Starting phenix.real_space_refine on Mon Jul 6 13:24:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r65_18947/07_2026/8r65_18947.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r65_18947/07_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_18947/07_2026/8r65_18947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r65_18947/07_2026/8r65_18947.map" model { file = "/net/cci-nas-00/data/ceres_data/8r65_18947/07_2026/8r65_18947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r65_18947/07_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-dev-6108/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: 4.98, per 1000 atoms: 0.14 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: 2.83 Conformation dependent library (CDL) restraints added in 800.4 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: 5.52 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: 8.64 Time building geometry restraints manager: 3.81 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.220 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 34.560 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.900 ------------------------------------------------------------------------------- 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= 0.243 Angle : 0.621 13.679 25043 Z= 0.363 Chirality : 0.053 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 0.00480 / 0.24 (18480) covalent geometry : angle 0.62101 / 0.36 (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 : 0.996 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: symmetry clash REVERT: A 1 MET cc_start: 0.8901 (ptm) cc_final: 0.8506 (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: 0.9128 (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: 0.6438 (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: 0.8934 (mp0) REVERT: B 519 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8623 (mt-10) REVERT: B 538 ASP cc_start: 0.9650 (m-30) cc_final: 0.9293 (p0) REVERT: B 599 TYR cc_start: 0.9272 (m-80) cc_final: 0.8622 (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: 0.3947 time to fit residues: 269.1645 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 : 1.038 ------------------------------------------------------------------------------- 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 452 HIS 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.107754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.095564 restraints weight = 488251.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.097910 restraints weight = 232415.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.099276 restraints weight = 132061.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.100014 restraints weight = 85301.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.100486 restraints weight = 62382.737| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 18480 Z= 0.308 Angle : 0.705 7.797 25043 Z= 0.400 Chirality : 0.042 0.452 2770 Planarity : 0.006 0.084 3147 Dihedral : 10.080 84.838 2762 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.84 % Favored : 93.93 % Rotamer: Outliers : 0.05 % Allowed : 1.96 % Favored : 97.99 % 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: -1.19 (0.17), residues: 2175 helix: 0.69 (0.16), residues: 952 sheet: -2.27 (0.31), residues: 230 loop : -1.91 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 583 TYR 0.025 0.002 TYR C 228 PHE 0.056 0.003 PHE B 333 TRP 0.028 0.002 TRP C 537 HIS 0.007 0.002 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.31 (18480) covalent geometry : angle 0.70484 / 0.40 (25043) hydrogen bonds : bond 0.05589 / 3.66 ( 792) hydrogen bonds : angle 5.61428 / 3.97 ( 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 339 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 338 time to evaluate : 1.027 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: A 311 MET cc_start: 0.9510 (mmp) cc_final: 0.9271 (mmm) REVERT: A 360 MET cc_start: 0.6293 (mmm) cc_final: 0.6003 (mmm) REVERT: A 460 MET cc_start: 0.9121 (ttp) cc_final: 0.8860 (tmm) REVERT: A 511 LEU cc_start: 0.9576 (mp) cc_final: 0.9224 (mp) REVERT: A 572 LYS cc_start: 0.9339 (ttmt) cc_final: 0.8918 (mtmt) REVERT: A 575 MET cc_start: 0.9339 (mtm) cc_final: 0.8997 (mtm) REVERT: A 581 MET cc_start: 0.9040 (ttm) cc_final: 0.8491 (ttm) REVERT: A 584 CYS cc_start: 0.9364 (m) cc_final: 0.9085 (m) REVERT: A 587 GLN cc_start: 0.9453 (tt0) cc_final: 0.8992 (mm-40) REVERT: A 607 MET cc_start: 0.9008 (mmt) cc_final: 0.8389 (mmm) REVERT: A 661 GLU cc_start: 0.9537 (mm-30) cc_final: 0.9334 (mt-10) REVERT: A 664 LYS cc_start: 0.9505 (tppp) cc_final: 0.9292 (tmtt) REVERT: A 694 LEU cc_start: 0.8583 (mt) cc_final: 0.8335 (mm) REVERT: C 90 MET cc_start: 0.9463 (mtp) cc_final: 0.9243 (mmm) REVERT: C 164 MET cc_start: 0.9198 (mtp) cc_final: 0.8655 (ptt) REVERT: C 483 MET cc_start: 0.6507 (mmp) cc_final: 0.6148 (mtp) REVERT: B 111 MET cc_start: 0.7354 (mtp) cc_final: 0.6969 (mtt) REVERT: B 131 TRP cc_start: 0.8889 (p-90) cc_final: 0.8413 (p-90) REVERT: B 137 GLN cc_start: 0.9536 (mm-40) cc_final: 0.9075 (mp10) REVERT: B 251 PHE cc_start: 0.9437 (m-80) cc_final: 0.9005 (m-80) REVERT: B 321 MET cc_start: 0.9522 (mtt) cc_final: 0.9019 (mtt) REVERT: B 414 MET cc_start: 0.7434 (mmm) cc_final: 0.7142 (tpp) REVERT: B 415 LEU cc_start: 0.9447 (tp) cc_final: 0.9175 (tp) REVERT: B 508 GLU cc_start: 0.8775 (mp0) cc_final: 0.8531 (mp0) REVERT: B 519 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8703 (mt-10) REVERT: B 527 VAL cc_start: 0.9620 (t) cc_final: 0.9355 (p) REVERT: B 546 MET cc_start: 0.9422 (mmp) cc_final: 0.9002 (mmp) REVERT: B 599 TYR cc_start: 0.9144 (m-80) cc_final: 0.8577 (m-10) REVERT: B 606 ILE cc_start: 0.8909 (mt) cc_final: 0.8490 (mp) REVERT: B 690 GLN cc_start: 0.9085 (pt0) cc_final: 0.8653 (pt0) outliers start: 1 outliers final: 0 residues processed: 339 average time/residue: 0.3858 time to fit residues: 188.0751 Evaluate side-chains 279 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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: 0.9980 chunk 43 optimal weight: 0.8980 chunk 160 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 158 optimal weight: 0.8980 chunk 142 optimal weight: 8.9990 chunk 98 optimal weight: 0.6980 chunk 104 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4388 r_free = 0.4388 target = 0.109792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.097886 restraints weight = 482704.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.100177 restraints weight = 228852.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.101521 restraints weight = 129310.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.102282 restraints weight = 83172.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.102688 restraints weight = 60336.146| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18480 Z= 0.131 Angle : 0.547 6.294 25043 Z= 0.295 Chirality : 0.040 0.421 2770 Planarity : 0.004 0.057 3147 Dihedral : 10.007 85.825 2762 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.47 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % 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: -0.81 (0.18), residues: 2175 helix: 1.04 (0.17), residues: 955 sheet: -1.94 (0.32), residues: 220 loop : -1.81 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 496 TYR 0.010 0.001 TYR C 531 PHE 0.030 0.001 PHE B 333 TRP 0.013 0.001 TRP A 619 HIS 0.003 0.001 HIS A 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (18480) covalent geometry : angle 0.54663 / 0.30 (25043) hydrogen bonds : bond 0.04707 / 3.12 ( 792) hydrogen bonds : angle 5.02383 / 3.60 ( 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 318 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 1.046 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: A 285 MET cc_start: 0.9342 (ttp) cc_final: 0.9020 (ttp) REVERT: A 311 MET cc_start: 0.9474 (mmp) cc_final: 0.9191 (mmp) REVERT: A 360 MET cc_start: 0.6304 (mmm) cc_final: 0.5960 (mmm) REVERT: A 446 PHE cc_start: 0.9573 (m-80) cc_final: 0.9257 (m-10) REVERT: A 460 MET cc_start: 0.9086 (ttp) cc_final: 0.8857 (tmm) REVERT: A 485 MET cc_start: 0.7970 (mtm) cc_final: 0.7657 (mtt) REVERT: A 581 MET cc_start: 0.8954 (ttm) cc_final: 0.8470 (ttm) REVERT: A 584 CYS cc_start: 0.9265 (m) cc_final: 0.9021 (m) REVERT: A 587 GLN cc_start: 0.9382 (tt0) cc_final: 0.8862 (mm110) REVERT: A 607 MET cc_start: 0.8987 (mmt) cc_final: 0.8444 (mmm) REVERT: A 661 GLU cc_start: 0.9500 (mm-30) cc_final: 0.9295 (mt-10) REVERT: C 50 MET cc_start: 0.9452 (tpt) cc_final: 0.9227 (tpp) REVERT: C 146 ASP cc_start: 0.8070 (m-30) cc_final: 0.7785 (t0) REVERT: C 483 MET cc_start: 0.6521 (mmp) cc_final: 0.6216 (mtp) REVERT: B 111 MET cc_start: 0.7214 (mtp) cc_final: 0.6805 (mtt) REVERT: B 137 GLN cc_start: 0.9510 (mm-40) cc_final: 0.9122 (mp10) REVERT: B 179 MET cc_start: 0.9168 (mmt) cc_final: 0.8952 (mmt) REVERT: B 251 PHE cc_start: 0.9473 (m-80) cc_final: 0.9029 (m-80) REVERT: B 348 MET cc_start: 0.9170 (mmt) cc_final: 0.8745 (mmt) REVERT: B 356 MET cc_start: 0.8101 (ttt) cc_final: 0.7877 (ttt) REVERT: B 408 MET cc_start: 0.7595 (tpt) cc_final: 0.7062 (tpt) REVERT: B 519 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8626 (mt-10) REVERT: B 527 VAL cc_start: 0.9620 (t) cc_final: 0.9301 (p) REVERT: B 532 ASN cc_start: 0.9541 (m110) cc_final: 0.9341 (m-40) REVERT: B 554 ASP cc_start: 0.9203 (t0) cc_final: 0.8999 (t0) REVERT: B 599 TYR cc_start: 0.9083 (m-80) cc_final: 0.8427 (m-10) REVERT: B 606 ILE cc_start: 0.8852 (mt) cc_final: 0.8355 (mp) REVERT: B 657 TYR cc_start: 0.8872 (p90) cc_final: 0.8113 (p90) outliers start: 0 outliers final: 0 residues processed: 318 average time/residue: 0.3659 time to fit residues: 168.7773 Evaluate side-chains 278 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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: 9.9990 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: 10.0000 chunk 170 optimal weight: 9.9990 chunk 27 optimal weight: 0.7980 chunk 201 optimal weight: 9.9990 chunk 82 optimal weight: 0.8980 overall best weight: 6.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.079945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.059748 restraints weight = 335568.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.062579 restraints weight = 201067.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.064547 restraints weight = 135165.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.065919 restraints weight = 99403.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.066738 restraints weight = 78596.619| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 18480 Z= 0.279 Angle : 0.638 8.101 25043 Z= 0.356 Chirality : 0.040 0.418 2770 Planarity : 0.005 0.053 3147 Dihedral : 9.987 82.570 2762 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.30 % Favored : 93.56 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % 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: -1.19 (0.17), residues: 2175 helix: 0.65 (0.16), residues: 952 sheet: -2.12 (0.31), residues: 243 loop : -1.90 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 369 TYR 0.024 0.002 TYR C 111 PHE 0.022 0.002 PHE B 505 TRP 0.019 0.002 TRP C 537 HIS 0.006 0.002 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.28 (18480) covalent geometry : angle 0.63824 / 0.36 (25043) hydrogen bonds : bond 0.04607 / 3.08 ( 792) hydrogen bonds : angle 5.21098 / 3.72 ( 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 295 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.927 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 311 MET cc_start: 0.9604 (mmp) cc_final: 0.9254 (mmp) REVERT: A 360 MET cc_start: 0.6683 (mmm) cc_final: 0.6166 (mmm) REVERT: A 511 LEU cc_start: 0.9544 (mp) cc_final: 0.9225 (mp) REVERT: A 572 LYS cc_start: 0.9241 (ttmt) cc_final: 0.8994 (mtmt) REVERT: A 581 MET cc_start: 0.9160 (ttm) cc_final: 0.8682 (ttm) REVERT: A 587 GLN cc_start: 0.9418 (tt0) cc_final: 0.9131 (tp40) REVERT: A 607 MET cc_start: 0.8943 (mmt) cc_final: 0.8564 (mmm) REVERT: A 612 PHE cc_start: 0.8748 (m-80) cc_final: 0.8382 (m-10) REVERT: A 661 GLU cc_start: 0.9564 (mm-30) cc_final: 0.9330 (mt-10) REVERT: A 664 LYS cc_start: 0.9520 (tppp) cc_final: 0.9297 (tmtt) REVERT: C 50 MET cc_start: 0.9543 (tpt) cc_final: 0.9310 (tpp) REVERT: C 483 MET cc_start: 0.6804 (mmp) cc_final: 0.6266 (mtp) REVERT: B 137 GLN cc_start: 0.9502 (mm-40) cc_final: 0.9062 (mp10) REVERT: B 179 MET cc_start: 0.9351 (mmt) cc_final: 0.9119 (mmm) REVERT: B 356 MET cc_start: 0.8421 (ttt) cc_final: 0.8156 (ttt) REVERT: B 477 MET cc_start: 0.8590 (mtm) cc_final: 0.8343 (mtm) REVERT: B 519 GLU cc_start: 0.9184 (mt-10) cc_final: 0.8845 (mt-10) REVERT: B 527 VAL cc_start: 0.9621 (t) cc_final: 0.9333 (p) REVERT: B 532 ASN cc_start: 0.9603 (m110) cc_final: 0.9381 (m110) REVERT: B 546 MET cc_start: 0.9456 (mmp) cc_final: 0.8988 (mmp) REVERT: B 599 TYR cc_start: 0.9259 (m-80) cc_final: 0.8697 (m-80) REVERT: B 606 ILE cc_start: 0.8994 (mt) cc_final: 0.8468 (mp) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.3582 time to fit residues: 156.1860 Evaluate side-chains 260 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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: 6.9990 chunk 119 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 139 optimal weight: 20.0000 chunk 194 optimal weight: 10.0000 chunk 148 optimal weight: 0.9990 chunk 213 optimal weight: 9.9990 chunk 159 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 HIS B 99 HIS B 136 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.077725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.057938 restraints weight = 337016.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.060607 restraints weight = 203071.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.062448 restraints weight = 137431.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.063754 restraints weight = 102058.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.064564 restraints weight = 81086.584| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 18480 Z= 0.256 Angle : 0.635 7.033 25043 Z= 0.358 Chirality : 0.041 0.412 2770 Planarity : 0.005 0.084 3147 Dihedral : 10.128 80.725 2762 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.11 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % 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: -1.45 (0.17), residues: 2175 helix: 0.37 (0.16), residues: 955 sheet: -2.18 (0.31), residues: 238 loop : -2.00 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 213 TYR 0.016 0.002 TYR C 704 PHE 0.031 0.002 PHE B 696 TRP 0.015 0.002 TRP A 422 HIS 0.012 0.002 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.26 (18480) covalent geometry : angle 0.63522 / 0.36 (25043) hydrogen bonds : bond 0.04561 / 3.01 ( 792) hydrogen bonds : angle 5.33232 / 3.81 ( 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 284 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 1.024 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: A 360 MET cc_start: 0.6905 (mmm) cc_final: 0.6255 (mmm) REVERT: A 460 MET cc_start: 0.9071 (tmm) cc_final: 0.8852 (tmm) REVERT: A 587 GLN cc_start: 0.9464 (tt0) cc_final: 0.8973 (tp40) REVERT: A 607 MET cc_start: 0.8836 (mmt) cc_final: 0.8383 (mmm) REVERT: A 612 PHE cc_start: 0.8668 (m-80) cc_final: 0.8348 (m-10) REVERT: A 661 GLU cc_start: 0.9575 (mm-30) cc_final: 0.9339 (mt-10) REVERT: A 664 LYS cc_start: 0.9536 (tppp) cc_final: 0.9318 (tmtt) REVERT: C 50 MET cc_start: 0.9569 (tpt) cc_final: 0.9327 (tpp) REVERT: C 297 ILE cc_start: 0.8713 (tp) cc_final: 0.8501 (pt) REVERT: C 483 MET cc_start: 0.7004 (mmp) cc_final: 0.6706 (mtp) REVERT: C 554 ILE cc_start: 0.6719 (mm) cc_final: 0.6517 (mm) REVERT: B 137 GLN cc_start: 0.9499 (mm-40) cc_final: 0.9267 (mp10) REVERT: B 527 VAL cc_start: 0.9625 (t) cc_final: 0.9208 (p) REVERT: B 532 ASN cc_start: 0.9603 (m110) cc_final: 0.9394 (m110) REVERT: B 546 MET cc_start: 0.9445 (mmp) cc_final: 0.8961 (mmp) REVERT: B 599 TYR cc_start: 0.9251 (m-80) cc_final: 0.8471 (m-80) REVERT: B 606 ILE cc_start: 0.9069 (mt) cc_final: 0.8433 (mp) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.3460 time to fit residues: 145.6245 Evaluate side-chains 248 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 1.248 ------------------------------------------------------------------------------- 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: 2.9990 chunk 117 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 153 optimal weight: 7.9990 chunk 143 optimal weight: 10.0000 chunk 188 optimal weight: 5.9990 chunk 196 optimal weight: 10.0000 chunk 162 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 406 GLN ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 ASN ** B 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3927 r_free = 0.3927 target = 0.077665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.057486 restraints weight = 331517.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.060220 restraints weight = 200938.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.062114 restraints weight = 135643.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.063421 restraints weight = 100454.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.064327 restraints weight = 80050.827| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18480 Z= 0.174 Angle : 0.562 6.311 25043 Z= 0.310 Chirality : 0.039 0.392 2770 Planarity : 0.004 0.075 3147 Dihedral : 10.044 80.382 2762 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.84 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % 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: -1.18 (0.17), residues: 2175 helix: 0.64 (0.16), residues: 958 sheet: -2.15 (0.29), residues: 251 loop : -1.87 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 638 TYR 0.021 0.001 TYR A 393 PHE 0.046 0.002 PHE C 330 TRP 0.013 0.001 TRP C 449 HIS 0.011 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 (18480) covalent geometry : angle 0.56232 / 0.31 (25043) hydrogen bonds : bond 0.04205 / 2.75 ( 792) hydrogen bonds : angle 5.11678 / 3.66 ( 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 280 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 1.057 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: A 311 MET cc_start: 0.9634 (mmp) cc_final: 0.9222 (mmp) REVERT: A 360 MET cc_start: 0.6795 (mmm) cc_final: 0.6171 (mmm) REVERT: A 485 MET cc_start: 0.8473 (mtm) cc_final: 0.7953 (mtm) REVERT: A 581 MET cc_start: 0.9170 (ttm) cc_final: 0.8802 (ttm) REVERT: A 587 GLN cc_start: 0.9440 (tt0) cc_final: 0.8909 (tp40) REVERT: A 607 MET cc_start: 0.8866 (mmt) cc_final: 0.8360 (mmm) REVERT: A 661 GLU cc_start: 0.9584 (mm-30) cc_final: 0.9359 (mm-30) REVERT: A 664 LYS cc_start: 0.9516 (tppp) cc_final: 0.9297 (tmtt) REVERT: C 50 MET cc_start: 0.9555 (tpt) cc_final: 0.9284 (tpp) REVERT: C 483 MET cc_start: 0.7054 (mmp) cc_final: 0.6704 (mtp) REVERT: B 137 GLN cc_start: 0.9492 (mm-40) cc_final: 0.9037 (mp10) REVERT: B 348 MET cc_start: 0.9028 (mmt) cc_final: 0.8722 (mmt) REVERT: B 532 ASN cc_start: 0.9599 (m110) cc_final: 0.9362 (m110) REVERT: B 533 ASN cc_start: 0.9415 (m110) cc_final: 0.9208 (m110) REVERT: B 546 MET cc_start: 0.9419 (mmp) cc_final: 0.8929 (mmp) REVERT: B 606 ILE cc_start: 0.9087 (mt) cc_final: 0.8836 (mp) REVERT: B 664 HIS cc_start: 0.9132 (m-70) cc_final: 0.8783 (m-70) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.3600 time to fit residues: 148.2899 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 : 0.919 ------------------------------------------------------------------------------- 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: 5.9990 chunk 193 optimal weight: 0.0970 chunk 161 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 182 optimal weight: 3.9990 chunk 216 optimal weight: 9.9990 chunk 43 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 152 optimal weight: 1.9990 chunk 111 optimal weight: 30.0000 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 591 GLN ** B 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4262 r_free = 0.4262 target = 0.100937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.088702 restraints weight = 497952.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.091022 restraints weight = 236473.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.092333 restraints weight = 132382.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.093044 restraints weight = 85397.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.093475 restraints weight = 63407.972| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.5230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 18480 Z= 0.134 Angle : 0.530 5.924 25043 Z= 0.288 Chirality : 0.039 0.383 2770 Planarity : 0.004 0.077 3147 Dihedral : 9.979 80.524 2762 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.41 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: -0.81 (0.18), residues: 2175 helix: 0.96 (0.16), residues: 954 sheet: -1.89 (0.31), residues: 238 loop : -1.72 (0.20), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 638 TYR 0.012 0.001 TYR B 82 PHE 0.024 0.002 PHE C 330 TRP 0.009 0.001 TRP B 55 HIS 0.007 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (18480) covalent geometry : angle 0.53003 / 0.29 (25043) hydrogen bonds : bond 0.04091 / 2.70 ( 792) hydrogen bonds : angle 4.90375 / 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 278 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 1.018 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: A 311 MET cc_start: 0.9576 (mmp) cc_final: 0.9216 (mmp) REVERT: A 360 MET cc_start: 0.6665 (mmm) cc_final: 0.6073 (mmm) REVERT: A 581 MET cc_start: 0.9085 (ttm) cc_final: 0.8691 (ttm) REVERT: A 587 GLN cc_start: 0.9398 (tt0) cc_final: 0.8876 (tp40) REVERT: A 607 MET cc_start: 0.8929 (mmt) cc_final: 0.8438 (mmm) REVERT: A 661 GLU cc_start: 0.9577 (mm-30) cc_final: 0.9362 (mm-30) REVERT: A 664 LYS cc_start: 0.9505 (tppp) cc_final: 0.9284 (tmtt) REVERT: C 50 MET cc_start: 0.9530 (tpt) cc_final: 0.9228 (tpp) REVERT: C 164 MET cc_start: 0.7777 (tmm) cc_final: 0.7497 (tmm) REVERT: C 483 MET cc_start: 0.6994 (mmp) cc_final: 0.6698 (mtp) REVERT: B 111 MET cc_start: 0.7087 (mtp) cc_final: 0.6560 (mtp) REVERT: B 137 GLN cc_start: 0.9480 (mm-40) cc_final: 0.9054 (mp10) REVERT: B 348 MET cc_start: 0.9069 (mmt) cc_final: 0.8716 (mmt) REVERT: B 530 ILE cc_start: 0.9804 (mm) cc_final: 0.9532 (tt) REVERT: B 532 ASN cc_start: 0.9550 (m110) cc_final: 0.9319 (m-40) REVERT: B 546 MET cc_start: 0.9381 (mmp) cc_final: 0.8901 (mmp) REVERT: B 593 ASP cc_start: 0.7391 (m-30) cc_final: 0.7191 (m-30) REVERT: B 606 ILE cc_start: 0.9069 (mt) cc_final: 0.8846 (mp) REVERT: B 664 HIS cc_start: 0.9128 (m-70) cc_final: 0.8721 (m-70) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.3545 time to fit residues: 144.9850 Evaluate side-chains 254 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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: 10.0000 chunk 70 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 109 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 184 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 27 optimal weight: 0.3980 chunk 55 optimal weight: 0.7980 chunk 182 optimal weight: 1.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN C 723 ASN 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 = 0.3922 r_free = 0.3922 target = 0.077648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.057821 restraints weight = 334764.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.060475 restraints weight = 201225.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.062304 restraints weight = 137542.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.063600 restraints weight = 101548.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.064524 restraints weight = 80415.423| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.5466 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= 0.161 Angle : 0.539 6.398 25043 Z= 0.296 Chirality : 0.038 0.394 2770 Planarity : 0.005 0.102 3147 Dihedral : 9.943 79.358 2762 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.98 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: -0.77 (0.18), residues: 2175 helix: 0.98 (0.16), residues: 960 sheet: -2.00 (0.31), residues: 236 loop : -1.64 (0.20), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 209 TYR 0.015 0.001 TYR C 205 PHE 0.027 0.002 PHE B 696 TRP 0.009 0.001 TRP B 55 HIS 0.005 0.001 HIS B 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (18480) covalent geometry : angle 0.53901 / 0.30 (25043) hydrogen bonds : bond 0.04008 / 2.66 ( 792) hydrogen bonds : angle 4.85386 / 3.49 ( 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 281 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.826 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: A 311 MET cc_start: 0.9632 (mmp) cc_final: 0.9226 (mmp) REVERT: A 360 MET cc_start: 0.6966 (mmm) cc_final: 0.6320 (mmm) REVERT: A 587 GLN cc_start: 0.9445 (tt0) cc_final: 0.8878 (tp40) REVERT: A 607 MET cc_start: 0.8904 (mmt) cc_final: 0.8437 (mmm) REVERT: A 661 GLU cc_start: 0.9569 (mm-30) cc_final: 0.9329 (mm-30) REVERT: A 664 LYS cc_start: 0.9517 (tppp) cc_final: 0.9294 (tmtt) REVERT: C 50 MET cc_start: 0.9554 (tpt) cc_final: 0.9256 (tpp) REVERT: C 164 MET cc_start: 0.7631 (tmm) cc_final: 0.7340 (tmm) REVERT: C 289 ILE cc_start: 0.7970 (mp) cc_final: 0.7750 (mp) REVERT: C 483 MET cc_start: 0.7074 (mmp) cc_final: 0.6676 (mtp) REVERT: B 111 MET cc_start: 0.7066 (mtp) cc_final: 0.6553 (mtp) REVERT: B 137 GLN cc_start: 0.9493 (mm-40) cc_final: 0.9068 (mp10) REVERT: B 348 MET cc_start: 0.9038 (mmt) cc_final: 0.8698 (mmt) REVERT: B 356 MET cc_start: 0.7740 (ttt) cc_final: 0.7479 (ttt) REVERT: B 530 ILE cc_start: 0.9803 (mm) cc_final: 0.9491 (tt) REVERT: B 546 MET cc_start: 0.9416 (mmp) cc_final: 0.8931 (mmp) REVERT: B 554 ASP cc_start: 0.9526 (m-30) cc_final: 0.9304 (m-30) REVERT: B 606 ILE cc_start: 0.9125 (mt) cc_final: 0.8895 (mp) REVERT: B 664 HIS cc_start: 0.9175 (m-70) cc_final: 0.8815 (m-70) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.3322 time to fit residues: 138.0045 Evaluate side-chains 250 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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: 5.9990 chunk 90 optimal weight: 0.9990 chunk 211 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 156 optimal weight: 0.5980 chunk 122 optimal weight: 8.9990 chunk 96 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 133 optimal weight: 8.9990 chunk 185 optimal weight: 9.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 236 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.077156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.057159 restraints weight = 330376.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.059851 restraints weight = 198944.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.061707 restraints weight = 134401.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.063008 restraints weight = 99383.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.063927 restraints weight = 78690.327| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.5614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18480 Z= 0.134 Angle : 0.529 7.523 25043 Z= 0.288 Chirality : 0.039 0.389 2770 Planarity : 0.004 0.073 3147 Dihedral : 9.926 78.791 2762 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.79 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: -0.62 (0.18), residues: 2175 helix: 1.09 (0.16), residues: 960 sheet: -1.85 (0.31), residues: 231 loop : -1.58 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 638 TYR 0.010 0.001 TYR B 82 PHE 0.059 0.002 PHE C 217 TRP 0.009 0.001 TRP B 55 HIS 0.009 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (18480) covalent geometry : angle 0.52938 / 0.29 (25043) hydrogen bonds : bond 0.03870 / 2.58 ( 792) hydrogen bonds : angle 4.79266 / 3.46 ( 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 283 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.757 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: A 47 MET cc_start: 0.1007 (ttm) cc_final: 0.0683 (ttm) REVERT: A 311 MET cc_start: 0.9636 (mmp) cc_final: 0.9216 (mmp) REVERT: A 360 MET cc_start: 0.6920 (mmm) cc_final: 0.6302 (mmm) REVERT: A 587 GLN cc_start: 0.9434 (tt0) cc_final: 0.8859 (tp40) REVERT: A 607 MET cc_start: 0.8918 (mmt) cc_final: 0.8451 (mmm) REVERT: A 612 PHE cc_start: 0.8705 (m-80) cc_final: 0.8443 (m-10) REVERT: A 661 GLU cc_start: 0.9571 (mm-30) cc_final: 0.9350 (mm-30) REVERT: A 664 LYS cc_start: 0.9514 (tppp) cc_final: 0.9175 (tptt) REVERT: C 50 MET cc_start: 0.9588 (tpt) cc_final: 0.9252 (tpp) REVERT: C 153 ASP cc_start: 0.8831 (t0) cc_final: 0.7999 (m-30) REVERT: C 483 MET cc_start: 0.7210 (mmp) cc_final: 0.6802 (mtp) REVERT: B 111 MET cc_start: 0.6978 (mtp) cc_final: 0.6484 (mtp) REVERT: B 137 GLN cc_start: 0.9444 (mm-40) cc_final: 0.9077 (mp10) REVERT: B 348 MET cc_start: 0.9005 (mmt) cc_final: 0.8647 (mmt) REVERT: B 530 ILE cc_start: 0.9804 (mm) cc_final: 0.9500 (tt) REVERT: B 546 MET cc_start: 0.9415 (mmp) cc_final: 0.8920 (mmp) REVERT: B 554 ASP cc_start: 0.9518 (m-30) cc_final: 0.9293 (m-30) REVERT: B 606 ILE cc_start: 0.9142 (mt) cc_final: 0.8935 (mp) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.3309 time to fit residues: 139.4286 Evaluate side-chains 257 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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: 20.0000 chunk 146 optimal weight: 6.9990 chunk 145 optimal weight: 20.0000 chunk 153 optimal weight: 10.0000 chunk 199 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 chunk 115 optimal weight: 0.8980 chunk 214 optimal weight: 7.9990 chunk 128 optimal weight: 5.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 GLN C 723 ASN ** B 600 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3865 r_free = 0.3865 target = 0.074052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.054329 restraints weight = 343987.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.056858 restraints weight = 209965.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.058673 restraints weight = 142536.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.059922 restraints weight = 106098.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.060793 restraints weight = 84744.058| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.6050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 18480 Z= 0.245 Angle : 0.621 9.243 25043 Z= 0.344 Chirality : 0.039 0.397 2770 Planarity : 0.005 0.066 3147 Dihedral : 10.018 75.680 2762 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.25 % Favored : 93.70 % 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: -1.11 (0.17), residues: 2175 helix: 0.58 (0.16), residues: 963 sheet: -2.05 (0.32), residues: 227 loop : -1.75 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 583 TYR 0.014 0.002 TYR X 22 PHE 0.031 0.002 PHE B 696 TRP 0.013 0.002 TRP A 368 HIS 0.010 0.002 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.24 (18480) covalent geometry : angle 0.62097 / 0.34 (25043) hydrogen bonds : bond 0.04323 / 2.88 ( 792) hydrogen bonds : angle 5.10817 / 3.67 ( 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 279 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 1.038 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: A 21 MET cc_start: 0.8913 (mtp) cc_final: 0.8629 (mtp) REVERT: A 311 MET cc_start: 0.9672 (mmp) cc_final: 0.9269 (mmp) REVERT: A 360 MET cc_start: 0.7024 (mmm) cc_final: 0.6516 (mmm) REVERT: A 587 GLN cc_start: 0.9495 (tt0) cc_final: 0.8949 (tp40) REVERT: A 607 MET cc_start: 0.8960 (mmt) cc_final: 0.8522 (mmm) REVERT: A 646 PHE cc_start: 0.9377 (m-80) cc_final: 0.8977 (m-80) REVERT: A 664 LYS cc_start: 0.9532 (tppp) cc_final: 0.9267 (tptp) REVERT: C 50 MET cc_start: 0.9591 (tpt) cc_final: 0.9223 (tpp) REVERT: C 164 MET cc_start: 0.7630 (tmm) cc_final: 0.7396 (tmm) REVERT: C 483 MET cc_start: 0.7275 (mmp) cc_final: 0.6889 (mtp) REVERT: B 348 MET cc_start: 0.8975 (mmt) cc_final: 0.8682 (mmt) REVERT: B 356 MET cc_start: 0.7874 (ttt) cc_final: 0.7558 (ttt) REVERT: B 508 GLU cc_start: 0.8749 (mp0) cc_final: 0.8204 (mp0) REVERT: B 532 ASN cc_start: 0.9621 (m110) cc_final: 0.9400 (m110) REVERT: B 546 MET cc_start: 0.9462 (mmp) cc_final: 0.8972 (mmm) REVERT: B 554 ASP cc_start: 0.9517 (m-30) cc_final: 0.9307 (m-30) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.3668 time to fit residues: 151.4919 Evaluate side-chains 249 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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: 5.9990 chunk 11 optimal weight: 10.0000 chunk 194 optimal weight: 8.9990 chunk 80 optimal weight: 0.8980 chunk 196 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 131 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 179 optimal weight: 8.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 ASN ** B 664 HIS ** 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 = 0.4205 r_free = 0.4205 target = 0.097131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.085350 restraints weight = 499017.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.087715 restraints weight = 253729.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.089172 restraints weight = 118976.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.089364 restraints weight = 70290.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.089464 restraints weight = 67620.007| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.6135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18480 Z= 0.148 Angle : 0.548 8.912 25043 Z= 0.300 Chirality : 0.039 0.395 2770 Planarity : 0.005 0.115 3147 Dihedral : 10.037 76.199 2762 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.93 % Favored : 94.02 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.88 (0.18), residues: 2175 helix: 0.80 (0.16), residues: 967 sheet: -1.82 (0.33), residues: 211 loop : -1.71 (0.19), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 641 TYR 0.013 0.001 TYR A 334 PHE 0.028 0.002 PHE C 217 TRP 0.013 0.001 TRP B 55 HIS 0.009 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 (18480) covalent geometry : angle 0.54826 / 0.30 (25043) hydrogen bonds : bond 0.03930 / 2.62 ( 792) hydrogen bonds : angle 4.91036 / 3.54 ( 2224) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6135.23 seconds wall clock time: 105 minutes 41.43 seconds (6341.43 seconds total)