Starting phenix.real_space_refine on Thu May 15 04:33:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n5v_49040/05_2025/9n5v_49040.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n5v_49040/05_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_49040/05_2025/9n5v_49040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n5v_49040/05_2025/9n5v_49040.map" model { file = "/net/cci-nas-00/data/ceres_data/9n5v_49040/05_2025/9n5v_49040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n5v_49040/05_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-5687/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: 7.97, per 1000 atoms: 0.63 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: 3.24 Conformation dependent library (CDL) restraints added in 1.7 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: 1.71 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: 4.83 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 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: 4.000 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: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 37.400 Find NCS groups from input model: 0.120 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:11.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.520 ------------------------------------------------------------------------------- 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 : 1.403 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: 1.4089 time to fit residues: 492.3835 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 : 1.534 ------------------------------------------------------------------------------- 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 = 0.063715 restraints weight = 26570.009| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.68 r_work: 0.2846 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 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 5.35732 ( 1380) metal coordination : bond 0.01372 ( 42) metal coordination : angle 12.72106 ( 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 : 1.355 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: 0.9340 (OUTLIER) cc_final: 0.7168 (mp10) REVERT: A 217 MET cc_start: 0.9167 (mtt) cc_final: 0.8819 (mtt) REVERT: A 350 ASP cc_start: 0.8442 (t0) cc_final: 0.8215 (p0) REVERT: A 351 VAL cc_start: 0.9214 (OUTLIER) cc_final: 0.8956 (t) REVERT: A 387 LYS cc_start: 0.8983 (ptmt) cc_final: 0.8680 (ttpp) REVERT: A 398 GLU cc_start: 0.8573 (pt0) cc_final: 0.8320 (pt0) REVERT: A 403 LYS cc_start: 0.8860 (tppt) cc_final: 0.8460 (tptp) REVERT: B 32 GLU cc_start: 0.8529 (tp30) cc_final: 0.8321 (tp30) REVERT: B 73 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.8296 (ptm160) REVERT: B 80 GLU cc_start: 0.9123 (OUTLIER) cc_final: 0.8759 (mp0) REVERT: B 485 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8403 (mp0) REVERT: C 6 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: C 66 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7577 (mm) outliers start: 53 outliers final: 21 residues processed: 266 average time/residue: 1.4386 time to fit residues: 411.8252 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 : 1.377 ------------------------------------------------------------------------------- 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: 2.9990 chunk 72 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 = 0.3295 r_free = 0.3295 target = 0.077999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.062443 restraints weight = 26612.538| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.76 r_work: 0.2823 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 13041 Z= 0.167 Angle : 1.132 66.236 17739 Z= 0.329 Chirality : 0.045 0.192 1963 Planarity : 0.005 0.055 2225 Dihedral : 8.140 74.148 1883 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.02 % Allowed : 16.44 % Favored : 79.54 % 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: -0.42 (0.21), residues: 1591 helix: 0.42 (0.21), residues: 595 sheet: -0.21 (0.34), residues: 236 loop : -0.79 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 186 HIS 0.003 0.001 HIS B 68 PHE 0.014 0.002 PHE B 157 TYR 0.023 0.002 TYR A 120 ARG 0.009 0.001 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.04209 ( 496) hydrogen bonds : angle 5.27553 ( 1380) metal coordination : bond 0.01385 ( 42) metal coordination : angle 12.75059 ( 99) covalent geometry : bond 0.00399 (12999) covalent geometry : angle 0.61320 (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 279 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 225 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 GLN cc_start: 0.9366 (OUTLIER) cc_final: 0.7232 (mp10) REVERT: A 219 HIS cc_start: 0.8727 (OUTLIER) cc_final: 0.7343 (m-70) REVERT: A 350 ASP cc_start: 0.8457 (t0) cc_final: 0.8225 (p0) REVERT: A 351 VAL cc_start: 0.9249 (OUTLIER) cc_final: 0.8983 (t) REVERT: A 387 LYS cc_start: 0.8983 (ptmt) cc_final: 0.8663 (ttpp) REVERT: A 398 GLU cc_start: 0.8513 (pt0) cc_final: 0.8261 (pt0) REVERT: A 773 ASN cc_start: 0.8657 (t0) cc_final: 0.8363 (p0) REVERT: A 820 ILE cc_start: 0.8265 (tp) cc_final: 0.8039 (pt) REVERT: B 32 GLU cc_start: 0.8597 (tp30) cc_final: 0.8375 (tp30) REVERT: B 73 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8341 (ptm160) REVERT: B 80 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8735 (mp0) REVERT: B 485 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8332 (mp0) REVERT: C 6 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: C 66 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7581 (mm) outliers start: 54 outliers final: 26 residues processed: 261 average time/residue: 1.4099 time to fit residues: 396.8036 Evaluate side-chains 244 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 210 time to evaluate : 1.530 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 151 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 141 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 465 ASN A 570 ASN B 61 ASN B 504 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.077916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.062405 restraints weight = 26640.879| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 1.95 r_work: 0.2803 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 13041 Z= 0.165 Angle : 1.140 64.748 17739 Z= 0.331 Chirality : 0.045 0.199 1963 Planarity : 0.005 0.054 2225 Dihedral : 7.992 73.868 1882 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.21 % Favored : 95.73 % Rotamer: Outliers : 3.94 % Allowed : 17.93 % Favored : 78.12 % 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: -0.31 (0.21), residues: 1591 helix: 0.53 (0.22), residues: 583 sheet: 0.02 (0.35), residues: 218 loop : -0.77 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 186 HIS 0.003 0.001 HIS B 68 PHE 0.028 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 0.04059 ( 496) hydrogen bonds : angle 5.20224 ( 1380) metal coordination : bond 0.01331 ( 42) metal coordination : angle 12.82761 ( 99) covalent geometry : bond 0.00395 (12999) covalent geometry : angle 0.61840 (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 271 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 218 time to evaluate : 1.362 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: 0.9352 (OUTLIER) cc_final: 0.7128 (mp10) REVERT: A 219 HIS cc_start: 0.8736 (OUTLIER) cc_final: 0.7323 (m-70) REVERT: A 296 MET cc_start: 0.7657 (ttp) cc_final: 0.7252 (ttm) REVERT: A 350 ASP cc_start: 0.8553 (t0) cc_final: 0.8286 (p0) REVERT: A 351 VAL cc_start: 0.9261 (OUTLIER) cc_final: 0.8985 (t) REVERT: A 393 LYS cc_start: 0.9063 (mmpt) cc_final: 0.8641 (mmmm) REVERT: A 397 VAL cc_start: 0.8474 (OUTLIER) cc_final: 0.8252 (m) REVERT: A 400 ILE cc_start: 0.8904 (pt) cc_final: 0.8649 (pp) REVERT: A 773 ASN cc_start: 0.8719 (t0) cc_final: 0.8442 (p0) REVERT: A 820 ILE cc_start: 0.8229 (tp) cc_final: 0.8002 (pt) REVERT: B 32 GLU cc_start: 0.8683 (tp30) cc_final: 0.8427 (tp30) REVERT: B 73 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8318 (ptm160) REVERT: B 80 GLU cc_start: 0.9190 (OUTLIER) cc_final: 0.8748 (mp0) REVERT: B 405 ASP cc_start: 0.7722 (p0) cc_final: 0.7455 (p0) REVERT: B 485 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8324 (mp0) REVERT: B 579 LYS cc_start: 0.6666 (OUTLIER) cc_final: 0.6224 (mtmm) REVERT: B 590 ASN cc_start: 0.7849 (p0) cc_final: 0.7645 (p0) REVERT: C 6 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7847 (mp0) REVERT: C 66 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7614 (mm) outliers start: 53 outliers final: 26 residues processed: 254 average time/residue: 1.4408 time to fit residues: 394.4025 Evaluate side-chains 246 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 210 time to evaluate : 1.368 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 22 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 145 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 280 GLN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 ASN B 61 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.078176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.062613 restraints weight = 27152.280| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.78 r_work: 0.2830 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 13041 Z= 0.158 Angle : 1.117 60.629 17739 Z= 0.331 Chirality : 0.045 0.196 1963 Planarity : 0.005 0.052 2225 Dihedral : 7.918 72.958 1880 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.27 % Favored : 95.66 % Rotamer: Outliers : 3.79 % Allowed : 19.49 % Favored : 76.71 % 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: -0.33 (0.21), residues: 1591 helix: 0.52 (0.22), residues: 589 sheet: 0.02 (0.35), residues: 217 loop : -0.82 (0.22), residues: 785 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 0.028 0.002 PHE A 783 TYR 0.023 0.002 TYR A 120 ARG 0.011 0.001 ARG A 837 Details of bonding type rmsd hydrogen bonds : bond 0.03936 ( 496) hydrogen bonds : angle 5.14107 ( 1380) metal coordination : bond 0.01281 ( 42) metal coordination : angle 12.43797 ( 99) covalent geometry : bond 0.00380 (12999) covalent geometry : angle 0.62148 (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 273 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 222 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 GLN cc_start: 0.9354 (OUTLIER) cc_final: 0.7179 (mp10) REVERT: A 219 HIS cc_start: 0.8714 (OUTLIER) cc_final: 0.7265 (m-70) REVERT: A 296 MET cc_start: 0.7593 (ttp) cc_final: 0.7258 (ttm) REVERT: A 351 VAL cc_start: 0.9261 (OUTLIER) cc_final: 0.8970 (t) REVERT: A 393 LYS cc_start: 0.9011 (mmpt) cc_final: 0.8644 (mmmm) REVERT: A 820 ILE cc_start: 0.8243 (tp) cc_final: 0.8017 (pt) REVERT: A 922 TYR cc_start: 0.7901 (p90) cc_final: 0.7293 (p90) REVERT: B 32 GLU cc_start: 0.8597 (tp30) cc_final: 0.8389 (tp30) REVERT: B 73 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8362 (ptm160) REVERT: B 80 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8724 (mp0) REVERT: B 219 MET cc_start: 0.9317 (mtp) cc_final: 0.9103 (mtp) REVERT: B 485 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8372 (mp0) REVERT: C 6 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7930 (mp0) REVERT: C 66 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7536 (mm) outliers start: 51 outliers final: 29 residues processed: 256 average time/residue: 1.3953 time to fit residues: 385.2870 Evaluate side-chains 257 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 220 time to evaluate : 1.451 ------------------------------------------------------------------------------- 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 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 351 VAL Chi-restraints excluded: chain A residue 394 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 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 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 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 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: 0.7980 chunk 46 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 120 optimal weight: 0.0570 chunk 145 optimal weight: 0.1980 chunk 54 optimal weight: 0.7980 chunk 83 optimal weight: 0.0870 chunk 125 optimal weight: 3.9990 overall best weight: 0.3876 ------------------------------------------------------------------------------- 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** A 570 ASN B 61 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.080162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.064784 restraints weight = 27195.221| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.92 r_work: 0.2872 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 13041 Z= 0.123 Angle : 1.082 58.066 17739 Z= 0.322 Chirality : 0.044 0.182 1963 Planarity : 0.005 0.058 2225 Dihedral : 7.729 71.622 1880 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.33 % Favored : 96.61 % Rotamer: Outliers : 3.65 % Allowed : 20.91 % Favored : 75.45 % 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: -0.03 (0.21), residues: 1591 helix: 0.88 (0.22), residues: 581 sheet: 0.03 (0.35), residues: 225 loop : -0.66 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 186 HIS 0.002 0.000 HIS A 651 PHE 0.030 0.001 PHE A 783 TYR 0.022 0.001 TYR A 437 ARG 0.012 0.001 ARG A 837 Details of bonding type rmsd hydrogen bonds : bond 0.03390 ( 496) hydrogen bonds : angle 4.91151 ( 1380) metal coordination : bond 0.01187 ( 42) metal coordination : angle 11.97620 ( 99) covalent geometry : bond 0.00289 (12999) covalent geometry : angle 0.60948 (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 280 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 231 time to evaluate : 1.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 HIS cc_start: 0.8690 (OUTLIER) cc_final: 0.7176 (m-70) REVERT: A 296 MET cc_start: 0.7657 (ttp) cc_final: 0.7323 (ttm) REVERT: A 773 ASN cc_start: 0.8772 (t0) cc_final: 0.8356 (p0) REVERT: A 820 ILE cc_start: 0.8170 (tp) cc_final: 0.7934 (pt) REVERT: B 80 GLU cc_start: 0.9183 (OUTLIER) cc_final: 0.8666 (mp0) REVERT: B 219 MET cc_start: 0.9289 (mtp) cc_final: 0.9089 (mtp) REVERT: B 485 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8358 (mp0) REVERT: B 585 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.6105 (tp30) REVERT: C 66 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7652 (mm) outliers start: 49 outliers final: 22 residues processed: 265 average time/residue: 1.4282 time to fit residues: 409.2681 Evaluate side-chains 242 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 215 time to evaluate : 1.400 ------------------------------------------------------------------------------- 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 418 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 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 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 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: 0.7980 chunk 119 optimal weight: 0.1980 chunk 15 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 90 optimal weight: 0.4980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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** A 570 ASN B 61 ASN B 504 GLN B 590 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.078690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.063072 restraints weight = 26808.553| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.76 r_work: 0.2848 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 13041 Z= 0.161 Angle : 1.111 52.705 17739 Z= 0.347 Chirality : 0.045 0.187 1963 Planarity : 0.005 0.057 2225 Dihedral : 7.642 72.623 1874 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.09 % Favored : 95.85 % Rotamer: Outliers : 3.50 % Allowed : 21.43 % Favored : 75.07 % 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: -0.17 (0.21), residues: 1591 helix: 0.72 (0.22), residues: 593 sheet: -0.14 (0.34), residues: 229 loop : -0.70 (0.22), residues: 769 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 0.032 0.002 PHE A 783 TYR 0.023 0.002 TYR A 120 ARG 0.012 0.001 ARG A 327 Details of bonding type rmsd hydrogen bonds : bond 0.03889 ( 496) hydrogen bonds : angle 5.03726 ( 1380) metal coordination : bond 0.01272 ( 42) metal coordination : angle 11.95854 ( 99) covalent geometry : bond 0.00391 (12999) covalent geometry : angle 0.66245 (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 260 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 213 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 GLN cc_start: 0.9365 (OUTLIER) cc_final: 0.7297 (mp10) REVERT: A 219 HIS cc_start: 0.8705 (OUTLIER) cc_final: 0.7267 (m-70) REVERT: A 296 MET cc_start: 0.7564 (ttp) cc_final: 0.7312 (ttm) REVERT: A 357 ARG cc_start: 0.9139 (mtt-85) cc_final: 0.8833 (mtt-85) REVERT: A 820 ILE cc_start: 0.8156 (tp) cc_final: 0.7934 (pt) REVERT: B 80 GLU cc_start: 0.9096 (OUTLIER) cc_final: 0.8655 (mp0) REVERT: B 389 LYS cc_start: 0.8265 (ttpt) cc_final: 0.7953 (tmtt) REVERT: B 485 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8375 (mp0) REVERT: B 573 ASN cc_start: 0.8018 (m-40) cc_final: 0.7682 (p0) REVERT: B 585 GLU cc_start: 0.6607 (OUTLIER) cc_final: 0.6090 (tp30) REVERT: B 590 ASN cc_start: 0.8828 (m-40) cc_final: 0.7624 (p0) REVERT: C 66 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7666 (mm) outliers start: 47 outliers final: 21 residues processed: 250 average time/residue: 1.4303 time to fit residues: 384.8836 Evaluate side-chains 235 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 208 time to evaluate : 1.356 ------------------------------------------------------------------------------- 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 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 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 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 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: 1.9990 chunk 113 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 114 optimal weight: 0.5980 chunk 146 optimal weight: 0.0670 chunk 33 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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** A 570 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 = 0.3337 r_free = 0.3337 target = 0.079780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.064206 restraints weight = 27157.911| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 1.79 r_work: 0.2875 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 13041 Z= 0.140 Angle : 1.098 53.232 17739 Z= 0.345 Chirality : 0.044 0.187 1963 Planarity : 0.005 0.057 2225 Dihedral : 7.579 71.439 1874 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.27 % Allowed : 21.95 % 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: -0.09 (0.21), residues: 1591 helix: 0.82 (0.22), residues: 594 sheet: -0.20 (0.34), residues: 229 loop : -0.65 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 186 HIS 0.003 0.001 HIS A 219 PHE 0.032 0.002 PHE A 783 TYR 0.021 0.002 TYR A 120 ARG 0.013 0.001 ARG A 424 Details of bonding type rmsd hydrogen bonds : bond 0.03664 ( 496) hydrogen bonds : angle 4.95253 ( 1380) metal coordination : bond 0.01056 ( 42) metal coordination : angle 11.76670 ( 99) covalent geometry : bond 0.00336 (12999) covalent geometry : angle 0.65963 (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 258 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 214 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 HIS cc_start: 0.8564 (OUTLIER) cc_final: 0.7318 (m-70) REVERT: A 296 MET cc_start: 0.7551 (ttp) cc_final: 0.7284 (ttm) REVERT: A 357 ARG cc_start: 0.9116 (mtt-85) cc_final: 0.8804 (ttm110) REVERT: A 773 ASN cc_start: 0.8713 (t0) cc_final: 0.8374 (p0) REVERT: A 820 ILE cc_start: 0.8129 (tp) cc_final: 0.7898 (pt) REVERT: B 80 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.8642 (mp0) REVERT: B 481 LEU cc_start: 0.9052 (mp) cc_final: 0.8695 (mt) REVERT: B 485 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8371 (mp0) REVERT: B 573 ASN cc_start: 0.8067 (m-40) cc_final: 0.7712 (p0) REVERT: B 585 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.6098 (tp30) REVERT: B 590 ASN cc_start: 0.8804 (m-40) cc_final: 0.7571 (p0) REVERT: C 66 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7646 (mm) outliers start: 44 outliers final: 23 residues processed: 244 average time/residue: 1.3643 time to fit residues: 359.3914 Evaluate side-chains 236 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 208 time to evaluate : 1.451 ------------------------------------------------------------------------------- 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 196 LYS 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 418 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 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 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 27 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: 3.9990 chunk 67 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 138 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 150 optimal weight: 9.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 A 570 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 = 0.3277 r_free = 0.3277 target = 0.077013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.061480 restraints weight = 26910.881| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.76 r_work: 0.2805 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.115 13041 Z= 0.226 Angle : 1.164 48.891 17739 Z= 0.394 Chirality : 0.048 0.233 1963 Planarity : 0.006 0.067 2225 Dihedral : 7.772 74.708 1870 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.98 % Allowed : 22.84 % Favored : 74.18 % 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: -0.46 (0.21), residues: 1591 helix: 0.39 (0.21), residues: 587 sheet: -0.17 (0.34), residues: 221 loop : -0.82 (0.22), residues: 783 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 0.031 0.002 PHE A 783 TYR 0.024 0.002 TYR A 120 ARG 0.014 0.001 ARG A 424 Details of bonding type rmsd hydrogen bonds : bond 0.04546 ( 496) hydrogen bonds : angle 5.26279 ( 1380) metal coordination : bond 0.01479 ( 42) metal coordination : angle 11.92973 ( 99) covalent geometry : bond 0.00553 (12999) covalent geometry : angle 0.75111 (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 255 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 215 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.8313 (mm-30) cc_final: 0.8082 (mm-30) REVERT: A 171 GLN cc_start: 0.9363 (OUTLIER) cc_final: 0.7261 (mp10) REVERT: A 219 HIS cc_start: 0.8667 (OUTLIER) cc_final: 0.7310 (m-70) REVERT: A 357 ARG cc_start: 0.9139 (mtt-85) cc_final: 0.8823 (ttm110) REVERT: A 387 LYS cc_start: 0.8956 (ttpp) cc_final: 0.8746 (tmmt) REVERT: A 820 ILE cc_start: 0.8146 (tp) cc_final: 0.7922 (pt) REVERT: B 80 GLU cc_start: 0.9147 (OUTLIER) cc_final: 0.8763 (mp0) REVERT: B 424 MET cc_start: 0.9151 (mmt) cc_final: 0.8921 (mmt) REVERT: B 481 LEU cc_start: 0.9048 (mp) cc_final: 0.8683 (mt) REVERT: B 485 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8373 (mp0) REVERT: B 573 ASN cc_start: 0.8125 (m-40) cc_final: 0.7721 (p0) REVERT: B 585 GLU cc_start: 0.6620 (OUTLIER) cc_final: 0.6149 (tp30) REVERT: B 590 ASN cc_start: 0.8887 (m-40) cc_final: 0.7640 (p0) REVERT: C 6 GLU cc_start: 0.8533 (tp30) cc_final: 0.7992 (mp0) REVERT: C 66 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7651 (mm) outliers start: 40 outliers final: 22 residues processed: 242 average time/residue: 1.3830 time to fit residues: 360.8641 Evaluate side-chains 237 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 209 time to evaluate : 1.357 ------------------------------------------------------------------------------- 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 196 LYS 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 421 SER 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 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 27 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: 2.9990 chunk 111 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 13 optimal weight: 0.0370 chunk 29 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 109 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.3064 ------------------------------------------------------------------------------- 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 394 GLN B 504 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.077273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.061724 restraints weight = 26898.523| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 1.77 r_work: 0.2811 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 13041 Z= 0.207 Angle : 1.163 50.794 17739 Z= 0.397 Chirality : 0.047 0.208 1963 Planarity : 0.006 0.065 2225 Dihedral : 7.846 74.153 1870 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.38 % Allowed : 22.92 % Favored : 74.70 % 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: -0.57 (0.20), residues: 1591 helix: 0.33 (0.21), residues: 588 sheet: -0.36 (0.34), residues: 227 loop : -0.87 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 186 HIS 0.004 0.001 HIS A 517 PHE 0.053 0.002 PHE B 445 TYR 0.024 0.002 TYR A 120 ARG 0.015 0.001 ARG A 424 Details of bonding type rmsd hydrogen bonds : bond 0.04408 ( 496) hydrogen bonds : angle 5.29636 ( 1380) metal coordination : bond 0.01398 ( 42) metal coordination : angle 11.83496 ( 99) covalent geometry : bond 0.00506 (12999) covalent geometry : angle 0.75787 (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 248 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 216 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.8306 (mm-30) cc_final: 0.8082 (mm-30) REVERT: A 171 GLN cc_start: 0.9365 (OUTLIER) cc_final: 0.7255 (mp10) REVERT: A 219 HIS cc_start: 0.8669 (OUTLIER) cc_final: 0.7357 (m-70) REVERT: A 304 ASP cc_start: 0.7807 (p0) cc_final: 0.7364 (p0) REVERT: A 706 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.7874 (mptt) REVERT: A 820 ILE cc_start: 0.8144 (tp) cc_final: 0.7901 (pt) REVERT: B 80 GLU cc_start: 0.9161 (OUTLIER) cc_final: 0.8754 (mp0) REVERT: B 481 LEU cc_start: 0.9062 (mp) cc_final: 0.8701 (mt) REVERT: B 485 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8352 (mp0) REVERT: B 573 ASN cc_start: 0.8112 (m-40) cc_final: 0.7617 (p0) REVERT: B 585 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.6184 (tp30) REVERT: B 590 ASN cc_start: 0.8866 (m-40) cc_final: 0.7575 (p0) REVERT: C 6 GLU cc_start: 0.8548 (tp30) cc_final: 0.8072 (mp0) REVERT: C 66 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7611 (mm) outliers start: 32 outliers final: 22 residues processed: 238 average time/residue: 1.4497 time to fit residues: 373.4794 Evaluate side-chains 235 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 206 time to evaluate : 1.363 ------------------------------------------------------------------------------- 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 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 418 ILE Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 706 LYS 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 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 27 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: 1.9990 chunk 144 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 142 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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** A 681 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.077409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.061916 restraints weight = 26839.445| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.74 r_work: 0.2818 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 13041 Z= 0.193 Angle : 1.156 51.777 17739 Z= 0.396 Chirality : 0.047 0.202 1963 Planarity : 0.006 0.066 2225 Dihedral : 7.788 74.308 1870 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.31 % Allowed : 23.59 % Favored : 74.11 % 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: -0.56 (0.21), residues: 1591 helix: 0.37 (0.21), residues: 588 sheet: -0.44 (0.34), residues: 226 loop : -0.86 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 186 HIS 0.004 0.001 HIS A 517 PHE 0.043 0.002 PHE B 445 TYR 0.023 0.002 TYR A 120 ARG 0.015 0.001 ARG A 424 Details of bonding type rmsd hydrogen bonds : bond 0.04280 ( 496) hydrogen bonds : angle 5.28926 ( 1380) metal coordination : bond 0.01314 ( 42) metal coordination : angle 11.73823 ( 99) covalent geometry : bond 0.00473 (12999) covalent geometry : angle 0.75464 (17640) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10939.72 seconds wall clock time: 188 minutes 30.39 seconds (11310.39 seconds total)