Starting phenix.real_space_refine on Fri Jul 3 13:31:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v46_64768/07_2026/9v46_64768.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v46_64768/07_2026/9v46_64768.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9v46_64768/07_2026/9v46_64768.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v46_64768/07_2026/9v46_64768.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v46_64768/07_2026/9v46_64768.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v46_64768/07_2026/9v46_64768.map" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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: 5 Type Number sf(0) Gaussians P 25 5.49 5 S 103 5.16 5 C 8752 2.51 5 N 2426 2.21 5 O 2699 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14005 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 692, 5621 Classifications: {'peptide': 692} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 661} Chain breaks: 3 Chain: "B" Number of atoms: 5844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5844 Classifications: {'peptide': 732} Link IDs: {'PTRANS': 32, 'TRANS': 699} Chain breaks: 2 Chain: "C" Number of atoms: 2002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2002 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 12, 'TRANS': 234} Chain: "E" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 185 Classifications: {'RNA': 9} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 1, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 6} Chain: "F" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 353 Classifications: {'RNA': 16} Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna3p_pur': 11, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 14} Time building chain proxies: 3.22, per 1000 atoms: 0.23 Number of scatterers: 14005 At special positions: 0 Unit cell: (103.88, 138.86, 111.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 103 16.00 P 25 15.00 O 2699 8.00 N 2426 7.00 C 8752 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 611.8 milliseconds 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3162 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 16 sheets defined 50.0% alpha, 9.1% beta 2 base pairs and 12 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 removed outlier: 3.640A pdb=" N CYS A 8 " --> pdb=" O PHE A 4 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE A 9 " --> pdb=" O VAL A 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4 through 9' Processing helix chain 'A' and resid 10 through 22 removed outlier: 3.925A pdb=" N ALA A 20 " --> pdb=" O LEU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 49 removed outlier: 3.948A pdb=" N ALA A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 97 Processing helix chain 'A' and resid 127 through 138 Processing helix chain 'A' and resid 156 through 160 Processing helix chain 'A' and resid 165 through 178 Processing helix chain 'A' and resid 179 through 184 removed outlier: 4.038A pdb=" N ASN A 184 " --> pdb=" O GLN A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 225 through 235 removed outlier: 4.117A pdb=" N GLY A 235 " --> pdb=" O ALA A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 249 Processing helix chain 'A' and resid 302 through 313 removed outlier: 4.135A pdb=" N THR A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 348 removed outlier: 3.560A pdb=" N LEU A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 341 " --> pdb=" O SER A 337 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU A 342 " --> pdb=" O TRP A 338 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA A 343 " --> pdb=" O LYS A 339 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 369 removed outlier: 3.818A pdb=" N ALA A 369 " --> pdb=" O GLN A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 416 removed outlier: 4.411A pdb=" N ASN A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU A 416 " --> pdb=" O ASN A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 452 removed outlier: 3.929A pdb=" N TYR A 445 " --> pdb=" O MET A 441 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N HIS A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 476 Processing helix chain 'A' and resid 529 through 538 removed outlier: 3.656A pdb=" N LEU A 532 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Proline residue: A 534 - end of helix removed outlier: 3.509A pdb=" N GLU A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 580 removed outlier: 3.570A pdb=" N GLU A 580 " --> pdb=" O LYS A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 604 removed outlier: 3.560A pdb=" N GLN A 587 " --> pdb=" O ARG A 583 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLN A 591 " --> pdb=" O GLN A 587 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET A 595 " --> pdb=" O GLN A 591 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A 598 " --> pdb=" O SER A 594 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU A 599 " --> pdb=" O MET A 595 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LYS A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU A 604 " --> pdb=" O SER A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 613 Processing helix chain 'A' and resid 632 through 650 removed outlier: 3.647A pdb=" N LYS A 643 " --> pdb=" O THR A 639 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER A 644 " --> pdb=" O LEU A 640 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 674 removed outlier: 4.555A pdb=" N LYS A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP A 674 " --> pdb=" O GLN A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 removed outlier: 3.583A pdb=" N LEU A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 713 Processing helix chain 'B' and resid 4 through 11 Processing helix chain 'B' and resid 17 through 22 removed outlier: 3.576A pdb=" N PHE B 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 removed outlier: 3.562A pdb=" N THR B 39 " --> pdb=" O GLY B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 99 removed outlier: 3.746A pdb=" N MET B 92 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 118 through 124 removed outlier: 3.651A pdb=" N ARG B 121 " --> pdb=" O ARG B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 153 removed outlier: 3.920A pdb=" N ASN B 153 " --> pdb=" O VAL B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.588A pdb=" N GLY B 161 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 174 removed outlier: 4.164A pdb=" N MET B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 221 Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 275 through 292 removed outlier: 3.946A pdb=" N LYS B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS B 288 " --> pdb=" O ASN B 284 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N MET B 289 " --> pdb=" O VAL B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 312 removed outlier: 3.586A pdb=" N GLU B 311 " --> pdb=" O LYS B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 removed outlier: 3.564A pdb=" N PHE B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.540A pdb=" N ALA B 340 " --> pdb=" O ILE B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix removed outlier: 3.828A pdb=" N ASN B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 376 Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' Processing helix chain 'B' and resid 414 through 426 Processing helix chain 'B' and resid 455 through 472 Processing helix chain 'B' and resid 519 through 536 removed outlier: 3.659A pdb=" N SER B 524 " --> pdb=" O SER B 520 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE B 525 " --> pdb=" O ALA B 521 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL B 527 " --> pdb=" O MET B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 572 through 582 removed outlier: 3.757A pdb=" N LEU B 576 " --> pdb=" O ARG B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 589 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 607 through 613 Processing helix chain 'B' and resid 614 through 616 No H-bonds generated for 'chain 'B' and resid 614 through 616' Processing helix chain 'B' and resid 617 through 626 removed outlier: 3.586A pdb=" N ASN B 626 " --> pdb=" O GLY B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 698 removed outlier: 3.601A pdb=" N GLU B 684 " --> pdb=" O ARG B 680 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE B 696 " --> pdb=" O CYS B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 705 removed outlier: 6.435A pdb=" N SER B 702 " --> pdb=" O PHE B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 733 removed outlier: 3.530A pdb=" N GLU B 731 " --> pdb=" O ARG B 727 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER B 732 " --> pdb=" O ILE B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 753 removed outlier: 4.041A pdb=" N PHE B 740 " --> pdb=" O LYS B 736 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU B 753 " --> pdb=" O THR B 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 13 removed outlier: 4.321A pdb=" N GLN C 13 " --> pdb=" O ASN C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 22 Processing helix chain 'C' and resid 24 through 32 removed outlier: 4.144A pdb=" N ALA C 29 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 51 removed outlier: 3.589A pdb=" N ARG C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 67 Processing helix chain 'C' and resid 93 through 100 removed outlier: 3.872A pdb=" N THR C 97 " --> pdb=" O PRO C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 removed outlier: 4.387A pdb=" N VAL C 114 " --> pdb=" O HIS C 110 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR C 115 " --> pdb=" O TYR C 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 110 through 115' Processing helix chain 'C' and resid 115 through 127 removed outlier: 3.907A pdb=" N LYS C 121 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL C 122 " --> pdb=" O TYR C 118 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N HIS C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 168 removed outlier: 3.559A pdb=" N VAL C 162 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE C 168 " --> pdb=" O MET C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 172 removed outlier: 3.652A pdb=" N VAL C 172 " --> pdb=" O PRO C 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 169 through 172' Processing helix chain 'C' and resid 179 through 193 Processing helix chain 'C' and resid 199 through 212 removed outlier: 3.501A pdb=" N VAL C 212 " --> pdb=" O GLU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 230 Processing helix chain 'C' and resid 231 through 236 removed outlier: 3.896A pdb=" N GLN C 236 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.858A pdb=" N LYS A 73 " --> pdb=" O ILE A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.601A pdb=" N GLU A 119 " --> pdb=" O HIS A 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 293 removed outlier: 8.248A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 546 " --> pdb=" O MET A 561 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU A 563 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N GLU A 544 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL A 565 " --> pdb=" O VAL A 542 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N VAL A 542 " --> pdb=" O VAL A 565 " (cutoff:3.500A) removed outlier: 10.502A pdb=" N CYS A 541 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ILE A 322 " --> pdb=" O CYS A 541 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N LEU A 543 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE A 545 " --> pdb=" O LYS A 318 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 290 through 293 removed outlier: 3.966A pdb=" N CYS A 489 " --> pdb=" O LYS A 497 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 377 through 378 Processing sheet with id=AA7, first strand: chain 'B' and resid 54 through 56 Processing sheet with id=AA8, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AA9, first strand: chain 'B' and resid 178 through 182 Processing sheet with id=AB1, first strand: chain 'B' and resid 240 through 243 removed outlier: 3.660A pdb=" N ARG B 350 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N THR B 226 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 437 through 442 removed outlier: 3.800A pdb=" N TRP B 437 " --> pdb=" O ASN B 452 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN B 452 " --> pdb=" O TRP B 437 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 489 through 492 Processing sheet with id=AB4, first strand: chain 'B' and resid 642 through 643 Processing sheet with id=AB5, first strand: chain 'B' and resid 667 through 668 removed outlier: 4.441A pdb=" N ILE B 667 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N MET C 81 " --> pdb=" O MET C 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 133 through 135 Processing sheet with id=AB7, first strand: chain 'C' and resid 141 through 146 567 hydrogen bonds defined for protein. 1590 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 5 hydrogen bonds 10 hydrogen bond angles 0 basepair planarities 2 basepair parallelities 12 stacking parallelities Total time for adding SS restraints: 2.43 Time building geometry restraints manager: 1.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4270 1.34 - 1.45: 2458 1.45 - 1.57: 7388 1.57 - 1.69: 48 1.69 - 1.81: 177 Bond restraints: 14341 Sorted by residual: bond pdb=" N ILE A 423 " pdb=" CA ILE A 423 " ideal model delta sigma weight residual 1.459 1.507 -0.048 1.25e-02 6.40e+03 1.45e+01 bond pdb=" N GLY B 275 " pdb=" CA GLY B 275 " ideal model delta sigma weight residual 1.447 1.475 -0.028 7.50e-03 1.78e+04 1.41e+01 bond pdb=" N GLU A 613 " pdb=" CA GLU A 613 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.19e-02 7.06e+03 1.04e+01 bond pdb=" N TYR A 464 " pdb=" CA TYR A 464 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.21e-02 6.83e+03 9.43e+00 bond pdb=" N LYS A 391 " pdb=" CA LYS A 391 " ideal model delta sigma weight residual 1.455 1.493 -0.039 1.27e-02 6.20e+03 9.27e+00 ... (remaining 14336 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 18775 2.49 - 4.98: 624 4.98 - 7.48: 52 7.48 - 9.97: 7 9.97 - 12.46: 2 Bond angle restraints: 19460 Sorted by residual: angle pdb=" N ARG A 179 " pdb=" CA ARG A 179 " pdb=" C ARG A 179 " ideal model delta sigma weight residual 112.57 100.76 11.81 1.13e+00 7.83e-01 1.09e+02 angle pdb=" N HIS C 110 " pdb=" CA HIS C 110 " pdb=" C HIS C 110 " ideal model delta sigma weight residual 113.02 104.07 8.95 1.20e+00 6.94e-01 5.56e+01 angle pdb=" N PRO B 272 " pdb=" CA PRO B 272 " pdb=" C PRO B 272 " ideal model delta sigma weight residual 112.33 99.87 12.46 1.87e+00 2.86e-01 4.44e+01 angle pdb=" N SER A 616 " pdb=" CA SER A 616 " pdb=" C SER A 616 " ideal model delta sigma weight residual 114.04 106.75 7.29 1.24e+00 6.50e-01 3.46e+01 angle pdb=" O GLY B 275 " pdb=" C GLY B 275 " pdb=" N ASN B 276 " ideal model delta sigma weight residual 121.85 124.74 -2.89 5.60e-01 3.19e+00 2.66e+01 ... (remaining 19455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.45: 8426 33.45 - 66.90: 338 66.90 - 100.35: 27 100.35 - 133.80: 2 133.80 - 167.25: 2 Dihedral angle restraints: 8795 sinusoidal: 3916 harmonic: 4879 Sorted by residual: dihedral pdb=" O4' C E 238 " pdb=" C1' C E 238 " pdb=" N1 C E 238 " pdb=" C2 C E 238 " ideal model delta sinusoidal sigma weight residual 200.00 52.06 147.94 1 1.50e+01 4.44e-03 7.88e+01 dihedral pdb=" O4' U E 239 " pdb=" C1' U E 239 " pdb=" N1 U E 239 " pdb=" C2 U E 239 " ideal model delta sinusoidal sigma weight residual -160.00 -68.18 -91.82 1 1.50e+01 4.44e-03 4.40e+01 dihedral pdb=" CA ASN A 184 " pdb=" C ASN A 184 " pdb=" N ARG A 185 " pdb=" CA ARG A 185 " ideal model delta harmonic sigma weight residual 180.00 154.60 25.40 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 8792 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1549 0.056 - 0.112: 455 0.112 - 0.168: 107 0.168 - 0.224: 29 0.224 - 0.280: 8 Chirality restraints: 2148 Sorted by residual: chirality pdb=" CG LEU B 282 " pdb=" CB LEU B 282 " pdb=" CD1 LEU B 282 " pdb=" CD2 LEU B 282 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C1' C E 238 " pdb=" O4' C E 238 " pdb=" C2' C E 238 " pdb=" N1 C E 238 " both_signs ideal model delta sigma weight residual False 2.47 2.21 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA ILE A 421 " pdb=" N ILE A 421 " pdb=" C ILE A 421 " pdb=" CB ILE A 421 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 2145 not shown) Planarity restraints: 2409 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 116 " -0.015 2.00e-02 2.50e+03 3.07e-02 9.42e+00 pdb=" C ARG A 116 " 0.053 2.00e-02 2.50e+03 pdb=" O ARG A 116 " -0.020 2.00e-02 2.50e+03 pdb=" N PHE A 117 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 699 " 0.014 2.00e-02 2.50e+03 2.87e-02 8.24e+00 pdb=" C PHE B 699 " -0.050 2.00e-02 2.50e+03 pdb=" O PHE B 699 " 0.018 2.00e-02 2.50e+03 pdb=" N PHE B 700 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 381 " 0.021 2.00e-02 2.50e+03 2.14e-02 8.01e+00 pdb=" CG PHE B 381 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE B 381 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE B 381 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 381 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 381 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 381 " 0.003 2.00e-02 2.50e+03 ... (remaining 2406 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 37 2.33 - 2.97: 7816 2.97 - 3.62: 20913 3.62 - 4.26: 31518 4.26 - 4.90: 50120 Nonbonded interactions: 110404 Sorted by model distance: nonbonded pdb=" ND2 ASN B 276 " pdb=" NH1 ARG C 142 " model vdw 1.688 3.200 nonbonded pdb=" O LEU B 258 " pdb=" OG SER B 261 " model vdw 2.125 3.040 nonbonded pdb=" O LYS A 635 " pdb=" OG1 THR A 639 " model vdw 2.131 3.040 nonbonded pdb=" OD1 ASP A 234 " pdb=" N GLY A 235 " model vdw 2.149 3.120 nonbonded pdb=" O PHE A 46 " pdb=" OG SER A 49 " model vdw 2.185 3.040 ... (remaining 110399 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: 7.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.930 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 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 : 0.007 0.058 14341 Z= 0.395 Angle : 1.011 12.459 19460 Z= 0.644 Chirality : 0.059 0.280 2148 Planarity : 0.006 0.062 2409 Dihedral : 17.358 167.246 5633 Min Nonbonded Distance : 1.688 Molprobity Statistics. All-atom Clashscore : 24.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.82 % Favored : 89.06 % Rotamer: Outliers : 3.42 % Allowed : 11.52 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.55 (0.17), residues: 1655 helix: -2.53 (0.15), residues: 749 sheet: -2.37 (0.42), residues: 133 loop : -3.67 (0.18), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 386 TYR 0.022 0.002 TYR A 393 PHE 0.049 0.002 PHE B 381 TRP 0.018 0.002 TRP A 368 HIS 0.007 0.001 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00710 / 0.39 (14341) covalent geometry : angle 1.01074 / 0.64 (19460) hydrogen bonds : bond 0.16486 / 11.51 ( 568) hydrogen bonds : angle 7.24847 / 5.00 ( 1600) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 390 time to evaluate : 0.566 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: A 16 LEU cc_start: 0.5333 (mt) cc_final: 0.4896 (tp) REVERT: A 66 ASP cc_start: 0.6332 (m-30) cc_final: 0.6107 (m-30) REVERT: A 92 ASN cc_start: 0.7787 (t0) cc_final: 0.7370 (t0) REVERT: A 155 MET cc_start: 0.3675 (ttt) cc_final: 0.2865 (ttm) REVERT: A 311 MET cc_start: 0.6801 (mmm) cc_final: 0.6552 (mtp) REVERT: A 406 TRP cc_start: 0.7901 (OUTLIER) cc_final: 0.6894 (p-90) REVERT: A 407 ILE cc_start: 0.6412 (mt) cc_final: 0.5666 (mp) REVERT: A 422 TRP cc_start: 0.8146 (m100) cc_final: 0.7656 (m100) REVERT: A 575 MET cc_start: 0.7115 (mtm) cc_final: 0.6854 (mtp) REVERT: A 629 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6985 (mm-30) REVERT: B 21 THR cc_start: 0.7746 (p) cc_final: 0.7467 (p) REVERT: B 41 ASP cc_start: 0.7697 (t0) cc_final: 0.7479 (t0) REVERT: B 52 LYS cc_start: 0.7702 (ptpt) cc_final: 0.7183 (tppt) REVERT: B 92 MET cc_start: 0.5913 (mtt) cc_final: 0.5712 (mtm) REVERT: B 121 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.7019 (tpt-90) REVERT: B 146 THR cc_start: 0.8157 (t) cc_final: 0.7933 (t) REVERT: B 264 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6839 (mp0) REVERT: B 318 PHE cc_start: 0.7035 (m-10) cc_final: 0.6780 (m-80) REVERT: B 447 PHE cc_start: 0.6287 (p90) cc_final: 0.5920 (p90) REVERT: B 485 ASN cc_start: 0.6965 (t0) cc_final: 0.6524 (p0) REVERT: B 492 PHE cc_start: 0.6207 (OUTLIER) cc_final: 0.4326 (p90) REVERT: B 496 PHE cc_start: 0.7560 (m-80) cc_final: 0.7251 (m-80) REVERT: B 507 MET cc_start: 0.7229 (ttt) cc_final: 0.6987 (ttm) REVERT: B 546 MET cc_start: 0.7353 (mmm) cc_final: 0.7062 (tpt) REVERT: B 560 ARG cc_start: 0.8466 (mpt180) cc_final: 0.8099 (mpt180) REVERT: B 565 ASP cc_start: 0.6112 (t0) cc_final: 0.5870 (t0) REVERT: B 582 GLN cc_start: 0.7319 (pm20) cc_final: 0.6939 (pm20) REVERT: B 621 GLN cc_start: 0.7378 (mt0) cc_final: 0.7057 (mt0) REVERT: B 672 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7653 (mtp180) REVERT: B 689 TYR cc_start: 0.6682 (m-10) cc_final: 0.6438 (m-10) REVERT: B 713 SER cc_start: 0.7290 (m) cc_final: 0.6833 (p) REVERT: B 744 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.7203 (mmp) REVERT: B 745 LYS cc_start: 0.7982 (pttt) cc_final: 0.7346 (mtmm) REVERT: C 42 ASN cc_start: 0.7799 (t0) cc_final: 0.7218 (t0) REVERT: C 45 LEU cc_start: 0.7670 (tp) cc_final: 0.7234 (tt) REVERT: C 51 MET cc_start: 0.6548 (mmm) cc_final: 0.6304 (mmm) REVERT: C 69 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7434 (tm-30) REVERT: C 100 ASN cc_start: 0.7780 (t0) cc_final: 0.7326 (t0) REVERT: C 101 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7494 (tpp80) REVERT: C 113 LYS cc_start: 0.7424 (mttt) cc_final: 0.7137 (mttt) REVERT: C 126 LYS cc_start: 0.7676 (tppt) cc_final: 0.7473 (tptp) REVERT: C 147 ILE cc_start: 0.8306 (pt) cc_final: 0.8086 (mp) REVERT: C 151 HIS cc_start: 0.7295 (OUTLIER) cc_final: 0.6158 (p-80) REVERT: C 164 MET cc_start: 0.6757 (mmt) cc_final: 0.6431 (mmt) outliers start: 51 outliers final: 23 residues processed: 419 average time/residue: 0.1508 time to fit residues: 86.6038 Evaluate side-chains 387 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 357 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 406 TRP Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 656 GLU Chi-restraints excluded: chain B residue 672 ARG Chi-restraints excluded: chain B residue 744 MET Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 101 ARG Chi-restraints excluded: chain C residue 110 HIS Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 217 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 98 optimal weight: 0.1980 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 ASN A 92 ASN A 136 ASN A 144 HIS A 340 GLN ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 GLN ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 GLN A 703 ASN ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 ASN B 186 GLN B 268 GLN B 335 ASN B 533 ASN ** B 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 ASN C 170 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.157617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.141809 restraints weight = 23682.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.145431 restraints weight = 12991.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.147802 restraints weight = 8025.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.149396 restraints weight = 5435.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.150496 restraints weight = 3962.964| |-----------------------------------------------------------------------------| r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6670 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14341 Z= 0.227 Angle : 0.782 9.924 19460 Z= 0.417 Chirality : 0.048 0.258 2148 Planarity : 0.006 0.058 2409 Dihedral : 14.956 159.218 2280 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 4.29 % Allowed : 18.08 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.35 (0.18), residues: 1655 helix: -1.35 (0.17), residues: 766 sheet: -1.81 (0.43), residues: 137 loop : -3.28 (0.19), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 213 TYR 0.023 0.002 TYR B 217 PHE 0.023 0.002 PHE B 700 TRP 0.014 0.002 TRP C 99 HIS 0.009 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.23 (14341) covalent geometry : angle 0.78200 / 0.42 (19460) hydrogen bonds : bond 0.06841 / 4.71 ( 568) hydrogen bonds : angle 5.59654 / 3.82 ( 1600) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 372 time to evaluate : 0.538 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: A 16 LEU cc_start: 0.5421 (mt) cc_final: 0.5160 (tp) REVERT: A 92 ASN cc_start: 0.7706 (OUTLIER) cc_final: 0.7395 (t0) REVERT: A 407 ILE cc_start: 0.6369 (mt) cc_final: 0.5536 (mp) REVERT: A 422 TRP cc_start: 0.8181 (m100) cc_final: 0.7950 (m100) REVERT: A 548 MET cc_start: 0.5656 (ttm) cc_final: 0.5252 (mtm) REVERT: A 617 GLU cc_start: 0.7740 (tt0) cc_final: 0.7480 (mt-10) REVERT: A 629 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6903 (mm-30) REVERT: B 1 MET cc_start: 0.6923 (tmm) cc_final: 0.6520 (tmm) REVERT: B 41 ASP cc_start: 0.7629 (t0) cc_final: 0.7429 (t0) REVERT: B 52 LYS cc_start: 0.7648 (ptpt) cc_final: 0.7371 (tppt) REVERT: B 104 GLU cc_start: 0.6852 (mm-30) cc_final: 0.5566 (mm-30) REVERT: B 105 ASN cc_start: 0.8261 (m-40) cc_final: 0.7920 (m-40) REVERT: B 130 ASP cc_start: 0.6497 (t0) cc_final: 0.6134 (t0) REVERT: B 135 ARG cc_start: 0.6072 (ttt-90) cc_final: 0.5868 (ttt-90) REVERT: B 146 THR cc_start: 0.8164 (t) cc_final: 0.7954 (t) REVERT: B 210 GLN cc_start: 0.6922 (pm20) cc_final: 0.6640 (pm20) REVERT: B 318 PHE cc_start: 0.6956 (m-10) cc_final: 0.6737 (m-80) REVERT: B 414 MET cc_start: 0.6520 (mmp) cc_final: 0.6280 (mmm) REVERT: B 447 PHE cc_start: 0.6218 (p90) cc_final: 0.5871 (p90) REVERT: B 485 ASN cc_start: 0.7080 (t0) cc_final: 0.6486 (p0) REVERT: B 496 PHE cc_start: 0.7517 (m-80) cc_final: 0.7206 (m-80) REVERT: B 560 ARG cc_start: 0.8460 (mpt180) cc_final: 0.8096 (mpt180) REVERT: B 582 GLN cc_start: 0.7210 (pm20) cc_final: 0.6880 (pt0) REVERT: B 602 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.6815 (mtm180) REVERT: B 672 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7886 (mtp180) REVERT: B 689 TYR cc_start: 0.6634 (m-10) cc_final: 0.6374 (m-10) REVERT: B 713 SER cc_start: 0.7128 (m) cc_final: 0.6766 (p) REVERT: B 745 LYS cc_start: 0.8158 (pttt) cc_final: 0.7502 (ptpp) REVERT: C 42 ASN cc_start: 0.7659 (t0) cc_final: 0.7091 (t0) REVERT: C 48 LYS cc_start: 0.8352 (mmtp) cc_final: 0.8127 (mmtp) REVERT: C 69 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7376 (tm-30) REVERT: C 100 ASN cc_start: 0.7824 (t0) cc_final: 0.7516 (t0) REVERT: C 113 LYS cc_start: 0.7464 (mttt) cc_final: 0.7154 (mttt) REVERT: C 147 ILE cc_start: 0.8289 (pt) cc_final: 0.8051 (mp) REVERT: C 164 MET cc_start: 0.6587 (mmt) cc_final: 0.6382 (mmt) REVERT: C 217 PHE cc_start: 0.5718 (OUTLIER) cc_final: 0.4838 (t80) outliers start: 64 outliers final: 38 residues processed: 401 average time/residue: 0.1483 time to fit residues: 82.1679 Evaluate side-chains 390 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 348 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 481 GLN Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 656 GLU Chi-restraints excluded: chain B residue 672 ARG Chi-restraints excluded: chain B residue 700 PHE Chi-restraints excluded: chain B residue 743 ILE Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 231 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 14 optimal weight: 0.0570 chunk 87 optimal weight: 1.9990 chunk 128 optimal weight: 0.0670 chunk 15 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 chunk 163 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 2 optimal weight: 0.4980 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN A 144 HIS A 326 HIS ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 HIS ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 ASN B 314 ASN B 518 ASN B 621 GLN ** B 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 HIS C 182 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.159493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.143615 restraints weight = 23539.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.147199 restraints weight = 12855.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.149560 restraints weight = 7963.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.151078 restraints weight = 5396.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.152244 restraints weight = 3978.917| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14341 Z= 0.170 Angle : 0.702 10.698 19460 Z= 0.373 Chirality : 0.045 0.199 2148 Planarity : 0.006 0.052 2409 Dihedral : 14.545 152.261 2260 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 5.22 % Allowed : 19.62 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.19), residues: 1655 helix: -0.76 (0.18), residues: 759 sheet: -1.60 (0.43), residues: 139 loop : -2.98 (0.20), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 754 TYR 0.021 0.002 TYR B 217 PHE 0.030 0.002 PHE B 381 TRP 0.021 0.002 TRP A 188 HIS 0.005 0.001 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (14341) covalent geometry : angle 0.70219 / 0.37 (19460) hydrogen bonds : bond 0.05772 / 3.93 ( 568) hydrogen bonds : angle 5.22694 / 3.57 ( 1600) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 360 time to evaluate : 0.500 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: A 1 MET cc_start: 0.4018 (mpp) cc_final: 0.3534 (mpp) REVERT: A 16 LEU cc_start: 0.5271 (mt) cc_final: 0.5046 (tp) REVERT: A 102 LYS cc_start: 0.8455 (tmtt) cc_final: 0.7810 (tmtt) REVERT: A 155 MET cc_start: 0.3802 (ttt) cc_final: 0.3027 (ttm) REVERT: A 285 MET cc_start: 0.7306 (OUTLIER) cc_final: 0.6763 (tpt) REVERT: A 311 MET cc_start: 0.6700 (mmm) cc_final: 0.6299 (mtm) REVERT: A 407 ILE cc_start: 0.6282 (mt) cc_final: 0.5555 (mp) REVERT: A 420 SER cc_start: 0.8208 (OUTLIER) cc_final: 0.7935 (p) REVERT: A 422 TRP cc_start: 0.8275 (m100) cc_final: 0.7769 (m100) REVERT: A 599 GLU cc_start: 0.6692 (tp30) cc_final: 0.6393 (tp30) REVERT: A 629 GLU cc_start: 0.7123 (mm-30) cc_final: 0.6886 (mm-30) REVERT: B 1 MET cc_start: 0.6952 (tmm) cc_final: 0.6636 (tmm) REVERT: B 52 LYS cc_start: 0.7623 (ptpt) cc_final: 0.7365 (tppt) REVERT: B 104 GLU cc_start: 0.6849 (mm-30) cc_final: 0.5402 (mm-30) REVERT: B 105 ASN cc_start: 0.8230 (m-40) cc_final: 0.7862 (m-40) REVERT: B 130 ASP cc_start: 0.6430 (t0) cc_final: 0.6206 (t0) REVERT: B 146 THR cc_start: 0.8160 (t) cc_final: 0.7889 (t) REVERT: B 208 LYS cc_start: 0.7696 (mptt) cc_final: 0.7443 (mptt) REVERT: B 356 MET cc_start: 0.4091 (OUTLIER) cc_final: 0.3656 (ttm) REVERT: B 447 PHE cc_start: 0.6177 (p90) cc_final: 0.5970 (p90) REVERT: B 485 ASN cc_start: 0.7017 (t0) cc_final: 0.6588 (p0) REVERT: B 560 ARG cc_start: 0.8437 (mpt180) cc_final: 0.8140 (mpt180) REVERT: B 582 GLN cc_start: 0.7187 (OUTLIER) cc_final: 0.6825 (pt0) REVERT: B 602 ARG cc_start: 0.7212 (OUTLIER) cc_final: 0.6915 (mtm180) REVERT: B 672 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7874 (mtp180) REVERT: B 745 LYS cc_start: 0.8121 (pttt) cc_final: 0.7470 (mtmm) REVERT: C 28 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7561 (ttm) REVERT: C 42 ASN cc_start: 0.7682 (t0) cc_final: 0.7186 (t0) REVERT: C 48 LYS cc_start: 0.8365 (mmtp) cc_final: 0.8134 (mmtp) REVERT: C 51 MET cc_start: 0.6545 (mmm) cc_final: 0.6247 (tpt) REVERT: C 113 LYS cc_start: 0.7389 (mttt) cc_final: 0.7111 (mttt) REVERT: C 147 ILE cc_start: 0.8300 (pt) cc_final: 0.8030 (mp) REVERT: C 217 PHE cc_start: 0.5737 (OUTLIER) cc_final: 0.4788 (t80) outliers start: 78 outliers final: 49 residues processed: 402 average time/residue: 0.1425 time to fit residues: 79.1960 Evaluate side-chains 400 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 343 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 616 MET Chi-restraints excluded: chain B residue 656 GLU Chi-restraints excluded: chain B residue 672 ARG Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 738 GLU Chi-restraints excluded: chain B residue 743 ILE Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 231 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 8 optimal weight: 0.9990 chunk 132 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 141 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 119 optimal weight: 0.5980 chunk 127 optimal weight: 0.4980 chunk 77 optimal weight: 0.8980 chunk 166 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 ASN A 144 HIS ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 ASN B 65 GLN ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 ASN B 312 ASN B 346 ASN B 518 ASN B 621 GLN ** B 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 HIS C 100 ASN C 160 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.158471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.142101 restraints weight = 23695.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.145801 restraints weight = 13059.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.148240 restraints weight = 8109.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.149810 restraints weight = 5518.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.150985 restraints weight = 4068.029| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14341 Z= 0.216 Angle : 0.728 10.483 19460 Z= 0.385 Chirality : 0.046 0.199 2148 Planarity : 0.006 0.053 2409 Dihedral : 14.434 147.582 2258 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 6.23 % Allowed : 19.96 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.19), residues: 1655 helix: -0.66 (0.18), residues: 758 sheet: -1.54 (0.44), residues: 137 loop : -2.87 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 468 TYR 0.020 0.002 TYR C 34 PHE 0.033 0.002 PHE B 381 TRP 0.016 0.002 TRP C 99 HIS 0.008 0.001 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.22 (14341) covalent geometry : angle 0.72816 / 0.39 (19460) hydrogen bonds : bond 0.05962 / 4.06 ( 568) hydrogen bonds : angle 5.19343 / 3.56 ( 1600) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 351 time to evaluate : 0.486 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: A 75 ARG cc_start: 0.4987 (OUTLIER) cc_final: 0.3506 (ttt-90) REVERT: A 102 LYS cc_start: 0.8451 (tmtt) cc_final: 0.7808 (tmtt) REVERT: A 128 HIS cc_start: 0.3726 (OUTLIER) cc_final: 0.2976 (t70) REVERT: A 155 MET cc_start: 0.3808 (ttt) cc_final: 0.3040 (ttm) REVERT: A 166 GLU cc_start: 0.5974 (pm20) cc_final: 0.5701 (pm20) REVERT: A 285 MET cc_start: 0.7333 (OUTLIER) cc_final: 0.6800 (tpt) REVERT: A 407 ILE cc_start: 0.6244 (mt) cc_final: 0.5447 (mp) REVERT: A 416 GLU cc_start: 0.7235 (mt-10) cc_final: 0.6982 (mt-10) REVERT: A 420 SER cc_start: 0.8230 (OUTLIER) cc_final: 0.7949 (p) REVERT: A 422 TRP cc_start: 0.8373 (m100) cc_final: 0.7913 (m100) REVERT: A 443 ARG cc_start: 0.7734 (mmm-85) cc_final: 0.7494 (mmm-85) REVERT: A 629 GLU cc_start: 0.7122 (mm-30) cc_final: 0.6895 (mm-30) REVERT: B 1 MET cc_start: 0.6939 (tmm) cc_final: 0.6641 (tmm) REVERT: B 52 LYS cc_start: 0.7605 (ptpt) cc_final: 0.7321 (tppt) REVERT: B 105 ASN cc_start: 0.8264 (m-40) cc_final: 0.7871 (m-40) REVERT: B 133 LEU cc_start: 0.8142 (mp) cc_final: 0.7653 (tp) REVERT: B 135 ARG cc_start: 0.6087 (ttt-90) cc_final: 0.5825 (ttt180) REVERT: B 146 THR cc_start: 0.8162 (t) cc_final: 0.7956 (t) REVERT: B 217 TYR cc_start: 0.6613 (t80) cc_final: 0.6402 (t80) REVERT: B 233 ARG cc_start: 0.6522 (OUTLIER) cc_final: 0.5855 (ptm160) REVERT: B 356 MET cc_start: 0.4197 (OUTLIER) cc_final: 0.3780 (ttm) REVERT: B 447 PHE cc_start: 0.6195 (p90) cc_final: 0.5986 (p90) REVERT: B 485 ASN cc_start: 0.7018 (t0) cc_final: 0.6626 (p0) REVERT: B 582 GLN cc_start: 0.7154 (OUTLIER) cc_final: 0.6887 (pt0) REVERT: B 602 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.6978 (mtm180) REVERT: B 713 SER cc_start: 0.7143 (m) cc_final: 0.6793 (p) REVERT: B 745 LYS cc_start: 0.8125 (pttt) cc_final: 0.7472 (mtmm) REVERT: C 28 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7642 (ttm) REVERT: C 42 ASN cc_start: 0.7507 (t0) cc_final: 0.7142 (t0) REVERT: C 61 LYS cc_start: 0.7140 (mppt) cc_final: 0.6694 (mppt) REVERT: C 83 ASP cc_start: 0.5605 (m-30) cc_final: 0.5016 (m-30) REVERT: C 118 TYR cc_start: 0.7955 (m-80) cc_final: 0.7754 (m-80) REVERT: C 147 ILE cc_start: 0.8329 (pt) cc_final: 0.8085 (mp) REVERT: C 217 PHE cc_start: 0.5959 (OUTLIER) cc_final: 0.4975 (t80) outliers start: 93 outliers final: 62 residues processed: 400 average time/residue: 0.1433 time to fit residues: 79.8179 Evaluate side-chains 421 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 349 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 253 TYR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 356 MET Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 656 GLU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 700 PHE Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 738 GLU Chi-restraints excluded: chain B residue 743 ILE Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 231 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 127 optimal weight: 0.0670 chunk 13 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 133 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 100 optimal weight: 0.1980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 HIS ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 GLN ** B 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 HIS C 100 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.160097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.143906 restraints weight = 23638.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.147556 restraints weight = 13149.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.149948 restraints weight = 8216.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.151535 restraints weight = 5613.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.152654 restraints weight = 4134.410| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14341 Z= 0.165 Angle : 0.681 11.706 19460 Z= 0.359 Chirality : 0.045 0.203 2148 Planarity : 0.005 0.050 2409 Dihedral : 14.276 147.249 2253 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 6.30 % Allowed : 21.43 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.19), residues: 1655 helix: -0.40 (0.18), residues: 760 sheet: -1.50 (0.43), residues: 139 loop : -2.73 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 727 TYR 0.016 0.001 TYR B 217 PHE 0.040 0.002 PHE B 381 TRP 0.015 0.001 TRP C 78 HIS 0.006 0.001 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (14341) covalent geometry : angle 0.68130 / 0.36 (19460) hydrogen bonds : bond 0.05316 / 3.59 ( 568) hydrogen bonds : angle 4.98584 / 3.42 ( 1600) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 353 time to evaluate : 0.503 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: A 1 MET cc_start: 0.4457 (mpp) cc_final: 0.3725 (mpp) REVERT: A 75 ARG cc_start: 0.4923 (OUTLIER) cc_final: 0.3481 (ttt-90) REVERT: A 92 ASN cc_start: 0.7679 (OUTLIER) cc_final: 0.7454 (t0) REVERT: A 128 HIS cc_start: 0.3487 (OUTLIER) cc_final: 0.2846 (t70) REVERT: A 155 MET cc_start: 0.3788 (ttt) cc_final: 0.3050 (ttm) REVERT: A 166 GLU cc_start: 0.5963 (pm20) cc_final: 0.5703 (pm20) REVERT: A 182 MET cc_start: 0.4482 (ppp) cc_final: 0.4096 (pmm) REVERT: A 285 MET cc_start: 0.7318 (OUTLIER) cc_final: 0.6795 (tpt) REVERT: A 309 LYS cc_start: 0.7215 (mmmm) cc_final: 0.6775 (mtmm) REVERT: A 407 ILE cc_start: 0.6212 (mt) cc_final: 0.5413 (mp) REVERT: A 416 GLU cc_start: 0.7219 (mt-10) cc_final: 0.7018 (mt-10) REVERT: A 420 SER cc_start: 0.8204 (OUTLIER) cc_final: 0.7949 (p) REVERT: A 422 TRP cc_start: 0.8306 (m100) cc_final: 0.7952 (m100) REVERT: B 1 MET cc_start: 0.6946 (tmm) cc_final: 0.6629 (tmm) REVERT: B 52 LYS cc_start: 0.7566 (ptpt) cc_final: 0.7336 (tppt) REVERT: B 105 ASN cc_start: 0.8232 (m-40) cc_final: 0.7858 (m-40) REVERT: B 121 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7328 (mmm-85) REVERT: B 133 LEU cc_start: 0.8046 (mp) cc_final: 0.7592 (tp) REVERT: B 135 ARG cc_start: 0.6067 (ttt-90) cc_final: 0.5803 (ttt180) REVERT: B 146 THR cc_start: 0.8075 (t) cc_final: 0.7847 (t) REVERT: B 233 ARG cc_start: 0.6468 (OUTLIER) cc_final: 0.6125 (ptm160) REVERT: B 358 GLU cc_start: 0.5362 (OUTLIER) cc_final: 0.5116 (mt-10) REVERT: B 447 PHE cc_start: 0.6197 (p90) cc_final: 0.5934 (p90) REVERT: B 485 ASN cc_start: 0.6956 (t0) cc_final: 0.6593 (p0) REVERT: B 496 PHE cc_start: 0.7204 (m-10) cc_final: 0.6907 (m-10) REVERT: B 582 GLN cc_start: 0.7072 (OUTLIER) cc_final: 0.6846 (pt0) REVERT: B 602 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6894 (mtm180) REVERT: B 745 LYS cc_start: 0.8090 (pttt) cc_final: 0.7494 (ptpp) REVERT: C 28 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7521 (ttm) REVERT: C 61 LYS cc_start: 0.7129 (mppt) cc_final: 0.6716 (mppt) REVERT: C 69 GLU cc_start: 0.7530 (tm-30) cc_final: 0.7291 (tm-30) REVERT: C 83 ASP cc_start: 0.5615 (m-30) cc_final: 0.5138 (m-30) REVERT: C 100 ASN cc_start: 0.7763 (t0) cc_final: 0.7488 (t0) REVERT: C 118 TYR cc_start: 0.7954 (m-80) cc_final: 0.7749 (m-80) REVERT: C 147 ILE cc_start: 0.8327 (pt) cc_final: 0.8063 (mp) REVERT: C 217 PHE cc_start: 0.6014 (OUTLIER) cc_final: 0.5017 (t80) outliers start: 94 outliers final: 61 residues processed: 403 average time/residue: 0.1343 time to fit residues: 75.5631 Evaluate side-chains 412 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 339 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 656 GLU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 700 PHE Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 738 GLU Chi-restraints excluded: chain B residue 743 ILE Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 231 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 158 optimal weight: 0.6980 chunk 105 optimal weight: 0.5980 chunk 29 optimal weight: 0.1980 chunk 66 optimal weight: 0.0970 chunk 73 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 HIS ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 587 GLN ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 HIS ** C 151 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 = 0.4061 r_free = 0.4061 target = 0.160928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.144731 restraints weight = 23675.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.148335 restraints weight = 13180.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.150695 restraints weight = 8250.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.152262 restraints weight = 5640.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.153335 restraints weight = 4162.466| |-----------------------------------------------------------------------------| r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14341 Z= 0.169 Angle : 0.687 11.279 19460 Z= 0.358 Chirality : 0.045 0.198 2148 Planarity : 0.005 0.061 2409 Dihedral : 14.129 147.103 2249 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 6.50 % Allowed : 21.97 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.20), residues: 1655 helix: -0.31 (0.18), residues: 757 sheet: -1.53 (0.42), residues: 143 loop : -2.62 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 638 TYR 0.017 0.001 TYR C 34 PHE 0.050 0.002 PHE B 381 TRP 0.016 0.002 TRP C 78 HIS 0.006 0.001 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (14341) covalent geometry : angle 0.68674 / 0.36 (19460) hydrogen bonds : bond 0.05257 / 3.54 ( 568) hydrogen bonds : angle 4.93474 / 3.38 ( 1600) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 344 time to evaluate : 0.328 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: A 1 MET cc_start: 0.4466 (mpp) cc_final: 0.3767 (mpp) REVERT: A 75 ARG cc_start: 0.4921 (OUTLIER) cc_final: 0.3482 (ttt-90) REVERT: A 128 HIS cc_start: 0.3517 (OUTLIER) cc_final: 0.2982 (t70) REVERT: A 155 MET cc_start: 0.3707 (ttt) cc_final: 0.2980 (ttm) REVERT: A 166 GLU cc_start: 0.6005 (pm20) cc_final: 0.5724 (pm20) REVERT: A 285 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6867 (tpt) REVERT: A 309 LYS cc_start: 0.7226 (mmmm) cc_final: 0.6798 (mtmm) REVERT: A 416 GLU cc_start: 0.7261 (mt-10) cc_final: 0.7046 (mt-10) REVERT: A 420 SER cc_start: 0.8196 (OUTLIER) cc_final: 0.7962 (p) REVERT: A 422 TRP cc_start: 0.8303 (m100) cc_final: 0.7905 (m100) REVERT: B 1 MET cc_start: 0.6961 (tmm) cc_final: 0.6656 (tmm) REVERT: B 52 LYS cc_start: 0.7562 (ptpt) cc_final: 0.7307 (tppt) REVERT: B 105 ASN cc_start: 0.8226 (m-40) cc_final: 0.7886 (m-40) REVERT: B 121 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.7336 (mmm-85) REVERT: B 133 LEU cc_start: 0.8049 (mp) cc_final: 0.7598 (tp) REVERT: B 135 ARG cc_start: 0.6127 (ttt-90) cc_final: 0.5875 (ttt180) REVERT: B 233 ARG cc_start: 0.6451 (OUTLIER) cc_final: 0.6241 (ptm160) REVERT: B 358 GLU cc_start: 0.5357 (OUTLIER) cc_final: 0.5105 (mt-10) REVERT: B 426 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7559 (tp) REVERT: B 447 PHE cc_start: 0.6158 (p90) cc_final: 0.5909 (p90) REVERT: B 485 ASN cc_start: 0.6910 (t0) cc_final: 0.6698 (p0) REVERT: B 496 PHE cc_start: 0.7220 (m-10) cc_final: 0.6949 (m-10) REVERT: B 533 ASN cc_start: 0.7552 (m-40) cc_final: 0.7322 (m-40) REVERT: B 582 GLN cc_start: 0.7093 (OUTLIER) cc_final: 0.6854 (pt0) REVERT: B 602 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6890 (mtm180) REVERT: B 745 LYS cc_start: 0.8103 (pttt) cc_final: 0.7476 (mtmm) REVERT: C 28 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7601 (ttm) REVERT: C 42 ASN cc_start: 0.7465 (t0) cc_final: 0.7157 (t0) REVERT: C 61 LYS cc_start: 0.7106 (mppt) cc_final: 0.6688 (mppt) REVERT: C 69 GLU cc_start: 0.7555 (tm-30) cc_final: 0.7310 (tm-30) REVERT: C 83 ASP cc_start: 0.5644 (m-30) cc_final: 0.5301 (m-30) REVERT: C 147 ILE cc_start: 0.8311 (pt) cc_final: 0.8044 (mp) REVERT: C 157 LYS cc_start: 0.6563 (mmtt) cc_final: 0.6360 (mmtt) REVERT: C 217 PHE cc_start: 0.6126 (OUTLIER) cc_final: 0.5149 (t80) outliers start: 97 outliers final: 64 residues processed: 398 average time/residue: 0.1224 time to fit residues: 68.0843 Evaluate side-chains 416 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 340 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 253 TYR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 492 PHE Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 656 GLU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 700 PHE Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 738 GLU Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 231 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 44 optimal weight: 0.5980 chunk 160 optimal weight: 0.9980 chunk 100 optimal weight: 0.1980 chunk 122 optimal weight: 0.6980 chunk 40 optimal weight: 0.3980 chunk 67 optimal weight: 0.1980 chunk 38 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 29 optimal weight: 0.0970 chunk 95 optimal weight: 0.0020 chunk 33 optimal weight: 0.2980 overall best weight: 0.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 HIS ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 664 HIS C 27 HIS C 100 ASN ** C 151 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 = 0.4095 r_free = 0.4095 target = 0.163582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.147298 restraints weight = 23528.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.150940 restraints weight = 13048.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.153236 restraints weight = 8117.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.154845 restraints weight = 5584.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.155914 restraints weight = 4108.930| |-----------------------------------------------------------------------------| r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6583 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14341 Z= 0.133 Angle : 0.664 11.995 19460 Z= 0.344 Chirality : 0.043 0.218 2148 Planarity : 0.005 0.050 2409 Dihedral : 13.966 146.946 2249 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 5.29 % Allowed : 23.84 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.20), residues: 1655 helix: -0.09 (0.19), residues: 759 sheet: -1.26 (0.43), residues: 135 loop : -2.49 (0.21), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 727 TYR 0.012 0.001 TYR B 467 PHE 0.053 0.002 PHE B 381 TRP 0.024 0.001 TRP A 188 HIS 0.004 0.001 HIS B 664 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (14341) covalent geometry : angle 0.66415 / 0.34 (19460) hydrogen bonds : bond 0.04529 / 3.02 ( 568) hydrogen bonds : angle 4.74283 / 3.25 ( 1600) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 343 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4130 (mpp) cc_final: 0.3693 (mpp) REVERT: A 75 ARG cc_start: 0.4770 (OUTLIER) cc_final: 0.3422 (ttt-90) REVERT: A 128 HIS cc_start: 0.3159 (OUTLIER) cc_final: 0.2662 (t70) REVERT: A 155 MET cc_start: 0.3663 (ttt) cc_final: 0.2995 (ttm) REVERT: A 166 GLU cc_start: 0.5898 (pm20) cc_final: 0.5634 (pm20) REVERT: A 285 MET cc_start: 0.7341 (tpt) cc_final: 0.6949 (tpt) REVERT: A 401 ARG cc_start: 0.7517 (tpp-160) cc_final: 0.7246 (tpp-160) REVERT: A 416 GLU cc_start: 0.7262 (mt-10) cc_final: 0.7050 (mt-10) REVERT: A 422 TRP cc_start: 0.8181 (m100) cc_final: 0.7923 (m-10) REVERT: A 443 ARG cc_start: 0.7562 (mmm-85) cc_final: 0.7160 (mtp85) REVERT: A 523 MET cc_start: 0.7110 (OUTLIER) cc_final: 0.6842 (ptp) REVERT: A 615 LYS cc_start: 0.6662 (OUTLIER) cc_final: 0.6356 (ptpp) REVERT: B 1 MET cc_start: 0.6976 (tmm) cc_final: 0.6630 (tmm) REVERT: B 51 GLU cc_start: 0.7647 (tp30) cc_final: 0.7431 (tm-30) REVERT: B 52 LYS cc_start: 0.7494 (ptpt) cc_final: 0.7263 (tppt) REVERT: B 105 ASN cc_start: 0.8180 (m-40) cc_final: 0.7867 (m-40) REVERT: B 121 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.7274 (mmm-85) REVERT: B 133 LEU cc_start: 0.8032 (mp) cc_final: 0.7622 (tp) REVERT: B 135 ARG cc_start: 0.6007 (ttt-90) cc_final: 0.5774 (ttt180) REVERT: B 148 GLU cc_start: 0.7573 (tt0) cc_final: 0.7364 (tt0) REVERT: B 358 GLU cc_start: 0.5220 (OUTLIER) cc_final: 0.4769 (mt-10) REVERT: B 447 PHE cc_start: 0.6054 (p90) cc_final: 0.5842 (p90) REVERT: B 485 ASN cc_start: 0.6997 (t0) cc_final: 0.6731 (p0) REVERT: B 496 PHE cc_start: 0.7162 (m-10) cc_final: 0.6880 (m-10) REVERT: B 582 GLN cc_start: 0.7010 (OUTLIER) cc_final: 0.6787 (pt0) REVERT: B 602 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6899 (ptt180) REVERT: B 745 LYS cc_start: 0.8059 (pttt) cc_final: 0.7430 (mtmm) REVERT: C 28 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7610 (ttm) REVERT: C 69 GLU cc_start: 0.7384 (tm-30) cc_final: 0.7105 (tm-30) REVERT: C 83 ASP cc_start: 0.5639 (m-30) cc_final: 0.5335 (m-30) REVERT: C 126 LYS cc_start: 0.7405 (tptp) cc_final: 0.7203 (tptp) REVERT: C 147 ILE cc_start: 0.8304 (pt) cc_final: 0.8063 (mp) REVERT: C 217 PHE cc_start: 0.5932 (OUTLIER) cc_final: 0.5049 (t80) outliers start: 79 outliers final: 51 residues processed: 393 average time/residue: 0.1318 time to fit residues: 72.5082 Evaluate side-chains 398 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 337 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 656 GLU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 738 GLU Chi-restraints excluded: chain B residue 743 ILE Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 231 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 158 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 119 optimal weight: 0.9980 chunk 153 optimal weight: 0.9990 chunk 116 optimal weight: 0.0060 chunk 69 optimal weight: 0.0970 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 154 optimal weight: 0.8980 chunk 140 optimal weight: 0.9980 chunk 129 optimal weight: 0.6980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 HIS ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN A 614 ASN B 137 GLN B 292 ASN C 27 HIS C 100 ASN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.161219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.144920 restraints weight = 23654.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.148472 restraints weight = 13192.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.150841 restraints weight = 8289.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.152429 restraints weight = 5677.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.153544 restraints weight = 4191.689| |-----------------------------------------------------------------------------| r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14341 Z= 0.168 Angle : 0.700 11.022 19460 Z= 0.361 Chirality : 0.045 0.194 2148 Planarity : 0.005 0.046 2409 Dihedral : 13.919 147.590 2238 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 5.89 % Allowed : 23.71 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.20), residues: 1655 helix: -0.12 (0.19), residues: 753 sheet: -1.30 (0.44), residues: 131 loop : -2.43 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 727 TYR 0.017 0.002 TYR C 34 PHE 0.048 0.002 PHE B 381 TRP 0.029 0.002 TRP A 188 HIS 0.006 0.001 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (14341) covalent geometry : angle 0.69998 / 0.36 (19460) hydrogen bonds : bond 0.04953 / 3.32 ( 568) hydrogen bonds : angle 4.81422 / 3.29 ( 1600) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 345 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4623 (mpp) cc_final: 0.4078 (mpp) REVERT: A 75 ARG cc_start: 0.4796 (OUTLIER) cc_final: 0.3424 (ttt-90) REVERT: A 110 TYR cc_start: 0.3850 (t80) cc_final: 0.3538 (t80) REVERT: A 128 HIS cc_start: 0.3219 (OUTLIER) cc_final: 0.2774 (t70) REVERT: A 155 MET cc_start: 0.3613 (ttt) cc_final: 0.2934 (ttm) REVERT: A 166 GLU cc_start: 0.5970 (pm20) cc_final: 0.5685 (pm20) REVERT: A 285 MET cc_start: 0.7351 (tpt) cc_final: 0.6958 (tpt) REVERT: A 401 ARG cc_start: 0.7544 (tpp-160) cc_final: 0.7253 (tpp-160) REVERT: A 416 GLU cc_start: 0.7272 (mt-10) cc_final: 0.7045 (mt-10) REVERT: A 422 TRP cc_start: 0.8322 (m100) cc_final: 0.8044 (m-10) REVERT: A 443 ARG cc_start: 0.7685 (mmm-85) cc_final: 0.7312 (mtp85) REVERT: A 615 LYS cc_start: 0.6608 (OUTLIER) cc_final: 0.6308 (ptpp) REVERT: B 1 MET cc_start: 0.6971 (tmm) cc_final: 0.6625 (tmm) REVERT: B 52 LYS cc_start: 0.7541 (ptpt) cc_final: 0.7337 (tppt) REVERT: B 105 ASN cc_start: 0.8217 (m-40) cc_final: 0.7877 (m-40) REVERT: B 121 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.7304 (mmm-85) REVERT: B 133 LEU cc_start: 0.8094 (mp) cc_final: 0.7605 (tp) REVERT: B 135 ARG cc_start: 0.6091 (ttt-90) cc_final: 0.5890 (ttt180) REVERT: B 148 GLU cc_start: 0.7626 (tt0) cc_final: 0.7411 (tt0) REVERT: B 582 GLN cc_start: 0.7076 (OUTLIER) cc_final: 0.6827 (pt0) REVERT: B 602 ARG cc_start: 0.7161 (OUTLIER) cc_final: 0.6955 (ptt180) REVERT: B 713 SER cc_start: 0.7065 (m) cc_final: 0.6764 (p) REVERT: B 745 LYS cc_start: 0.8068 (pttt) cc_final: 0.7453 (mtmm) REVERT: C 28 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7678 (ttm) REVERT: C 69 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7353 (tm-30) REVERT: C 83 ASP cc_start: 0.5616 (m-30) cc_final: 0.5345 (m-30) REVERT: C 126 LYS cc_start: 0.7428 (tptp) cc_final: 0.7195 (tptp) REVERT: C 147 ILE cc_start: 0.8367 (pt) cc_final: 0.8106 (mp) REVERT: C 217 PHE cc_start: 0.6141 (OUTLIER) cc_final: 0.5165 (t80) outliers start: 88 outliers final: 59 residues processed: 398 average time/residue: 0.1322 time to fit residues: 74.0800 Evaluate side-chains 413 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 346 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 253 TYR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 656 GLU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 738 GLU Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 231 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 27 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 101 optimal weight: 0.0060 chunk 52 optimal weight: 1.9990 chunk 154 optimal weight: 0.6980 chunk 47 optimal weight: 0.0970 chunk 76 optimal weight: 0.8980 chunk 157 optimal weight: 0.9990 chunk 38 optimal weight: 0.0060 chunk 24 optimal weight: 0.0970 overall best weight: 0.1808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 HIS ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN C 27 HIS C 160 GLN ** C 236 GLN ** 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 = 0.4095 r_free = 0.4095 target = 0.163180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.146889 restraints weight = 23685.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.150471 restraints weight = 13145.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.152872 restraints weight = 8233.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.154480 restraints weight = 5612.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.155590 restraints weight = 4135.730| |-----------------------------------------------------------------------------| r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14341 Z= 0.139 Angle : 0.694 13.073 19460 Z= 0.355 Chirality : 0.043 0.219 2148 Planarity : 0.005 0.045 2409 Dihedral : 13.808 147.326 2238 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.76 % Allowed : 24.98 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.20), residues: 1655 helix: 0.04 (0.19), residues: 751 sheet: -1.10 (0.45), residues: 126 loop : -2.36 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 727 TYR 0.014 0.001 TYR B 217 PHE 0.038 0.002 PHE B 381 TRP 0.030 0.001 TRP A 188 HIS 0.004 0.001 HIS A 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (14341) covalent geometry : angle 0.69393 / 0.36 (19460) hydrogen bonds : bond 0.04431 / 2.94 ( 568) hydrogen bonds : angle 4.73397 / 3.25 ( 1600) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 342 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4470 (mpp) cc_final: 0.4048 (mpp) REVERT: A 75 ARG cc_start: 0.4730 (OUTLIER) cc_final: 0.3430 (ttt-90) REVERT: A 110 TYR cc_start: 0.3744 (t80) cc_final: 0.3468 (t80) REVERT: A 128 HIS cc_start: 0.3181 (OUTLIER) cc_final: 0.2585 (t70) REVERT: A 155 MET cc_start: 0.3519 (ttt) cc_final: 0.2893 (ttm) REVERT: A 166 GLU cc_start: 0.5907 (pm20) cc_final: 0.5630 (pm20) REVERT: A 401 ARG cc_start: 0.7521 (tpp-160) cc_final: 0.7235 (tpp-160) REVERT: A 416 GLU cc_start: 0.7299 (mt-10) cc_final: 0.7050 (mt-10) REVERT: A 422 TRP cc_start: 0.8229 (m100) cc_final: 0.7986 (m-10) REVERT: A 443 ARG cc_start: 0.7665 (mmm-85) cc_final: 0.7362 (mtp85) REVERT: A 523 MET cc_start: 0.7146 (OUTLIER) cc_final: 0.6909 (ptp) REVERT: A 615 LYS cc_start: 0.6673 (OUTLIER) cc_final: 0.6362 (ptpp) REVERT: B 1 MET cc_start: 0.6938 (tmm) cc_final: 0.6586 (tmm) REVERT: B 52 LYS cc_start: 0.7529 (ptpt) cc_final: 0.7322 (tppt) REVERT: B 105 ASN cc_start: 0.8177 (m-40) cc_final: 0.7749 (m110) REVERT: B 121 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.7291 (mmm-85) REVERT: B 133 LEU cc_start: 0.7996 (mp) cc_final: 0.7533 (tp) REVERT: B 135 ARG cc_start: 0.6036 (ttt-90) cc_final: 0.5827 (ttt180) REVERT: B 146 THR cc_start: 0.7809 (t) cc_final: 0.7470 (p) REVERT: B 148 GLU cc_start: 0.7602 (tt0) cc_final: 0.7380 (tt0) REVERT: B 356 MET cc_start: 0.4002 (ttm) cc_final: 0.3732 (ttp) REVERT: B 582 GLN cc_start: 0.7009 (OUTLIER) cc_final: 0.6768 (pt0) REVERT: B 745 LYS cc_start: 0.8074 (pttt) cc_final: 0.7441 (mtmm) REVERT: C 28 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7655 (ttm) REVERT: C 69 GLU cc_start: 0.7413 (tm-30) cc_final: 0.7154 (tm-30) REVERT: C 83 ASP cc_start: 0.5545 (m-30) cc_final: 0.5319 (m-30) REVERT: C 147 ILE cc_start: 0.8340 (pt) cc_final: 0.8082 (mp) REVERT: C 217 PHE cc_start: 0.6006 (OUTLIER) cc_final: 0.5104 (t80) outliers start: 71 outliers final: 52 residues processed: 384 average time/residue: 0.1285 time to fit residues: 69.3827 Evaluate side-chains 397 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 337 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 656 GLU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 738 GLU Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 217 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 17 optimal weight: 0.7980 chunk 70 optimal weight: 0.0010 chunk 114 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 152 optimal weight: 0.6980 chunk 118 optimal weight: 0.5980 chunk 81 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 HIS ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 687 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 HIS ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.160830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.144462 restraints weight = 23748.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.148045 restraints weight = 13265.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.150415 restraints weight = 8335.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.152030 restraints weight = 5722.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.153094 restraints weight = 4221.808| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 14341 Z= 0.186 Angle : 0.735 13.404 19460 Z= 0.377 Chirality : 0.045 0.202 2148 Planarity : 0.005 0.049 2409 Dihedral : 13.822 147.831 2234 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 4.49 % Allowed : 25.32 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.20), residues: 1655 helix: 0.00 (0.19), residues: 746 sheet: -1.06 (0.46), residues: 126 loop : -2.29 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 707 TYR 0.020 0.002 TYR B 217 PHE 0.027 0.002 PHE B 466 TRP 0.041 0.002 TRP A 188 HIS 0.007 0.001 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (14341) covalent geometry : angle 0.73536 / 0.38 (19460) hydrogen bonds : bond 0.05040 / 3.37 ( 568) hydrogen bonds : angle 4.84772 / 3.33 ( 1600) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3310 Ramachandran restraints generated. 1655 Oldfield, 0 Emsley, 1655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 339 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5090 (mpp) cc_final: 0.4701 (mpp) REVERT: A 75 ARG cc_start: 0.4794 (OUTLIER) cc_final: 0.3447 (ttt-90) REVERT: A 110 TYR cc_start: 0.3893 (t80) cc_final: 0.3631 (t80) REVERT: A 128 HIS cc_start: 0.3217 (OUTLIER) cc_final: 0.2660 (t70) REVERT: A 155 MET cc_start: 0.3521 (ttt) cc_final: 0.2881 (ttm) REVERT: A 166 GLU cc_start: 0.5962 (pm20) cc_final: 0.5659 (pm20) REVERT: A 401 ARG cc_start: 0.7510 (tpp-160) cc_final: 0.7220 (tpp-160) REVERT: A 416 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6918 (mt-10) REVERT: A 422 TRP cc_start: 0.8359 (m100) cc_final: 0.8031 (m-10) REVERT: A 443 ARG cc_start: 0.7659 (mmm-85) cc_final: 0.7151 (mtp85) REVERT: A 524 GLU cc_start: 0.7083 (mp0) cc_final: 0.6876 (mp0) REVERT: B 1 MET cc_start: 0.6930 (tmm) cc_final: 0.6559 (tmm) REVERT: B 52 LYS cc_start: 0.7545 (ptpt) cc_final: 0.7289 (tppt) REVERT: B 105 ASN cc_start: 0.8247 (m-40) cc_final: 0.7903 (m-40) REVERT: B 121 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.7316 (mmm-85) REVERT: B 133 LEU cc_start: 0.8070 (mp) cc_final: 0.7583 (tp) REVERT: B 135 ARG cc_start: 0.6170 (ttt-90) cc_final: 0.5955 (ttt180) REVERT: B 146 THR cc_start: 0.7823 (t) cc_final: 0.6639 (p) REVERT: B 148 GLU cc_start: 0.7613 (tt0) cc_final: 0.7361 (mm-30) REVERT: B 356 MET cc_start: 0.4224 (ttm) cc_final: 0.3984 (ttp) REVERT: B 582 GLN cc_start: 0.7059 (OUTLIER) cc_final: 0.6822 (pt0) REVERT: B 713 SER cc_start: 0.7153 (m) cc_final: 0.6851 (p) REVERT: B 745 LYS cc_start: 0.8084 (pttt) cc_final: 0.7456 (mtmm) REVERT: C 28 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7782 (ttm) REVERT: C 61 LYS cc_start: 0.7059 (mppt) cc_final: 0.6505 (mppt) REVERT: C 69 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7317 (tm-30) REVERT: C 83 ASP cc_start: 0.5597 (m-30) cc_final: 0.5332 (m-30) REVERT: C 147 ILE cc_start: 0.8339 (pt) cc_final: 0.8116 (mp) REVERT: C 217 PHE cc_start: 0.6200 (OUTLIER) cc_final: 0.5199 (t80) outliers start: 67 outliers final: 54 residues processed: 381 average time/residue: 0.1341 time to fit residues: 71.8228 Evaluate side-chains 395 residues out of total 1493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 335 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ARG Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 160 ASP Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 615 LYS Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 210 GLN Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 287 ARG Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 336 ILE Chi-restraints excluded: chain B residue 344 PHE Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 642 ASN Chi-restraints excluded: chain B residue 656 GLU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 714 MET Chi-restraints excluded: chain B residue 738 GLU Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 217 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 136 optimal weight: 0.0470 chunk 27 optimal weight: 0.9980 chunk 8 optimal weight: 0.1980 chunk 125 optimal weight: 0.6980 chunk 46 optimal weight: 0.1980 chunk 18 optimal weight: 0.6980 chunk 51 optimal weight: 0.0870 chunk 98 optimal weight: 0.3980 chunk 112 optimal weight: 0.1980 chunk 4 optimal weight: 0.6980 chunk 129 optimal weight: 0.7980 overall best weight: 0.1456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 HIS ** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 HIS ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.163987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.147395 restraints weight = 23609.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.151053 restraints weight = 13110.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.153477 restraints weight = 8195.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.155085 restraints weight = 5606.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.156213 restraints weight = 4131.828| |-----------------------------------------------------------------------------| r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14341 Z= 0.136 Angle : 0.708 12.991 19460 Z= 0.362 Chirality : 0.043 0.197 2148 Planarity : 0.005 0.062 2409 Dihedral : 13.653 147.246 2234 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.09 % Allowed : 25.65 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.20), residues: 1655 helix: 0.14 (0.19), residues: 741 sheet: -1.09 (0.46), residues: 129 loop : -2.18 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 638 TYR 0.022 0.001 TYR B 217 PHE 0.048 0.002 PHE B 381 TRP 0.037 0.002 TRP A 188 HIS 0.004 0.001 HIS A 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (14341) covalent geometry : angle 0.70847 / 0.36 (19460) hydrogen bonds : bond 0.04296 / 2.84 ( 568) hydrogen bonds : angle 4.70040 / 3.23 ( 1600) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2608.71 seconds wall clock time: 45 minutes 52.75 seconds (2752.75 seconds total)