) covalent geometry : angle 0.62474 (43700) hydrogen bonds : bond 0.04028 ( 1505) hydrogen bonds : angle 4.61773 ( 4317) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 370 time to evaluate : 1.234 Fit side-chains revert: symmetry clash REVERT: 1 11 MET cc_start: 0.7820 (mmp) cc_final: 0.7296 (ptm) REVERT: 1 274 ILE cc_start: 0.7768 (pt) cc_final: 0.7224 (mp) REVERT: 1 426 ASN cc_start: 0.6613 (t0) cc_final: 0.6263 (t0) REVERT: 2 469 PHE cc_start: 0.7402 (OUTLIER) cc_final: 0.7170 (p90) REVERT: 5 93 GLU cc_start: 0.6203 (mm-30) cc_final: 0.5617 (mm-30) REVERT: 5 324 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7945 (tt) REVERT: 7 21 MET cc_start: 0.7767 (ttp) cc_final: 0.7274 (ttp) REVERT: 7 389 LYS cc_start: 0.7819 (tptt) cc_final: 0.7055 (tttt) REVERT: 7 441 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8182 (tp) REVERT: 7 671 TYR cc_start: 0.8191 (m-10) cc_final: 0.7669 (m-10) REVERT: 7 700 LEU cc_start: 0.7408 (mm) cc_final: 0.7145 (mt) REVERT: 8 171 TYR cc_start: 0.7637 (m-80) cc_final: 0.6786 (m-10) REVERT: 8 258 ASP cc_start: 0.7866 (t70) cc_final: 0.7531 (t70) REVERT: 8 265 ASN cc_start: 0.8019 (m-40) cc_final: 0.7491 (m110) REVERT: 8 293 ASN cc_start: 0.8298 (p0) cc_final: 0.7930 (p0) REVERT: 9 480 GLU cc_start: 0.6707 (mm-30) cc_final: 0.6296 (tm-30) REVERT: 9 686 ASP cc_start: 0.7537 (OUTLIER) cc_final: 0.7071 (t70) REVERT: 3 73 GLN cc_start: 0.7656 (mm-40) cc_final: 0.7334 (mm110) REVERT: 3 78 ASN cc_start: 0.6603 (m110) cc_final: 0.6021 (m110) REVERT: 3 171 GLN cc_start: 0.7159 (mm-40) cc_final: 0.6861 (mm-40) outliers start: 99 outliers final: 78 residues processed: 450 average time/residue: 0.1907 time to fit residues: 141.7877 Evaluate side-chains 436 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 354 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 11 VAL Chi-restraints excluded: chain 0 residue 12 LEU Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 33 LEU Chi-restraints excluded: chain 1 residue 10 SER Chi-restraints excluded: chain 1 residue 105 SER Chi-restraints excluded: chain 1 residue 198 THR Chi-restraints excluded: chain 1 residue 202 THR Chi-restraints excluded: chain 1 residue 220 VAL Chi-restraints excluded: chain 1 residue 362 VAL Chi-restraints excluded: chain 1 residue 488 LEU Chi-restraints excluded: chain 1 residue 502 THR Chi-restraints excluded: chain 1 residue 505 LEU Chi-restraints excluded: chain 1 residue 552 VAL Chi-restraints excluded: chain 1 residue 582 ILE Chi-restraints excluded: chain 2 residue 123 ILE Chi-restraints excluded: chain 2 residue 181 VAL Chi-restraints excluded: chain 2 residue 212 MET Chi-restraints excluded: chain 2 residue 293 VAL Chi-restraints excluded: chain 2 residue 341 LEU Chi-restraints excluded: chain 2 residue 377 ILE Chi-restraints excluded: chain 2 residue 469 PHE Chi-restraints excluded: chain 2 residue 499 VAL Chi-restraints excluded: chain 2 residue 546 ILE Chi-restraints excluded: chain 2 residue 610 LEU Chi-restraints excluded: chain 4 residue 79 LEU Chi-restraints excluded: chain 4 residue 177 ILE Chi-restraints excluded: chain 4 residue 190 ILE Chi-restraints excluded: chain 4 residue 245 MET Chi-restraints excluded: chain 5 residue 17 VAL Chi-restraints excluded: chain 5 residue 40 THR Chi-restraints excluded: chain 5 residue 57 ILE Chi-restraints excluded: chain 5 residue 79 ILE Chi-restraints excluded: chain 5 residue 80 THR Chi-restraints excluded: chain 5 residue 97 VAL Chi-restraints excluded: chain 5 residue 120 LEU Chi-restraints excluded: chain 5 residue 201 ILE Chi-restraints excluded: chain 5 residue 232 VAL Chi-restraints excluded: chain 5 residue 241 GLU Chi-restraints excluded: chain 5 residue 324 ILE Chi-restraints excluded: chain 7 residue 77 THR Chi-restraints excluded: chain 7 residue 174 VAL Chi-restraints excluded: chain 7 residue 192 VAL Chi-restraints excluded: chain 7 residue 381 VAL Chi-restraints excluded: chain 7 residue 441 LEU Chi-restraints excluded: chain 7 residue 461 ILE Chi-restraints excluded: chain 7 residue 508 THR Chi-restraints excluded: chain 7 residue 609 ILE Chi-restraints excluded: chain 7 residue 650 LEU Chi-restraints excluded: chain 8 residue 39 LEU Chi-restraints excluded: chain 8 residue 99 THR Chi-restraints excluded: chain 8 residue 133 THR Chi-restraints excluded: chain 8 residue 204 GLU Chi-restraints excluded: chain 8 residue 262 THR Chi-restraints excluded: chain 8 residue 399 THR Chi-restraints excluded: chain 9 residue 9 TRP Chi-restraints excluded: chain 9 residue 134 THR Chi-restraints excluded: chain 9 residue 157 VAL Chi-restraints excluded: chain 9 residue 189 ARG Chi-restraints excluded: chain 9 residue 205 TYR Chi-restraints excluded: chain 9 residue 341 LEU Chi-restraints excluded: chain 9 residue 361 THR Chi-restraints excluded: chain 9 residue 364 SER Chi-restraints excluded: chain 9 residue 395 VAL Chi-restraints excluded: chain 9 residue 413 VAL Chi-restraints excluded: chain 9 residue 414 SER Chi-restraints excluded: chain 9 residue 460 TYR Chi-restraints excluded: chain 9 residue 461 VAL Chi-restraints excluded: chain 9 residue 488 SER Chi-restraints excluded: chain 9 residue 505 VAL Chi-restraints excluded: chain 9 residue 531 LEU Chi-restraints excluded: chain 9 residue 546 HIS Chi-restraints excluded: chain 9 residue 552 THR Chi-restraints excluded: chain 9 residue 575 VAL Chi-restraints excluded: chain 9 residue 642 LEU Chi-restraints excluded: chain 9 residue 686 ASP Chi-restraints excluded: chain 9 residue 688 THR Chi-restraints excluded: chain 9 residue 747 ASP Chi-restraints excluded: chain 9 residue 763 THR Chi-restraints excluded: chain 3 residue 112 LEU Chi-restraints excluded: chain 3 residue 132 MET Chi-restraints excluded: chain 3 residue 141 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 285 optimal weight: 2.9990 chunk 225 optimal weight: 7.9990 chunk 198 optimal weight: 5.9990 chunk 161 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 319 optimal weight: 0.9980 chunk 123 optimal weight: 0.8980 chunk 311 optimal weight: 7.9990 chunk 290 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 36 GLN 2 343 GLN ** 2 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 249 HIS ** 7 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 309 ASN 3 35 ASN 3 114 ASN ** 3 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.159794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.136635 restraints weight = 48466.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.136407 restraints weight = 61381.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.137746 restraints weight = 55486.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.137700 restraints weight = 38357.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.138071 restraints weight = 35979.884| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 32289 Z= 0.174 Angle : 0.620 9.032 43700 Z= 0.316 Chirality : 0.044 0.205 4974 Planarity : 0.004 0.050 5596 Dihedral : 5.648 139.028 4310 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 3.18 % Allowed : 20.29 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.14), residues: 3944 helix: 1.67 (0.14), residues: 1365 sheet: -0.94 (0.17), residues: 985 loop : -1.83 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 5 129 TYR 0.031 0.002 TYR 9 207 PHE 0.023 0.002 PHE 7 58 TRP 0.023 0.002 TRP 3 176 HIS 0.012 0.001 HIS 3 115 Details of bonding type rmsd covalent geometry : bond 0.00415 (32289) covalent geometry : angle 0.62035 (43700) hydrogen bonds : bond 0.03957 ( 1505) hydrogen bonds : angle 4.62605 ( 4317) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 373 time to evaluate : 1.203 Fit side-chains REVERT: 1 11 MET cc_start: 0.7858 (mmp) cc_final: 0.7296 (ptm) REVERT: 1 274 ILE cc_start: 0.7779 (pt) cc_final: 0.7205 (mp) REVERT: 1 426 ASN cc_start: 0.6644 (t0) cc_final: 0.6288 (t0) REVERT: 4 134 ASP cc_start: 0.4830 (p0) cc_final: 0.4480 (p0) REVERT: 4 137 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.7818 (mp) REVERT: 5 93 GLU cc_start: 0.6214 (mm-30) cc_final: 0.5668 (mm-30) REVERT: 5 324 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7929 (tt) REVERT: 7 21 MET cc_start: 0.7768 (ttp) cc_final: 0.7277 (ttp) REVERT: 7 389 LYS cc_start: 0.7819 (tptt) cc_final: 0.7059 (tttt) REVERT: 7 441 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8165 (tp) REVERT: 7 671 TYR cc_start: 0.8196 (m-10) cc_final: 0.7616 (m-10) REVERT: 7 700 LEU cc_start: 0.7403 (mm) cc_final: 0.7167 (mt) REVERT: 8 10 TYR cc_start: 0.8150 (m-80) cc_final: 0.7788 (m-10) REVERT: 8 171 TYR cc_start: 0.7623 (m-80) cc_final: 0.6764 (m-10) REVERT: 8 258 ASP cc_start: 0.7857 (t70) cc_final: 0.7521 (t70) REVERT: 8 265 ASN cc_start: 0.7982 (m-40) cc_final: 0.7676 (m110) REVERT: 8 293 ASN cc_start: 0.8300 (p0) cc_final: 0.7932 (p0) REVERT: 9 480 GLU cc_start: 0.6709 (mm-30) cc_final: 0.6293 (tm-30) REVERT: 9 686 ASP cc_start: 0.7524 (OUTLIER) cc_final: 0.7046 (t70) REVERT: 3 78 ASN cc_start: 0.6578 (m110) cc_final: 0.5999 (m110) REVERT: 3 171 GLN cc_start: 0.7141 (mm-40) cc_final: 0.6859 (mm-40) outliers start: 111 outliers final: 91 residues processed: 462 average time/residue: 0.1883 time to fit residues: 144.6850 Evaluate side-chains 451 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 356 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 11 VAL Chi-restraints excluded: chain 0 residue 12 LEU Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 33 LEU Chi-restraints excluded: chain 1 residue 10 SER Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 1 residue 50 VAL Chi-restraints excluded: chain 1 residue 55 THR Chi-restraints excluded: chain 1 residue 105 SER Chi-restraints excluded: chain 1 residue 198 THR Chi-restraints excluded: chain 1 residue 202 THR Chi-restraints excluded: chain 1 residue 220 VAL Chi-restraints excluded: chain 1 residue 362 VAL Chi-restraints excluded: chain 1 residue 369 THR Chi-restraints excluded: chain 1 residue 488 LEU Chi-restraints excluded: chain 1 residue 502 THR Chi-restraints excluded: chain 1 residue 505 LEU Chi-restraints excluded: chain 1 residue 552 VAL Chi-restraints excluded: chain 1 residue 582 ILE Chi-restraints excluded: chain 2 residue 123 ILE Chi-restraints excluded: chain 2 residue 124 VAL Chi-restraints excluded: chain 2 residue 181 VAL Chi-restraints excluded: chain 2 residue 212 MET Chi-restraints excluded: chain 2 residue 293 VAL Chi-restraints excluded: chain 2 residue 341 LEU Chi-restraints excluded: chain 2 residue 377 ILE Chi-restraints excluded: chain 2 residue 384 HIS Chi-restraints excluded: chain 2 residue 441 VAL Chi-restraints excluded: chain 2 residue 453 VAL Chi-restraints excluded: chain 2 residue 499 VAL Chi-restraints excluded: chain 2 residue 526 ILE Chi-restraints excluded: chain 2 residue 546 ILE Chi-restraints excluded: chain 2 residue 548 ILE Chi-restraints excluded: chain 2 residue 610 LEU Chi-restraints excluded: chain 2 residue 634 MET Chi-restraints excluded: chain 4 residue 79 LEU Chi-restraints excluded: chain 4 residue 137 ILE Chi-restraints excluded: chain 4 residue 177 ILE Chi-restraints excluded: chain 4 residue 190 ILE Chi-restraints excluded: chain 4 residue 245 MET Chi-restraints excluded: chain 4 residue 373 LEU Chi-restraints excluded: chain 5 residue 17 VAL Chi-restraints excluded: chain 5 residue 40 THR Chi-restraints excluded: chain 5 residue 57 ILE Chi-restraints excluded: chain 5 residue 79 ILE Chi-restraints excluded: chain 5 residue 80 THR Chi-restraints excluded: chain 5 residue 97 VAL Chi-restraints excluded: chain 5 residue 120 LEU Chi-restraints excluded: chain 5 residue 201 ILE Chi-restraints excluded: chain 5 residue 232 VAL Chi-restraints excluded: chain 5 residue 241 GLU Chi-restraints excluded: chain 5 residue 324 ILE Chi-restraints excluded: chain 7 residue 77 THR Chi-restraints excluded: chain 7 residue 174 VAL Chi-restraints excluded: chain 7 residue 180 VAL Chi-restraints excluded: chain 7 residue 192 VAL Chi-restraints excluded: chain 7 residue 381 VAL Chi-restraints excluded: chain 7 residue 441 LEU Chi-restraints excluded: chain 7 residue 452 THR Chi-restraints excluded: chain 7 residue 461 ILE Chi-restraints excluded: chain 7 residue 508 THR Chi-restraints excluded: chain 7 residue 609 ILE Chi-restraints excluded: chain 7 residue 650 LEU Chi-restraints excluded: chain 8 residue 39 LEU Chi-restraints excluded: chain 8 residue 99 THR Chi-restraints excluded: chain 8 residue 133 THR Chi-restraints excluded: chain 8 residue 204 GLU Chi-restraints excluded: chain 8 residue 262 THR Chi-restraints excluded: chain 8 residue 399 THR Chi-restraints excluded: chain 9 residue 9 TRP Chi-restraints excluded: chain 9 residue 81 VAL Chi-restraints excluded: chain 9 residue 134 THR Chi-restraints excluded: chain 9 residue 157 VAL Chi-restraints excluded: chain 9 residue 189 ARG Chi-restraints excluded: chain 9 residue 205 TYR Chi-restraints excluded: chain 9 residue 303 THR Chi-restraints excluded: chain 9 residue 341 LEU Chi-restraints excluded: chain 9 residue 364 SER Chi-restraints excluded: chain 9 residue 395 VAL Chi-restraints excluded: chain 9 residue 413 VAL Chi-restraints excluded: chain 9 residue 414 SER Chi-restraints excluded: chain 9 residue 460 TYR Chi-restraints excluded: chain 9 residue 461 VAL Chi-restraints excluded: chain 9 residue 488 SER Chi-restraints excluded: chain 9 residue 505 VAL Chi-restraints excluded: chain 9 residue 531 LEU Chi-restraints excluded: chain 9 residue 552 THR Chi-restraints excluded: chain 9 residue 575 VAL Chi-restraints excluded: chain 9 residue 642 LEU Chi-restraints excluded: chain 9 residue 686 ASP Chi-restraints excluded: chain 9 residue 688 THR Chi-restraints excluded: chain 9 residue 747 ASP Chi-restraints excluded: chain 9 residue 763 THR Chi-restraints excluded: chain 3 residue 132 MET Chi-restraints excluded: chain 3 residue 141 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 395 optimal weight: 9.9990 chunk 160 optimal weight: 0.8980 chunk 231 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 146 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 213 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 36 GLN 2 343 GLN ** 2 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 436 HIS ** 4 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 74 ASN ** 7 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 309 ASN ** 3 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 82 HIS 3 114 ASN ** 3 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.161045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.137963 restraints weight = 48389.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.137828 restraints weight = 57011.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.138815 restraints weight = 52147.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.139066 restraints weight = 35856.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.139335 restraints weight = 35505.793| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32289 Z= 0.143 Angle : 0.604 9.460 43700 Z= 0.307 Chirality : 0.043 0.204 4974 Planarity : 0.004 0.051 5596 Dihedral : 5.546 141.183 4309 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.83 % Allowed : 20.86 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.14), residues: 3944 helix: 1.77 (0.14), residues: 1370 sheet: -0.84 (0.17), residues: 989 loop : -1.76 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 5 129 TYR 0.028 0.001 TYR 9 207 PHE 0.022 0.002 PHE 7 58 TRP 0.026 0.001 TRP 3 176 HIS 0.014 0.001 HIS 3 82 Details of bonding type rmsd covalent geometry : bond 0.00336 (32289) covalent geometry : angle 0.60382 (43700) hydrogen bonds : bond 0.03791 ( 1505) hydrogen bonds : angle 4.55255 ( 4317) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7888 Ramachandran restraints generated. 3944 Oldfield, 0 Emsley, 3944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 370 time to evaluate : 1.263 Fit side-chains REVERT: 1 11 MET cc_start: 0.7833 (mmp) cc_final: 0.7316 (ptm) REVERT: 1 274 ILE cc_start: 0.7788 (pt) cc_final: 0.7224 (mp) REVERT: 1 426 ASN cc_start: 0.6630 (t0) cc_final: 0.6267 (t0) REVERT: 2 469 PHE cc_start: 0.7306 (OUTLIER) cc_final: 0.6565 (p90) REVERT: 4 134 ASP cc_start: 0.4699 (p0) cc_final: 0.4351 (p0) REVERT: 4 137 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.7793 (mp) REVERT: 5 93 GLU cc_start: 0.6278 (mm-30) cc_final: 0.5748 (mm-30) REVERT: 5 324 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7905 (tt) REVERT: 7 21 MET cc_start: 0.7646 (ttp) cc_final: 0.7191 (ttp) REVERT: 7 389 LYS cc_start: 0.7804 (tptt) cc_final: 0.7072 (tttt) REVERT: 7 441 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8145 (tp) REVERT: 7 671 TYR cc_start: 0.8176 (m-10) cc_final: 0.7618 (m-10) REVERT: 7 700 LEU cc_start: 0.7396 (mm) cc_final: 0.7166 (mt) REVERT: 8 10 TYR cc_start: 0.8143 (m-80) cc_final: 0.7791 (m-10) REVERT: 8 171 TYR cc_start: 0.7528 (m-80) cc_final: 0.6766 (m-10) REVERT: 8 258 ASP cc_start: 0.7790 (t70) cc_final: 0.7466 (t70) REVERT: 8 265 ASN cc_start: 0.7955 (m-40) cc_final: 0.7696 (m110) REVERT: 8 293 ASN cc_start: 0.8266 (p0) cc_final: 0.7927 (p0) REVERT: 9 480 GLU cc_start: 0.6717 (mm-30) cc_final: 0.6209 (tm-30) REVERT: 9 686 ASP cc_start: 0.7468 (OUTLIER) cc_final: 0.6995 (t70) REVERT: 3 78 ASN cc_start: 0.6705 (m110) cc_final: 0.6219 (m110) REVERT: 3 171 GLN cc_start: 0.7124 (mm-40) cc_final: 0.6851 (mm-40) outliers start: 99 outliers final: 88 residues processed: 450 average time/residue: 0.1908 time to fit residues: 142.1387 Evaluate side-chains 450 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 357 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 11 VAL Chi-restraints excluded: chain 0 residue 12 LEU Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 33 LEU Chi-restraints excluded: chain 1 residue 10 SER Chi-restraints excluded: chain 1 residue 39 LEU Chi-restraints excluded: chain 1 residue 55 THR Chi-restraints excluded: chain 1 residue 105 SER Chi-restraints excluded: chain 1 residue 198 THR Chi-restraints excluded: chain 1 residue 202 THR Chi-restraints excluded: chain 1 residue 220 VAL Chi-restraints excluded: chain 1 residue 246 SER Chi-restraints excluded: chain 1 residue 362 VAL Chi-restraints excluded: chain 1 residue 369 THR Chi-restraints excluded: chain 1 residue 488 LEU Chi-restraints excluded: chain 1 residue 502 THR Chi-restraints excluded: chain 1 residue 505 LEU Chi-restraints excluded: chain 1 residue 552 VAL Chi-restraints excluded: chain 1 residue 582 ILE Chi-restraints excluded: chain 2 residue 123 ILE Chi-restraints excluded: chain 2 residue 181 VAL Chi-restraints excluded: chain 2 residue 212 MET Chi-restraints excluded: chain 2 residue 293 VAL Chi-restraints excluded: chain 2 residue 341 LEU Chi-restraints excluded: chain 2 residue 377 ILE Chi-restraints excluded: chain 2 residue 384 HIS Chi-restraints excluded: chain 2 residue 453 VAL Chi-restraints excluded: chain 2 residue 469 PHE Chi-restraints excluded: chain 2 residue 499 VAL Chi-restraints excluded: chain 2 residue 546 ILE Chi-restraints excluded: chain 2 residue 548 ILE Chi-restraints excluded: chain 2 residue 610 LEU Chi-restraints excluded: chain 2 residue 634 MET Chi-restraints excluded: chain 4 residue 79 LEU Chi-restraints excluded: chain 4 residue 137 ILE Chi-restraints excluded: chain 4 residue 177 ILE Chi-restraints excluded: chain 4 residue 190 ILE Chi-restraints excluded: chain 4 residue 245 MET Chi-restraints excluded: chain 4 residue 373 LEU Chi-restraints excluded: chain 5 residue 17 VAL Chi-restraints excluded: chain 5 residue 40 THR Chi-restraints excluded: chain 5 residue 57 ILE Chi-restraints excluded: chain 5 residue 74 ASN Chi-restraints excluded: chain 5 residue 79 ILE Chi-restraints excluded: chain 5 residue 80 THR Chi-restraints excluded: chain 5 residue 97 VAL Chi-restraints excluded: chain 5 residue 120 LEU Chi-restraints excluded: chain 5 residue 201 ILE Chi-restraints excluded: chain 5 residue 232 VAL Chi-restraints excluded: chain 5 residue 241 GLU Chi-restraints excluded: chain 5 residue 324 ILE Chi-restraints excluded: chain 7 residue 77 THR Chi-restraints excluded: chain 7 residue 174 VAL Chi-restraints excluded: chain 7 residue 180 VAL Chi-restraints excluded: chain 7 residue 192 VAL Chi-restraints excluded: chain 7 residue 291 SER Chi-restraints excluded: chain 7 residue 381 VAL Chi-restraints excluded: chain 7 residue 441 LEU Chi-restraints excluded: chain 7 residue 508 THR Chi-restraints excluded: chain 7 residue 609 ILE Chi-restraints excluded: chain 7 residue 650 LEU Chi-restraints excluded: chain 8 residue 39 LEU Chi-restraints excluded: chain 8 residue 99 THR Chi-restraints excluded: chain 8 residue 133 THR Chi-restraints excluded: chain 8 residue 204 GLU Chi-restraints excluded: chain 8 residue 262 THR Chi-restraints excluded: chain 9 residue 9 TRP Chi-restraints excluded: chain 9 residue 81 VAL Chi-restraints excluded: chain 9 residue 134 THR Chi-restraints excluded: chain 9 residue 157 VAL Chi-restraints excluded: chain 9 residue 189 ARG Chi-restraints excluded: chain 9 residue 205 TYR Chi-restraints excluded: chain 9 residue 303 THR Chi-restraints excluded: chain 9 residue 341 LEU Chi-restraints excluded: chain 9 residue 364 SER Chi-restraints excluded: chain 9 residue 395 VAL Chi-restraints excluded: chain 9 residue 413 VAL Chi-restraints excluded: chain 9 residue 414 SER Chi-restraints excluded: chain 9 residue 460 TYR Chi-restraints excluded: chain 9 residue 461 VAL Chi-restraints excluded: chain 9 residue 488 SER Chi-restraints excluded: chain 9 residue 505 VAL Chi-restraints excluded: chain 9 residue 531 LEU Chi-restraints excluded: chain 9 residue 546 HIS Chi-restraints excluded: chain 9 residue 552 THR Chi-restraints excluded: chain 9 residue 575 VAL Chi-restraints excluded: chain 9 residue 642 LEU Chi-restraints excluded: chain 9 residue 686 ASP Chi-restraints excluded: chain 9 residue 688 THR Chi-restraints excluded: chain 9 residue 747 ASP Chi-restraints excluded: chain 3 residue 82 HIS Chi-restraints excluded: chain 3 residue 132 MET Chi-restraints excluded: chain 3 residue 141 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 289 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 263 optimal weight: 0.0370 chunk 220 optimal weight: 7.9990 chunk 47 optimal weight: 0.2980 chunk 255 optimal weight: 3.9990 chunk 202 optimal weight: 3.9990 chunk 59 optimal weight: 0.3980 chunk 267 optimal weight: 3.9990 chunk 349 optimal weight: 0.9980 chunk 297 optimal weight: 2.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 36 GLN 2 343 GLN ** 2 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 74 ASN ** 7 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 309 ASN 3 82 HIS 3 114 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.163658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.140978 restraints weight = 48479.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.140666 restraints weight = 59211.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.141850 restraints weight = 49812.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.141917 restraints weight = 37165.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.142251 restraints weight = 37311.004| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 32289 Z= 0.113 Angle : 0.588 9.717 43700 Z= 0.299 Chirality : 0.042 0.199 4974 Planarity : 0.004 0.051 5596 Dihedral : 5.399 144.545 4309 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.72 % Allowed : 21.12 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.14), residues: 3944 helix: 1.97 (0.14), residues: 1370 sheet: -0.67 (0.17), residues: 988 loop : -1.74 (0.15), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 5 129 TYR 0.070 0.001 TYR 3 83 PHE 0.021 0.001 PHE 7 58 TRP 0.022 0.001 TRP 3 176 HIS 0.030 0.001 HIS 3 82 Details of bonding type rmsd covalent geometry : bond 0.00249 (32289) covalent geometry : angle 0.58829 (43700) hydrogen bonds : bond 0.03550 ( 1505) hydrogen bonds : angle 4.42756 ( 4317) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5074.76 seconds wall clock time: 89 minutes 7.55 seconds (5347.55 seconds total)