Starting phenix.real_space_refine on Sun Aug 9 14:40:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r65_18947/08_2026/8r65_18947.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r65_18947/08_2026/8r65_18947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r65_18947/08_2026/8r65_18947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r65_18947/08_2026/8r65_18947.map" model { file = "/net/cci-nas-00/data/ceres_data/8r65_18947/08_2026/8r65_18947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r65_18947/08_2026/8r65_18947.cif" } resolution = 4.23 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= 0.003 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 26 5.49 5 S 124 5.16 5 C 11292 2.51 5 N 3161 2.21 5 O 3476 1.98 5 H 17462 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35541 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 11519 Classifications: {'peptide': 716} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 31, 'TRANS': 684} Chain: "C" Number of atoms: 11651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 11651 Classifications: {'peptide': 737} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 29, 'TRANS': 707} Chain: "D" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 491 Classifications: {'RNA': 15} Modifications used: {'3*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 3} Link IDs: {'rna2p': 3, 'rna3p': 11} Chain: "E" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 255 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 6} Chain: "X" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 197 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 7, 'TRANS': 17} Chain: "B" Number of atoms: 11428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 718, 11428 Classifications: {'peptide': 718} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 30, 'TRANS': 687} Chain breaks: 2 Time building chain proxies: 4.56, per 1000 atoms: 0.13 Number of scatterers: 35541 At special positions: 0 Unit cell: (133.35, 114.45, 143.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 124 16.00 P 26 15.00 O 3476 8.00 N 3161 7.00 C 11292 6.00 H 17462 1.00 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: 3.05 Conformation dependent library (CDL) restraints added in 973.2 milliseconds 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4134 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 24 sheets defined 47.3% alpha, 10.7% beta 2 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 5.11 Creating SS restraints... Processing helix chain 'A' and resid 1 through 9 removed outlier: 3.641A pdb=" N VAL A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE A 9 " --> pdb=" O VAL A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 25 Processing helix chain 'A' and resid 31 through 50 Processing helix chain 'A' and resid 83 through 99 Processing helix chain 'A' and resid 126 through 138 Processing helix chain 'A' and resid 164 through 186 Processing helix chain 'A' and resid 187 through 194 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.880A pdb=" N SER A 247 " --> pdb=" O GLU A 243 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 312 Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 405 through 414 removed outlier: 3.685A pdb=" N SER A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 452 removed outlier: 3.962A pdb=" N HIS A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 476 removed outlier: 3.766A pdb=" N GLU A 457 " --> pdb=" O CYS A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 580 removed outlier: 3.658A pdb=" N LYS A 576 " --> pdb=" O LYS A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 603 removed outlier: 4.061A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 613 Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 3.771A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 694 removed outlier: 3.657A pdb=" N LEU A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N CYS A 693 " --> pdb=" O ALA A 689 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU A 694 " --> pdb=" O ILE A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 714 Processing helix chain 'C' and resid 2 through 13 removed outlier: 4.272A pdb=" N GLN C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 62 through 67 Processing helix chain 'C' and resid 92 through 103 removed outlier: 3.803A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 115 through 127 removed outlier: 3.501A pdb=" N PHE C 119 " --> pdb=" O TYR C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 168 Processing helix chain 'C' and resid 169 through 173 removed outlier: 3.704A pdb=" N VAL C 172 " --> pdb=" O PRO C 169 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY C 173 " --> pdb=" O ASN C 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 169 through 173' Processing helix chain 'C' and resid 179 through 193 Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 225 through 231 removed outlier: 4.121A pdb=" N VAL C 231 " --> pdb=" O VAL C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 273 removed outlier: 3.877A pdb=" N VAL C 272 " --> pdb=" O ARG C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 285 Processing helix chain 'C' and resid 294 through 301 Processing helix chain 'C' and resid 305 through 315 Processing helix chain 'C' and resid 390 through 406 removed outlier: 3.652A pdb=" N GLN C 406 " --> pdb=" O MET C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 412 Processing helix chain 'C' and resid 429 through 438 Processing helix chain 'C' and resid 442 through 450 removed outlier: 4.789A pdb=" N GLY C 450 " --> pdb=" O PHE C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 460 removed outlier: 3.959A pdb=" N GLY C 459 " --> pdb=" O ASN C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 556 Processing helix chain 'C' and resid 556 through 564 removed outlier: 4.355A pdb=" N ILE C 562 " --> pdb=" O GLU C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 573 Processing helix chain 'C' and resid 577 through 582 Processing helix chain 'C' and resid 588 through 606 removed outlier: 3.658A pdb=" N TYR C 592 " --> pdb=" O ALA C 588 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C 606 " --> pdb=" O GLN C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 619 Processing helix chain 'C' and resid 620 through 622 No H-bonds generated for 'chain 'C' and resid 620 through 622' Processing helix chain 'C' and resid 709 through 713 removed outlier: 4.029A pdb=" N LEU C 713 " --> pdb=" O ILE C 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 11 Processing helix chain 'B' and resid 17 through 22 removed outlier: 3.592A pdb=" N PHE B 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 removed outlier: 3.785A pdb=" N MET B 40 " --> pdb=" O THR B 36 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 118 through 124 Processing helix chain 'B' and resid 138 through 153 Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 162 through 175 removed outlier: 3.507A pdb=" N MET B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP B 175 " --> pdb=" O MET B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 248 through 265 removed outlier: 3.801A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 293 removed outlier: 3.519A pdb=" N ASN B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 313 removed outlier: 3.549A pdb=" N ASN B 312 " --> pdb=" O TRP B 309 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN B 313 " --> pdb=" O ASN B 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 309 through 313' Processing helix chain 'B' and resid 314 through 326 removed outlier: 3.600A pdb=" N PHE B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 345 removed outlier: 4.761A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 369 through 374 removed outlier: 3.827A pdb=" N ALA B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 393 Processing helix chain 'B' and resid 412 through 426 Processing helix chain 'B' and resid 455 through 473 Processing helix chain 'B' and resid 508 through 512 Processing helix chain 'B' and resid 518 through 536 Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 585 through 589 removed outlier: 3.860A pdb=" N LEU B 589 " --> pdb=" O LYS B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 662 through 666 removed outlier: 3.912A pdb=" N TRP B 666 " --> pdb=" O THR B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 677 removed outlier: 3.787A pdb=" N LEU B 675 " --> pdb=" O ARG B 672 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN B 676 " --> pdb=" O SER B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 700 removed outlier: 4.229A pdb=" N GLU B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 704 removed outlier: 4.034A pdb=" N SER B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 701 through 704' Processing helix chain 'B' and resid 713 through 732 Processing helix chain 'B' and resid 736 through 756 Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.312A pdb=" N PHE A 117 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N HIS A 146 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N GLU A 119 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N PHE A 148 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLY A 121 " --> pdb=" O PHE A 148 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET A 155 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AA3, first strand: chain 'A' and resid 292 through 293 Processing sheet with id=AA4, first strand: chain 'A' and resid 317 through 322 removed outlier: 5.862A pdb=" N ILE A 545 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N LEU A 543 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU A 524 " --> pdb=" O TYR A 564 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 521 " --> pdb=" O ILE A 505 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 317 through 322 removed outlier: 5.862A pdb=" N ILE A 545 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N LEU A 543 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU A 524 " --> pdb=" O TYR A 564 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 570 " --> pdb=" O VAL A 518 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 377 through 379 removed outlier: 4.024A pdb=" N GLN B 367 " --> pdb=" O VAL A 379 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 619 through 624 removed outlier: 4.476A pdb=" N GLU A 629 " --> pdb=" O ILE A 621 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLU A 623 " --> pdb=" O GLY A 627 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLY A 627 " --> pdb=" O GLU A 623 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 78 through 82 removed outlier: 3.767A pdb=" N MET C 90 " --> pdb=" O SER C 79 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE B 667 " --> pdb=" O THR C 58 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 129 through 135 removed outlier: 6.052A pdb=" N PHE C 130 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR C 245 " --> pdb=" O PHE C 130 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N MET C 243 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 143 through 146 Processing sheet with id=AB2, first strand: chain 'C' and resid 292 through 293 Processing sheet with id=AB3, first strand: chain 'C' and resid 324 through 325 Processing sheet with id=AB4, first strand: chain 'C' and resid 331 through 334 removed outlier: 6.143A pdb=" N GLU C 362 " --> pdb=" O THR C 333 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR C 371 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N VAL C 386 " --> pdb=" O THR C 371 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE C 373 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEU C 384 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ARG C 375 " --> pdb=" O ILE C 382 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 342 through 345 Processing sheet with id=AB6, first strand: chain 'C' and resid 452 through 453 removed outlier: 3.737A pdb=" N SER C 474 " --> pdb=" O GLU C 452 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 504 through 505 removed outlier: 6.497A pdb=" N VAL C 504 " --> pdb=" O LEU C 512 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 635 through 639 Processing sheet with id=AB9, first strand: chain 'C' and resid 656 through 658 removed outlier: 5.762A pdb=" N LEU C 665 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 694 through 699 removed outlier: 6.913A pdb=" N LEU C 733 " --> pdb=" O LEU C 697 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N LYS C 699 " --> pdb=" O VAL C 731 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N VAL C 731 " --> pdb=" O LYS C 699 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AC3, first strand: chain 'B' and resid 128 through 129 Processing sheet with id=AC4, first strand: chain 'B' and resid 178 through 181 Processing sheet with id=AC5, first strand: chain 'B' and resid 240 through 244 removed outlier: 6.388A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 437 through 443 removed outlier: 3.615A pdb=" N ALA B 453 " --> pdb=" O LEU B 298 " (cutoff:3.500A) 796 hydrogen bonds defined for protein. 2214 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 5 hydrogen bonds 10 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 7.68 Time building geometry restraints manager: 4.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.00: 17432 1.00 - 1.21: 31 1.21 - 1.41: 7434 1.41 - 1.61: 10824 1.61 - 1.81: 221 Bond restraints: 35942 Sorted by residual: bond pdb=" C ILE C 319 " pdb=" O ILE C 319 " ideal model delta sigma weight residual 1.235 1.164 0.072 1.05e-02 9.07e+03 4.67e+01 bond pdb=" N ILE C 319 " pdb=" CA ILE C 319 " ideal model delta sigma weight residual 1.457 1.503 -0.046 1.15e-02 7.56e+03 1.63e+01 bond pdb=" N SER C 320 " pdb=" CA SER C 320 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.14e-02 7.69e+03 1.05e+01 bond pdb=" N VAL C 494 " pdb=" CA VAL C 494 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.94e+00 bond pdb=" NE2 GLN C 426 " pdb="HE22 GLN C 426 " ideal model delta sigma weight residual 0.860 0.803 0.057 2.00e-02 2.50e+03 8.02e+00 ... (remaining 35937 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.26: 64757 5.26 - 10.51: 15 10.51 - 15.77: 5 15.77 - 21.03: 3 21.03 - 26.29: 3 Bond angle restraints: 64783 Sorted by residual: angle pdb=" N MET C 536 " pdb=" CA MET C 536 " pdb=" C MET C 536 " ideal model delta sigma weight residual 108.07 121.75 -13.68 1.38e+00 5.25e-01 9.83e+01 angle pdb=" C MET C 536 " pdb=" CA MET C 536 " pdb=" HA MET C 536 " ideal model delta sigma weight residual 110.00 83.71 26.29 3.00e+00 1.11e-01 7.68e+01 angle pdb=" N MET C 536 " pdb=" CA MET C 536 " pdb=" HA MET C 536 " ideal model delta sigma weight residual 110.00 83.87 26.13 3.00e+00 1.11e-01 7.59e+01 angle pdb=" N PRO C 542 " pdb=" CA PRO C 542 " pdb=" C PRO C 542 " ideal model delta sigma weight residual 113.53 102.89 10.64 1.39e+00 5.18e-01 5.86e+01 angle pdb=" CB MET C 536 " pdb=" CA MET C 536 " pdb=" HA MET C 536 " ideal model delta sigma weight residual 109.00 86.32 22.68 3.00e+00 1.11e-01 5.72e+01 ... (remaining 64778 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 15281 17.93 - 35.86: 1158 35.86 - 53.79: 336 53.79 - 71.71: 118 71.71 - 89.64: 28 Dihedral angle restraints: 16921 sinusoidal: 9540 harmonic: 7381 Sorted by residual: dihedral pdb=" C MET C 536 " pdb=" N MET C 536 " pdb=" CA MET C 536 " pdb=" CB MET C 536 " ideal model delta harmonic sigma weight residual -122.60 -161.29 38.69 0 2.50e+00 1.60e-01 2.39e+02 dihedral pdb=" N MET C 536 " pdb=" C MET C 536 " pdb=" CA MET C 536 " pdb=" CB MET C 536 " ideal model delta harmonic sigma weight residual 122.80 161.21 -38.41 0 2.50e+00 1.60e-01 2.36e+02 dihedral pdb=" CD ARG C 493 " pdb=" NE ARG C 493 " pdb=" CZ ARG C 493 " pdb=" NH1 ARG C 493 " ideal model delta sinusoidal sigma weight residual 0.00 -39.85 39.85 1 1.00e+01 1.00e-02 2.23e+01 ... (remaining 16918 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.332: 2769 0.332 - 0.663: 0 0.663 - 0.995: 0 0.995 - 1.327: 0 1.327 - 1.658: 1 Chirality restraints: 2770 Sorted by residual: chirality pdb=" CA MET C 536 " pdb=" N MET C 536 " pdb=" C MET C 536 " pdb=" CB MET C 536 " both_signs ideal model delta sigma weight residual False 2.51 0.85 1.66 2.00e-01 2.50e+01 6.87e+01 chirality pdb=" CA ILE C 319 " pdb=" N ILE C 319 " pdb=" C ILE C 319 " pdb=" CB ILE C 319 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA VAL C 495 " pdb=" N VAL C 495 " pdb=" C VAL C 495 " pdb=" CB VAL C 495 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 2767 not shown) Planarity restraints: 5236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 641 " 0.413 9.50e-02 1.11e+02 4.66e-01 4.48e+03 pdb=" NE ARG C 641 " 0.117 2.00e-02 2.50e+03 pdb=" CZ ARG C 641 " 0.032 2.00e-02 2.50e+03 pdb=" NH1 ARG C 641 " 0.027 2.00e-02 2.50e+03 pdb=" NH2 ARG C 641 " -0.061 2.00e-02 2.50e+03 pdb="HH11 ARG C 641 " -0.543 2.00e-02 2.50e+03 pdb="HH12 ARG C 641 " 0.592 2.00e-02 2.50e+03 pdb="HH21 ARG C 641 " -0.834 2.00e-02 2.50e+03 pdb="HH22 ARG C 641 " 0.652 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 548 " 0.048 2.00e-02 2.50e+03 4.40e-01 2.91e+03 pdb=" CG ASN C 548 " -0.007 2.00e-02 2.50e+03 pdb=" OD1 ASN C 548 " -0.046 2.00e-02 2.50e+03 pdb=" ND2 ASN C 548 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN C 548 " 0.764 2.00e-02 2.50e+03 pdb="HD22 ASN C 548 " -0.759 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 493 " -0.676 9.50e-02 1.11e+02 2.60e-01 4.31e+02 pdb=" NE ARG C 493 " 0.069 2.00e-02 2.50e+03 pdb=" CZ ARG C 493 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG C 493 " -0.029 2.00e-02 2.50e+03 pdb=" NH2 ARG C 493 " 0.018 2.00e-02 2.50e+03 pdb="HH11 ARG C 493 " -0.200 2.00e-02 2.50e+03 pdb="HH12 ARG C 493 " 0.113 2.00e-02 2.50e+03 pdb="HH21 ARG C 493 " 0.237 2.00e-02 2.50e+03 pdb="HH22 ARG C 493 " -0.194 2.00e-02 2.50e+03 ... (remaining 5233 not shown) Histogram of nonbonded interaction distances: 1.01 - 1.73: 58 1.73 - 2.45: 21426 2.45 - 3.17: 108856 3.17 - 3.88: 141016 3.88 - 4.60: 227413 Nonbonded interactions: 498769 Sorted by model distance: nonbonded pdb=" H GLY C 223 " pdb=" OE2 GLU C 525 " model vdw 1.014 2.450 nonbonded pdb=" HE1 HIS A 437 " pdb="HH12 ARG C 646 " model vdw 1.085 2.100 nonbonded pdb="HH12 ARG C 143 " pdb=" OG1 THR C 524 " model vdw 1.216 2.450 nonbonded pdb=" HB3 PRO C 276 " pdb="HD11 LEU C 502 " model vdw 1.338 2.440 nonbonded pdb="HH22 ARG C 143 " pdb="HG21 THR C 524 " model vdw 1.354 2.270 ... (remaining 498764 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: 1.010 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: 0.230 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 32.960 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 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 : 0.005 0.086 18480 Z= 0.244 Angle : 0.629 13.679 25043 Z= 0.374 Chirality : 0.054 1.658 2770 Planarity : 0.007 0.307 3147 Dihedral : 14.382 89.080 7214 Min Nonbonded Distance : 1.637 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.71 % Favored : 92.78 % Rotamer: Outliers : 1.85 % Allowed : 6.85 % Favored : 91.29 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.18), residues: 2175 helix: 1.04 (0.17), residues: 944 sheet: -2.50 (0.32), residues: 221 loop : -1.99 (0.18), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 505 TYR 0.011 0.001 TYR B 555 PHE 0.020 0.001 PHE C 323 TRP 0.014 0.001 TRP C 537 HIS 0.005 0.001 HIS C 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.24 (18480) covalent geometry : angle 0.62923 / 0.37 (25043) hydrogen bonds : bond 0.16723 / 11.20 ( 792) hydrogen bonds : angle 6.42830 / 4.58 ( 2224) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 108 is missing expected H atoms. Skipping. Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue VAL 655 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue ALA 674 is missing expected H atoms. Skipping. Residue THR 676 is missing expected H atoms. Skipping. Residue ALA 684 is missing expected H atoms. Skipping. Evaluate side-chains 485 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 449 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8901 (ptm) cc_final: 0.8505 (tpt) REVERT: A 540 TYR cc_start: 0.8608 (m-80) cc_final: 0.8063 (m-80) REVERT: A 584 CYS cc_start: 0.9378 (m) cc_final: 0.9127 (m) REVERT: A 587 GLN cc_start: 0.9419 (tt0) cc_final: 0.9058 (tp-100) REVERT: A 594 SER cc_start: 0.9898 (t) cc_final: 0.9680 (p) REVERT: A 649 LEU cc_start: 0.9086 (mt) cc_final: 0.8877 (mt) REVERT: C 26 ASP cc_start: 0.8215 (m-30) cc_final: 0.7844 (m-30) REVERT: C 69 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8594 (tp30) REVERT: C 90 MET cc_start: 0.9378 (mmm) cc_final: 0.9157 (mmm) REVERT: C 153 ASP cc_start: 0.8865 (t70) cc_final: 0.7974 (m-30) REVERT: C 164 MET cc_start: 0.9138 (mtp) cc_final: 0.8933 (ptt) REVERT: C 429 ASN cc_start: 0.6692 (t0) cc_final: 0.6439 (m-40) REVERT: C 483 MET cc_start: 0.6425 (mmp) cc_final: 0.6136 (ptp) REVERT: B 131 TRP cc_start: 0.8706 (p-90) cc_final: 0.7715 (p-90) REVERT: B 137 GLN cc_start: 0.9525 (mm-40) cc_final: 0.9290 (mp10) REVERT: B 303 THR cc_start: 0.7790 (OUTLIER) cc_final: 0.7490 (p) REVERT: B 450 ILE cc_start: 0.9648 (mt) cc_final: 0.9441 (tp) REVERT: B 508 GLU cc_start: 0.9253 (mp0) cc_final: 0.8935 (mp0) REVERT: B 519 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8625 (mt-10) REVERT: B 538 ASP cc_start: 0.9650 (m-30) cc_final: 0.9292 (p0) REVERT: B 599 TYR cc_start: 0.9272 (m-80) cc_final: 0.8621 (m-80) REVERT: B 606 ILE cc_start: 0.8709 (mt) cc_final: 0.8197 (mp) REVERT: B 657 TYR cc_start: 0.8920 (p90) cc_final: 0.8047 (p90) REVERT: B 687 GLN cc_start: 0.9189 (OUTLIER) cc_final: 0.8597 (mm-40) outliers start: 36 outliers final: 15 residues processed: 478 average time/residue: 0.3412 time to fit residues: 234.1419 Evaluate side-chains 340 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 322 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 10.0000 chunk 212 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 ASN C 27 HIS C 100 ASN ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 456 ASN B 136 ASN ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 ASN B 532 ASN B 567 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.108002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.095834 restraints weight = 487503.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.098184 restraints weight = 233048.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.099564 restraints weight = 131962.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.100332 restraints weight = 85004.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.100782 restraints weight = 61816.525| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.127 18480 Z= 0.299 Angle : 0.686 7.319 25043 Z= 0.385 Chirality : 0.042 0.483 2770 Planarity : 0.006 0.082 3147 Dihedral : 10.039 85.895 2762 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.84 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.12 (0.17), residues: 2175 helix: 0.77 (0.16), residues: 952 sheet: -2.24 (0.31), residues: 224 loop : -1.91 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 583 TYR 0.023 0.002 TYR C 228 PHE 0.054 0.003 PHE B 333 TRP 0.026 0.002 TRP C 537 HIS 0.010 0.002 HIS C 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.30 (18480) covalent geometry : angle 0.68611 / 0.39 (25043) hydrogen bonds : bond 0.05674 / 3.72 ( 792) hydrogen bonds : angle 5.59537 / 3.96 ( 2224) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 108 is missing expected H atoms. Skipping. Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue VAL 655 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue ALA 674 is missing expected H atoms. Skipping. Residue THR 676 is missing expected H atoms. Skipping. Residue ALA 684 is missing expected H atoms. Skipping. Evaluate side-chains 337 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 MET cc_start: 0.9480 (mmp) cc_final: 0.9179 (mmm) REVERT: A 360 MET cc_start: 0.6308 (mmm) cc_final: 0.6009 (mmm) REVERT: A 460 MET cc_start: 0.9114 (ttp) cc_final: 0.8855 (tmm) REVERT: A 511 LEU cc_start: 0.9575 (mp) cc_final: 0.9202 (mp) REVERT: A 572 LYS cc_start: 0.9364 (ttmt) cc_final: 0.8902 (mtmt) REVERT: A 575 MET cc_start: 0.9333 (mtm) cc_final: 0.8994 (mtm) REVERT: A 581 MET cc_start: 0.9036 (ttm) cc_final: 0.8483 (ttm) REVERT: A 584 CYS cc_start: 0.9357 (m) cc_final: 0.9087 (m) REVERT: A 587 GLN cc_start: 0.9437 (tt0) cc_final: 0.9012 (tp-100) REVERT: A 607 MET cc_start: 0.8950 (mmt) cc_final: 0.8290 (mmm) REVERT: A 661 GLU cc_start: 0.9533 (mm-30) cc_final: 0.9329 (mt-10) REVERT: A 664 LYS cc_start: 0.9497 (tppp) cc_final: 0.9286 (tmtt) REVERT: A 694 LEU cc_start: 0.8540 (mt) cc_final: 0.8259 (mm) REVERT: C 46 ARG cc_start: 0.9307 (mmm160) cc_final: 0.8375 (tpp-160) REVERT: C 90 MET cc_start: 0.9468 (mtp) cc_final: 0.9246 (mmm) REVERT: C 164 MET cc_start: 0.9198 (mtp) cc_final: 0.8653 (ptt) REVERT: C 483 MET cc_start: 0.6510 (mmp) cc_final: 0.6157 (mtp) REVERT: B 111 MET cc_start: 0.7368 (mtp) cc_final: 0.6980 (mtt) REVERT: B 131 TRP cc_start: 0.8884 (p-90) cc_final: 0.8414 (p-90) REVERT: B 137 GLN cc_start: 0.9535 (mm-40) cc_final: 0.9075 (mp10) REVERT: B 251 PHE cc_start: 0.9429 (m-80) cc_final: 0.8999 (m-80) REVERT: B 321 MET cc_start: 0.9524 (mtt) cc_final: 0.9054 (mtt) REVERT: B 414 MET cc_start: 0.7430 (mmm) cc_final: 0.7148 (tpp) REVERT: B 415 LEU cc_start: 0.9447 (tp) cc_final: 0.9179 (tp) REVERT: B 508 GLU cc_start: 0.8774 (mp0) cc_final: 0.8532 (mp0) REVERT: B 519 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8682 (mt-10) REVERT: B 527 VAL cc_start: 0.9621 (t) cc_final: 0.9286 (p) REVERT: B 546 MET cc_start: 0.9406 (mmp) cc_final: 0.8976 (mmp) REVERT: B 599 TYR cc_start: 0.9134 (m-80) cc_final: 0.8559 (m-10) REVERT: B 606 ILE cc_start: 0.8890 (mt) cc_final: 0.8470 (mp) REVERT: B 690 GLN cc_start: 0.9069 (pt0) cc_final: 0.8644 (pt0) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.3272 time to fit residues: 159.6696 Evaluate side-chains 285 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 186 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 160 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 158 optimal weight: 1.9990 chunk 142 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 104 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 ASN ** C 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.108741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.096708 restraints weight = 484737.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.099003 restraints weight = 230505.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.100331 restraints weight = 129559.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.101100 restraints weight = 83780.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.101566 restraints weight = 60380.792| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 18480 Z= 0.141 Angle : 0.551 6.174 25043 Z= 0.299 Chirality : 0.039 0.423 2770 Planarity : 0.004 0.057 3147 Dihedral : 9.961 85.693 2762 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.56 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.18), residues: 2175 helix: 0.98 (0.17), residues: 961 sheet: -1.98 (0.31), residues: 226 loop : -1.87 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 706 TYR 0.012 0.001 TYR C 228 PHE 0.030 0.002 PHE A 446 TRP 0.012 0.001 TRP A 619 HIS 0.003 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (18480) covalent geometry : angle 0.55132 / 0.30 (25043) hydrogen bonds : bond 0.04662 / 3.09 ( 792) hydrogen bonds : angle 5.06514 / 3.63 ( 2224) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 108 is missing expected H atoms. Skipping. Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue VAL 655 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue ALA 674 is missing expected H atoms. Skipping. Residue THR 676 is missing expected H atoms. Skipping. Residue ALA 684 is missing expected H atoms. Skipping. Evaluate side-chains 317 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 MET cc_start: 0.9358 (ttp) cc_final: 0.9025 (ttp) REVERT: A 311 MET cc_start: 0.9481 (mmp) cc_final: 0.9188 (mmp) REVERT: A 360 MET cc_start: 0.6280 (mmm) cc_final: 0.5911 (mmm) REVERT: A 460 MET cc_start: 0.9104 (ttp) cc_final: 0.8868 (tmm) REVERT: A 581 MET cc_start: 0.8988 (ttm) cc_final: 0.8513 (ttm) REVERT: A 584 CYS cc_start: 0.9263 (m) cc_final: 0.8985 (m) REVERT: A 587 GLN cc_start: 0.9386 (tt0) cc_final: 0.8849 (mm110) REVERT: A 607 MET cc_start: 0.9010 (mmt) cc_final: 0.8514 (mmm) REVERT: A 661 GLU cc_start: 0.9510 (mm-30) cc_final: 0.9299 (mt-10) REVERT: A 664 LYS cc_start: 0.9480 (tppp) cc_final: 0.9258 (tmtt) REVERT: C 46 ARG cc_start: 0.9195 (mmm160) cc_final: 0.8384 (tpp-160) REVERT: C 483 MET cc_start: 0.6574 (mmp) cc_final: 0.6239 (mtp) REVERT: B 137 GLN cc_start: 0.9505 (mm-40) cc_final: 0.9113 (mp10) REVERT: B 179 MET cc_start: 0.9233 (mmt) cc_final: 0.8812 (mpp) REVERT: B 251 PHE cc_start: 0.9510 (m-80) cc_final: 0.9074 (m-80) REVERT: B 348 MET cc_start: 0.9126 (mmt) cc_final: 0.8707 (mmt) REVERT: B 356 MET cc_start: 0.8117 (ttt) cc_final: 0.7863 (ttt) REVERT: B 408 MET cc_start: 0.7583 (tpt) cc_final: 0.7056 (tpt) REVERT: B 519 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8695 (mt-10) REVERT: B 527 VAL cc_start: 0.9634 (t) cc_final: 0.9247 (p) REVERT: B 599 TYR cc_start: 0.9112 (m-80) cc_final: 0.8479 (m-10) REVERT: B 606 ILE cc_start: 0.8890 (mt) cc_final: 0.8422 (mp) REVERT: B 657 TYR cc_start: 0.8893 (p90) cc_final: 0.8127 (p90) outliers start: 0 outliers final: 0 residues processed: 317 average time/residue: 0.3351 time to fit residues: 155.0988 Evaluate side-chains 277 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 180 optimal weight: 10.0000 chunk 139 optimal weight: 20.0000 chunk 136 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 118 optimal weight: 30.0000 chunk 146 optimal weight: 30.0000 chunk 170 optimal weight: 10.0000 chunk 27 optimal weight: 0.0470 chunk 201 optimal weight: 10.0000 chunk 82 optimal weight: 0.9990 overall best weight: 6.2092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 HIS C 75 GLN ** C 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN B 582 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.079399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.058967 restraints weight = 332836.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.061809 restraints weight = 198852.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.063813 restraints weight = 133422.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.065207 restraints weight = 97721.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.066165 restraints weight = 76812.140| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 18480 Z= 0.272 Angle : 0.646 10.200 25043 Z= 0.358 Chirality : 0.040 0.410 2770 Planarity : 0.005 0.094 3147 Dihedral : 9.984 82.087 2762 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.93 % Favored : 93.93 % Rotamer: Outliers : 0.05 % Allowed : 1.55 % Favored : 98.40 % Cbeta Deviations : 0.05 % 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: -1.25 (0.17), residues: 2175 helix: 0.60 (0.16), residues: 958 sheet: -2.14 (0.31), residues: 241 loop : -1.95 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG C 213 TYR 0.024 0.002 TYR C 111 PHE 0.020 0.002 PHE B 512 TRP 0.038 0.002 TRP C 537 HIS 0.023 0.002 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.27 (18480) covalent geometry : angle 0.64574 / 0.36 (25043) hydrogen bonds : bond 0.04605 / 3.08 ( 792) hydrogen bonds : angle 5.20699 / 3.73 ( 2224) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 108 is missing expected H atoms. Skipping. Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue VAL 655 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue ALA 674 is missing expected H atoms. Skipping. Residue THR 676 is missing expected H atoms. Skipping. Residue ALA 684 is missing expected H atoms. Skipping. Evaluate side-chains 297 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 296 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 MET cc_start: 0.9629 (mmp) cc_final: 0.9264 (mmp) REVERT: A 360 MET cc_start: 0.6654 (mmm) cc_final: 0.6106 (mmm) REVERT: A 581 MET cc_start: 0.9191 (ttm) cc_final: 0.8742 (ttm) REVERT: A 587 GLN cc_start: 0.9414 (tt0) cc_final: 0.8977 (tp40) REVERT: A 607 MET cc_start: 0.8932 (mmt) cc_final: 0.8501 (mmm) REVERT: A 612 PHE cc_start: 0.8671 (m-80) cc_final: 0.8342 (m-10) REVERT: A 661 GLU cc_start: 0.9590 (mm-30) cc_final: 0.9373 (mm-30) REVERT: A 664 LYS cc_start: 0.9526 (tppp) cc_final: 0.9309 (tmtt) REVERT: C 46 ARG cc_start: 0.9361 (mmm160) cc_final: 0.8569 (tpp-160) REVERT: C 483 MET cc_start: 0.6833 (mmp) cc_final: 0.6291 (mtp) REVERT: B 137 GLN cc_start: 0.9496 (mm-40) cc_final: 0.9058 (mp10) REVERT: B 179 MET cc_start: 0.9389 (mmt) cc_final: 0.9158 (mmm) REVERT: B 356 MET cc_start: 0.8428 (ttt) cc_final: 0.8171 (ttt) REVERT: B 414 MET cc_start: 0.7646 (mmm) cc_final: 0.7374 (tpp) REVERT: B 477 MET cc_start: 0.8571 (mtm) cc_final: 0.8321 (mtm) REVERT: B 527 VAL cc_start: 0.9614 (t) cc_final: 0.9286 (p) REVERT: B 546 MET cc_start: 0.9461 (mmp) cc_final: 0.8990 (mmp) REVERT: B 599 TYR cc_start: 0.9256 (m-80) cc_final: 0.8693 (m-80) REVERT: B 606 ILE cc_start: 0.9041 (mt) cc_final: 0.8504 (mp) outliers start: 1 outliers final: 1 residues processed: 297 average time/residue: 0.2957 time to fit residues: 130.5039 Evaluate side-chains 263 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 262 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 35 optimal weight: 0.9980 chunk 119 optimal weight: 0.0070 chunk 5 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 139 optimal weight: 30.0000 chunk 194 optimal weight: 7.9990 chunk 148 optimal weight: 8.9990 chunk 213 optimal weight: 5.9990 chunk 159 optimal weight: 9.9990 overall best weight: 4.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 HIS ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 HIS B 136 ASN ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.080106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.060130 restraints weight = 338692.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.062966 restraints weight = 200340.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.064961 restraints weight = 133084.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.066380 restraints weight = 96973.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.067349 restraints weight = 75494.044| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.4656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 18480 Z= 0.198 Angle : 0.577 6.471 25043 Z= 0.322 Chirality : 0.039 0.394 2770 Planarity : 0.004 0.067 3147 Dihedral : 10.000 81.661 2762 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.70 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.05 % 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: -1.10 (0.18), residues: 2175 helix: 0.74 (0.16), residues: 956 sheet: -2.10 (0.31), residues: 239 loop : -1.88 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 442 TYR 0.016 0.001 TYR C 704 PHE 0.026 0.002 PHE B 333 TRP 0.012 0.001 TRP A 422 HIS 0.008 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.20 (18480) covalent geometry : angle 0.57718 / 0.32 (25043) hydrogen bonds : bond 0.04390 / 2.89 ( 792) hydrogen bonds : angle 5.08951 / 3.65 ( 2224) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 108 is missing expected H atoms. Skipping. Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue VAL 655 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue ALA 674 is missing expected H atoms. Skipping. Residue THR 676 is missing expected H atoms. Skipping. Residue ALA 684 is missing expected H atoms. Skipping. Evaluate side-chains 291 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 MET cc_start: 0.6736 (mmm) cc_final: 0.6127 (mmm) REVERT: A 446 PHE cc_start: 0.9378 (m-80) cc_final: 0.9148 (m-10) REVERT: A 587 GLN cc_start: 0.9406 (tt0) cc_final: 0.8977 (tp40) REVERT: A 607 MET cc_start: 0.8874 (mmt) cc_final: 0.8455 (mmm) REVERT: A 612 PHE cc_start: 0.8651 (m-80) cc_final: 0.8315 (m-10) REVERT: A 661 GLU cc_start: 0.9577 (mm-30) cc_final: 0.9335 (mt-10) REVERT: A 664 LYS cc_start: 0.9515 (tppp) cc_final: 0.9288 (tmtt) REVERT: C 46 ARG cc_start: 0.9327 (mmm160) cc_final: 0.8550 (tpp-160) REVERT: C 297 ILE cc_start: 0.8673 (tp) cc_final: 0.8414 (pt) REVERT: C 483 MET cc_start: 0.6921 (mmp) cc_final: 0.6616 (mtp) REVERT: B 137 GLN cc_start: 0.9486 (mm-40) cc_final: 0.9063 (mp10) REVERT: B 477 MET cc_start: 0.8553 (mtm) cc_final: 0.8341 (mtm) REVERT: B 527 VAL cc_start: 0.9648 (t) cc_final: 0.9447 (p) REVERT: B 546 MET cc_start: 0.9407 (mmp) cc_final: 0.8899 (mmp) REVERT: B 606 ILE cc_start: 0.9077 (mt) cc_final: 0.8824 (mp) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.3001 time to fit residues: 130.2502 Evaluate side-chains 261 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 53 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 153 optimal weight: 9.9990 chunk 143 optimal weight: 9.9990 chunk 188 optimal weight: 7.9990 chunk 196 optimal weight: 3.9990 chunk 162 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 165 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 ASN B 532 ASN ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.079411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.059075 restraints weight = 329393.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.061939 restraints weight = 195345.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.063954 restraints weight = 130423.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.065304 restraints weight = 95579.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.066239 restraints weight = 75416.244| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18480 Z= 0.134 Angle : 0.532 5.927 25043 Z= 0.289 Chirality : 0.039 0.392 2770 Planarity : 0.004 0.075 3147 Dihedral : 9.920 81.517 2762 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.33 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.05 % 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: -0.79 (0.18), residues: 2175 helix: 1.02 (0.16), residues: 957 sheet: -1.95 (0.31), residues: 234 loop : -1.74 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 638 TYR 0.011 0.001 TYR C 704 PHE 0.044 0.002 PHE C 330 TRP 0.009 0.001 TRP A 422 HIS 0.003 0.001 HIS A 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (18480) covalent geometry : angle 0.53217 / 0.29 (25043) hydrogen bonds : bond 0.04075 / 2.67 ( 792) hydrogen bonds : angle 4.94415 / 3.53 ( 2224) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 108 is missing expected H atoms. Skipping. Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue VAL 655 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue ALA 674 is missing expected H atoms. Skipping. Residue THR 676 is missing expected H atoms. Skipping. Residue ALA 684 is missing expected H atoms. Skipping. Evaluate side-chains 292 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 MET cc_start: 0.6647 (mmm) cc_final: 0.6061 (mmm) REVERT: A 446 PHE cc_start: 0.9339 (m-80) cc_final: 0.9110 (m-10) REVERT: A 581 MET cc_start: 0.9115 (ttm) cc_final: 0.8732 (ttm) REVERT: A 587 GLN cc_start: 0.9384 (tt0) cc_final: 0.8925 (tp40) REVERT: A 607 MET cc_start: 0.8782 (mmt) cc_final: 0.8422 (mmm) REVERT: A 612 PHE cc_start: 0.8639 (m-80) cc_final: 0.8353 (m-10) REVERT: A 661 GLU cc_start: 0.9575 (mm-30) cc_final: 0.9358 (mm-30) REVERT: A 664 LYS cc_start: 0.9508 (tppp) cc_final: 0.9286 (tmtt) REVERT: C 46 ARG cc_start: 0.9326 (mmm160) cc_final: 0.8527 (tpp-160) REVERT: C 297 ILE cc_start: 0.8649 (tp) cc_final: 0.8435 (pt) REVERT: C 483 MET cc_start: 0.6985 (mmp) cc_final: 0.6626 (mtp) REVERT: C 553 ILE cc_start: 0.8046 (tp) cc_final: 0.7795 (tp) REVERT: C 554 ILE cc_start: 0.6436 (mm) cc_final: 0.6221 (mm) REVERT: B 137 GLN cc_start: 0.9477 (mm-40) cc_final: 0.9060 (mp10) REVERT: B 348 MET cc_start: 0.9037 (mmt) cc_final: 0.8687 (mmt) REVERT: B 414 MET cc_start: 0.7825 (mmm) cc_final: 0.7491 (tpp) REVERT: B 477 MET cc_start: 0.8539 (mtm) cc_final: 0.8318 (mtm) REVERT: B 527 VAL cc_start: 0.9643 (t) cc_final: 0.9442 (p) REVERT: B 546 MET cc_start: 0.9386 (mmp) cc_final: 0.8864 (mmp) REVERT: B 593 ASP cc_start: 0.7366 (m-30) cc_final: 0.7139 (m-30) REVERT: B 606 ILE cc_start: 0.9103 (mt) cc_final: 0.8863 (mp) REVERT: B 664 HIS cc_start: 0.9020 (m-70) cc_final: 0.8594 (m-70) outliers start: 0 outliers final: 0 residues processed: 292 average time/residue: 0.2994 time to fit residues: 129.3788 Evaluate side-chains 259 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 26 optimal weight: 6.9990 chunk 193 optimal weight: 10.0000 chunk 161 optimal weight: 9.9990 chunk 76 optimal weight: 8.9990 chunk 182 optimal weight: 6.9990 chunk 216 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 chunk 99 optimal weight: 9.9990 chunk 152 optimal weight: 0.8980 chunk 111 optimal weight: 20.0000 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 236 GLN C 406 GLN ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 591 GLN B 136 ASN ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.078862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.058749 restraints weight = 329712.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.061487 restraints weight = 196596.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.063460 restraints weight = 132458.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.064806 restraints weight = 97351.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.065715 restraints weight = 76932.148| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 18480 Z= 0.168 Angle : 0.542 5.836 25043 Z= 0.297 Chirality : 0.038 0.389 2770 Planarity : 0.004 0.077 3147 Dihedral : 9.902 80.640 2762 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.66 % Favored : 94.25 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.05 % 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: -0.72 (0.18), residues: 2175 helix: 1.08 (0.16), residues: 951 sheet: -1.94 (0.31), residues: 247 loop : -1.67 (0.20), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 442 TYR 0.011 0.001 TYR B 82 PHE 0.024 0.002 PHE C 330 TRP 0.008 0.001 TRP A 422 HIS 0.004 0.001 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.17 (18480) covalent geometry : angle 0.54159 / 0.30 (25043) hydrogen bonds : bond 0.04156 / 2.73 ( 792) hydrogen bonds : angle 4.91735 / 3.51 ( 2224) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 108 is missing expected H atoms. Skipping. Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue VAL 655 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue ALA 674 is missing expected H atoms. Skipping. Residue THR 676 is missing expected H atoms. Skipping. Residue ALA 684 is missing expected H atoms. Skipping. Evaluate side-chains 285 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 360 MET cc_start: 0.6745 (mmm) cc_final: 0.6145 (mmm) REVERT: A 446 PHE cc_start: 0.9322 (m-80) cc_final: 0.9073 (m-10) REVERT: A 581 MET cc_start: 0.9130 (ttm) cc_final: 0.8786 (ttm) REVERT: A 587 GLN cc_start: 0.9395 (tt0) cc_final: 0.8950 (tp40) REVERT: A 607 MET cc_start: 0.8890 (mmt) cc_final: 0.8448 (mmm) REVERT: A 612 PHE cc_start: 0.8642 (m-80) cc_final: 0.8389 (m-10) REVERT: A 661 GLU cc_start: 0.9578 (mm-30) cc_final: 0.9339 (mm-30) REVERT: A 664 LYS cc_start: 0.9525 (tppp) cc_final: 0.9309 (tmtt) REVERT: C 297 ILE cc_start: 0.8655 (tp) cc_final: 0.8455 (pt) REVERT: C 483 MET cc_start: 0.7011 (mmp) cc_final: 0.6673 (mtp) REVERT: C 553 ILE cc_start: 0.8145 (tp) cc_final: 0.7884 (tp) REVERT: C 554 ILE cc_start: 0.6481 (mm) cc_final: 0.6248 (mm) REVERT: B 111 MET cc_start: 0.7174 (mtp) cc_final: 0.6669 (mtp) REVERT: B 137 GLN cc_start: 0.9487 (mm-40) cc_final: 0.9036 (mp10) REVERT: B 348 MET cc_start: 0.9019 (mmt) cc_final: 0.8671 (mmt) REVERT: B 414 MET cc_start: 0.7868 (mmm) cc_final: 0.7545 (tpp) REVERT: B 477 MET cc_start: 0.8565 (mtm) cc_final: 0.8352 (mtm) REVERT: B 527 VAL cc_start: 0.9668 (t) cc_final: 0.9407 (p) REVERT: B 530 ILE cc_start: 0.9804 (mt) cc_final: 0.9593 (tt) REVERT: B 546 MET cc_start: 0.9394 (mmp) cc_final: 0.8878 (mmp) REVERT: B 554 ASP cc_start: 0.9533 (m-30) cc_final: 0.9319 (m-30) REVERT: B 606 ILE cc_start: 0.9093 (mt) cc_final: 0.8846 (mp) REVERT: B 664 HIS cc_start: 0.9092 (m-70) cc_final: 0.8721 (m-70) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.3161 time to fit residues: 133.2194 Evaluate side-chains 253 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 186 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 109 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 27 optimal weight: 0.0670 chunk 55 optimal weight: 3.9990 chunk 182 optimal weight: 9.9990 overall best weight: 3.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN B 136 ASN ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.077958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.057709 restraints weight = 332036.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.060538 restraints weight = 197633.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.062501 restraints weight = 132128.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.063858 restraints weight = 96723.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.064772 restraints weight = 76280.258| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 18480 Z= 0.174 Angle : 0.556 5.891 25043 Z= 0.304 Chirality : 0.039 0.396 2770 Planarity : 0.004 0.074 3147 Dihedral : 9.944 79.432 2762 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.89 % Favored : 94.02 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.05 % 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: -0.71 (0.18), residues: 2175 helix: 1.08 (0.16), residues: 953 sheet: -2.04 (0.30), residues: 245 loop : -1.64 (0.20), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 442 TYR 0.021 0.001 TYR B 355 PHE 0.053 0.002 PHE C 217 TRP 0.010 0.001 TRP B 55 HIS 0.004 0.001 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.17 (18480) covalent geometry : angle 0.55573 / 0.30 (25043) hydrogen bonds : bond 0.04074 / 2.69 ( 792) hydrogen bonds : angle 4.87497 / 3.50 ( 2224) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 108 is missing expected H atoms. Skipping. Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue VAL 655 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue ALA 674 is missing expected H atoms. Skipping. Residue THR 676 is missing expected H atoms. Skipping. Residue ALA 684 is missing expected H atoms. Skipping. Evaluate side-chains 280 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 MET cc_start: 0.9640 (mmp) cc_final: 0.9251 (mmp) REVERT: A 360 MET cc_start: 0.6759 (mmm) cc_final: 0.6173 (mmm) REVERT: A 446 PHE cc_start: 0.9264 (m-80) cc_final: 0.9058 (m-10) REVERT: A 581 MET cc_start: 0.9134 (ttm) cc_final: 0.8800 (ttm) REVERT: A 587 GLN cc_start: 0.9424 (tt0) cc_final: 0.8980 (tp40) REVERT: A 607 MET cc_start: 0.8893 (mmt) cc_final: 0.8498 (mmm) REVERT: A 612 PHE cc_start: 0.8627 (m-80) cc_final: 0.8376 (m-10) REVERT: A 661 GLU cc_start: 0.9572 (mm-30) cc_final: 0.9333 (mm-30) REVERT: A 664 LYS cc_start: 0.9517 (tppp) cc_final: 0.9294 (tmtt) REVERT: C 483 MET cc_start: 0.7015 (mmp) cc_final: 0.6639 (mtp) REVERT: B 111 MET cc_start: 0.7090 (mtp) cc_final: 0.6586 (mtp) REVERT: B 137 GLN cc_start: 0.9479 (mm-40) cc_final: 0.9049 (mp10) REVERT: B 348 MET cc_start: 0.9056 (mmt) cc_final: 0.8753 (mmt) REVERT: B 414 MET cc_start: 0.7885 (mmm) cc_final: 0.7645 (tpp) REVERT: B 415 LEU cc_start: 0.9675 (mp) cc_final: 0.9469 (mp) REVERT: B 477 MET cc_start: 0.8565 (mtm) cc_final: 0.8363 (mtm) REVERT: B 508 GLU cc_start: 0.8520 (mp0) cc_final: 0.8031 (mp0) REVERT: B 527 VAL cc_start: 0.9667 (t) cc_final: 0.9400 (p) REVERT: B 530 ILE cc_start: 0.9790 (mt) cc_final: 0.9588 (tt) REVERT: B 546 MET cc_start: 0.9400 (mmp) cc_final: 0.8883 (mmp) REVERT: B 554 ASP cc_start: 0.9509 (m-30) cc_final: 0.9280 (m-30) REVERT: B 606 ILE cc_start: 0.9140 (mt) cc_final: 0.8894 (mp) REVERT: B 664 HIS cc_start: 0.9169 (m-70) cc_final: 0.8822 (m-70) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.3116 time to fit residues: 130.1101 Evaluate side-chains 253 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 85 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 211 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 156 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 chunk 133 optimal weight: 5.9990 chunk 185 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 GLN C 723 ASN B 136 ASN ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.074710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.054857 restraints weight = 337299.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.057472 restraints weight = 205298.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.059310 restraints weight = 139371.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.060547 restraints weight = 103437.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.061447 restraints weight = 82683.264| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.5791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 18480 Z= 0.238 Angle : 0.619 10.479 25043 Z= 0.342 Chirality : 0.039 0.395 2770 Planarity : 0.005 0.135 3147 Dihedral : 10.049 76.827 2762 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.62 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.05 % 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: -0.98 (0.18), residues: 2175 helix: 0.74 (0.16), residues: 951 sheet: -2.03 (0.31), residues: 241 loop : -1.68 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 209 TYR 0.023 0.002 TYR C 205 PHE 0.032 0.002 PHE B 696 TRP 0.030 0.002 TRP C 449 HIS 0.008 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.24 (18480) covalent geometry : angle 0.61915 / 0.34 (25043) hydrogen bonds : bond 0.04350 / 2.90 ( 792) hydrogen bonds : angle 5.03662 / 3.62 ( 2224) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 108 is missing expected H atoms. Skipping. Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue VAL 655 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue ALA 674 is missing expected H atoms. Skipping. Residue THR 676 is missing expected H atoms. Skipping. Residue ALA 684 is missing expected H atoms. Skipping. Evaluate side-chains 281 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.8929 (mtp) cc_final: 0.8643 (mtp) REVERT: A 311 MET cc_start: 0.9662 (mmp) cc_final: 0.9222 (mmp) REVERT: A 360 MET cc_start: 0.6965 (mmm) cc_final: 0.6434 (mmm) REVERT: A 485 MET cc_start: 0.8426 (mtm) cc_final: 0.7958 (mtm) REVERT: A 587 GLN cc_start: 0.9467 (tt0) cc_final: 0.9015 (tp40) REVERT: A 607 MET cc_start: 0.8986 (mmt) cc_final: 0.8576 (mmm) REVERT: A 664 LYS cc_start: 0.9528 (tppp) cc_final: 0.9194 (tptt) REVERT: C 46 ARG cc_start: 0.9310 (mmm160) cc_final: 0.8690 (tpp-160) REVERT: C 153 ASP cc_start: 0.8820 (t0) cc_final: 0.7958 (m-30) REVERT: C 483 MET cc_start: 0.7093 (mmp) cc_final: 0.6646 (mtp) REVERT: B 111 MET cc_start: 0.7111 (mtp) cc_final: 0.6623 (mtp) REVERT: B 137 GLN cc_start: 0.9468 (mm-40) cc_final: 0.9042 (mp10) REVERT: B 348 MET cc_start: 0.8989 (mmt) cc_final: 0.8699 (mmt) REVERT: B 414 MET cc_start: 0.7970 (mmm) cc_final: 0.7604 (tpp) REVERT: B 508 GLU cc_start: 0.8521 (mp0) cc_final: 0.8048 (mp0) REVERT: B 527 VAL cc_start: 0.9679 (t) cc_final: 0.9427 (p) REVERT: B 546 MET cc_start: 0.9442 (mmp) cc_final: 0.8961 (mmm) REVERT: B 554 ASP cc_start: 0.9499 (m-30) cc_final: 0.9281 (m-30) REVERT: B 606 ILE cc_start: 0.9207 (mt) cc_final: 0.8977 (mp) REVERT: B 664 HIS cc_start: 0.9280 (m-70) cc_final: 0.8976 (m-70) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.3092 time to fit residues: 129.0355 Evaluate side-chains 246 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 130 optimal weight: 0.8980 chunk 146 optimal weight: 20.0000 chunk 145 optimal weight: 8.9990 chunk 153 optimal weight: 8.9990 chunk 199 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 144 optimal weight: 20.0000 chunk 118 optimal weight: 20.0000 chunk 115 optimal weight: 10.0000 chunk 214 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 723 ASN B 136 ASN B 532 ASN ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.076920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.057297 restraints weight = 334523.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.060035 restraints weight = 197560.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.061949 restraints weight = 131608.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.063307 restraints weight = 96163.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.064270 restraints weight = 75236.960| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.5843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18480 Z= 0.130 Angle : 0.552 8.208 25043 Z= 0.298 Chirality : 0.039 0.395 2770 Planarity : 0.004 0.070 3147 Dihedral : 9.991 77.054 2762 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.89 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.05 % 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: -0.69 (0.18), residues: 2175 helix: 1.00 (0.16), residues: 958 sheet: -1.84 (0.31), residues: 239 loop : -1.57 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 638 TYR 0.013 0.001 TYR B 82 PHE 0.023 0.002 PHE B 696 TRP 0.014 0.001 TRP C 449 HIS 0.008 0.001 HIS C 432 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (18480) covalent geometry : angle 0.55196 / 0.30 (25043) hydrogen bonds : bond 0.04000 / 2.66 ( 792) hydrogen bonds : angle 4.80732 / 3.47 ( 2224) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 108 is missing expected H atoms. Skipping. Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue VAL 655 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue ALA 674 is missing expected H atoms. Skipping. Residue THR 676 is missing expected H atoms. Skipping. Residue ALA 684 is missing expected H atoms. Skipping. Evaluate side-chains 283 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.1025 (ttm) cc_final: 0.0693 (ttm) REVERT: A 311 MET cc_start: 0.9648 (mmp) cc_final: 0.9205 (mmp) REVERT: A 360 MET cc_start: 0.7137 (mmm) cc_final: 0.6398 (mmm) REVERT: A 446 PHE cc_start: 0.9426 (m-10) cc_final: 0.9194 (m-10) REVERT: A 485 MET cc_start: 0.8456 (mtm) cc_final: 0.8010 (mtm) REVERT: A 587 GLN cc_start: 0.9443 (tt0) cc_final: 0.8983 (tp40) REVERT: A 607 MET cc_start: 0.8952 (mmt) cc_final: 0.8580 (mmm) REVERT: A 646 PHE cc_start: 0.9324 (m-80) cc_final: 0.8900 (m-80) REVERT: A 664 LYS cc_start: 0.9512 (tppp) cc_final: 0.9281 (tmtt) REVERT: C 153 ASP cc_start: 0.8769 (t0) cc_final: 0.7946 (m-30) REVERT: C 483 MET cc_start: 0.7316 (mmp) cc_final: 0.6940 (mtp) REVERT: B 7 LEU cc_start: 0.9617 (tp) cc_final: 0.9400 (tp) REVERT: B 111 MET cc_start: 0.6962 (mtp) cc_final: 0.6477 (mtp) REVERT: B 137 GLN cc_start: 0.9463 (mm-40) cc_final: 0.9089 (mp10) REVERT: B 227 MET cc_start: 0.8298 (pmm) cc_final: 0.7901 (pmm) REVERT: B 348 MET cc_start: 0.8951 (mmt) cc_final: 0.8622 (mmt) REVERT: B 414 MET cc_start: 0.7717 (mmm) cc_final: 0.7329 (mmt) REVERT: B 508 GLU cc_start: 0.8493 (mp0) cc_final: 0.7983 (mp0) REVERT: B 527 VAL cc_start: 0.9611 (t) cc_final: 0.9361 (p) REVERT: B 546 MET cc_start: 0.9370 (mmp) cc_final: 0.8876 (mmp) REVERT: B 554 ASP cc_start: 0.9487 (m-30) cc_final: 0.9260 (m-30) REVERT: B 606 ILE cc_start: 0.9196 (mt) cc_final: 0.8968 (mp) REVERT: B 664 HIS cc_start: 0.9235 (m-70) cc_final: 0.8889 (m-70) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.3082 time to fit residues: 129.1367 Evaluate side-chains 258 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 114 optimal weight: 10.0000 chunk 11 optimal weight: 0.6980 chunk 194 optimal weight: 0.0370 chunk 80 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 chunk 131 optimal weight: 9.9990 chunk 141 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 179 optimal weight: 2.9990 overall best weight: 2.3464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 723 ASN B 136 ASN ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.077175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.057750 restraints weight = 335411.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.060455 restraints weight = 198616.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.062342 restraints weight = 132637.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.063622 restraints weight = 97377.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.064516 restraints weight = 76851.702| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.5974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18480 Z= 0.139 Angle : 0.541 7.009 25043 Z= 0.293 Chirality : 0.039 0.378 2770 Planarity : 0.004 0.068 3147 Dihedral : 9.934 77.253 2762 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.11 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.05 % 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: -0.53 (0.18), residues: 2175 helix: 1.12 (0.17), residues: 952 sheet: -1.71 (0.32), residues: 227 loop : -1.48 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 702 TYR 0.033 0.001 TYR A 445 PHE 0.023 0.002 PHE B 696 TRP 0.043 0.001 TRP C 537 HIS 0.007 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (18480) covalent geometry : angle 0.54053 / 0.29 (25043) hydrogen bonds : bond 0.03893 / 2.60 ( 792) hydrogen bonds : angle 4.79180 / 3.44 ( 2224) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5468.00 seconds wall clock time: 94 minutes 6.66 seconds (5646.66 seconds total)