Starting phenix.real_space_refine on Wed Jun 11 10:09:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n5v_49040/06_2025/9n5v_49040.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n5v_49040/06_2025/9n5v_49040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n5v_49040/06_2025/9n5v_49040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n5v_49040/06_2025/9n5v_49040.map" model { file = "/net/cci-nas-00/data/ceres_data/9n5v_49040/06_2025/9n5v_49040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n5v_49040/06_2025/9n5v_49040.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= -0.038 sd= 0.555 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: 7 Type Number sf(0) Gaussians Fe 34 7.16 5 Zn 2 6.06 5 P 5 5.49 5 S 118 5.16 5 C 8052 2.51 5 N 2131 2.21 5 O 2369 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12711 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 947, 7424 Classifications: {'peptide': 947} Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 898} Chain breaks: 1 Chain: "B" Number of atoms: 4549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4549 Classifications: {'peptide': 590} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 560} Chain breaks: 1 Chain: "C" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 540 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 6, 'TRANS': 57} Chain: "A" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 97 Unusual residues: {'FAD': 1, 'FES': 1, 'SF4': 5} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 101 Unusual residues: {' ZN': 2, 'FMN': 1, 'NAD': 1, 'SF4': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4939 SG CYS A 640 49.601 66.212 77.717 1.00 7.66 S ATOM 4960 SG CYS A 643 43.895 62.819 78.294 1.00 5.65 S ATOM 4979 SG CYS A 646 49.446 59.953 79.207 1.00 3.64 S ATOM 5359 SG CYS A 693 47.195 61.903 73.423 1.00 18.89 S ATOM 788 SG CYS A 111 43.462 73.468 46.394 1.00 24.61 S ATOM 1091 SG CYS A 150 46.016 75.757 40.702 1.00 37.95 S ATOM 1120 SG CYS A 154 49.653 73.600 45.622 1.00 9.96 S ATOM 4537 SG CYS A 590 54.635 66.685 52.380 1.00 11.79 S ATOM 4557 SG CYS A 593 54.595 70.997 56.750 1.00 15.88 S ATOM 761 SG CYS A 107 49.877 71.016 52.102 1.00 13.67 S ATOM 1153 SG CYS A 158 55.359 73.311 50.849 1.00 39.08 S ATOM 4619 SG CYS A 601 42.796 66.928 68.327 1.00 29.78 S ATOM 736 SG CYS A 103 43.810 71.333 63.817 1.00 13.06 S ATOM 4567 SG CYS A 595 48.024 66.604 65.175 1.00 4.83 S ATOM 5817 SG CYS A 752 51.332 41.894 72.089 1.00 48.77 S ATOM 5603 SG CYS A 726 44.807 40.140 73.131 1.00 60.93 S ATOM 5575 SG CYS A 722 49.248 35.793 72.698 1.00 74.54 S ATOM 5557 SG CYS A 719 48.080 39.395 67.639 1.00 72.35 S ATOM 256 SG CYS A 41 38.961 64.629 82.505 1.00 24.50 S ATOM 343 SG CYS A 52 37.404 67.110 80.304 1.00 26.53 S ATOM 368 SG CYS A 55 32.466 66.231 82.592 1.00 28.30 S ATOM 455 SG CYS A 67 33.856 63.938 84.803 1.00 28.68 S ATOM 11281 SG CYS B 500 41.739 72.863 94.131 1.00 12.59 S ATOM 10969 SG CYS B 460 43.898 76.428 89.458 1.00 14.42 S ATOM 10945 SG CYS B 457 40.871 72.769 87.345 1.00 10.50 S ATOM 10926 SG CYS B 454 46.040 70.242 90.998 1.00 27.07 S ATOM 11684 SG CYS B 553 68.741 110.743 95.717 1.00145.34 S ATOM 11649 SG CYS B 547 68.391 116.935 96.679 1.00136.12 S ATOM 11666 SG CYS B 550 70.510 112.810 101.757 1.00148.75 S ATOM 11842 SG CYS B 580 65.357 101.114 92.513 1.00129.21 S ATOM 11819 SG CYS B 577 65.835 106.004 88.111 1.00134.21 S ATOM 11711 SG CYS B 557 69.195 104.256 93.070 1.00127.64 S ATOM 10789 SG CYS B 437 47.380 99.748 91.682 1.00 67.55 S ATOM 11508 SG CYS B 529 49.427 102.871 90.747 1.00 92.99 S ATOM 11542 SG CYS B 534 50.525 99.487 89.452 1.00 72.06 S ATOM 7513 SG CYS B 14 54.513 84.244 117.937 1.00 66.64 S ATOM 7751 SG CYS B 45 51.976 84.943 119.886 1.00 70.45 S ATOM 7776 SG CYS B 49 51.333 87.158 117.062 1.00 78.62 S Time building chain proxies: 7.46, per 1000 atoms: 0.59 Number of scatterers: 12711 At special positions: 0 Unit cell: (89.424, 130.824, 154.008, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Fe 34 26.01 S 118 16.00 P 5 15.00 O 2369 8.00 N 2131 7.00 C 8052 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.88 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A1007 " pdb="FE2 FES A1007 " - pdb=" SG CYS A 55 " pdb="FE1 FES A1007 " - pdb=" SG CYS A 52 " pdb="FE1 FES A1007 " - pdb=" SG CYS A 41 " pdb="FE2 FES A1007 " - pdb=" SG CYS A 67 " pdb=" SF4 A1001 " pdb="FE2 SF4 A1001 " - pdb=" SG CYS A 643 " pdb="FE1 SF4 A1001 " - pdb=" SG CYS A 640 " pdb="FE3 SF4 A1001 " - pdb=" SG CYS A 646 " pdb="FE4 SF4 A1001 " - pdb=" SG CYS A 693 " pdb=" SF4 A1002 " pdb="FE4 SF4 A1002 " - pdb=" SG CYS A 154 " pdb="FE1 SF4 A1002 " - pdb=" SG CYS A 111 " pdb="FE2 SF4 A1002 " - pdb=" SG CYS A 150 " pdb=" SF4 A1003 " pdb="FE4 SF4 A1003 " - pdb=" SG CYS A 158 " pdb="FE2 SF4 A1003 " - pdb=" SG CYS A 593 " pdb="FE3 SF4 A1003 " - pdb=" SG CYS A 107 " pdb="FE1 SF4 A1003 " - pdb=" SG CYS A 590 " pdb=" SF4 A1004 " pdb="FE4 SF4 A1004 " - pdb=" ND1 HIS A 99 " pdb="FE2 SF4 A1004 " - pdb=" SG CYS A 103 " pdb="FE1 SF4 A1004 " - pdb=" SG CYS A 601 " pdb="FE3 SF4 A1004 " - pdb=" SG CYS A 595 " pdb=" SF4 A1006 " pdb="FE1 SF4 A1006 " - pdb=" SG CYS A 752 " pdb="FE3 SF4 A1006 " - pdb=" SG CYS A 722 " pdb="FE2 SF4 A1006 " - pdb=" SG CYS A 726 " pdb="FE4 SF4 A1006 " - pdb=" SG CYS A 719 " pdb=" SF4 B 701 " pdb="FE1 SF4 B 701 " - pdb=" SG CYS B 500 " pdb="FE3 SF4 B 701 " - pdb=" SG CYS B 457 " pdb="FE2 SF4 B 701 " - pdb=" SG CYS B 460 " pdb="FE4 SF4 B 701 " - pdb=" SG CYS B 454 " pdb=" SF4 B 703 " pdb="FE1 SF4 B 703 " - pdb=" SG CYS B 553 " pdb="FE4 SF4 B 703 " - pdb=" SG CYS B 550 " pdb="FE3 SF4 B 703 " - pdb=" SG CYS B 547 " pdb="FE2 SF4 B 703 " - pdb=" SG CYS B 587 " pdb=" SF4 B 704 " pdb="FE4 SF4 B 704 " - pdb=" SG CYS B 557 " pdb="FE3 SF4 B 704 " - pdb=" SG CYS B 577 " pdb="FE1 SF4 B 704 " - pdb=" SG CYS B 580 " pdb="FE4 SF4 B 704 " - pdb=" SG CYS B 583 " Number of angles added : 96 Zn2+ tetrahedral coordination pdb=" ZN B 706 " pdb="ZN ZN B 706 " - pdb=" NE2 HIS B 524 " pdb="ZN ZN B 706 " - pdb=" SG CYS B 529 " pdb="ZN ZN B 706 " - pdb=" SG CYS B 534 " pdb="ZN ZN B 706 " - pdb=" SG CYS B 437 " pdb=" ZN B 707 " pdb="ZN ZN B 707 " - pdb=" SG CYS B 45 " pdb="ZN ZN B 707 " - pdb=" SG CYS B 49 " pdb="ZN ZN B 707 " - pdb=" SG CYS B 14 " Number of angles added : 3 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2908 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 18 sheets defined 43.3% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.18 Creating SS restraints... Processing helix chain 'A' and resid 26 through 35 removed outlier: 4.164A pdb=" N PHE A 30 " --> pdb=" O SER A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 99 removed outlier: 3.668A pdb=" N ASP A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 111 removed outlier: 3.542A pdb=" N ASN A 109 " --> pdb=" O GLY A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 127 Processing helix chain 'A' and resid 128 through 138 removed outlier: 3.683A pdb=" N GLU A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 150 Processing helix chain 'A' and resid 168 through 183 Processing helix chain 'A' and resid 204 through 216 Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 244 through 257 Processing helix chain 'A' and resid 273 through 280 Processing helix chain 'A' and resid 309 through 319 removed outlier: 3.566A pdb=" N GLY A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 347 removed outlier: 3.616A pdb=" N ARG A 346 " --> pdb=" O ARG A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 376 Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 481 through 501 Processing helix chain 'A' and resid 503 through 513 Processing helix chain 'A' and resid 514 through 516 No H-bonds generated for 'chain 'A' and resid 514 through 516' Processing helix chain 'A' and resid 517 through 524 Processing helix chain 'A' and resid 524 through 535 Processing helix chain 'A' and resid 544 through 549 removed outlier: 3.519A pdb=" N TYR A 548 " --> pdb=" O GLU A 545 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU A 549 " --> pdb=" O LYS A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 568 Processing helix chain 'A' and resid 579 through 588 removed outlier: 3.503A pdb=" N VAL A 583 " --> pdb=" O ASP A 579 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU A 584 " --> pdb=" O GLU A 580 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR A 585 " --> pdb=" O GLU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 610 removed outlier: 3.543A pdb=" N GLU A 605 " --> pdb=" O CYS A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 640 Processing helix chain 'A' and resid 644 through 653 Processing helix chain 'A' and resid 664 through 668 removed outlier: 3.984A pdb=" N LYS A 667 " --> pdb=" O ARG A 664 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR A 668 " --> pdb=" O GLY A 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 664 through 668' Processing helix chain 'A' and resid 677 through 681 Processing helix chain 'A' and resid 688 through 693 Processing helix chain 'A' and resid 752 through 758 Processing helix chain 'A' and resid 759 through 763 removed outlier: 4.023A pdb=" N GLN A 763 " --> pdb=" O PRO A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 787 Processing helix chain 'A' and resid 798 through 813 Processing helix chain 'A' and resid 828 through 835 Processing helix chain 'A' and resid 848 through 854 removed outlier: 4.012A pdb=" N LEU A 852 " --> pdb=" O PRO A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 893 removed outlier: 4.029A pdb=" N LEU A 892 " --> pdb=" O ALA A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 Processing helix chain 'A' and resid 929 through 933 Processing helix chain 'B' and resid 12 through 19 Processing helix chain 'B' and resid 19 through 34 Processing helix chain 'B' and resid 48 through 52 removed outlier: 4.085A pdb=" N GLU B 52 " --> pdb=" O CYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 82 Processing helix chain 'B' and resid 130 through 137 removed outlier: 3.684A pdb=" N TYR B 134 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 148 Processing helix chain 'B' and resid 150 through 161 removed outlier: 3.514A pdb=" N SER B 161 " --> pdb=" O PHE B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 183 Processing helix chain 'B' and resid 202 through 211 Processing helix chain 'B' and resid 211 through 227 removed outlier: 3.786A pdb=" N VAL B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 256 Processing helix chain 'B' and resid 262 through 266 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 311 through 315 removed outlier: 3.517A pdb=" N GLY B 314 " --> pdb=" O GLY B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 341 removed outlier: 3.581A pdb=" N VAL B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) Proline residue: B 329 - end of helix removed outlier: 6.678A pdb=" N TRP B 336 " --> pdb=" O ILE B 332 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N GLU B 337 " --> pdb=" O LYS B 333 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA B 338 " --> pdb=" O HIS B 334 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR B 339 " --> pdb=" O GLY B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 379 Processing helix chain 'B' and resid 397 through 400 Processing helix chain 'B' and resid 406 through 408 No H-bonds generated for 'chain 'B' and resid 406 through 408' Processing helix chain 'B' and resid 413 through 421 Processing helix chain 'B' and resid 437 through 453 Processing helix chain 'B' and resid 457 through 476 removed outlier: 4.050A pdb=" N LYS B 465 " --> pdb=" O ARG B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 498 Proline residue: B 492 - end of helix Processing helix chain 'B' and resid 500 through 505 Processing helix chain 'B' and resid 507 through 517 Processing helix chain 'B' and resid 517 through 526 removed outlier: 3.736A pdb=" N TYR B 521 " --> pdb=" O PHE B 517 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE B 525 " --> pdb=" O TYR B 521 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU B 526 " --> pdb=" O LEU B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 557 removed outlier: 4.020A pdb=" N CYS B 557 " --> pdb=" O CYS B 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 11 removed outlier: 3.992A pdb=" N TYR C 7 " --> pdb=" O GLN C 4 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE C 8 " --> pdb=" O LEU C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 16 No H-bonds generated for 'chain 'C' and resid 14 through 16' Processing helix chain 'C' and resid 17 through 30 Processing helix chain 'C' and resid 33 through 45 Processing helix chain 'C' and resid 47 through 58 removed outlier: 3.687A pdb=" N TYR C 58 " --> pdb=" O VAL C 54 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 20 removed outlier: 9.296A pdb=" N ILE A 77 " --> pdb=" O LYS A 11 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N THR A 13 " --> pdb=" O ILE A 77 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 59 Processing sheet with id=AA3, first strand: chain 'A' and resid 261 through 264 removed outlier: 6.665A pdb=" N VAL A 221 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LYS A 263 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ILE A 223 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE A 198 " --> pdb=" O THR A 222 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N PHE A 224 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL A 200 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA A 283 " --> pdb=" O ARG A 197 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 306 through 308 removed outlier: 6.639A pdb=" N VAL A 328 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N VAL A 354 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL A 330 " --> pdb=" O VAL A 354 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL A 351 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N MET A 380 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N VAL A 353 " --> pdb=" O MET A 380 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 383 through 389 removed outlier: 6.842A pdb=" N GLU A 398 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ILE A 388 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLU A 396 " --> pdb=" O ILE A 388 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET A 416 " --> pdb=" O LYS A 403 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 383 through 389 removed outlier: 6.842A pdb=" N GLU A 398 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ILE A 388 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLU A 396 " --> pdb=" O ILE A 388 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 450 through 451 Processing sheet with id=AA8, first strand: chain 'A' and resid 633 through 635 Processing sheet with id=AA9, first strand: chain 'A' and resid 660 through 662 Processing sheet with id=AB1, first strand: chain 'A' and resid 713 through 718 removed outlier: 3.607A pdb=" N ARG A 739 " --> pdb=" O GLU A 731 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N TYR A 733 " --> pdb=" O LEU A 737 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU A 737 " --> pdb=" O TYR A 733 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 773 through 774 removed outlier: 6.594A pdb=" N TYR A 906 " --> pdb=" O LEU A 923 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LEU A 925 " --> pdb=" O TYR A 906 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL A 908 " --> pdb=" O LEU A 925 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N LEU A 791 " --> pdb=" O GLY A 817 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 858 through 859 removed outlier: 6.550A pdb=" N ARG A 837 " --> pdb=" O VAL A 866 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ILE A 868 " --> pdb=" O ARG A 837 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU A 839 " --> pdb=" O ILE A 868 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N GLU A 870 " --> pdb=" O LEU A 839 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 935 through 938 Processing sheet with id=AB5, first strand: chain 'B' and resid 39 through 43 removed outlier: 3.535A pdb=" N ALA B 6 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LEU B 54 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLY B 67 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL B 92 " --> pdb=" O GLY B 67 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 271 through 277 removed outlier: 6.142A pdb=" N GLY B 231 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LYS B 275 " --> pdb=" O GLY B 231 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ILE B 233 " --> pdb=" O LYS B 275 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLY B 277 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL B 235 " --> pdb=" O GLY B 277 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ARG B 236 " --> pdb=" O ALA B 194 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 363 through 368 removed outlier: 7.717A pdb=" N MET B 429 " --> pdb=" O VAL B 352 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ALA B 354 " --> pdb=" O MET B 429 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL B 431 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N SER B 356 " --> pdb=" O VAL B 431 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N ASP B 433 " --> pdb=" O SER B 356 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 371 through 372 removed outlier: 3.768A pdb=" N ILE B 371 " --> pdb=" O VAL B 412 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 541 through 542 499 hydrogen bonds defined for protein. 1380 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.98 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 5256 1.43 - 1.65: 7522 1.65 - 1.86: 121 1.86 - 2.07: 0 2.07 - 2.28: 100 Bond restraints: 12999 Sorted by residual: bond pdb=" C4 FMN B 702 " pdb=" C4A FMN B 702 " ideal model delta sigma weight residual 1.485 1.386 0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" O3P FAD A1005 " pdb=" P FAD A1005 " ideal model delta sigma weight residual 1.660 1.581 0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C4A FMN B 702 " pdb=" N5 FMN B 702 " ideal model delta sigma weight residual 1.300 1.378 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" O5' FMN B 702 " pdb=" P FMN B 702 " ideal model delta sigma weight residual 1.676 1.605 0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" O5B FAD A1005 " pdb=" PA FAD A1005 " ideal model delta sigma weight residual 1.634 1.569 0.065 2.00e-02 2.50e+03 1.07e+01 ... (remaining 12994 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 17389 1.96 - 3.91: 211 3.91 - 5.87: 29 5.87 - 7.82: 9 7.82 - 9.78: 2 Bond angle restraints: 17640 Sorted by residual: angle pdb=" N ARG B 303 " pdb=" CA ARG B 303 " pdb=" C ARG B 303 " ideal model delta sigma weight residual 109.81 119.59 -9.78 2.21e+00 2.05e-01 1.96e+01 angle pdb=" CA TYR A 120 " pdb=" CB TYR A 120 " pdb=" CG TYR A 120 " ideal model delta sigma weight residual 113.90 119.53 -5.63 1.80e+00 3.09e-01 9.77e+00 angle pdb=" PA NAD B 705 " pdb=" O3 NAD B 705 " pdb=" PN NAD B 705 " ideal model delta sigma weight residual 126.50 135.50 -9.00 3.00e+00 1.11e-01 9.00e+00 angle pdb=" CA ARG B 303 " pdb=" C ARG B 303 " pdb=" N PRO B 304 " ideal model delta sigma weight residual 118.44 122.54 -4.10 1.59e+00 3.96e-01 6.64e+00 angle pdb=" O1P FAD A1005 " pdb=" P FAD A1005 " pdb=" O2P FAD A1005 " ideal model delta sigma weight residual 122.50 114.78 7.72 3.00e+00 1.11e-01 6.62e+00 ... (remaining 17635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 7334 17.65 - 35.30: 427 35.30 - 52.94: 76 52.94 - 70.59: 33 70.59 - 88.24: 4 Dihedral angle restraints: 7874 sinusoidal: 3312 harmonic: 4562 Sorted by residual: dihedral pdb=" CA PRO B 304 " pdb=" C PRO B 304 " pdb=" N PRO B 305 " pdb=" CA PRO B 305 " ideal model delta harmonic sigma weight residual 180.00 155.74 24.26 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA PHE A 40 " pdb=" C PHE A 40 " pdb=" N CYS A 41 " pdb=" CA CYS A 41 " ideal model delta harmonic sigma weight residual -180.00 -160.77 -19.23 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA PRO B 305 " pdb=" C PRO B 305 " pdb=" N TYR B 306 " pdb=" CA TYR B 306 " ideal model delta harmonic sigma weight residual -180.00 -163.29 -16.71 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 7871 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1393 0.044 - 0.088: 438 0.088 - 0.132: 124 0.132 - 0.177: 6 0.177 - 0.221: 2 Chirality restraints: 1963 Sorted by residual: chirality pdb=" C3B NAD B 705 " pdb=" C2B NAD B 705 " pdb=" C4B NAD B 705 " pdb=" O3B NAD B 705 " both_signs ideal model delta sigma weight residual False -2.71 -2.49 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA ARG B 303 " pdb=" N ARG B 303 " pdb=" C ARG B 303 " pdb=" CB ARG B 303 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" C1D NAD B 705 " pdb=" C2D NAD B 705 " pdb=" N1N NAD B 705 " pdb=" O4D NAD B 705 " both_signs ideal model delta sigma weight residual False 2.41 2.57 -0.16 2.00e-01 2.50e+01 6.33e-01 ... (remaining 1960 not shown) Planarity restraints: 2225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 304 " -0.041 5.00e-02 4.00e+02 6.27e-02 6.28e+00 pdb=" N PRO B 305 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 305 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 305 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 303 " 0.036 5.00e-02 4.00e+02 5.38e-02 4.64e+00 pdb=" N PRO B 304 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 304 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 304 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 59 " -0.030 5.00e-02 4.00e+02 4.47e-02 3.19e+00 pdb=" N PRO A 60 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 60 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 60 " -0.025 5.00e-02 4.00e+02 ... (remaining 2222 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1605 2.75 - 3.29: 12087 3.29 - 3.83: 21182 3.83 - 4.36: 25961 4.36 - 4.90: 44696 Nonbonded interactions: 105531 Sorted by model distance: nonbonded pdb=" OG1 THR B 70 " pdb=" OD1 ASP B 72 " model vdw 2.215 3.040 nonbonded pdb=" OE1 GLU B 285 " pdb=" OG1 THR B 287 " model vdw 2.236 3.040 nonbonded pdb=" OD1 ASP A 474 " pdb=" OG SER A 480 " model vdw 2.241 3.040 nonbonded pdb=" OG1 THR A 59 " pdb=" O GLY A 62 " model vdw 2.250 3.040 nonbonded pdb=" OG1 THR A 794 " pdb=" O ILE A 909 " model vdw 2.252 3.040 ... (remaining 105526 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 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: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 37.090 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 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 : 0.014 1.207 13041 Z= 0.450 Angle : 1.092 59.816 17739 Z= 0.302 Chirality : 0.045 0.221 1963 Planarity : 0.005 0.063 2225 Dihedral : 12.024 88.238 4966 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 4.24 % Allowed : 5.88 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.20), residues: 1591 helix: -0.02 (0.21), residues: 590 sheet: 0.19 (0.36), residues: 215 loop : -0.84 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 186 HIS 0.003 0.001 HIS B 68 PHE 0.014 0.002 PHE B 157 TYR 0.025 0.002 TYR A 120 ARG 0.003 0.000 ARG B 297 Details of bonding type rmsd hydrogen bonds : bond 0.17926 ( 496) hydrogen bonds : angle 6.83576 ( 1380) metal coordination : bond 0.24363 ( 42) metal coordination : angle 12.39100 ( 99) covalent geometry : bond 0.00429 (12999) covalent geometry : angle 0.58128 (17640) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 280 time to evaluate : 1.469 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: A 87 MET cc_start: 0.8602 (mtp) cc_final: 0.8270 (mtt) REVERT: A 304 ASP cc_start: 0.6962 (t0) cc_final: 0.6552 (t70) REVERT: A 351 VAL cc_start: 0.9084 (OUTLIER) cc_final: 0.8836 (t) REVERT: A 387 LYS cc_start: 0.8738 (ptmt) cc_final: 0.8301 (ttpp) REVERT: A 396 GLU cc_start: 0.7946 (pt0) cc_final: 0.7697 (pt0) REVERT: A 398 GLU cc_start: 0.8254 (pt0) cc_final: 0.7756 (pt0) REVERT: A 769 ILE cc_start: 0.8763 (mt) cc_final: 0.8445 (mm) REVERT: A 922 TYR cc_start: 0.7581 (p90) cc_final: 0.7091 (p90) REVERT: B 32 GLU cc_start: 0.7997 (tp30) cc_final: 0.7682 (tp30) REVERT: B 80 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8136 (mp0) REVERT: B 219 MET cc_start: 0.9089 (mtp) cc_final: 0.8885 (mtp) REVERT: B 504 GLN cc_start: 0.8850 (mt0) cc_final: 0.8634 (mt0) REVERT: C 6 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7410 (mp0) outliers start: 57 outliers final: 19 residues processed: 325 average time/residue: 1.6108 time to fit residues: 563.0383 Evaluate side-chains 249 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 227 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 951 ARG Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 568 LYS Chi-restraints excluded: chain B residue 577 CYS Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 46 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 0.9990 chunk 120 optimal weight: 0.0370 chunk 66 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN B 262 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.078732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.063714 restraints weight = 26570.159| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.68 r_work: 0.2846 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 13041 Z= 0.149 Angle : 1.118 65.549 17739 Z= 0.319 Chirality : 0.044 0.189 1963 Planarity : 0.005 0.057 2225 Dihedral : 8.698 72.364 1894 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.94 % Allowed : 14.73 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.21), residues: 1591 helix: 0.47 (0.22), residues: 589 sheet: 0.25 (0.36), residues: 213 loop : -0.75 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 186 HIS 0.003 0.001 HIS B 68 PHE 0.024 0.002 PHE B 445 TYR 0.023 0.002 TYR A 120 ARG 0.009 0.001 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.04391 ( 496) hydrogen bonds : angle 5.35731 ( 1380) metal coordination : bond 0.01372 ( 42) metal coordination : angle 12.72104 ( 99) covalent geometry : bond 0.00351 (12999) covalent geometry : angle 0.59120 (17640) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 231 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 GLN cc_start: 0.9338 (OUTLIER) cc_final: 0.7167 (mp10) REVERT: A 217 MET cc_start: 0.9166 (mtt) cc_final: 0.8815 (mtt) REVERT: A 350 ASP cc_start: 0.8435 (t0) cc_final: 0.8209 (p0) REVERT: A 351 VAL cc_start: 0.9214 (OUTLIER) cc_final: 0.8956 (t) REVERT: A 387 LYS cc_start: 0.9003 (ptmt) cc_final: 0.8701 (ttpp) REVERT: A 398 GLU cc_start: 0.8566 (pt0) cc_final: 0.8315 (pt0) REVERT: A 403 LYS cc_start: 0.8862 (tppt) cc_final: 0.8469 (tptp) REVERT: B 32 GLU cc_start: 0.8550 (tp30) cc_final: 0.8332 (tp30) REVERT: B 73 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8295 (ptm160) REVERT: B 80 GLU cc_start: 0.9113 (OUTLIER) cc_final: 0.8750 (mp0) REVERT: B 485 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8401 (mp0) REVERT: C 6 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7902 (mp0) REVERT: C 66 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7599 (mm) outliers start: 53 outliers final: 21 residues processed: 266 average time/residue: 1.7298 time to fit residues: 495.4200 Evaluate side-chains 243 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 215 time to evaluate : 2.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 568 LYS Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 66 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 118 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 74 optimal weight: 0.0020 chunk 125 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 126 optimal weight: 0.5980 chunk 121 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN B 364 ASN B 504 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.077081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.061468 restraints weight = 26570.212| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 1.76 r_work: 0.2797 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 13041 Z= 0.198 Angle : 1.154 65.806 17739 Z= 0.344 Chirality : 0.046 0.203 1963 Planarity : 0.005 0.057 2225 Dihedral : 8.193 75.097 1883 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.46 % Allowed : 16.44 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.20), residues: 1591 helix: 0.33 (0.21), residues: 583 sheet: -0.13 (0.34), residues: 229 loop : -0.83 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 186 HIS 0.004 0.001 HIS B 68 PHE 0.015 0.002 PHE B 157 TYR 0.024 0.002 TYR A 120 ARG 0.010 0.001 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.04549 ( 496) hydrogen bonds : angle 5.39409 ( 1380) metal coordination : bond 0.01561 ( 42) metal coordination : angle 12.87044 ( 99) covalent geometry : bond 0.00477 (12999) covalent geometry : angle 0.64071 (17640) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 227 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 GLN cc_start: 0.9367 (OUTLIER) cc_final: 0.7180 (mp10) REVERT: A 219 HIS cc_start: 0.8761 (OUTLIER) cc_final: 0.7462 (m-70) REVERT: A 350 ASP cc_start: 0.8492 (t0) cc_final: 0.8252 (p0) REVERT: A 351 VAL cc_start: 0.9278 (OUTLIER) cc_final: 0.8989 (t) REVERT: A 384 ASN cc_start: 0.8481 (p0) cc_final: 0.8278 (p0) REVERT: A 397 VAL cc_start: 0.8509 (OUTLIER) cc_final: 0.8306 (m) REVERT: A 773 ASN cc_start: 0.8660 (t0) cc_final: 0.8354 (p0) REVERT: B 32 GLU cc_start: 0.8641 (tp30) cc_final: 0.8441 (tp30) REVERT: B 73 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8352 (ptm160) REVERT: B 80 GLU cc_start: 0.9145 (OUTLIER) cc_final: 0.8741 (mp0) REVERT: B 485 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8290 (mp0) REVERT: C 6 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7873 (mp0) REVERT: C 66 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7529 (mm) outliers start: 60 outliers final: 27 residues processed: 267 average time/residue: 1.4895 time to fit residues: 429.0318 Evaluate side-chains 251 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 215 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 568 LYS Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 66 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 93 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 141 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 ASN A 280 GLN A 465 ASN A 570 ASN B 61 ASN B 504 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.076896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.061375 restraints weight = 26725.882| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 1.77 r_work: 0.2795 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 13041 Z= 0.197 Angle : 1.164 64.108 17739 Z= 0.348 Chirality : 0.046 0.212 1963 Planarity : 0.005 0.055 2225 Dihedral : 8.084 75.092 1882 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.46 % Favored : 95.47 % Rotamer: Outliers : 3.94 % Allowed : 18.45 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.20), residues: 1591 helix: 0.31 (0.21), residues: 583 sheet: -0.00 (0.35), residues: 213 loop : -0.88 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 186 HIS 0.004 0.001 HIS B 68 PHE 0.027 0.002 PHE A 783 TYR 0.023 0.002 TYR A 120 ARG 0.009 0.001 ARG A 327 Details of bonding type rmsd hydrogen bonds : bond 0.04392 ( 496) hydrogen bonds : angle 5.36630 ( 1380) metal coordination : bond 0.01525 ( 42) metal coordination : angle 12.93030 ( 99) covalent geometry : bond 0.00477 (12999) covalent geometry : angle 0.65167 (17640) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 217 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 GLN cc_start: 0.9381 (OUTLIER) cc_final: 0.7212 (mp10) REVERT: A 219 HIS cc_start: 0.8771 (OUTLIER) cc_final: 0.7371 (m-70) REVERT: A 296 MET cc_start: 0.7624 (ttp) cc_final: 0.7261 (ttm) REVERT: A 351 VAL cc_start: 0.9280 (OUTLIER) cc_final: 0.9002 (t) REVERT: A 400 ILE cc_start: 0.8892 (pt) cc_final: 0.8660 (pp) REVERT: A 922 TYR cc_start: 0.7769 (p90) cc_final: 0.7211 (p90) REVERT: B 73 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8322 (ptm160) REVERT: B 80 GLU cc_start: 0.9138 (OUTLIER) cc_final: 0.8766 (mp0) REVERT: B 485 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8281 (mp0) REVERT: B 568 LYS cc_start: 0.7038 (OUTLIER) cc_final: 0.6723 (tmtt) REVERT: B 579 LYS cc_start: 0.6789 (OUTLIER) cc_final: 0.6337 (mtmm) REVERT: C 6 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7922 (mp0) REVERT: C 66 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7519 (mm) outliers start: 53 outliers final: 28 residues processed: 252 average time/residue: 1.4931 time to fit residues: 405.1450 Evaluate side-chains 252 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 214 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 951 ARG Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 568 LYS Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 66 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 22 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 145 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.078216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.063193 restraints weight = 27079.172| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.75 r_work: 0.2829 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 13041 Z= 0.151 Angle : 1.119 60.143 17739 Z= 0.334 Chirality : 0.044 0.198 1963 Planarity : 0.005 0.051 2225 Dihedral : 7.915 73.029 1882 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.02 % Favored : 95.91 % Rotamer: Outliers : 3.72 % Allowed : 19.49 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.21), residues: 1591 helix: 0.61 (0.22), residues: 575 sheet: 0.13 (0.35), residues: 211 loop : -0.78 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 186 HIS 0.002 0.000 HIS B 68 PHE 0.028 0.002 PHE A 783 TYR 0.021 0.002 TYR A 120 ARG 0.011 0.001 ARG A 424 Details of bonding type rmsd hydrogen bonds : bond 0.03858 ( 496) hydrogen bonds : angle 5.17621 ( 1380) metal coordination : bond 0.01440 ( 42) metal coordination : angle 12.41632 ( 99) covalent geometry : bond 0.00360 (12999) covalent geometry : angle 0.62679 (17640) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 226 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 GLN cc_start: 0.9366 (OUTLIER) cc_final: 0.7154 (mp10) REVERT: A 219 HIS cc_start: 0.8717 (OUTLIER) cc_final: 0.7265 (m-70) REVERT: A 296 MET cc_start: 0.7624 (ttp) cc_final: 0.7289 (ttm) REVERT: A 393 LYS cc_start: 0.8995 (mmpt) cc_final: 0.8621 (mmmm) REVERT: A 820 ILE cc_start: 0.8149 (tp) cc_final: 0.7923 (pt) REVERT: B 73 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8346 (ptm160) REVERT: B 80 GLU cc_start: 0.9148 (OUTLIER) cc_final: 0.8744 (mp0) REVERT: B 219 MET cc_start: 0.9315 (mtp) cc_final: 0.9111 (mtp) REVERT: B 405 ASP cc_start: 0.7571 (p0) cc_final: 0.7322 (p0) REVERT: B 485 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8324 (mp0) REVERT: B 568 LYS cc_start: 0.6919 (OUTLIER) cc_final: 0.6590 (tmtt) REVERT: C 6 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7881 (mp0) REVERT: C 66 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7561 (mm) outliers start: 50 outliers final: 27 residues processed: 257 average time/residue: 1.5793 time to fit residues: 437.1591 Evaluate side-chains 246 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 211 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 951 ARG Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 557 CYS Chi-restraints excluded: chain B residue 568 LYS Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 66 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 53 optimal weight: 0.4980 chunk 46 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 145 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 83 optimal weight: 0.0970 chunk 125 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN B 504 GLN B 590 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.078781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.063777 restraints weight = 27275.866| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.71 r_work: 0.2848 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 13041 Z= 0.143 Angle : 1.102 56.924 17739 Z= 0.335 Chirality : 0.044 0.202 1963 Planarity : 0.005 0.060 2225 Dihedral : 7.841 72.340 1879 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.02 % Favored : 95.91 % Rotamer: Outliers : 3.87 % Allowed : 20.31 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.21), residues: 1591 helix: 0.69 (0.22), residues: 586 sheet: 0.02 (0.35), residues: 217 loop : -0.77 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 186 HIS 0.002 0.000 HIS B 68 PHE 0.029 0.002 PHE A 783 TYR 0.021 0.002 TYR A 120 ARG 0.012 0.001 ARG A 424 Details of bonding type rmsd hydrogen bonds : bond 0.03767 ( 496) hydrogen bonds : angle 5.07082 ( 1380) metal coordination : bond 0.01210 ( 42) metal coordination : angle 12.07478 ( 99) covalent geometry : bond 0.00344 (12999) covalent geometry : angle 0.63525 (17640) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 227 time to evaluate : 2.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 HIS cc_start: 0.8715 (OUTLIER) cc_final: 0.7192 (m-70) REVERT: A 296 MET cc_start: 0.7569 (ttp) cc_final: 0.7300 (ttm) REVERT: A 820 ILE cc_start: 0.8138 (tp) cc_final: 0.7917 (pt) REVERT: A 922 TYR cc_start: 0.7650 (p90) cc_final: 0.7098 (p90) REVERT: B 80 GLU cc_start: 0.9138 (OUTLIER) cc_final: 0.8675 (mp0) REVERT: B 481 LEU cc_start: 0.9059 (mp) cc_final: 0.8691 (mt) REVERT: B 485 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8356 (mp0) REVERT: B 568 LYS cc_start: 0.6910 (OUTLIER) cc_final: 0.6611 (tmtt) REVERT: B 585 GLU cc_start: 0.6603 (OUTLIER) cc_final: 0.6097 (tp30) REVERT: B 590 ASN cc_start: 0.8765 (m-40) cc_final: 0.7511 (p0) REVERT: C 6 GLU cc_start: 0.8440 (tp30) cc_final: 0.7906 (mp0) REVERT: C 66 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7555 (mm) outliers start: 52 outliers final: 25 residues processed: 262 average time/residue: 1.5759 time to fit residues: 445.4796 Evaluate side-chains 246 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 215 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 951 ARG Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain B residue 568 LYS Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 585 GLU Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 66 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 154 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 140 optimal weight: 0.5980 chunk 32 optimal weight: 0.3980 chunk 72 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 121 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 ASN B 61 ASN B 504 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.077559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.062055 restraints weight = 26846.390| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.76 r_work: 0.2819 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 13041 Z= 0.183 Angle : 1.130 51.126 17739 Z= 0.359 Chirality : 0.046 0.215 1963 Planarity : 0.005 0.053 2225 Dihedral : 7.769 73.816 1874 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.59 % Favored : 95.35 % Rotamer: Outliers : 3.65 % Allowed : 20.83 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.21), residues: 1591 helix: 0.49 (0.21), residues: 587 sheet: -0.14 (0.34), residues: 223 loop : -0.80 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 186 HIS 0.004 0.001 HIS B 68 PHE 0.021 0.002 PHE B 445 TYR 0.023 0.002 TYR A 120 ARG 0.012 0.001 ARG A 424 Details of bonding type rmsd hydrogen bonds : bond 0.04170 ( 496) hydrogen bonds : angle 5.22732 ( 1380) metal coordination : bond 0.01282 ( 42) metal coordination : angle 12.06769 ( 99) covalent geometry : bond 0.00445 (12999) covalent geometry : angle 0.68240 (17640) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 217 time to evaluate : 2.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 GLN cc_start: 0.9362 (OUTLIER) cc_final: 0.7269 (mp10) REVERT: A 219 HIS cc_start: 0.8654 (OUTLIER) cc_final: 0.7299 (m-70) REVERT: A 296 MET cc_start: 0.7659 (ttp) cc_final: 0.7440 (ttm) REVERT: A 820 ILE cc_start: 0.8144 (tp) cc_final: 0.7920 (pt) REVERT: B 80 GLU cc_start: 0.9103 (OUTLIER) cc_final: 0.8670 (mp0) REVERT: B 481 LEU cc_start: 0.9072 (mp) cc_final: 0.8556 (mt) REVERT: B 485 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8289 (mp0) REVERT: B 573 ASN cc_start: 0.8017 (m-40) cc_final: 0.7672 (p0) REVERT: B 585 GLU cc_start: 0.6639 (OUTLIER) cc_final: 0.6134 (tp30) REVERT: B 590 ASN cc_start: 0.8836 (m-40) cc_final: 0.7562 (p0) REVERT: C 6 GLU cc_start: 0.8467 (tp30) cc_final: 0.7881 (mp0) REVERT: C 66 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7586 (mm) outliers start: 49 outliers final: 27 residues processed: 256 average time/residue: 2.1431 time to fit residues: 596.1858 Evaluate side-chains 248 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 215 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 951 ARG Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain B residue 568 LYS Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 585 GLU Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 66 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 66 optimal weight: 0.4980 chunk 113 optimal weight: 0.4980 chunk 112 optimal weight: 0.6980 chunk 115 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 114 optimal weight: 0.0020 chunk 146 optimal weight: 0.0070 chunk 33 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.3006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.080607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.065564 restraints weight = 27139.414| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.77 r_work: 0.2901 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13041 Z= 0.127 Angle : 1.095 53.961 17739 Z= 0.345 Chirality : 0.043 0.201 1963 Planarity : 0.005 0.053 2225 Dihedral : 7.537 71.280 1874 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.98 % Allowed : 21.88 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.21), residues: 1591 helix: 0.88 (0.22), residues: 582 sheet: -0.30 (0.34), residues: 237 loop : -0.63 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 186 HIS 0.002 0.000 HIS A 651 PHE 0.033 0.001 PHE A 783 TYR 0.023 0.001 TYR A 437 ARG 0.013 0.001 ARG A 424 Details of bonding type rmsd hydrogen bonds : bond 0.03386 ( 496) hydrogen bonds : angle 4.90919 ( 1380) metal coordination : bond 0.00922 ( 42) metal coordination : angle 11.74345 ( 99) covalent geometry : bond 0.00301 (12999) covalent geometry : angle 0.65751 (17640) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 229 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8099 (mm-30) REVERT: A 219 HIS cc_start: 0.8579 (OUTLIER) cc_final: 0.7123 (m-70) REVERT: A 296 MET cc_start: 0.7542 (ttp) cc_final: 0.7296 (ttm) REVERT: A 304 ASP cc_start: 0.7860 (p0) cc_final: 0.7366 (p0) REVERT: A 773 ASN cc_start: 0.8733 (t0) cc_final: 0.8382 (p0) REVERT: A 820 ILE cc_start: 0.8142 (tp) cc_final: 0.7915 (pt) REVERT: B 80 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.8567 (mp0) REVERT: B 485 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8359 (mp0) REVERT: B 573 ASN cc_start: 0.8160 (m-40) cc_final: 0.7798 (p0) REVERT: B 585 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.6187 (tp30) REVERT: B 590 ASN cc_start: 0.8822 (m-40) cc_final: 0.7580 (p0) REVERT: C 6 GLU cc_start: 0.8500 (tp30) cc_final: 0.7978 (mp0) REVERT: C 66 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7665 (mm) outliers start: 40 outliers final: 19 residues processed: 259 average time/residue: 1.5931 time to fit residues: 443.9008 Evaluate side-chains 238 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 214 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 924 ILE Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain B residue 568 LYS Chi-restraints excluded: chain B residue 585 GLU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 66 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 107 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 148 optimal weight: 20.0000 chunk 155 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 150 optimal weight: 10.0000 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN B 504 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.076804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.061259 restraints weight = 26882.196| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.75 r_work: 0.2799 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 13041 Z= 0.232 Angle : 1.170 49.540 17739 Z= 0.399 Chirality : 0.048 0.242 1963 Planarity : 0.006 0.067 2225 Dihedral : 7.812 75.179 1870 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.38 % Allowed : 22.84 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.21), residues: 1591 helix: 0.37 (0.21), residues: 587 sheet: -0.16 (0.34), residues: 219 loop : -0.85 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 186 HIS 0.004 0.001 HIS A 517 PHE 0.054 0.003 PHE B 445 TYR 0.024 0.002 TYR A 120 ARG 0.014 0.001 ARG A 424 Details of bonding type rmsd hydrogen bonds : bond 0.04558 ( 496) hydrogen bonds : angle 5.32363 ( 1380) metal coordination : bond 0.01542 ( 42) metal coordination : angle 11.97457 ( 99) covalent geometry : bond 0.00568 (12999) covalent geometry : angle 0.75663 (17640) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 225 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8103 (mm-30) REVERT: A 171 GLN cc_start: 0.9364 (OUTLIER) cc_final: 0.7267 (mp10) REVERT: A 219 HIS cc_start: 0.8783 (OUTLIER) cc_final: 0.7482 (m-70) REVERT: A 394 VAL cc_start: 0.8307 (OUTLIER) cc_final: 0.7892 (t) REVERT: A 820 ILE cc_start: 0.8138 (tp) cc_final: 0.7894 (pt) REVERT: B 80 GLU cc_start: 0.9148 (OUTLIER) cc_final: 0.8778 (mp0) REVERT: B 424 MET cc_start: 0.9143 (mmt) cc_final: 0.8933 (mmt) REVERT: B 481 LEU cc_start: 0.9058 (mp) cc_final: 0.8663 (mt) REVERT: B 485 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8331 (mp0) REVERT: B 532 LYS cc_start: 0.8706 (mmmm) cc_final: 0.8494 (tptm) REVERT: B 573 ASN cc_start: 0.8220 (m-40) cc_final: 0.7812 (p0) REVERT: B 585 GLU cc_start: 0.6641 (OUTLIER) cc_final: 0.6132 (tp30) REVERT: B 590 ASN cc_start: 0.8905 (m-40) cc_final: 0.7652 (p0) REVERT: C 6 GLU cc_start: 0.8549 (tp30) cc_final: 0.8072 (mp0) REVERT: C 66 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7619 (mm) outliers start: 32 outliers final: 20 residues processed: 249 average time/residue: 1.5138 time to fit residues: 405.5996 Evaluate side-chains 239 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 212 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain B residue 568 LYS Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 585 GLU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 66 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 136 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 29 optimal weight: 6.9990 chunk 127 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 ASN B 61 ASN B 394 GLN B 504 GLN C 23 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.078270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.062765 restraints weight = 26961.020| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.77 r_work: 0.2841 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 13041 Z= 0.169 Angle : 1.153 50.843 17739 Z= 0.394 Chirality : 0.046 0.269 1963 Planarity : 0.006 0.063 2225 Dihedral : 7.754 72.593 1870 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.16 % Allowed : 23.44 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.21), residues: 1591 helix: 0.48 (0.22), residues: 593 sheet: -0.36 (0.34), residues: 225 loop : -0.82 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 186 HIS 0.003 0.001 HIS B 68 PHE 0.040 0.002 PHE B 445 TYR 0.020 0.002 TYR A 120 ARG 0.015 0.001 ARG A 424 Details of bonding type rmsd hydrogen bonds : bond 0.03966 ( 496) hydrogen bonds : angle 5.21800 ( 1380) metal coordination : bond 0.01194 ( 42) metal coordination : angle 11.71073 ( 99) covalent geometry : bond 0.00411 (12999) covalent geometry : angle 0.75370 (17640) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 218 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8095 (mm-30) REVERT: A 219 HIS cc_start: 0.8666 (OUTLIER) cc_final: 0.7283 (m-70) REVERT: A 400 ILE cc_start: 0.8880 (pt) cc_final: 0.8674 (pp) REVERT: A 820 ILE cc_start: 0.8147 (tp) cc_final: 0.7888 (pt) REVERT: B 80 GLU cc_start: 0.9134 (OUTLIER) cc_final: 0.8694 (mp0) REVERT: B 481 LEU cc_start: 0.9064 (mp) cc_final: 0.8695 (mt) REVERT: B 485 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8344 (mp0) REVERT: B 532 LYS cc_start: 0.8756 (mmmm) cc_final: 0.8551 (tptm) REVERT: B 573 ASN cc_start: 0.8198 (m-40) cc_final: 0.7796 (p0) REVERT: B 585 GLU cc_start: 0.6675 (OUTLIER) cc_final: 0.6162 (tp30) REVERT: B 590 ASN cc_start: 0.8897 (m-40) cc_final: 0.7611 (p0) REVERT: C 6 GLU cc_start: 0.8559 (tp30) cc_final: 0.8098 (mp0) REVERT: C 66 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7651 (mm) outliers start: 29 outliers final: 19 residues processed: 241 average time/residue: 1.5073 time to fit residues: 392.5525 Evaluate side-chains 237 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 213 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain B residue 568 LYS Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 585 GLU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 66 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 122 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 85 optimal weight: 0.0370 chunk 76 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 0.0870 chunk 108 optimal weight: 2.9990 overall best weight: 0.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.078436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.062959 restraints weight = 26778.381| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.75 r_work: 0.2847 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 13041 Z= 0.168 Angle : 1.163 51.623 17739 Z= 0.387 Chirality : 0.046 0.241 1963 Planarity : 0.006 0.063 2225 Dihedral : 7.729 72.672 1870 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.93 % Allowed : 23.66 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.21), residues: 1591 helix: 0.53 (0.22), residues: 587 sheet: -0.43 (0.33), residues: 233 loop : -0.81 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 186 HIS 0.002 0.001 HIS B 68 PHE 0.035 0.002 PHE B 445 TYR 0.022 0.002 TYR A 120 ARG 0.015 0.001 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.03944 ( 496) hydrogen bonds : angle 5.16295 ( 1380) metal coordination : bond 0.01174 ( 42) metal coordination : angle 12.03973 ( 99) covalent geometry : bond 0.00410 (12999) covalent geometry : angle 0.73927 (17640) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12390.94 seconds wall clock time: 217 minutes 38.14 seconds (13058.14 seconds total)