Starting phenix.real_space_refine on Tue Aug 26 10:08:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r65_18947/08_2025/8r65_18947.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r65_18947/08_2025/8r65_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 { model { file = "/net/cci-nas-00/data/ceres_data/8r65_18947/08_2025/8r65_18947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r65_18947/08_2025/8r65_18947.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8r65_18947/08_2025/8r65_18947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r65_18947/08_2025/8r65_18947.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.11, per 1000 atoms: 0.17 Number of scatterers: 35541 At special positions: 0 Unit cell: (133.35, 114.45, 143.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 124 16.00 P 26 15.00 O 3476 8.00 N 3161 7.00 C 11292 6.00 H 17462 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.38 Conformation dependent library (CDL) restraints added in 967.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 6.10 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: 9.10 Time building geometry restraints manager: 4.63 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.220 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 39.100 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 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= 0.235 Angle : 0.621 13.679 25043 Z= 0.359 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 aren 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 covalent geometry : bond 0.00480 (18480) covalent geometry : angle 0.62101 (25043) hydrogen bonds : bond 0.16723 ( 792) hydrogen bonds : angle 6.42830 ( 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 : 0.979 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: 0.8595 (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: 0.3953 time to fit residues: 265.3810 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 : 1.004 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 HIS C 100 ASN ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 456 ASN B 136 ASN B 485 ASN B 532 ASN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 567 GLN B 582 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.081086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.060182 restraints weight = 325659.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.063018 restraints weight = 194395.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.065066 restraints weight = 130405.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.066516 restraints weight = 95317.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.067522 restraints weight = 74826.286| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.136 18480 Z= 0.307 Angle : 0.734 6.542 25043 Z= 0.409 Chirality : 0.043 0.570 2770 Planarity : 0.006 0.064 3147 Dihedral : 10.175 85.849 2762 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.70 % Favored : 94.07 % Rotamer: Outliers : 0.10 % Allowed : 2.47 % Favored : 97.42 % 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 aren not related in a simple way. whole: -1.31 (0.17), residues: 2175 helix: 0.52 (0.16), residues: 951 sheet: -2.22 (0.30), residues: 239 loop : -1.92 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 583 TYR 0.025 0.002 TYR C 111 PHE 0.034 0.003 PHE C 330 TRP 0.028 0.002 TRP C 537 HIS 0.009 0.002 HIS A 452 Details of bonding type rmsd covalent geometry : bond 0.00611 (18480) covalent geometry : angle 0.73450 (25043) hydrogen bonds : bond 0.05096 ( 792) hydrogen bonds : angle 5.52887 ( 2224) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 108 is missing expected H atoms. Skipping. Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue VAL 655 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue ALA 674 is missing expected H atoms. Skipping. Residue THR 676 is missing expected H atoms. Skipping. Residue ALA 684 is missing expected H atoms. Skipping. Evaluate side-chains 337 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 335 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 MET cc_start: 0.9560 (mmp) cc_final: 0.9286 (mmm) REVERT: A 460 MET cc_start: 0.9178 (ttp) cc_final: 0.8766 (tmm) REVERT: A 485 MET cc_start: 0.6593 (mtm) cc_final: 0.5903 (ptp) REVERT: A 511 LEU cc_start: 0.9597 (mp) cc_final: 0.9221 (mp) REVERT: A 572 LYS cc_start: 0.9346 (ttmt) cc_final: 0.9003 (mtmt) REVERT: A 581 MET cc_start: 0.9201 (ttm) cc_final: 0.8713 (ttm) REVERT: A 584 CYS cc_start: 0.9434 (m) cc_final: 0.9176 (m) REVERT: A 587 GLN cc_start: 0.9470 (tt0) cc_final: 0.8960 (mm110) REVERT: A 594 SER cc_start: 0.9846 (t) cc_final: 0.9599 (m) REVERT: A 607 MET cc_start: 0.9008 (mmt) cc_final: 0.8501 (mmm) REVERT: A 612 PHE cc_start: 0.8588 (m-80) cc_final: 0.8230 (m-10) REVERT: A 661 GLU cc_start: 0.9536 (mm-30) cc_final: 0.9316 (mt-10) REVERT: A 664 LYS cc_start: 0.9541 (tppp) cc_final: 0.9334 (tmtt) REVERT: C 164 MET cc_start: 0.9240 (mtp) cc_final: 0.8620 (ptt) REVERT: C 213 ARG cc_start: 0.9495 (ptm-80) cc_final: 0.9259 (tmm-80) REVERT: C 283 MET cc_start: 0.9532 (mmp) cc_final: 0.9259 (tpp) REVERT: C 483 MET cc_start: 0.6786 (mmp) cc_final: 0.6288 (mtp) REVERT: B 32 HIS cc_start: 0.7647 (m-70) cc_final: 0.7437 (m170) REVERT: B 111 MET cc_start: 0.7383 (mtp) cc_final: 0.6992 (mtt) REVERT: B 131 TRP cc_start: 0.8981 (p-90) cc_final: 0.8379 (p-90) REVERT: B 137 GLN cc_start: 0.9503 (mm-40) cc_final: 0.9027 (mp10) REVERT: B 251 PHE cc_start: 0.9522 (m-80) cc_final: 0.9116 (m-80) REVERT: B 321 MET cc_start: 0.9495 (mtt) cc_final: 0.8986 (mtt) REVERT: B 414 MET cc_start: 0.7552 (mmm) cc_final: 0.7234 (tpp) REVERT: B 415 LEU cc_start: 0.9467 (tp) cc_final: 0.9172 (tp) REVERT: B 508 GLU cc_start: 0.8784 (mp0) cc_final: 0.8560 (mp0) REVERT: B 519 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8820 (mt-10) REVERT: B 527 VAL cc_start: 0.9596 (t) cc_final: 0.9244 (p) REVERT: B 546 MET cc_start: 0.9453 (mmp) cc_final: 0.9012 (mmp) REVERT: B 599 TYR cc_start: 0.9231 (m-80) cc_final: 0.8745 (m-80) REVERT: B 606 ILE cc_start: 0.8965 (mt) cc_final: 0.8559 (mp) REVERT: B 696 PHE cc_start: 0.9352 (t80) cc_final: 0.9088 (t80) outliers start: 2 outliers final: 1 residues processed: 336 average time/residue: 0.3462 time to fit residues: 167.7849 Evaluate side-chains 281 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 280 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 186 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 158 optimal weight: 3.9990 chunk 142 optimal weight: 0.4980 chunk 98 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 GLN C 27 HIS C 75 GLN C 591 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.106652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.094541 restraints weight = 488902.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.096898 restraints weight = 230907.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.098235 restraints weight = 129520.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.098974 restraints weight = 83426.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.099398 restraints weight = 60539.900| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18480 Z= 0.125 Angle : 0.542 6.254 25043 Z= 0.290 Chirality : 0.039 0.416 2770 Planarity : 0.004 0.060 3147 Dihedral : 9.988 84.158 2762 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.15 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % 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 aren not related in a simple way. whole: -0.81 (0.18), residues: 2175 helix: 1.05 (0.17), residues: 960 sheet: -2.01 (0.30), residues: 247 loop : -1.78 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 706 TYR 0.013 0.001 TYR A 393 PHE 0.025 0.001 PHE A 446 TRP 0.012 0.001 TRP C 537 HIS 0.003 0.001 HIS A 510 Details of bonding type rmsd covalent geometry : bond 0.00273 (18480) covalent geometry : angle 0.54159 (25043) hydrogen bonds : bond 0.04328 ( 792) hydrogen bonds : angle 4.90230 ( 2224) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 108 is missing expected H atoms. Skipping. Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue VAL 655 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue ALA 674 is missing expected H atoms. Skipping. Residue THR 676 is missing expected H atoms. Skipping. Residue ALA 684 is missing expected H atoms. Skipping. Evaluate side-chains 317 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 0.947 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: A 311 MET cc_start: 0.9491 (mmp) cc_final: 0.9194 (mmp) REVERT: A 360 MET cc_start: 0.5974 (mmm) cc_final: 0.5704 (mmm) REVERT: A 485 MET cc_start: 0.6457 (mtm) cc_final: 0.5807 (ptp) REVERT: A 581 MET cc_start: 0.9023 (ttm) cc_final: 0.8558 (ttm) REVERT: A 587 GLN cc_start: 0.9383 (tt0) cc_final: 0.8862 (mm110) REVERT: A 607 MET cc_start: 0.9054 (mmt) cc_final: 0.8486 (mmm) REVERT: A 661 GLU cc_start: 0.9513 (mm-30) cc_final: 0.9289 (mt-10) REVERT: A 664 LYS cc_start: 0.9482 (tppp) cc_final: 0.9256 (tmtt) REVERT: C 146 ASP cc_start: 0.8100 (m-30) cc_final: 0.7704 (t70) REVERT: C 297 ILE cc_start: 0.8490 (tp) cc_final: 0.8234 (pt) REVERT: C 460 MET cc_start: -0.2513 (ptt) cc_final: -0.2893 (ptt) REVERT: C 483 MET cc_start: 0.6756 (mmp) cc_final: 0.6454 (mtp) REVERT: B 137 GLN cc_start: 0.9491 (mm-40) cc_final: 0.9081 (mp10) REVERT: B 348 MET cc_start: 0.9144 (mmt) cc_final: 0.8731 (mmt) REVERT: B 519 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8658 (mt-10) REVERT: B 527 VAL cc_start: 0.9645 (t) cc_final: 0.9199 (p) REVERT: B 532 ASN cc_start: 0.9538 (m110) cc_final: 0.9308 (m-40) REVERT: B 533 ASN cc_start: 0.9257 (m110) cc_final: 0.8960 (m110) REVERT: B 554 ASP cc_start: 0.9296 (m-30) cc_final: 0.9082 (m-30) REVERT: B 599 TYR cc_start: 0.9075 (m-80) cc_final: 0.8311 (m-10) REVERT: B 606 ILE cc_start: 0.8906 (mt) cc_final: 0.8450 (mp) REVERT: B 657 TYR cc_start: 0.8894 (p90) cc_final: 0.8116 (p90) outliers start: 0 outliers final: 0 residues processed: 317 average time/residue: 0.3411 time to fit residues: 156.5721 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 : 0.937 ------------------------------------------------------------------------------- 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: 9.9990 chunk 139 optimal weight: 30.0000 chunk 136 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 118 optimal weight: 20.0000 chunk 146 optimal weight: 10.0000 chunk 170 optimal weight: 7.9990 chunk 27 optimal weight: 0.2980 chunk 201 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 overall best weight: 6.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 HIS B 136 ASN ** B 600 ASN ** 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 = 0.3894 r_free = 0.3894 target = 0.076050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.055848 restraints weight = 345223.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.058411 restraints weight = 209961.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.060261 restraints weight = 142957.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.061514 restraints weight = 106337.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.062366 restraints weight = 85148.296| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 18480 Z= 0.296 Angle : 0.714 8.344 25043 Z= 0.396 Chirality : 0.042 0.379 2770 Planarity : 0.005 0.084 3147 Dihedral : 10.195 78.855 2762 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.34 % Favored : 93.56 % Rotamer: Outliers : 0.10 % Allowed : 2.42 % Favored : 97.48 % 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 aren not related in a simple way. whole: -1.60 (0.17), residues: 2175 helix: 0.18 (0.16), residues: 956 sheet: -2.02 (0.32), residues: 217 loop : -2.09 (0.18), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 442 TYR 0.020 0.002 TYR A 393 PHE 0.056 0.003 PHE C 330 TRP 0.017 0.002 TRP A 422 HIS 0.018 0.002 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00583 (18480) covalent geometry : angle 0.71386 (25043) hydrogen bonds : bond 0.04812 ( 792) hydrogen bonds : angle 5.35856 ( 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 300 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 298 time to evaluate : 0.869 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 360 MET cc_start: 0.6740 (mmm) cc_final: 0.6110 (mmm) REVERT: A 587 GLN cc_start: 0.9451 (tt0) cc_final: 0.9150 (tp40) REVERT: A 607 MET cc_start: 0.9058 (mmt) cc_final: 0.8682 (mmm) REVERT: A 664 LYS cc_start: 0.9540 (tppp) cc_final: 0.9334 (tmtt) REVERT: C 50 MET cc_start: 0.9515 (tpt) cc_final: 0.9277 (tpp) REVERT: C 146 ASP cc_start: 0.8606 (m-30) cc_final: 0.8175 (t70) REVERT: C 283 MET cc_start: 0.9537 (mmp) cc_final: 0.9312 (tpp) REVERT: C 297 ILE cc_start: 0.8705 (tp) cc_final: 0.8472 (pt) REVERT: C 458 MET cc_start: 0.1147 (ptt) cc_final: 0.0946 (ptm) REVERT: C 460 MET cc_start: -0.1312 (ptt) cc_final: -0.1979 (ptt) REVERT: C 483 MET cc_start: 0.6851 (mmp) cc_final: 0.6436 (mtp) REVERT: B 111 MET cc_start: 0.7214 (mtp) cc_final: 0.6714 (mtp) REVERT: B 137 GLN cc_start: 0.9482 (mm-40) cc_final: 0.9244 (mp10) REVERT: B 508 GLU cc_start: 0.8556 (mp0) cc_final: 0.8077 (mp0) REVERT: B 527 VAL cc_start: 0.9654 (t) cc_final: 0.9373 (p) REVERT: B 530 ILE cc_start: 0.9818 (mt) cc_final: 0.9577 (tt) REVERT: B 532 ASN cc_start: 0.9621 (m110) cc_final: 0.9374 (m110) REVERT: B 533 ASN cc_start: 0.9480 (m110) cc_final: 0.9238 (m110) REVERT: B 546 MET cc_start: 0.9440 (mmp) cc_final: 0.8986 (mmp) REVERT: B 606 ILE cc_start: 0.9119 (mt) cc_final: 0.8891 (mp) REVERT: B 696 PHE cc_start: 0.9349 (t80) cc_final: 0.9071 (t80) outliers start: 2 outliers final: 2 residues processed: 300 average time/residue: 0.3415 time to fit residues: 148.6658 Evaluate side-chains 264 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 262 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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: 10.0000 chunk 119 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 139 optimal weight: 20.0000 chunk 194 optimal weight: 7.9990 chunk 148 optimal weight: 2.9990 chunk 213 optimal weight: 9.9990 chunk 159 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 GLN ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN C 591 GLN B 136 ASN ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.076042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.056130 restraints weight = 344192.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.058826 restraints weight = 206206.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.060641 restraints weight = 138891.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.061884 restraints weight = 102885.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.062752 restraints weight = 82138.208| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.5469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18480 Z= 0.188 Angle : 0.574 5.713 25043 Z= 0.317 Chirality : 0.039 0.398 2770 Planarity : 0.005 0.058 3147 Dihedral : 10.125 78.574 2762 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.84 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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 aren not related in a simple way. whole: -1.30 (0.17), residues: 2175 helix: 0.47 (0.16), residues: 963 sheet: -2.02 (0.30), residues: 229 loop : -1.94 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 583 TYR 0.017 0.001 TYR B 82 PHE 0.015 0.002 PHE B 505 TRP 0.013 0.001 TRP B 55 HIS 0.013 0.001 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00373 (18480) covalent geometry : angle 0.57425 (25043) hydrogen bonds : bond 0.04280 ( 792) hydrogen bonds : angle 5.12674 ( 2224) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 108 is missing expected H atoms. Skipping. Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue VAL 655 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue ALA 674 is missing expected H atoms. Skipping. Residue THR 676 is missing expected H atoms. Skipping. Residue ALA 684 is missing expected H atoms. Skipping. Evaluate side-chains 291 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.933 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 311 MET cc_start: 0.9666 (mmp) cc_final: 0.9224 (mmp) REVERT: A 360 MET cc_start: 0.6830 (mmm) cc_final: 0.6131 (mmm) REVERT: A 587 GLN cc_start: 0.9479 (tt0) cc_final: 0.9146 (tp40) REVERT: A 607 MET cc_start: 0.8929 (mmt) cc_final: 0.8463 (mmm) REVERT: A 664 LYS cc_start: 0.9511 (tppp) cc_final: 0.9297 (tmtt) REVERT: C 50 MET cc_start: 0.9497 (tpt) cc_final: 0.9263 (tpp) REVERT: C 146 ASP cc_start: 0.8602 (m-30) cc_final: 0.8178 (t70) REVERT: C 283 MET cc_start: 0.9556 (mmp) cc_final: 0.9221 (tpp) REVERT: C 297 ILE cc_start: 0.8663 (tp) cc_final: 0.8456 (pt) REVERT: C 460 MET cc_start: -0.0944 (ptt) cc_final: -0.1412 (ptt) REVERT: C 483 MET cc_start: 0.7261 (mmp) cc_final: 0.6875 (mtp) REVERT: B 21 THR cc_start: 0.8889 (p) cc_final: 0.8668 (p) REVERT: B 111 MET cc_start: 0.7250 (mtp) cc_final: 0.6748 (mtp) REVERT: B 137 GLN cc_start: 0.9442 (mm-40) cc_final: 0.8956 (mp10) REVERT: B 348 MET cc_start: 0.9044 (mmt) cc_final: 0.8738 (mmt) REVERT: B 519 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8880 (mt-10) REVERT: B 527 VAL cc_start: 0.9686 (t) cc_final: 0.9422 (p) REVERT: B 532 ASN cc_start: 0.9603 (m110) cc_final: 0.9360 (m110) REVERT: B 546 MET cc_start: 0.9418 (mmp) cc_final: 0.8962 (mmp) REVERT: B 606 ILE cc_start: 0.9149 (mt) cc_final: 0.8912 (mp) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.3471 time to fit residues: 145.3434 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 : 0.835 ------------------------------------------------------------------------------- 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: 0.9980 chunk 117 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 153 optimal weight: 6.9990 chunk 143 optimal weight: 9.9990 chunk 188 optimal weight: 6.9990 chunk 196 optimal weight: 6.9990 chunk 162 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 165 optimal weight: 0.7980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 723 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 = 0.4251 r_free = 0.4251 target = 0.099816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.087616 restraints weight = 498023.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.089859 restraints weight = 233583.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.091141 restraints weight = 131281.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.091839 restraints weight = 85119.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.092252 restraints weight = 63388.346| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 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 0.037 18480 Z= 0.119 Angle : 0.520 6.333 25043 Z= 0.280 Chirality : 0.039 0.393 2770 Planarity : 0.004 0.068 3147 Dihedral : 9.986 79.048 2762 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.52 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % 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 aren not related in a simple way. whole: -0.81 (0.18), residues: 2175 helix: 0.93 (0.16), residues: 964 sheet: -1.87 (0.30), residues: 233 loop : -1.70 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 209 TYR 0.018 0.001 TYR C 205 PHE 0.024 0.001 PHE C 580 TRP 0.008 0.001 TRP B 55 HIS 0.017 0.001 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00255 (18480) covalent geometry : angle 0.51996 (25043) hydrogen bonds : bond 0.03861 ( 792) hydrogen bonds : angle 4.79509 ( 2224) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 108 is missing expected H atoms. Skipping. Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue VAL 655 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue ALA 674 is missing expected H atoms. Skipping. Residue THR 676 is missing expected H atoms. Skipping. Residue ALA 684 is missing expected H atoms. Skipping. Evaluate side-chains 292 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 1.071 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: 0.9626 (mmp) cc_final: 0.9195 (mmp) REVERT: A 360 MET cc_start: 0.6778 (mmm) cc_final: 0.6120 (mmm) REVERT: A 485 MET cc_start: 0.7031 (mtm) cc_final: 0.6665 (mtt) REVERT: A 587 GLN cc_start: 0.9375 (tt0) cc_final: 0.9070 (tp40) REVERT: A 607 MET cc_start: 0.9002 (mmt) cc_final: 0.8516 (mmm) REVERT: A 664 LYS cc_start: 0.9505 (tppp) cc_final: 0.9257 (tmtt) REVERT: C 50 MET cc_start: 0.9507 (tpt) cc_final: 0.9230 (tpp) REVERT: C 146 ASP cc_start: 0.8408 (m-30) cc_final: 0.8029 (t70) REVERT: C 283 MET cc_start: 0.9557 (mmp) cc_final: 0.9278 (tpp) REVERT: C 297 ILE cc_start: 0.8530 (tp) cc_final: 0.8245 (pt) REVERT: C 460 MET cc_start: -0.1789 (ptt) cc_final: -0.2181 (ptt) REVERT: C 483 MET cc_start: 0.7241 (mmp) cc_final: 0.6913 (mtp) REVERT: B 111 MET cc_start: 0.7083 (mtp) cc_final: 0.6610 (mtp) REVERT: B 137 GLN cc_start: 0.9439 (mm-40) cc_final: 0.9036 (mp10) REVERT: B 348 MET cc_start: 0.8961 (mmt) cc_final: 0.8595 (mmt) REVERT: B 519 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8906 (mt-10) REVERT: B 527 VAL cc_start: 0.9605 (t) cc_final: 0.9362 (p) REVERT: B 532 ASN cc_start: 0.9544 (m110) cc_final: 0.9277 (m110) REVERT: B 546 MET cc_start: 0.9381 (mmp) cc_final: 0.8941 (mmp) REVERT: B 554 ASP cc_start: 0.9485 (m-30) cc_final: 0.9244 (m-30) REVERT: B 606 ILE cc_start: 0.9185 (mt) cc_final: 0.8971 (mp) outliers start: 0 outliers final: 0 residues processed: 292 average time/residue: 0.3218 time to fit residues: 137.2094 Evaluate side-chains 258 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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: 7.9990 chunk 193 optimal weight: 5.9990 chunk 161 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 chunk 182 optimal weight: 9.9990 chunk 216 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 158 optimal weight: 0.8980 chunk 99 optimal weight: 10.0000 chunk 152 optimal weight: 10.0000 chunk 111 optimal weight: 30.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 GLN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 GLN C 723 ASN B 136 ASN ** B 600 ASN ** 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 = 0.3875 r_free = 0.3875 target = 0.075390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.055424 restraints weight = 341469.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.057948 restraints weight = 206400.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.059776 restraints weight = 140826.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.061062 restraints weight = 104820.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.061953 restraints weight = 83461.936| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.6051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 18480 Z= 0.221 Angle : 0.590 10.907 25043 Z= 0.327 Chirality : 0.039 0.404 2770 Planarity : 0.004 0.067 3147 Dihedral : 10.057 75.724 2762 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.57 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % 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 aren not related in a simple way. whole: -1.12 (0.17), residues: 2175 helix: 0.59 (0.16), residues: 970 sheet: -2.01 (0.30), residues: 237 loop : -1.79 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 646 TYR 0.015 0.002 TYR C 228 PHE 0.036 0.002 PHE B 696 TRP 0.010 0.001 TRP A 422 HIS 0.011 0.001 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00432 (18480) covalent geometry : angle 0.58994 (25043) hydrogen bonds : bond 0.04241 ( 792) hydrogen bonds : angle 5.05888 ( 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 282 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 MET cc_start: 0.9666 (mmp) cc_final: 0.9239 (mmp) REVERT: A 360 MET cc_start: 0.6812 (mmm) cc_final: 0.6267 (mmm) REVERT: A 446 PHE cc_start: 0.9369 (m-80) cc_final: 0.8947 (m-10) REVERT: A 587 GLN cc_start: 0.9475 (tt0) cc_final: 0.9160 (tp40) REVERT: A 607 MET cc_start: 0.8929 (mmt) cc_final: 0.8478 (mmm) REVERT: A 612 PHE cc_start: 0.8723 (m-80) cc_final: 0.8360 (m-80) REVERT: A 646 PHE cc_start: 0.9398 (m-80) cc_final: 0.8858 (m-80) REVERT: A 664 LYS cc_start: 0.9504 (tppp) cc_final: 0.9299 (tmtt) REVERT: A 699 TRP cc_start: 0.9329 (t-100) cc_final: 0.8849 (t-100) REVERT: C 146 ASP cc_start: 0.8685 (m-30) cc_final: 0.8369 (t0) REVERT: C 283 MET cc_start: 0.9587 (mmp) cc_final: 0.9245 (tpp) REVERT: C 297 ILE cc_start: 0.8655 (tp) cc_final: 0.8368 (pt) REVERT: C 460 MET cc_start: -0.1246 (ptt) cc_final: -0.1623 (ptt) REVERT: C 483 MET cc_start: 0.7282 (mmp) cc_final: 0.6927 (mtp) REVERT: B 111 MET cc_start: 0.7235 (mtp) cc_final: 0.6741 (mtp) REVERT: B 137 GLN cc_start: 0.9455 (mm-40) cc_final: 0.9016 (mp10) REVERT: B 348 MET cc_start: 0.8987 (mmt) cc_final: 0.8677 (mmt) REVERT: B 527 VAL cc_start: 0.9615 (t) cc_final: 0.9346 (p) REVERT: B 532 ASN cc_start: 0.9575 (m110) cc_final: 0.9354 (m110) REVERT: B 534 MET cc_start: 0.9298 (tpp) cc_final: 0.8999 (tpp) REVERT: B 546 MET cc_start: 0.9421 (mmp) cc_final: 0.8956 (mmp) REVERT: B 554 ASP cc_start: 0.9477 (m-30) cc_final: 0.9258 (m-30) REVERT: B 606 ILE cc_start: 0.9164 (mt) cc_final: 0.8937 (mp) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.3284 time to fit residues: 134.6588 Evaluate side-chains 252 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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: 8.9990 chunk 70 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 184 optimal weight: 0.9990 chunk 44 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 chunk 182 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 548 ASN C 723 ASN B 136 ASN ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.097276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.085487 restraints weight = 499277.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.087913 restraints weight = 252333.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.089247 restraints weight = 117242.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.089491 restraints weight = 71164.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.089590 restraints weight = 69704.377| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.6206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18480 Z= 0.136 Angle : 0.533 9.753 25043 Z= 0.287 Chirality : 0.039 0.399 2770 Planarity : 0.004 0.070 3147 Dihedral : 10.000 77.730 2762 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.93 % Favored : 94.02 % 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 aren not related in a simple way. whole: -0.79 (0.18), residues: 2175 helix: 0.89 (0.16), residues: 974 sheet: -1.84 (0.30), residues: 241 loop : -1.67 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 646 TYR 0.015 0.001 TYR A 130 PHE 0.027 0.001 PHE B 696 TRP 0.024 0.001 TRP C 537 HIS 0.010 0.001 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00281 (18480) covalent geometry : angle 0.53266 (25043) hydrogen bonds : bond 0.03871 ( 792) hydrogen bonds : angle 4.79872 ( 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 282 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 1.016 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 21 MET cc_start: 0.8818 (mtp) cc_final: 0.8479 (mtp) REVERT: A 47 MET cc_start: 0.1402 (ttm) cc_final: 0.1093 (ttm) REVERT: A 311 MET cc_start: 0.9647 (mmp) cc_final: 0.9209 (mmp) REVERT: A 360 MET cc_start: 0.6669 (mmm) cc_final: 0.6088 (mmm) REVERT: A 446 PHE cc_start: 0.9395 (m-80) cc_final: 0.8949 (m-10) REVERT: A 485 MET cc_start: 0.6954 (mtm) cc_final: 0.6547 (mtt) REVERT: A 587 GLN cc_start: 0.9483 (tt0) cc_final: 0.9129 (tp40) REVERT: A 607 MET cc_start: 0.8983 (mmt) cc_final: 0.8518 (mmm) REVERT: A 612 PHE cc_start: 0.8603 (m-80) cc_final: 0.8306 (m-80) REVERT: A 646 PHE cc_start: 0.9335 (m-80) cc_final: 0.8740 (m-80) REVERT: A 664 LYS cc_start: 0.9530 (tppp) cc_final: 0.9302 (tmtt) REVERT: A 699 TRP cc_start: 0.9280 (t-100) cc_final: 0.8784 (t-100) REVERT: C 46 ARG cc_start: 0.9132 (tpp-160) cc_final: 0.8877 (tpp-160) REVERT: C 50 MET cc_start: 0.9395 (tpt) cc_final: 0.9112 (tpp) REVERT: C 146 ASP cc_start: 0.8728 (m-30) cc_final: 0.8258 (t70) REVERT: C 283 MET cc_start: 0.9569 (mmp) cc_final: 0.9279 (tpp) REVERT: C 297 ILE cc_start: 0.8500 (tp) cc_final: 0.8228 (pt) REVERT: C 460 MET cc_start: -0.1804 (ptt) cc_final: -0.2136 (ptt) REVERT: B 111 MET cc_start: 0.7092 (mtp) cc_final: 0.6664 (mtp) REVERT: B 137 GLN cc_start: 0.9425 (mm-40) cc_final: 0.9017 (mp10) REVERT: B 348 MET cc_start: 0.8962 (mmt) cc_final: 0.8619 (mmt) REVERT: B 519 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8890 (mt-10) REVERT: B 527 VAL cc_start: 0.9614 (t) cc_final: 0.9352 (p) REVERT: B 532 ASN cc_start: 0.9502 (m110) cc_final: 0.9244 (m110) REVERT: B 546 MET cc_start: 0.9348 (mmp) cc_final: 0.8888 (mmp) REVERT: B 554 ASP cc_start: 0.9477 (m-30) cc_final: 0.9250 (m-30) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.3525 time to fit residues: 146.8165 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 : 0.947 ------------------------------------------------------------------------------- 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: 8.9990 chunk 90 optimal weight: 3.9990 chunk 211 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 chunk 156 optimal weight: 7.9990 chunk 122 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 133 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 723 ASN B 136 ASN B 137 GLN ** 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 = 0.3860 r_free = 0.3860 target = 0.074175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.054219 restraints weight = 336197.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.056818 restraints weight = 204464.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.058636 restraints weight = 137914.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.059874 restraints weight = 102290.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.060790 restraints weight = 82342.606| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.6503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18480 Z= 0.176 Angle : 0.555 9.053 25043 Z= 0.306 Chirality : 0.039 0.397 2770 Planarity : 0.004 0.065 3147 Dihedral : 9.982 73.981 2762 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.62 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.18), residues: 2175 helix: 0.86 (0.16), residues: 969 sheet: -1.87 (0.31), residues: 235 loop : -1.69 (0.20), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 179 TYR 0.014 0.001 TYR A 334 PHE 0.029 0.002 PHE B 696 TRP 0.010 0.001 TRP B 55 HIS 0.009 0.001 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00350 (18480) covalent geometry : angle 0.55546 (25043) hydrogen bonds : bond 0.04005 ( 792) hydrogen bonds : angle 4.84496 ( 2224) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4350 Ramachandran restraints generated. 2175 Oldfield, 0 Emsley, 2175 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 108 is missing expected H atoms. Skipping. Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Residue ALA 588 is missing expected H atoms. Skipping. Residue THR 612 is missing expected H atoms. Skipping. Residue VAL 613 is missing expected H atoms. Skipping. Residue VAL 655 is missing expected H atoms. Skipping. Residue ALA 661 is missing expected H atoms. Skipping. Residue VAL 667 is missing expected H atoms. Skipping. Residue ALA 674 is missing expected H atoms. Skipping. Residue THR 676 is missing expected H atoms. Skipping. Residue ALA 684 is missing expected H atoms. Skipping. Evaluate side-chains 281 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.976 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 21 MET cc_start: 0.8911 (mtp) cc_final: 0.8622 (mtp) REVERT: A 360 MET cc_start: 0.6738 (mmm) cc_final: 0.6426 (mmm) REVERT: A 446 PHE cc_start: 0.9373 (m-80) cc_final: 0.8995 (m-10) REVERT: A 587 GLN cc_start: 0.9515 (tt0) cc_final: 0.9152 (tp40) REVERT: A 607 MET cc_start: 0.8916 (mmt) cc_final: 0.8461 (mmm) REVERT: A 646 PHE cc_start: 0.9383 (m-80) cc_final: 0.8952 (m-80) REVERT: A 664 LYS cc_start: 0.9569 (tppp) cc_final: 0.9262 (tptt) REVERT: C 50 MET cc_start: 0.9346 (tpt) cc_final: 0.9092 (tpp) REVERT: C 121 LYS cc_start: 0.9590 (ttmt) cc_final: 0.9383 (tppt) REVERT: C 146 ASP cc_start: 0.8553 (m-30) cc_final: 0.8170 (t70) REVERT: C 283 MET cc_start: 0.9571 (mmp) cc_final: 0.9234 (tpp) REVERT: C 297 ILE cc_start: 0.8680 (tp) cc_final: 0.8391 (pt) REVERT: C 460 MET cc_start: -0.0454 (ptt) cc_final: -0.0756 (ptt) REVERT: B 348 MET cc_start: 0.8932 (mmt) cc_final: 0.8605 (mmt) REVERT: B 527 VAL cc_start: 0.9593 (t) cc_final: 0.9133 (p) REVERT: B 532 ASN cc_start: 0.9551 (m110) cc_final: 0.9312 (m110) REVERT: B 546 MET cc_start: 0.9393 (mmp) cc_final: 0.8915 (mmm) REVERT: B 554 ASP cc_start: 0.9462 (m-30) cc_final: 0.9239 (m-30) REVERT: B 599 TYR cc_start: 0.9146 (m-80) cc_final: 0.8706 (m-80) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.3616 time to fit residues: 148.8328 Evaluate side-chains 251 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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: 10.0000 chunk 146 optimal weight: 30.0000 chunk 145 optimal weight: 20.0000 chunk 153 optimal weight: 4.9990 chunk 199 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 214 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 723 ASN B 136 ASN B 292 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 = 0.4185 r_free = 0.4185 target = 0.095302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.083234 restraints weight = 505069.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.085427 restraints weight = 233265.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.086692 restraints weight = 131893.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.087364 restraints weight = 86100.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.087771 restraints weight = 64990.368| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.6718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18480 Z= 0.149 Angle : 0.540 8.380 25043 Z= 0.293 Chirality : 0.039 0.402 2770 Planarity : 0.004 0.066 3147 Dihedral : 9.950 75.590 2762 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.25 % Favored : 93.70 % 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 aren not related in a simple way. whole: -0.74 (0.18), residues: 2175 helix: 0.92 (0.16), residues: 978 sheet: -1.62 (0.32), residues: 219 loop : -1.70 (0.20), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 260 TYR 0.016 0.001 TYR A 334 PHE 0.022 0.002 PHE B 696 TRP 0.010 0.001 TRP B 55 HIS 0.010 0.001 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00302 (18480) covalent geometry : angle 0.53960 (25043) hydrogen bonds : bond 0.03787 ( 792) hydrogen bonds : angle 4.76490 ( 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 282 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 MET cc_start: 0.8843 (mtp) cc_final: 0.8493 (mtp) REVERT: A 47 MET cc_start: 0.1560 (ttm) cc_final: 0.1229 (ttm) REVERT: A 360 MET cc_start: 0.6803 (mmm) cc_final: 0.6497 (mmm) REVERT: A 431 ASP cc_start: 0.8967 (p0) cc_final: 0.8703 (m-30) REVERT: A 446 PHE cc_start: 0.9388 (m-80) cc_final: 0.9017 (m-10) REVERT: A 587 GLN cc_start: 0.9509 (tt0) cc_final: 0.9117 (tp40) REVERT: A 607 MET cc_start: 0.8935 (mmt) cc_final: 0.8449 (mmm) REVERT: A 664 LYS cc_start: 0.9580 (tppp) cc_final: 0.9260 (tptt) REVERT: C 46 ARG cc_start: 0.9192 (tpp-160) cc_final: 0.8966 (tpp-160) REVERT: C 50 MET cc_start: 0.9312 (tpt) cc_final: 0.9081 (tpp) REVERT: C 146 ASP cc_start: 0.8597 (m-30) cc_final: 0.8079 (t70) REVERT: C 151 HIS cc_start: 0.8834 (p90) cc_final: 0.8494 (p90) REVERT: C 153 ASP cc_start: 0.8648 (t0) cc_final: 0.8008 (m-30) REVERT: C 283 MET cc_start: 0.9581 (mmp) cc_final: 0.9267 (tpp) REVERT: C 297 ILE cc_start: 0.8539 (tp) cc_final: 0.8256 (pt) REVERT: C 460 MET cc_start: -0.0230 (ptt) cc_final: -0.0502 (ptt) REVERT: B 7 LEU cc_start: 0.9600 (tp) cc_final: 0.9380 (tp) REVERT: B 174 MET cc_start: 0.8627 (tpt) cc_final: 0.8383 (tpt) REVERT: B 348 MET cc_start: 0.8910 (mmt) cc_final: 0.8571 (mmt) REVERT: B 447 PHE cc_start: 0.8287 (p90) cc_final: 0.7753 (p90) REVERT: B 508 GLU cc_start: 0.8842 (mp0) cc_final: 0.8621 (mp0) REVERT: B 527 VAL cc_start: 0.9609 (t) cc_final: 0.9112 (p) REVERT: B 532 ASN cc_start: 0.9492 (m110) cc_final: 0.9228 (m110) REVERT: B 546 MET cc_start: 0.9344 (mmp) cc_final: 0.8879 (mmm) REVERT: B 554 ASP cc_start: 0.9480 (m-30) cc_final: 0.9256 (m-30) REVERT: B 599 TYR cc_start: 0.9059 (m-80) cc_final: 0.8639 (m-80) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.3607 time to fit residues: 150.0504 Evaluate side-chains 252 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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: 6.9990 chunk 11 optimal weight: 10.0000 chunk 194 optimal weight: 0.4980 chunk 80 optimal weight: 10.0000 chunk 196 optimal weight: 0.6980 chunk 47 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 131 optimal weight: 8.9990 chunk 141 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 179 optimal weight: 4.9990 overall best weight: 4.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 723 ASN B 136 ASN B 292 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.072676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.053704 restraints weight = 348393.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.056202 restraints weight = 208038.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.057919 restraints weight = 140493.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.059145 restraints weight = 104429.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.059941 restraints weight = 83342.920| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.7003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18480 Z= 0.179 Angle : 0.563 8.302 25043 Z= 0.309 Chirality : 0.039 0.407 2770 Planarity : 0.004 0.080 3147 Dihedral : 9.967 73.564 2762 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.39 % Favored : 93.56 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.18), residues: 2175 helix: 0.69 (0.16), residues: 983 sheet: -1.62 (0.32), residues: 221 loop : -1.78 (0.19), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 646 TYR 0.016 0.002 TYR A 334 PHE 0.030 0.002 PHE A 707 TRP 0.011 0.001 TRP B 55 HIS 0.010 0.001 HIS B 605 Details of bonding type rmsd covalent geometry : bond 0.00355 (18480) covalent geometry : angle 0.56332 (25043) hydrogen bonds : bond 0.03925 ( 792) hydrogen bonds : angle 4.88325 ( 2224) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6142.80 seconds wall clock time: 105 minutes 39.83 seconds (6339.83 seconds total)