Starting phenix.real_space_refine on Mon Sep 14 15:53:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vbv_21145/09_2026/6vbv_21145.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vbv_21145/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6vbv_21145/09_2026/6vbv_21145.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vbv_21145/09_2026/6vbv_21145.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vbv_21145/09_2026/6vbv_21145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vbv_21145/09_2026/6vbv_21145.map" model { file = "/net/cci-nas-00/data/ceres_data/6vbv_21145/09_2026/6vbv_21145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vbv_21145/09_2026/6vbv_21145.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 7.01, per 1000 atoms: 0.22 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: 2.83 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: 1.06 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: 7.80 Time building geometry restraints manager: 3.79 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: 2.980 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: 0.030 Extract box with map and model: 0.470 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 31.210 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 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/Z covalent geometry : bond 0.00415 / 0.24 (32289) covalent geometry : angle 0.71442 / 0.42 (43700) hydrogen bonds : bond 0.13214 / 8.53 ( 1505) hydrogen bonds : angle 6.28776 / 4.30 ( 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 : 1.279 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: 0.2209 time to fit residues: 285.2107 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 : 1.603 ------------------------------------------------------------------------------- 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... 0 17 GLN 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 7 228 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 8 454 HIS 8 456 ASN 8 496 GLN 9 22 GLN 9 37 GLN 9 201 GLN 9 276 GLN 9 652 HIS 9 693 GLN ** 9 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 60 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.164562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.142126 restraints weight = 48469.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.142048 restraints weight = 57531.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.143112 restraints weight = 50094.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.143396 restraints weight = 34243.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.143627 restraints weight = 33482.071| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 32289 Z= 0.142 Angle : 0.631 9.963 43700 Z= 0.323 Chirality : 0.044 0.178 4974 Planarity : 0.004 0.057 5596 Dihedral : 6.914 160.392 4331 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.23 % Allowed : 13.39 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.75 (0.13), residues: 3944 helix: 0.75 (0.14), residues: 1383 sheet: -1.68 (0.16), residues: 1016 loop : -2.56 (0.15), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 8 469 TYR 0.027 0.001 TYR 7 660 PHE 0.024 0.002 PHE 4 413 TRP 0.013 0.001 TRP 9 237 HIS 0.013 0.001 HIS 7 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (32289) covalent geometry : angle 0.63052 / 0.32 (43700) hydrogen bonds : bond 0.04233 / 2.78 ( 1505) hydrogen bonds : angle 4.91231 / 3.37 ( 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 552 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 474 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 11 MET cc_start: 0.7690 (mmp) cc_final: 0.7204 (ptt) REVERT: 1 274 ILE cc_start: 0.7377 (pt) cc_final: 0.7076 (mp) REVERT: 1 479 SER cc_start: 0.7563 (m) cc_final: 0.7323 (t) REVERT: 2 287 SER cc_start: 0.8479 (t) cc_final: 0.8145 (p) REVERT: 4 134 ASP cc_start: 0.5905 (p0) cc_final: 0.4891 (p0) REVERT: 4 137 ILE cc_start: 0.8080 (mt) cc_final: 0.7646 (mp) REVERT: 4 178 PHE cc_start: 0.7971 (m-10) cc_final: 0.7731 (m-10) REVERT: 4 411 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7390 (mt) REVERT: 5 93 GLU cc_start: 0.6277 (mm-30) cc_final: 0.5542 (mm-30) REVERT: 5 233 LEU cc_start: 0.8384 (mm) cc_final: 0.7938 (mp) REVERT: 7 325 GLU cc_start: 0.7083 (pp20) cc_final: 0.6090 (pm20) REVERT: 7 389 LYS cc_start: 0.7678 (tptt) cc_final: 0.7258 (ttpt) REVERT: 7 461 ILE cc_start: 0.7500 (OUTLIER) cc_final: 0.7211 (mp) REVERT: 7 671 TYR cc_start: 0.7837 (m-10) cc_final: 0.7607 (m-10) REVERT: 7 700 LEU cc_start: 0.6983 (mm) cc_final: 0.6489 (mm) REVERT: 8 10 TYR cc_start: 0.7893 (m-10) cc_final: 0.7476 (m-80) REVERT: 8 171 TYR cc_start: 0.7636 (m-80) cc_final: 0.7002 (m-80) REVERT: 8 293 ASN cc_start: 0.8330 (p0) cc_final: 0.7961 (p0) REVERT: 9 480 GLU cc_start: 0.6420 (mm-30) cc_final: 0.5592 (tm-30) REVERT: 3 142 LYS cc_start: 0.7367 (mmtt) cc_final: 0.7144 (mmmt) REVERT: 3 171 GLN cc_start: 0.7300 (mm-40) cc_final: 0.7019 (mm-40) outliers start: 78 outliers final: 37 residues processed: 522 average time/residue: 0.1993 time to fit residues: 170.5814 Evaluate side-chains 437 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 398 time to evaluate : 1.271 ------------------------------------------------------------------------------- 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 488 LEU 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 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: 3.9990 chunk 171 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 313 optimal weight: 3.9990 chunk 152 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 360 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 268 optimal weight: 5.9990 chunk 182 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 308 GLN 1 545 ASN 2 36 GLN ** 2 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 436 HIS ** 2 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 91 GLN 4 140 ASN 5 60 HIS ** 7 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 635 HIS 9 309 ASN 9 367 GLN 9 694 HIS ** 9 748 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 27 ASN 3 158 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.163015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.140113 restraints weight = 48695.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.139963 restraints weight = 59910.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.141108 restraints weight = 52543.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.141382 restraints weight = 34996.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.141621 restraints weight = 33938.980| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32289 Z= 0.150 Angle : 0.597 8.868 43700 Z= 0.306 Chirality : 0.044 0.189 4974 Planarity : 0.004 0.054 5596 Dihedral : 6.401 157.557 4317 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.80 % Allowed : 15.88 % Favored : 81.32 % 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: -1.21 (0.13), residues: 3944 helix: 1.29 (0.14), residues: 1367 sheet: -1.40 (0.16), residues: 996 loop : -2.29 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 9 75 TYR 0.019 0.001 TYR 9 623 PHE 0.024 0.002 PHE 2 250 TRP 0.014 0.001 TRP 9 237 HIS 0.008 0.001 HIS 7 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (32289) covalent geometry : angle 0.59678 / 0.31 (43700) hydrogen bonds : bond 0.04019 / 2.64 ( 1505) hydrogen bonds : angle 4.71318 / 3.22 ( 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 528 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 430 time to evaluate : 1.265 Fit side-chains revert: symmetry clash REVERT: 1 11 MET cc_start: 0.7831 (mmp) cc_final: 0.7182 (ptt) REVERT: 1 274 ILE cc_start: 0.7492 (pt) cc_final: 0.7132 (mp) REVERT: 1 426 ASN cc_start: 0.6609 (t0) cc_final: 0.6358 (t0) REVERT: 1 479 SER cc_start: 0.7620 (m) cc_final: 0.7341 (t) REVERT: 2 614 MET cc_start: 0.7518 (mtm) cc_final: 0.7317 (mtm) REVERT: 4 134 ASP cc_start: 0.6071 (p0) cc_final: 0.5066 (p0) REVERT: 4 137 ILE cc_start: 0.8229 (mt) cc_final: 0.7788 (mp) REVERT: 4 411 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7411 (mt) REVERT: 4 412 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6646 (tp30) REVERT: 5 93 GLU cc_start: 0.6281 (mm-30) cc_final: 0.5729 (mm-30) REVERT: 5 154 LEU cc_start: 0.8317 (mt) cc_final: 0.7974 (mt) REVERT: 5 233 LEU cc_start: 0.8383 (mm) cc_final: 0.7939 (mp) REVERT: 7 325 GLU cc_start: 0.7156 (pp20) cc_final: 0.6138 (pm20) REVERT: 7 461 ILE cc_start: 0.7470 (OUTLIER) cc_final: 0.7134 (mp) REVERT: 7 671 TYR cc_start: 0.7899 (m-10) cc_final: 0.7564 (m-10) REVERT: 7 700 LEU cc_start: 0.7381 (mm) cc_final: 0.6837 (mt) REVERT: 8 10 TYR cc_start: 0.7979 (m-10) cc_final: 0.7544 (m-10) REVERT: 8 171 TYR cc_start: 0.7631 (m-80) cc_final: 0.6955 (m-10) REVERT: 8 293 ASN cc_start: 0.8368 (p0) cc_final: 0.7988 (p0) REVERT: 9 311 MET cc_start: 0.8143 (mtp) cc_final: 0.7924 (ttm) REVERT: 9 480 GLU cc_start: 0.6465 (mm-30) cc_final: 0.5833 (tm-30) REVERT: 9 686 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7332 (t0) REVERT: 3 73 GLN cc_start: 0.7758 (mm-40) cc_final: 0.7513 (mm-40) REVERT: 3 78 ASN cc_start: 0.6334 (m110) cc_final: 0.5606 (m110) outliers start: 98 outliers final: 52 residues processed: 498 average time/residue: 0.1937 time to fit residues: 159.0968 Evaluate side-chains 439 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 383 time to evaluate : 1.126 ------------------------------------------------------------------------------- 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 502 THR Chi-restraints excluded: chain 1 residue 514 ILE Chi-restraints excluded: chain 1 residue 552 VAL Chi-restraints excluded: chain 2 residue 36 GLN Chi-restraints excluded: chain 2 residue 123 ILE Chi-restraints excluded: chain 2 residue 138 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 404 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 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 192 VAL 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 461 ILE Chi-restraints excluded: chain 7 residue 593 ILE Chi-restraints excluded: chain 7 residue 650 LEU Chi-restraints excluded: chain 7 residue 709 ILE 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 29 ASP 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 395 VAL Chi-restraints excluded: chain 9 residue 413 VAL Chi-restraints excluded: chain 9 residue 461 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 141 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 329 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 2 optimal weight: 0.6980 chunk 388 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 343 optimal weight: 1.9990 chunk 391 optimal weight: 10.0000 chunk 394 optimal weight: 5.9990 chunk 202 optimal weight: 4.9990 chunk 324 optimal weight: 10.0000 chunk 209 optimal weight: 10.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 359 HIS 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 ** 2 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 91 GLN 4 103 ASN 5 102 ASN 7 76 ASN 7 99 GLN ** 7 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 188 HIS 9 53 ASN 9 73 HIS 3 158 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.158744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.135504 restraints weight = 48805.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.134942 restraints weight = 64219.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.136127 restraints weight = 56804.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.136519 restraints weight = 38246.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.136774 restraints weight = 36806.736| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 32289 Z= 0.216 Angle : 0.649 8.588 43700 Z= 0.332 Chirality : 0.045 0.195 4974 Planarity : 0.004 0.057 5596 Dihedral : 6.334 153.847 4316 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 3.69 % Allowed : 17.05 % Favored : 79.26 % 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: -1.14 (0.13), residues: 3944 helix: 1.28 (0.14), residues: 1369 sheet: -1.36 (0.17), residues: 998 loop : -2.19 (0.15), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 5 129 TYR 0.021 0.002 TYR 2 229 PHE 0.025 0.002 PHE 4 413 TRP 0.017 0.002 TRP 9 237 HIS 0.006 0.001 HIS 1 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.22 (32289) covalent geometry : angle 0.64939 / 0.33 (43700) hydrogen bonds : bond 0.04307 / 2.83 ( 1505) hydrogen bonds : angle 4.79794 / 3.29 ( 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 538 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 409 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 274 ILE cc_start: 0.7529 (pt) cc_final: 0.7106 (mp) REVERT: 1 426 ASN cc_start: 0.6866 (t0) cc_final: 0.6599 (t0) REVERT: 1 479 SER cc_start: 0.7819 (m) cc_final: 0.7393 (t) REVERT: 2 206 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8432 (mm) REVERT: 4 134 ASP cc_start: 0.6394 (p0) cc_final: 0.5428 (t70) REVERT: 4 411 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7316 (mt) REVERT: 5 93 GLU cc_start: 0.6260 (mm-30) cc_final: 0.5652 (mm-30) REVERT: 5 324 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.8054 (tt) REVERT: 7 325 GLU cc_start: 0.7312 (pp20) cc_final: 0.6329 (pm20) REVERT: 7 461 ILE cc_start: 0.7407 (OUTLIER) cc_final: 0.7061 (mp) REVERT: 7 671 TYR cc_start: 0.8034 (m-10) cc_final: 0.7527 (m-80) REVERT: 7 700 LEU cc_start: 0.7486 (mm) cc_final: 0.7039 (mt) REVERT: 8 10 TYR cc_start: 0.8092 (m-10) cc_final: 0.7662 (m-80) REVERT: 8 103 ARG cc_start: 0.6417 (mmt90) cc_final: 0.6198 (mmm160) REVERT: 8 171 TYR cc_start: 0.7737 (m-80) cc_final: 0.6925 (m-10) REVERT: 8 293 ASN cc_start: 0.8326 (p0) cc_final: 0.7900 (p0) REVERT: 9 480 GLU cc_start: 0.6539 (mm-30) cc_final: 0.5883 (tm-30) REVERT: 9 686 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.7263 (t70) REVERT: 9 765 GLU cc_start: 0.6961 (mm-30) cc_final: 0.6659 (mm-30) REVERT: 3 78 ASN cc_start: 0.6650 (m110) cc_final: 0.5986 (m110) REVERT: 3 171 GLN cc_start: 0.7311 (mm-40) cc_final: 0.7042 (mm-40) outliers start: 129 outliers final: 77 residues processed: 505 average time/residue: 0.1917 time to fit residues: 159.7891 Evaluate side-chains 459 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 377 time to evaluate : 1.228 ------------------------------------------------------------------------------- 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 202 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 545 ASN 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 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 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 40 THR Chi-restraints excluded: chain 5 residue 57 ILE Chi-restraints excluded: chain 5 residue 97 VAL 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 82 ILE 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 349 LEU 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 452 THR Chi-restraints excluded: chain 7 residue 461 ILE Chi-restraints excluded: chain 7 residue 593 ILE Chi-restraints excluded: chain 8 residue 39 LEU Chi-restraints excluded: chain 8 residue 161 ILE 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 134 THR 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 461 VAL Chi-restraints excluded: chain 9 residue 488 SER 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 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 128 PHE 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: 0.7980 chunk 187 optimal weight: 1.9990 chunk 353 optimal weight: 6.9990 chunk 198 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 278 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 364 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 355 optimal weight: 9.9990 chunk 390 optimal weight: 20.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ** 2 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 706 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 91 GLN ** 7 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 265 ASN 9 155 GLN 3 27 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 = 0.3932 r_free = 0.3932 target = 0.157033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.134982 restraints weight = 49142.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.134780 restraints weight = 61173.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.135755 restraints weight = 55189.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.135886 restraints weight = 38160.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.136332 restraints weight = 38392.675| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 32289 Z= 0.217 Angle : 0.651 8.445 43700 Z= 0.333 Chirality : 0.045 0.186 4974 Planarity : 0.004 0.056 5596 Dihedral : 6.102 146.947 4314 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 3.83 % Allowed : 18.23 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.14), residues: 3944 helix: 1.35 (0.14), residues: 1367 sheet: -1.30 (0.17), residues: 994 loop : -2.10 (0.15), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 5 186 TYR 0.031 0.002 TYR 7 660 PHE 0.027 0.002 PHE 4 413 TRP 0.019 0.002 TRP 9 9 HIS 0.007 0.001 HIS 1 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.22 (32289) covalent geometry : angle 0.65056 / 0.33 (43700) hydrogen bonds : bond 0.04274 / 2.81 ( 1505) hydrogen bonds : angle 4.80707 / 3.29 ( 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 532 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 398 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 274 ILE cc_start: 0.7649 (pt) cc_final: 0.7103 (mp) REVERT: 1 426 ASN cc_start: 0.6949 (t0) cc_final: 0.6431 (t0) REVERT: 1 479 SER cc_start: 0.7822 (m) cc_final: 0.7430 (t) REVERT: 2 128 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7912 (mp) REVERT: 2 138 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8106 (tt) REVERT: 2 206 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8427 (mm) REVERT: 2 299 MET cc_start: 0.8141 (mmm) cc_final: 0.7711 (mmm) REVERT: 5 324 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7985 (tt) REVERT: 7 389 LYS cc_start: 0.7887 (tptt) cc_final: 0.7231 (tttt) REVERT: 7 461 ILE cc_start: 0.7388 (OUTLIER) cc_final: 0.7052 (mp) REVERT: 7 671 TYR cc_start: 0.8047 (m-10) cc_final: 0.7517 (m-80) REVERT: 7 700 LEU cc_start: 0.7472 (mm) cc_final: 0.7103 (mt) REVERT: 8 10 TYR cc_start: 0.8081 (m-10) cc_final: 0.7714 (m-80) REVERT: 8 103 ARG cc_start: 0.6487 (mmt90) cc_final: 0.6273 (mmm160) REVERT: 8 171 TYR cc_start: 0.7693 (m-80) cc_final: 0.6892 (m-10) REVERT: 8 258 ASP cc_start: 0.7688 (t70) cc_final: 0.7343 (t70) REVERT: 8 265 ASN cc_start: 0.7645 (m-40) cc_final: 0.7205 (m110) REVERT: 8 293 ASN cc_start: 0.8329 (p0) cc_final: 0.7973 (p0) REVERT: 9 480 GLU cc_start: 0.6662 (mm-30) cc_final: 0.6141 (tm-30) REVERT: 9 624 PHE cc_start: 0.6720 (m-10) cc_final: 0.6412 (m-10) REVERT: 9 686 ASP cc_start: 0.7612 (OUTLIER) cc_final: 0.7169 (t70) REVERT: 3 73 GLN cc_start: 0.7616 (mm-40) cc_final: 0.7378 (mm-40) REVERT: 3 78 ASN cc_start: 0.6673 (m110) cc_final: 0.6061 (m110) REVERT: 3 158 HIS cc_start: 0.6740 (t-90) cc_final: 0.6229 (t70) REVERT: 3 171 GLN cc_start: 0.7126 (mm-40) cc_final: 0.6879 (mm-40) outliers start: 134 outliers final: 92 residues processed: 502 average time/residue: 0.1956 time to fit residues: 161.1072 Evaluate side-chains 469 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 371 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 11 VAL 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 55 THR Chi-restraints excluded: chain 1 residue 198 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 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 1 residue 590 LEU 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 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 383 HIS Chi-restraints excluded: chain 2 residue 441 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 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 75 CYS Chi-restraints excluded: chain 5 residue 79 ILE 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 82 ILE 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 291 SER 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 420 VAL Chi-restraints excluded: chain 7 residue 461 ILE Chi-restraints excluded: chain 7 residue 593 ILE 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 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 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 461 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 103 VAL Chi-restraints excluded: chain 3 residue 111 THR Chi-restraints excluded: chain 3 residue 112 LEU 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: 9.9990 chunk 267 optimal weight: 1.9990 chunk 359 optimal weight: 5.9990 chunk 191 optimal weight: 10.0000 chunk 374 optimal weight: 0.8980 chunk 225 optimal weight: 0.9980 chunk 116 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 4 224 HIS 9 155 GLN 3 27 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 = 0.3971 r_free = 0.3971 target = 0.160249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.137202 restraints weight = 48431.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.136860 restraints weight = 59355.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.137961 restraints weight = 51390.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.138191 restraints weight = 37530.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.138459 restraints weight = 35166.173| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32289 Z= 0.148 Angle : 0.600 7.838 43700 Z= 0.307 Chirality : 0.043 0.182 4974 Planarity : 0.004 0.051 5596 Dihedral : 5.762 138.354 4312 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 3.18 % Allowed : 19.43 % Favored : 77.40 % 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: -0.76 (0.14), residues: 3944 helix: 1.61 (0.14), residues: 1364 sheet: -1.12 (0.17), residues: 973 loop : -1.99 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG 8 12 TYR 0.022 0.001 TYR 7 660 PHE 0.026 0.002 PHE 4 413 TRP 0.016 0.001 TRP 9 9 HIS 0.006 0.001 HIS 1 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (32289) covalent geometry : angle 0.60023 / 0.31 (43700) hydrogen bonds : bond 0.03917 / 2.58 ( 1505) hydrogen bonds : angle 4.62815 / 3.17 ( 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 519 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 408 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 11 MET cc_start: 0.7782 (mmp) cc_final: 0.7171 (ptm) REVERT: 1 274 ILE cc_start: 0.7642 (pt) cc_final: 0.7118 (mp) REVERT: 1 426 ASN cc_start: 0.6942 (t0) cc_final: 0.6552 (t0) REVERT: 2 299 MET cc_start: 0.8121 (mmm) cc_final: 0.7693 (mmm) REVERT: 2 469 PHE cc_start: 0.7407 (OUTLIER) cc_final: 0.6911 (p90) REVERT: 2 526 ILE cc_start: 0.4838 (OUTLIER) cc_final: 0.4324 (tp) REVERT: 4 278 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7851 (mmt) REVERT: 5 93 GLU cc_start: 0.6315 (mm-30) cc_final: 0.5797 (mm-30) REVERT: 5 324 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7894 (tt) REVERT: 7 389 LYS cc_start: 0.7847 (tptt) cc_final: 0.7154 (tttt) REVERT: 7 441 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8107 (tp) REVERT: 7 461 ILE cc_start: 0.7453 (OUTLIER) cc_final: 0.7152 (mp) REVERT: 7 671 TYR cc_start: 0.8042 (m-10) cc_final: 0.7530 (m-80) REVERT: 7 700 LEU cc_start: 0.7365 (mm) cc_final: 0.7093 (mt) REVERT: 8 10 TYR cc_start: 0.8076 (m-10) cc_final: 0.7752 (m-80) REVERT: 8 103 ARG cc_start: 0.6446 (mmt90) cc_final: 0.6246 (mmm160) REVERT: 8 171 TYR cc_start: 0.7604 (m-80) cc_final: 0.6789 (m-10) REVERT: 8 258 ASP cc_start: 0.7762 (t70) cc_final: 0.7393 (t70) REVERT: 8 265 ASN cc_start: 0.7838 (m-40) cc_final: 0.7520 (m110) REVERT: 8 293 ASN cc_start: 0.8280 (p0) cc_final: 0.7968 (p0) REVERT: 9 480 GLU cc_start: 0.6680 (mm-30) cc_final: 0.6230 (tm-30) REVERT: 9 686 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.7099 (t70) REVERT: 3 73 GLN cc_start: 0.7624 (mm-40) cc_final: 0.7315 (mm-40) REVERT: 3 78 ASN cc_start: 0.6665 (m110) cc_final: 0.6048 (m110) REVERT: 3 158 HIS cc_start: 0.6749 (t-90) cc_final: 0.6106 (t-90) REVERT: 3 171 GLN cc_start: 0.7159 (mm-40) cc_final: 0.6858 (mm-40) outliers start: 111 outliers final: 77 residues processed: 490 average time/residue: 0.1943 time to fit residues: 155.5969 Evaluate side-chains 460 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 376 time to evaluate : 1.249 ------------------------------------------------------------------------------- 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 33 LEU Chi-restraints excluded: chain 1 residue 10 SER 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 552 VAL Chi-restraints excluded: chain 1 residue 582 ILE Chi-restraints excluded: chain 2 residue 123 ILE 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 293 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 526 ILE Chi-restraints excluded: chain 2 residue 546 ILE Chi-restraints excluded: chain 2 residue 548 ILE 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 278 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 11 LEU 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 296 CYS 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 441 LEU Chi-restraints excluded: chain 7 residue 461 ILE Chi-restraints excluded: chain 7 residue 508 THR Chi-restraints excluded: chain 7 residue 593 ILE 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 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 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 413 VAL Chi-restraints excluded: chain 9 residue 461 VAL Chi-restraints excluded: chain 9 residue 488 SER 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 141 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 205 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 343 optimal weight: 3.9990 chunk 284 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 245 optimal weight: 5.9990 chunk 276 optimal weight: 0.7980 chunk 279 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** 2 706 ASN 4 45 GLN 4 91 GLN ** 7 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 309 ASN 9 811 HIS ** 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 = 0.4000 r_free = 0.4000 target = 0.162662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.139788 restraints weight = 48527.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.139696 restraints weight = 60360.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.140744 restraints weight = 49842.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.140923 restraints weight = 35692.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.141095 restraints weight = 35824.075| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3560 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= 0.119 Angle : 0.578 8.982 43700 Z= 0.294 Chirality : 0.042 0.247 4974 Planarity : 0.004 0.051 5596 Dihedral : 5.526 134.034 4311 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.80 % Allowed : 20.34 % Favored : 76.85 % 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: -0.48 (0.14), residues: 3944 helix: 1.86 (0.14), residues: 1363 sheet: -0.97 (0.17), residues: 983 loop : -1.84 (0.15), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 5 129 TYR 0.018 0.001 TYR 7 132 PHE 0.023 0.001 PHE 4 413 TRP 0.018 0.001 TRP 3 176 HIS 0.005 0.001 HIS 7 521 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (32289) covalent geometry : angle 0.57762 / 0.29 (43700) hydrogen bonds : bond 0.03629 / 2.37 ( 1505) hydrogen bonds : angle 4.46578 / 3.06 ( 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 508 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 410 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 11 MET cc_start: 0.7678 (mmp) cc_final: 0.7200 (ptm) REVERT: 1 274 ILE cc_start: 0.7577 (pt) cc_final: 0.7114 (mp) REVERT: 2 299 MET cc_start: 0.8112 (mmm) cc_final: 0.7678 (mmm) REVERT: 2 469 PHE cc_start: 0.7397 (OUTLIER) cc_final: 0.6891 (p90) REVERT: 2 526 ILE cc_start: 0.4466 (OUTLIER) cc_final: 0.4128 (tp) REVERT: 5 93 GLU cc_start: 0.6317 (mm-30) cc_final: 0.5756 (mm-30) REVERT: 5 324 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7882 (tt) REVERT: 7 389 LYS cc_start: 0.7772 (tptt) cc_final: 0.7036 (tttt) REVERT: 7 461 ILE cc_start: 0.7319 (OUTLIER) cc_final: 0.7015 (mp) REVERT: 7 671 TYR cc_start: 0.8013 (m-10) cc_final: 0.7508 (m-80) REVERT: 7 700 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.7094 (mt) REVERT: 8 6 LEU cc_start: 0.8508 (tp) cc_final: 0.7887 (tp) REVERT: 8 10 TYR cc_start: 0.8065 (m-10) cc_final: 0.7862 (m-80) REVERT: 8 171 TYR cc_start: 0.7495 (m-80) cc_final: 0.6804 (m-10) REVERT: 8 258 ASP cc_start: 0.7818 (t70) cc_final: 0.7462 (t70) REVERT: 8 261 LEU cc_start: 0.8542 (mt) cc_final: 0.8164 (mt) REVERT: 8 265 ASN cc_start: 0.7899 (m-40) cc_final: 0.7541 (m110) REVERT: 8 269 GLN cc_start: 0.8511 (tt0) cc_final: 0.8273 (tt0) REVERT: 8 293 ASN cc_start: 0.8308 (p0) cc_final: 0.7904 (p0) REVERT: 9 480 GLU cc_start: 0.6662 (mm-30) cc_final: 0.6130 (tm-30) REVERT: 9 686 ASP cc_start: 0.7411 (OUTLIER) cc_final: 0.6971 (t70) REVERT: 3 78 ASN cc_start: 0.6703 (m110) cc_final: 0.6129 (m110) REVERT: 3 171 GLN cc_start: 0.7052 (mm-40) cc_final: 0.6769 (mm-40) outliers start: 98 outliers final: 67 residues processed: 482 average time/residue: 0.1947 time to fit residues: 154.1648 Evaluate side-chains 449 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 376 time to evaluate : 1.231 ------------------------------------------------------------------------------- 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 362 VAL Chi-restraints excluded: chain 1 residue 369 THR Chi-restraints excluded: chain 1 residue 392 THR Chi-restraints excluded: chain 1 residue 552 VAL Chi-restraints excluded: chain 1 residue 582 ILE Chi-restraints excluded: chain 1 residue 590 LEU 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 526 ILE Chi-restraints excluded: chain 2 residue 546 ILE 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 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 244 VAL Chi-restraints excluded: chain 7 residue 287 GLU 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 420 VAL Chi-restraints excluded: chain 7 residue 461 ILE Chi-restraints excluded: chain 7 residue 609 ILE Chi-restraints excluded: chain 7 residue 650 LEU Chi-restraints excluded: chain 7 residue 700 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 399 THR Chi-restraints excluded: chain 9 residue 9 TRP Chi-restraints excluded: chain 9 residue 29 ASP Chi-restraints excluded: chain 9 residue 134 THR Chi-restraints excluded: chain 9 residue 157 VAL Chi-restraints excluded: chain 9 residue 205 TYR Chi-restraints excluded: chain 9 residue 361 THR Chi-restraints excluded: chain 9 residue 395 VAL Chi-restraints excluded: chain 9 residue 413 VAL Chi-restraints excluded: chain 9 residue 461 VAL Chi-restraints excluded: chain 9 residue 488 SER Chi-restraints excluded: chain 9 residue 546 HIS 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 112 LEU 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: 6.9990 chunk 222 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 363 optimal weight: 8.9990 chunk 320 optimal weight: 7.9990 chunk 165 optimal weight: 10.0000 chunk 110 optimal weight: 0.8980 chunk 158 optimal weight: 9.9990 chunk 285 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 308 GLN 1 426 ASN 1 545 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** ** 7 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 155 GLN 9 309 ASN 3 114 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.156916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.133974 restraints weight = 48952.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.133416 restraints weight = 61497.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.134401 restraints weight = 58010.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.134719 restraints weight = 37671.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.135023 restraints weight = 36553.099| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 32289 Z= 0.265 Angle : 0.690 10.027 43700 Z= 0.351 Chirality : 0.047 0.216 4974 Planarity : 0.005 0.056 5596 Dihedral : 5.860 135.290 4310 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 3.49 % Allowed : 20.26 % Favored : 76.25 % 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: -0.84 (0.14), residues: 3944 helix: 1.42 (0.14), residues: 1375 sheet: -1.12 (0.17), residues: 999 loop : -1.96 (0.15), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG 2 632 TYR 0.025 0.002 TYR 7 660 PHE 0.028 0.002 PHE 4 413 TRP 0.023 0.002 TRP 3 176 HIS 0.007 0.001 HIS 1 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.27 (32289) covalent geometry : angle 0.68958 / 0.35 (43700) hydrogen bonds : bond 0.04405 / 2.90 ( 1505) hydrogen bonds : angle 4.80920 / 3.29 ( 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 510 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 388 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 11 MET cc_start: 0.7843 (mmp) cc_final: 0.7263 (ptm) REVERT: 1 274 ILE cc_start: 0.7753 (pt) cc_final: 0.7233 (mp) REVERT: 1 426 ASN cc_start: 0.6569 (t0) cc_final: 0.6237 (t0) REVERT: 2 128 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.8010 (mp) REVERT: 2 138 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.8115 (tt) REVERT: 2 469 PHE cc_start: 0.7512 (OUTLIER) cc_final: 0.7191 (p90) REVERT: 7 389 LYS cc_start: 0.7883 (tptt) cc_final: 0.7182 (tttt) REVERT: 7 441 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8162 (tp) REVERT: 7 461 ILE cc_start: 0.7389 (OUTLIER) cc_final: 0.7072 (mp) REVERT: 7 506 MET cc_start: 0.7491 (tpp) cc_final: 0.7093 (tpp) REVERT: 7 671 TYR cc_start: 0.8154 (m-10) cc_final: 0.7603 (m-80) REVERT: 7 700 LEU cc_start: 0.7424 (mm) cc_final: 0.7157 (mt) REVERT: 8 171 TYR cc_start: 0.7653 (m-80) cc_final: 0.6824 (m-10) REVERT: 8 258 ASP cc_start: 0.7851 (t70) cc_final: 0.7512 (t70) REVERT: 8 265 ASN cc_start: 0.7783 (m-40) cc_final: 0.7379 (m110) REVERT: 8 293 ASN cc_start: 0.8384 (p0) cc_final: 0.7953 (p0) REVERT: 9 480 GLU cc_start: 0.6766 (mm-30) cc_final: 0.6325 (tm-30) REVERT: 9 686 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.7128 (t70) REVERT: 3 78 ASN cc_start: 0.6535 (m110) cc_final: 0.6132 (m110) REVERT: 3 158 HIS cc_start: 0.6893 (t70) cc_final: 0.6649 (t70) REVERT: 3 171 GLN cc_start: 0.7146 (mm-40) cc_final: 0.6904 (mm-40) outliers start: 122 outliers final: 91 residues processed: 487 average time/residue: 0.1989 time to fit residues: 158.5793 Evaluate side-chains 460 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 363 time to evaluate : 1.151 ------------------------------------------------------------------------------- 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 50 VAL 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 224 GLU Chi-restraints excluded: chain 1 residue 346 VAL Chi-restraints excluded: chain 1 residue 362 VAL Chi-restraints excluded: chain 1 residue 366 VAL Chi-restraints excluded: chain 1 residue 369 THR 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 545 ASN Chi-restraints excluded: chain 1 residue 552 VAL Chi-restraints excluded: chain 1 residue 582 ILE Chi-restraints excluded: chain 1 residue 590 LEU 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 293 VAL Chi-restraints excluded: chain 2 residue 341 LEU Chi-restraints excluded: chain 2 residue 377 ILE Chi-restraints excluded: chain 2 residue 441 VAL 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 526 ILE Chi-restraints excluded: chain 2 residue 546 ILE Chi-restraints excluded: chain 2 residue 548 ILE 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 4 residue 373 LEU Chi-restraints excluded: chain 4 residue 409 SER 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 174 VAL Chi-restraints excluded: chain 7 residue 180 VAL Chi-restraints excluded: chain 7 residue 192 VAL Chi-restraints excluded: chain 7 residue 244 VAL Chi-restraints excluded: chain 7 residue 287 GLU Chi-restraints excluded: chain 7 residue 381 VAL Chi-restraints excluded: chain 7 residue 420 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 593 ILE 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 195 THR 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 395 VAL Chi-restraints excluded: chain 9 residue 413 VAL Chi-restraints excluded: chain 9 residue 414 SER Chi-restraints excluded: chain 9 residue 461 VAL Chi-restraints excluded: chain 9 residue 488 SER Chi-restraints excluded: chain 9 residue 531 LEU 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 111 THR Chi-restraints excluded: chain 3 residue 112 LEU 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: 0.7980 chunk 225 optimal weight: 1.9990 chunk 198 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 319 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 311 optimal weight: 3.9990 chunk 290 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 36 GLN 2 343 GLN ** 7 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 309 ASN 3 35 ASN 3 114 ASN 3 145 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.160397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.137510 restraints weight = 48357.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.137303 restraints weight = 56464.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.138310 restraints weight = 52198.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.138511 restraints weight = 35274.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.138773 restraints weight = 35863.912| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32289 Z= 0.148 Angle : 0.620 13.886 43700 Z= 0.315 Chirality : 0.044 0.207 4974 Planarity : 0.004 0.051 5596 Dihedral : 5.647 139.728 4309 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 2.72 % Allowed : 21.34 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.14), residues: 3944 helix: 1.65 (0.14), residues: 1373 sheet: -0.99 (0.17), residues: 983 loop : -1.89 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 5 129 TYR 0.035 0.001 TYR 5 131 PHE 0.023 0.002 PHE 4 413 TRP 0.028 0.001 TRP 3 176 HIS 0.006 0.001 HIS 7 521 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (32289) covalent geometry : angle 0.61985 / 0.32 (43700) hydrogen bonds : bond 0.03871 / 2.54 ( 1505) hydrogen bonds : angle 4.62401 / 3.17 ( 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 475 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 380 time to evaluate : 1.250 Fit side-chains REVERT: 1 11 MET cc_start: 0.7772 (mmp) cc_final: 0.7225 (ptm) REVERT: 1 274 ILE cc_start: 0.7694 (pt) cc_final: 0.7129 (mp) REVERT: 1 426 ASN cc_start: 0.6609 (t0) cc_final: 0.6268 (t0) REVERT: 2 299 MET cc_start: 0.8187 (mmm) cc_final: 0.7723 (mmm) REVERT: 5 93 GLU cc_start: 0.6389 (mm-30) cc_final: 0.5813 (mm-30) REVERT: 7 389 LYS cc_start: 0.7835 (tptt) cc_final: 0.7071 (tttt) REVERT: 7 441 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8106 (tp) REVERT: 7 461 ILE cc_start: 0.7279 (OUTLIER) cc_final: 0.6948 (mp) REVERT: 7 506 MET cc_start: 0.7394 (tpp) cc_final: 0.6962 (tpp) REVERT: 7 671 TYR cc_start: 0.8140 (m-10) cc_final: 0.7499 (m-80) REVERT: 7 700 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.7142 (mt) REVERT: 8 10 TYR cc_start: 0.8087 (m-80) cc_final: 0.7748 (m-10) REVERT: 8 171 TYR cc_start: 0.7562 (m-80) cc_final: 0.6764 (m-10) REVERT: 8 258 ASP cc_start: 0.7736 (t70) cc_final: 0.7384 (t70) REVERT: 8 265 ASN cc_start: 0.7947 (m-40) cc_final: 0.7666 (m110) REVERT: 8 293 ASN cc_start: 0.8288 (p0) cc_final: 0.7929 (p0) REVERT: 9 480 GLU cc_start: 0.6711 (mm-30) cc_final: 0.6283 (tm-30) REVERT: 9 686 ASP cc_start: 0.7478 (OUTLIER) cc_final: 0.7020 (t70) REVERT: 3 78 ASN cc_start: 0.6472 (m110) cc_final: 0.6102 (m110) REVERT: 3 158 HIS cc_start: 0.6932 (t70) cc_final: 0.6671 (t70) REVERT: 3 171 GLN cc_start: 0.7028 (mm-40) cc_final: 0.6791 (mm-40) outliers start: 95 outliers final: 79 residues processed: 453 average time/residue: 0.1971 time to fit residues: 147.3467 Evaluate side-chains 449 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 366 time to evaluate : 1.266 ------------------------------------------------------------------------------- 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 39 LEU Chi-restraints excluded: chain 1 residue 50 VAL Chi-restraints excluded: chain 1 residue 202 THR Chi-restraints excluded: chain 1 residue 220 VAL Chi-restraints excluded: chain 1 residue 346 VAL Chi-restraints excluded: chain 1 residue 362 VAL Chi-restraints excluded: chain 1 residue 369 THR 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 552 VAL Chi-restraints excluded: chain 1 residue 582 ILE Chi-restraints excluded: chain 1 residue 590 LEU 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 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 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 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 174 VAL Chi-restraints excluded: chain 7 residue 180 VAL Chi-restraints excluded: chain 7 residue 192 VAL Chi-restraints excluded: chain 7 residue 244 VAL Chi-restraints excluded: chain 7 residue 381 VAL Chi-restraints excluded: chain 7 residue 390 ASP 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 593 ILE Chi-restraints excluded: chain 7 residue 609 ILE Chi-restraints excluded: chain 7 residue 650 LEU Chi-restraints excluded: chain 7 residue 700 LEU Chi-restraints excluded: chain 8 residue 99 THR Chi-restraints excluded: chain 8 residue 133 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 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 461 VAL Chi-restraints excluded: chain 9 residue 488 SER Chi-restraints excluded: chain 9 residue 531 LEU Chi-restraints excluded: chain 9 residue 546 HIS 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 111 THR Chi-restraints excluded: chain 3 residue 112 LEU 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: 5.9990 chunk 160 optimal weight: 3.9990 chunk 231 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 101 optimal weight: 8.9990 chunk 146 optimal weight: 5.9990 chunk 153 optimal weight: 10.0000 chunk 50 optimal weight: 0.0970 chunk 213 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.160035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.136981 restraints weight = 48504.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.136756 restraints weight = 57092.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.138007 restraints weight = 50740.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.137971 restraints weight = 35358.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.138267 restraints weight = 36033.423| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 32289 Z= 0.157 Angle : 0.625 14.358 43700 Z= 0.317 Chirality : 0.044 0.205 4974 Planarity : 0.004 0.051 5596 Dihedral : 5.619 141.172 4309 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 2.75 % Allowed : 21.40 % Favored : 75.85 % 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: 1374 sheet: -0.93 (0.17), residues: 990 loop : -1.86 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 2 216 TYR 0.030 0.002 TYR 5 131 PHE 0.023 0.002 PHE 4 413 TRP 0.031 0.002 TRP 3 176 HIS 0.015 0.001 HIS 3 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (32289) covalent geometry : angle 0.62464 / 0.32 (43700) hydrogen bonds : bond 0.03891 / 2.56 ( 1505) hydrogen bonds : angle 4.60906 / 3.16 ( 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 458 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 362 time to evaluate : 1.122 Fit side-chains REVERT: 1 11 MET cc_start: 0.7820 (mmp) cc_final: 0.7263 (ptm) REVERT: 1 274 ILE cc_start: 0.7731 (pt) cc_final: 0.7154 (mp) REVERT: 1 426 ASN cc_start: 0.6715 (t0) cc_final: 0.6367 (t0) REVERT: 2 229 TYR cc_start: 0.8432 (OUTLIER) cc_final: 0.8016 (m-80) REVERT: 2 299 MET cc_start: 0.8196 (mmm) cc_final: 0.7740 (mmm) REVERT: 5 93 GLU cc_start: 0.6279 (mm-30) cc_final: 0.5727 (mm-30) REVERT: 7 441 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8118 (tp) REVERT: 7 461 ILE cc_start: 0.7327 (OUTLIER) cc_final: 0.7017 (mp) REVERT: 7 506 MET cc_start: 0.7462 (tpp) cc_final: 0.7050 (tpp) REVERT: 7 671 TYR cc_start: 0.8155 (m-10) cc_final: 0.7505 (m-80) REVERT: 7 700 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7154 (mt) REVERT: 8 171 TYR cc_start: 0.7546 (m-80) cc_final: 0.6757 (m-10) REVERT: 8 258 ASP cc_start: 0.7769 (t70) cc_final: 0.7428 (t70) REVERT: 8 265 ASN cc_start: 0.7813 (m-40) cc_final: 0.7460 (m110) REVERT: 8 293 ASN cc_start: 0.8299 (p0) cc_final: 0.7943 (p0) REVERT: 8 466 ASP cc_start: 0.8218 (t0) cc_final: 0.7929 (t70) REVERT: 9 480 GLU cc_start: 0.6713 (mm-30) cc_final: 0.6288 (tm-30) REVERT: 9 686 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.7002 (t70) REVERT: 3 73 GLN cc_start: 0.7661 (mm-40) cc_final: 0.7432 (mm-40) REVERT: 3 78 ASN cc_start: 0.6510 (m110) cc_final: 0.6118 (m110) REVERT: 3 171 GLN cc_start: 0.7086 (mm-40) cc_final: 0.6838 (mm-40) outliers start: 96 outliers final: 85 residues processed: 440 average time/residue: 0.1831 time to fit residues: 134.1104 Evaluate side-chains 450 residues out of total 3495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 360 time to evaluate : 1.295 ------------------------------------------------------------------------------- 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 39 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 220 VAL Chi-restraints excluded: chain 1 residue 246 SER Chi-restraints excluded: chain 1 residue 346 VAL Chi-restraints excluded: chain 1 residue 362 VAL Chi-restraints excluded: chain 1 residue 369 THR 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 552 VAL Chi-restraints excluded: chain 1 residue 582 ILE Chi-restraints excluded: chain 1 residue 590 LEU 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 228 VAL 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 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 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 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 11 LEU 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 244 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 593 ILE Chi-restraints excluded: chain 7 residue 609 ILE Chi-restraints excluded: chain 7 residue 650 LEU Chi-restraints excluded: chain 7 residue 700 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 251 VAL 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 461 VAL Chi-restraints excluded: chain 9 residue 488 SER Chi-restraints excluded: chain 9 residue 531 LEU 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 82 HIS Chi-restraints excluded: chain 3 residue 111 THR Chi-restraints excluded: chain 3 residue 112 LEU 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: 2.9990 chunk 2 optimal weight: 1.9990 chunk 263 optimal weight: 0.6980 chunk 220 optimal weight: 10.0000 chunk 47 optimal weight: 0.6980 chunk 255 optimal weight: 2.9990 chunk 202 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 267 optimal weight: 0.8980 chunk 349 optimal weight: 5.9990 chunk 297 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 1 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 36 GLN 2 343 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.160906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.137887 restraints weight = 48571.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.137857 restraints weight = 56724.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.138871 restraints weight = 51797.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.139075 restraints weight = 35844.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.139257 restraints weight = 35479.204| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 32289 Z= 0.143 Angle : 0.614 14.287 43700 Z= 0.311 Chirality : 0.044 0.203 4974 Planarity : 0.004 0.051 5596 Dihedral : 5.570 143.060 4309 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.15 % Allowed : 21.03 % Favored : 75.82 % 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: -0.48 (0.14), residues: 3944 helix: 1.72 (0.14), residues: 1377 sheet: -0.84 (0.17), residues: 982 loop : -1.84 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 5 129 TYR 0.037 0.001 TYR 3 83 PHE 0.022 0.002 PHE 7 58 TRP 0.029 0.001 TRP 3 176 HIS 0.017 0.001 HIS 3 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (32289) covalent geometry : angle 0.61408 / 0.31 (43700) hydrogen bonds : bond 0.03810 / 2.50 ( 1505) hydrogen bonds : angle 4.56758 / 3.13 ( 4317) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5282.78 seconds wall clock time: 92 minutes 41.95 seconds (5561.95 seconds total)