Starting phenix.real_space_refine on Sat Aug 23 14:31:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n5v_49040/08_2025/9n5v_49040.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n5v_49040/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9n5v_49040/08_2025/9n5v_49040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n5v_49040/08_2025/9n5v_49040.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n5v_49040/08_2025/9n5v_49040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n5v_49040/08_2025/9n5v_49040.map" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.038 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.16, per 1000 atoms: 0.25 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: 1.30 Conformation dependent library (CDL) restraints added in 581.4 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.59 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: 2.53 Time building geometry restraints manager: 1.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 5256 1.43 - 1.65: 7522 1.65 - 1.86: 121 1.86 - 2.07: 0 2.07 - 2.28: 100 Bond restraints: 12999 Sorted by residual: bond pdb=" C4 FMN B 702 " pdb=" C4A FMN B 702 " ideal model delta sigma weight residual 1.485 1.386 0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" O3P FAD A1005 " pdb=" P FAD A1005 " ideal model delta sigma weight residual 1.660 1.581 0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" C4A FMN B 702 " pdb=" N5 FMN B 702 " ideal model delta sigma weight residual 1.300 1.378 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" O5' FMN B 702 " pdb=" P FMN B 702 " ideal model delta sigma weight residual 1.676 1.605 0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" O5B FAD A1005 " pdb=" PA FAD A1005 " ideal model delta sigma weight residual 1.634 1.569 0.065 2.00e-02 2.50e+03 1.07e+01 ... (remaining 12994 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 17389 1.96 - 3.91: 211 3.91 - 5.87: 29 5.87 - 7.82: 9 7.82 - 9.78: 2 Bond angle restraints: 17640 Sorted by residual: angle pdb=" N ARG B 303 " pdb=" CA ARG B 303 " pdb=" C ARG B 303 " ideal model delta sigma weight residual 109.81 119.59 -9.78 2.21e+00 2.05e-01 1.96e+01 angle pdb=" CA TYR A 120 " pdb=" CB TYR A 120 " pdb=" CG TYR A 120 " ideal model delta sigma weight residual 113.90 119.53 -5.63 1.80e+00 3.09e-01 9.77e+00 angle pdb=" PA NAD B 705 " pdb=" O3 NAD B 705 " pdb=" PN NAD B 705 " ideal model delta sigma weight residual 126.50 135.50 -9.00 3.00e+00 1.11e-01 9.00e+00 angle pdb=" CA ARG B 303 " pdb=" C ARG B 303 " pdb=" N PRO B 304 " ideal model delta sigma weight residual 118.44 122.54 -4.10 1.59e+00 3.96e-01 6.64e+00 angle pdb=" O1P FAD A1005 " pdb=" P FAD A1005 " pdb=" O2P FAD A1005 " ideal model delta sigma weight residual 122.50 114.78 7.72 3.00e+00 1.11e-01 6.62e+00 ... (remaining 17635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 7334 17.65 - 35.30: 427 35.30 - 52.94: 76 52.94 - 70.59: 33 70.59 - 88.24: 4 Dihedral angle restraints: 7874 sinusoidal: 3312 harmonic: 4562 Sorted by residual: dihedral pdb=" CA PRO B 304 " pdb=" C PRO B 304 " pdb=" N PRO B 305 " pdb=" CA PRO B 305 " ideal model delta harmonic sigma weight residual 180.00 155.74 24.26 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA PHE A 40 " pdb=" C PHE A 40 " pdb=" N CYS A 41 " pdb=" CA CYS A 41 " ideal model delta harmonic sigma weight residual -180.00 -160.77 -19.23 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA PRO B 305 " pdb=" C PRO B 305 " pdb=" N TYR B 306 " pdb=" CA TYR B 306 " ideal model delta harmonic sigma weight residual -180.00 -163.29 -16.71 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 7871 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1393 0.044 - 0.088: 438 0.088 - 0.132: 124 0.132 - 0.177: 6 0.177 - 0.221: 2 Chirality restraints: 1963 Sorted by residual: chirality pdb=" C3B NAD B 705 " pdb=" C2B NAD B 705 " pdb=" C4B NAD B 705 " pdb=" O3B NAD B 705 " both_signs ideal model delta sigma weight residual False -2.71 -2.49 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA ARG B 303 " pdb=" N ARG B 303 " pdb=" C ARG B 303 " pdb=" CB ARG B 303 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" C1D NAD B 705 " pdb=" C2D NAD B 705 " pdb=" N1N NAD B 705 " pdb=" O4D NAD B 705 " both_signs ideal model delta sigma weight residual False 2.41 2.57 -0.16 2.00e-01 2.50e+01 6.33e-01 ... (remaining 1960 not shown) Planarity restraints: 2225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 304 " -0.041 5.00e-02 4.00e+02 6.27e-02 6.28e+00 pdb=" N PRO B 305 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 305 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 305 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 303 " 0.036 5.00e-02 4.00e+02 5.38e-02 4.64e+00 pdb=" N PRO B 304 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 304 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 304 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 59 " -0.030 5.00e-02 4.00e+02 4.47e-02 3.19e+00 pdb=" N PRO A 60 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 60 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 60 " -0.025 5.00e-02 4.00e+02 ... (remaining 2222 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1605 2.75 - 3.29: 12087 3.29 - 3.83: 21182 3.83 - 4.36: 25961 4.36 - 4.90: 44696 Nonbonded interactions: 105531 Sorted by model distance: nonbonded pdb=" OG1 THR B 70 " pdb=" OD1 ASP B 72 " model vdw 2.215 3.040 nonbonded pdb=" OE1 GLU B 285 " pdb=" OG1 THR B 287 " model vdw 2.236 3.040 nonbonded pdb=" OD1 ASP A 474 " pdb=" OG SER A 480 " model vdw 2.241 3.040 nonbonded pdb=" OG1 THR A 59 " pdb=" O GLY A 62 " model vdw 2.250 3.040 nonbonded pdb=" OG1 THR A 794 " pdb=" O ILE A 909 " model vdw 2.252 3.040 ... (remaining 105526 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.750 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.280 ------------------------------------------------------------------------------- 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 : 6.37 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (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 ARG 0.003 0.000 ARG B 297 TYR 0.025 0.002 TYR A 120 PHE 0.014 0.002 PHE B 157 TRP 0.010 0.002 TRP A 186 HIS 0.003 0.001 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00429 (12999) covalent geometry : angle 0.58128 (17640) hydrogen bonds : bond 0.17926 ( 496) hydrogen bonds : angle 6.83576 ( 1380) metal coordination : bond 0.24363 ( 42) metal coordination : angle 12.39100 ( 99) *********************** 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 : 0.534 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: 0.7209 time to fit residues: 250.7641 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 : 0.521 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 8.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 570 ASN B 61 ASN B 262 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.077927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.062952 restraints weight = 26620.958| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.64 r_work: 0.2825 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 13041 Z= 0.175 Angle : 1.134 64.388 17739 Z= 0.331 Chirality : 0.045 0.197 1963 Planarity : 0.005 0.059 2225 Dihedral : 8.742 73.419 1894 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.09 % Allowed : 14.58 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.21), residues: 1591 helix: 0.35 (0.21), residues: 589 sheet: 0.21 (0.36), residues: 213 loop : -0.77 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 600 TYR 0.024 0.002 TYR A 120 PHE 0.026 0.002 PHE B 445 TRP 0.012 0.002 TRP A 186 HIS 0.003 0.001 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00414 (12999) covalent geometry : angle 0.61235 (17640) hydrogen bonds : bond 0.04575 ( 496) hydrogen bonds : angle 5.44361 ( 1380) metal coordination : bond 0.01535 ( 42) metal coordination : angle 12.79313 ( 99) *********************** 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 286 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 231 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 GLN cc_start: 0.9351 (OUTLIER) cc_final: 0.7201 (mp10) REVERT: A 217 MET cc_start: 0.9172 (mtt) cc_final: 0.8823 (mtt) REVERT: A 219 HIS cc_start: 0.8661 (OUTLIER) cc_final: 0.7314 (m-70) REVERT: A 350 ASP cc_start: 0.8458 (t0) cc_final: 0.8212 (p0) REVERT: A 351 VAL cc_start: 0.9241 (OUTLIER) cc_final: 0.8972 (t) REVERT: A 387 LYS cc_start: 0.9000 (ptmt) cc_final: 0.8692 (ttpp) REVERT: A 398 GLU cc_start: 0.8583 (pt0) cc_final: 0.8313 (pt0) REVERT: A 403 LYS cc_start: 0.8869 (tppt) cc_final: 0.8470 (tptp) REVERT: A 677 ARG cc_start: 0.8718 (mmm-85) cc_final: 0.8517 (mmm-85) REVERT: A 932 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7651 (mt-10) REVERT: A 951 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.7826 (ptm160) REVERT: B 32 GLU cc_start: 0.8569 (tp30) cc_final: 0.8362 (tp30) REVERT: B 73 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8314 (ptm160) REVERT: B 80 GLU cc_start: 0.9125 (OUTLIER) cc_final: 0.8755 (mp0) REVERT: B 219 MET cc_start: 0.9263 (mtp) cc_final: 0.9050 (mtp) REVERT: B 485 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8361 (mp0) REVERT: B 535 LYS cc_start: 0.8405 (mtpm) cc_final: 0.8169 (tptm) REVERT: C 6 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7911 (mp0) REVERT: C 66 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7563 (mm) outliers start: 55 outliers final: 20 residues processed: 266 average time/residue: 0.7473 time to fit residues: 213.4595 Evaluate side-chains 244 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 215 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 171 GLN Chi-restraints excluded: chain A residue 219 HIS 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 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 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 109 optimal weight: 0.5980 chunk 116 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 570 ASN B 61 ASN B 364 ASN B 504 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.077751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.062117 restraints weight = 26828.562| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.76 r_work: 0.2814 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 13041 Z= 0.170 Angle : 1.129 63.831 17739 Z= 0.330 Chirality : 0.045 0.198 1963 Planarity : 0.005 0.055 2225 Dihedral : 8.207 74.270 1887 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.46 % Allowed : 16.52 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.21), residues: 1591 helix: 0.42 (0.22), residues: 583 sheet: -0.02 (0.35), residues: 224 loop : -0.84 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 600 TYR 0.023 0.002 TYR A 120 PHE 0.015 0.002 PHE B 281 TRP 0.012 0.002 TRP A 186 HIS 0.003 0.001 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00407 (12999) covalent geometry : angle 0.61590 (17640) hydrogen bonds : bond 0.04267 ( 496) hydrogen bonds : angle 5.31367 ( 1380) metal coordination : bond 0.01391 ( 42) metal coordination : angle 12.68558 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 227 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 GLN cc_start: 0.9368 (OUTLIER) cc_final: 0.7178 (mp10) REVERT: A 219 HIS cc_start: 0.8706 (OUTLIER) cc_final: 0.7346 (m-70) REVERT: A 350 ASP cc_start: 0.8463 (t0) cc_final: 0.8237 (p0) REVERT: A 351 VAL cc_start: 0.9295 (OUTLIER) cc_final: 0.9039 (t) REVERT: A 387 LYS cc_start: 0.8999 (ptmt) cc_final: 0.8667 (ttpp) REVERT: A 396 GLU cc_start: 0.7998 (pt0) cc_final: 0.7259 (pp20) REVERT: A 398 GLU cc_start: 0.8555 (pt0) cc_final: 0.8260 (pt0) REVERT: A 773 ASN cc_start: 0.8668 (t0) cc_final: 0.8367 (p0) REVERT: A 820 ILE cc_start: 0.8271 (tp) cc_final: 0.8045 (pt) REVERT: B 32 GLU cc_start: 0.8610 (tp30) cc_final: 0.8396 (tp30) REVERT: B 73 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8334 (ptm160) REVERT: B 80 GLU cc_start: 0.9135 (OUTLIER) cc_final: 0.8752 (mp0) REVERT: B 219 MET cc_start: 0.9267 (mtp) cc_final: 0.9049 (mtp) REVERT: B 405 ASP cc_start: 0.7576 (p0) cc_final: 0.7355 (p0) REVERT: B 485 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8382 (mp0) REVERT: C 6 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7811 (mp0) REVERT: C 66 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7551 (mm) outliers start: 60 outliers final: 28 residues processed: 266 average time/residue: 0.7172 time to fit residues: 205.3023 Evaluate side-chains 251 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 215 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 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 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 92 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 133 optimal weight: 0.0570 chunk 93 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 overall best weight: 1.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 ASN A 280 GLN A 465 ASN A 570 ASN B 61 ASN B 504 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.075621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.059876 restraints weight = 26995.048| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 1.79 r_work: 0.2756 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.128 13041 Z= 0.265 Angle : 1.207 61.479 17739 Z= 0.380 Chirality : 0.049 0.224 1963 Planarity : 0.006 0.061 2225 Dihedral : 8.279 76.595 1882 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.59 % Favored : 95.35 % Rotamer: Outliers : 4.32 % Allowed : 18.08 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.20), residues: 1591 helix: -0.02 (0.21), residues: 586 sheet: -0.24 (0.34), residues: 222 loop : -1.02 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 424 TYR 0.025 0.003 TYR A 120 PHE 0.027 0.002 PHE A 783 TRP 0.015 0.003 TRP A 186 HIS 0.005 0.001 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00643 (12999) covalent geometry : angle 0.71218 (17640) hydrogen bonds : bond 0.05020 ( 496) hydrogen bonds : angle 5.59620 ( 1380) metal coordination : bond 0.01885 ( 42) metal coordination : angle 13.07133 ( 99) *********************** 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 281 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 223 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 GLN cc_start: 0.9380 (OUTLIER) cc_final: 0.7229 (mp10) REVERT: A 219 HIS cc_start: 0.8815 (OUTLIER) cc_final: 0.7546 (m-70) REVERT: A 296 MET cc_start: 0.7822 (ttp) cc_final: 0.7533 (ttm) REVERT: A 350 ASP cc_start: 0.8508 (t0) cc_final: 0.8270 (p0) REVERT: A 351 VAL cc_start: 0.9361 (OUTLIER) cc_final: 0.9026 (t) REVERT: A 922 TYR cc_start: 0.7809 (p90) cc_final: 0.7247 (p90) REVERT: B 73 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8381 (ptm160) REVERT: B 80 GLU cc_start: 0.9167 (OUTLIER) cc_final: 0.8812 (mp0) REVERT: B 485 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8260 (mp0) REVERT: B 556 MET cc_start: 0.6469 (ptm) cc_final: 0.6172 (ptm) REVERT: B 568 LYS cc_start: 0.7008 (OUTLIER) cc_final: 0.6698 (tmtt) REVERT: C 6 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7936 (mp0) REVERT: C 66 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7544 (mm) outliers start: 58 outliers final: 27 residues processed: 260 average time/residue: 0.7086 time to fit residues: 198.2733 Evaluate side-chains 248 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 212 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 PHE 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 560 LYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain B residue 535 LYS 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 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 39 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 146 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 157 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.077095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.061560 restraints weight = 27118.522| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 1.77 r_work: 0.2800 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 13041 Z= 0.178 Angle : 1.136 57.686 17739 Z= 0.347 Chirality : 0.045 0.204 1963 Planarity : 0.005 0.058 2225 Dihedral : 8.029 74.965 1882 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.96 % Favored : 95.98 % Rotamer: Outliers : 4.46 % Allowed : 19.05 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.20), residues: 1591 helix: 0.25 (0.21), residues: 587 sheet: -0.06 (0.35), residues: 211 loop : -0.96 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 600 TYR 0.022 0.002 TYR A 120 PHE 0.028 0.002 PHE A 783 TRP 0.014 0.002 TRP A 186 HIS 0.003 0.001 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00431 (12999) covalent geometry : angle 0.65300 (17640) hydrogen bonds : bond 0.04206 ( 496) hydrogen bonds : angle 5.30913 ( 1380) metal coordination : bond 0.01459 ( 42) metal coordination : angle 12.46207 ( 99) *********************** 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 287 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 227 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7491 (tm-30) cc_final: 0.7028 (tm-30) REVERT: A 171 GLN cc_start: 0.9374 (OUTLIER) cc_final: 0.7189 (mp10) REVERT: A 219 HIS cc_start: 0.8716 (OUTLIER) cc_final: 0.7284 (m-70) REVERT: A 296 MET cc_start: 0.7669 (ttp) cc_final: 0.7436 (ttm) REVERT: A 351 VAL cc_start: 0.9310 (OUTLIER) cc_final: 0.8997 (t) REVERT: A 393 LYS cc_start: 0.9018 (mmpt) cc_final: 0.8643 (mmmm) REVERT: A 820 ILE cc_start: 0.8144 (tp) cc_final: 0.7908 (pt) REVERT: B 73 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8322 (ptm160) REVERT: B 80 GLU cc_start: 0.9147 (OUTLIER) cc_final: 0.8766 (mp0) REVERT: B 481 LEU cc_start: 0.9075 (mp) cc_final: 0.8718 (mt) REVERT: B 485 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8370 (mp0) REVERT: B 568 LYS cc_start: 0.6997 (OUTLIER) cc_final: 0.6662 (tmtt) REVERT: C 6 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7939 (mp0) REVERT: C 66 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7551 (mm) outliers start: 60 outliers final: 29 residues processed: 265 average time/residue: 0.6851 time to fit residues: 195.5219 Evaluate side-chains 253 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 215 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 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 775 VAL Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 101 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 ASN B 61 ASN B 590 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.076740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.061230 restraints weight = 26886.784| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 1.92 r_work: 0.2780 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 13041 Z= 0.191 Angle : 1.148 55.848 17739 Z= 0.362 Chirality : 0.046 0.204 1963 Planarity : 0.005 0.053 2225 Dihedral : 8.013 74.918 1882 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.78 % Favored : 95.16 % Rotamer: Outliers : 3.65 % Allowed : 21.13 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.21), residues: 1591 helix: 0.25 (0.21), residues: 587 sheet: -0.02 (0.35), residues: 211 loop : -0.93 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 837 TYR 0.023 0.002 TYR A 120 PHE 0.028 0.002 PHE A 783 TRP 0.014 0.002 TRP A 186 HIS 0.003 0.001 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00467 (12999) covalent geometry : angle 0.68248 (17640) hydrogen bonds : bond 0.04303 ( 496) hydrogen bonds : angle 5.32737 ( 1380) metal coordination : bond 0.01539 ( 42) metal coordination : angle 12.37974 ( 99) *********************** 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 265 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 216 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7277 (tm-30) cc_final: 0.6961 (tm-30) REVERT: A 171 GLN cc_start: 0.9336 (OUTLIER) cc_final: 0.7186 (mp10) REVERT: A 219 HIS cc_start: 0.8789 (OUTLIER) cc_final: 0.7382 (m-70) REVERT: A 296 MET cc_start: 0.7857 (ttp) cc_final: 0.7643 (ttm) REVERT: A 820 ILE cc_start: 0.8165 (tp) cc_final: 0.7932 (pt) REVERT: A 922 TYR cc_start: 0.7787 (p90) cc_final: 0.7159 (p90) REVERT: B 73 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8400 (ptm160) REVERT: B 80 GLU cc_start: 0.9215 (OUTLIER) cc_final: 0.8798 (mp0) REVERT: B 481 LEU cc_start: 0.9037 (mp) cc_final: 0.8696 (mt) REVERT: B 485 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8374 (mp0) REVERT: B 568 LYS cc_start: 0.6965 (OUTLIER) cc_final: 0.6640 (tmtt) REVERT: B 590 ASN cc_start: 0.8835 (m-40) cc_final: 0.7582 (p0) REVERT: C 6 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7885 (mp0) REVERT: C 66 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7606 (mm) outliers start: 49 outliers final: 29 residues processed: 247 average time/residue: 0.6864 time to fit residues: 182.3048 Evaluate side-chains 249 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 212 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 533 ASP 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 775 VAL 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 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 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 24 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 103 optimal weight: 0.0030 chunk 4 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.078259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.062826 restraints weight = 26936.021| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.75 r_work: 0.2842 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 13041 Z= 0.143 Angle : 1.099 52.028 17739 Z= 0.341 Chirality : 0.044 0.192 1963 Planarity : 0.005 0.050 2225 Dihedral : 7.863 73.347 1881 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.46 % Favored : 96.48 % Rotamer: Outliers : 3.42 % Allowed : 21.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.21), residues: 1591 helix: 0.56 (0.22), residues: 586 sheet: -0.06 (0.35), residues: 215 loop : -0.86 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 452 TYR 0.021 0.002 TYR A 120 PHE 0.019 0.002 PHE A 423 TRP 0.012 0.001 TRP A 186 HIS 0.002 0.000 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00344 (12999) covalent geometry : angle 0.64649 (17640) hydrogen bonds : bond 0.03771 ( 496) hydrogen bonds : angle 5.11188 ( 1380) metal coordination : bond 0.01251 ( 42) metal coordination : angle 11.91096 ( 99) *********************** 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 274 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 228 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 GLN cc_start: 0.9364 (OUTLIER) cc_final: 0.7205 (mp10) REVERT: A 219 HIS cc_start: 0.8682 (OUTLIER) cc_final: 0.7153 (m-70) REVERT: A 296 MET cc_start: 0.7624 (ttp) cc_final: 0.7411 (ttm) REVERT: A 820 ILE cc_start: 0.8131 (tp) cc_final: 0.7915 (pt) REVERT: B 48 MET cc_start: 0.8695 (mtm) cc_final: 0.8380 (mtm) REVERT: B 80 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.8698 (mp0) REVERT: B 481 LEU cc_start: 0.9069 (mp) cc_final: 0.8727 (mt) REVERT: B 485 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8374 (mp0) REVERT: B 568 LYS cc_start: 0.7015 (OUTLIER) cc_final: 0.6640 (tmtt) REVERT: B 579 LYS cc_start: 0.7180 (OUTLIER) cc_final: 0.6827 (mptt) REVERT: B 585 GLU cc_start: 0.6626 (OUTLIER) cc_final: 0.6175 (tp30) REVERT: B 590 ASN cc_start: 0.8854 (m-40) cc_final: 0.7567 (p0) REVERT: C 6 GLU cc_start: 0.8482 (tp30) cc_final: 0.7909 (mp0) REVERT: C 66 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7600 (mm) outliers start: 46 outliers final: 24 residues processed: 263 average time/residue: 0.6727 time to fit residues: 189.9164 Evaluate side-chains 247 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 215 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 98 ASP Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 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 776 SER Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 15 optimal weight: 3.9990 chunk 128 optimal weight: 0.0970 chunk 69 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 504 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.078336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.062907 restraints weight = 26587.634| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.73 r_work: 0.2845 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2516 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= 0.151 Angle : 1.118 48.660 17739 Z= 0.356 Chirality : 0.045 0.187 1963 Planarity : 0.005 0.053 2225 Dihedral : 7.659 72.843 1874 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.21 % Favored : 95.73 % Rotamer: Outliers : 2.98 % Allowed : 22.47 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.21), residues: 1591 helix: 0.59 (0.22), residues: 593 sheet: -0.08 (0.35), residues: 221 loop : -0.80 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 452 TYR 0.021 0.002 TYR A 437 PHE 0.032 0.002 PHE A 783 TRP 0.011 0.001 TRP A 186 HIS 0.003 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00368 (12999) covalent geometry : angle 0.68259 (17640) hydrogen bonds : bond 0.03837 ( 496) hydrogen bonds : angle 5.06369 ( 1380) metal coordination : bond 0.01070 ( 42) metal coordination : angle 11.87102 ( 99) *********************** 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 264 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 224 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 HIS cc_start: 0.8695 (OUTLIER) cc_final: 0.7323 (m-70) REVERT: A 296 MET cc_start: 0.7643 (ttp) cc_final: 0.7433 (ttm) REVERT: A 393 LYS cc_start: 0.9030 (mmpt) cc_final: 0.8669 (mmmm) REVERT: A 418 ILE cc_start: 0.8963 (mp) cc_final: 0.8625 (mt) REVERT: A 820 ILE cc_start: 0.8125 (tp) cc_final: 0.7911 (pt) REVERT: B 80 GLU cc_start: 0.9124 (OUTLIER) cc_final: 0.8665 (mp0) REVERT: B 481 LEU cc_start: 0.9066 (mp) cc_final: 0.8705 (mt) REVERT: B 485 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8371 (mp0) REVERT: B 568 LYS cc_start: 0.7058 (OUTLIER) cc_final: 0.6661 (tmtt) REVERT: B 579 LYS cc_start: 0.7126 (OUTLIER) cc_final: 0.6767 (mptt) REVERT: B 590 ASN cc_start: 0.8837 (m-40) cc_final: 0.7540 (p0) REVERT: C 66 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7609 (mm) outliers start: 40 outliers final: 22 residues processed: 254 average time/residue: 0.6183 time to fit residues: 168.7841 Evaluate side-chains 238 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 210 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 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 776 SER Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain 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 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 96 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 46 optimal weight: 0.1980 chunk 146 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN B 504 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.077747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.062246 restraints weight = 27016.400| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.75 r_work: 0.2828 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 13041 Z= 0.174 Angle : 1.134 50.157 17739 Z= 0.374 Chirality : 0.046 0.193 1963 Planarity : 0.005 0.051 2225 Dihedral : 7.679 73.213 1874 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.46 % Favored : 95.47 % Rotamer: Outliers : 2.83 % Allowed : 22.69 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.21), residues: 1591 helix: 0.50 (0.22), residues: 593 sheet: -0.27 (0.34), residues: 227 loop : -0.85 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 42 TYR 0.022 0.002 TYR A 120 PHE 0.032 0.002 PHE A 783 TRP 0.012 0.002 TRP A 186 HIS 0.003 0.001 HIS B 68 Details of bonding type rmsd covalent geometry : bond 0.00427 (12999) covalent geometry : angle 0.71588 (17640) hydrogen bonds : bond 0.04063 ( 496) hydrogen bonds : angle 5.14182 ( 1380) metal coordination : bond 0.01225 ( 42) metal coordination : angle 11.78804 ( 99) *********************** 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 253 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 215 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.8294 (mm-30) cc_final: 0.8083 (mm-30) REVERT: A 171 GLN cc_start: 0.9361 (OUTLIER) cc_final: 0.7272 (mp10) REVERT: A 219 HIS cc_start: 0.8720 (OUTLIER) cc_final: 0.7302 (m-70) REVERT: A 357 ARG cc_start: 0.9115 (mtm-85) cc_final: 0.8800 (ttm110) REVERT: A 393 LYS cc_start: 0.9044 (mmpt) cc_final: 0.8823 (mmmt) REVERT: A 402 MET cc_start: 0.7551 (mtm) cc_final: 0.7331 (mtp) REVERT: A 820 ILE cc_start: 0.8142 (tp) cc_final: 0.7903 (pt) REVERT: B 61 ASN cc_start: 0.8656 (m-40) cc_final: 0.8243 (m-40) REVERT: B 80 GLU cc_start: 0.9124 (OUTLIER) cc_final: 0.8697 (mp0) REVERT: B 481 LEU cc_start: 0.9084 (mp) cc_final: 0.8720 (mt) REVERT: B 485 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8354 (mp0) REVERT: B 532 LYS cc_start: 0.8895 (mmmt) cc_final: 0.8673 (mmmm) REVERT: B 579 LYS cc_start: 0.7168 (OUTLIER) cc_final: 0.6788 (mptt) REVERT: B 590 ASN cc_start: 0.8900 (m-40) cc_final: 0.7608 (p0) REVERT: C 6 GLU cc_start: 0.8513 (tp30) cc_final: 0.8036 (mp0) REVERT: C 66 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7599 (mm) outliers start: 38 outliers final: 22 residues processed: 243 average time/residue: 0.6413 time to fit residues: 167.0951 Evaluate side-chains 238 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 210 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 924 ILE 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 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 26 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 111 optimal weight: 0.1980 chunk 129 optimal weight: 0.8980 chunk 114 optimal weight: 0.2980 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 A 834 ASN B 394 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.078955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.063261 restraints weight = 27041.177| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 1.79 r_work: 0.2851 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 13041 Z= 0.156 Angle : 1.131 51.840 17739 Z= 0.379 Chirality : 0.045 0.194 1963 Planarity : 0.005 0.064 2225 Dihedral : 7.702 72.516 1874 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.60 % Allowed : 22.99 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.21), residues: 1591 helix: 0.65 (0.22), residues: 593 sheet: -0.36 (0.33), residues: 235 loop : -0.76 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 528 TYR 0.021 0.002 TYR A 120 PHE 0.045 0.002 PHE B 445 TRP 0.011 0.001 TRP A 186 HIS 0.002 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00382 (12999) covalent geometry : angle 0.72609 (17640) hydrogen bonds : bond 0.03829 ( 496) hydrogen bonds : angle 5.05040 ( 1380) metal coordination : bond 0.01043 ( 42) metal coordination : angle 11.62660 ( 99) ********************** 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 252 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 217 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLU cc_start: 0.8314 (mm-30) cc_final: 0.8111 (mm-30) REVERT: A 219 HIS cc_start: 0.8688 (OUTLIER) cc_final: 0.7255 (m-70) REVERT: A 393 LYS cc_start: 0.9040 (mmpt) cc_final: 0.8837 (mmmt) REVERT: A 773 ASN cc_start: 0.8802 (t0) cc_final: 0.8385 (p0) REVERT: A 820 ILE cc_start: 0.8140 (tp) cc_final: 0.7898 (pt) REVERT: B 80 GLU cc_start: 0.9134 (OUTLIER) cc_final: 0.8647 (mp0) REVERT: B 481 LEU cc_start: 0.9079 (mp) cc_final: 0.8712 (mt) REVERT: B 485 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8354 (mp0) REVERT: B 579 LYS cc_start: 0.7143 (OUTLIER) cc_final: 0.6777 (mptt) REVERT: B 585 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.6087 (tp30) REVERT: B 590 ASN cc_start: 0.8869 (m-40) cc_final: 0.7607 (p0) REVERT: C 6 GLU cc_start: 0.8518 (tp30) cc_final: 0.8049 (mp0) REVERT: C 66 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7597 (mm) outliers start: 35 outliers final: 23 residues processed: 242 average time/residue: 0.6372 time to fit residues: 165.9608 Evaluate side-chains 236 residues out of total 1344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 207 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 219 HIS Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 560 LYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 776 SER Chi-restraints excluded: chain A residue 825 SER Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 882 ILE Chi-restraints excluded: chain A residue 887 VAL Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 924 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 60 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 120 optimal weight: 0.0570 chunk 149 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 ASN B 61 ASN B 504 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.077123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.061536 restraints weight = 26829.203| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.75 r_work: 0.2811 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 13041 Z= 0.201 Angle : 1.160 53.649 17739 Z= 0.398 Chirality : 0.048 0.209 1963 Planarity : 0.006 0.070 2225 Dihedral : 7.852 73.803 1874 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.38 % Allowed : 23.81 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.21), residues: 1591 helix: 0.37 (0.21), residues: 588 sheet: -0.18 (0.34), residues: 221 loop : -0.86 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 357 TYR 0.023 0.002 TYR A 120 PHE 0.039 0.002 PHE B 445 TRP 0.012 0.002 TRP A 186 HIS 0.003 0.001 HIS A 517 Details of bonding type rmsd covalent geometry : bond 0.00495 (12999) covalent geometry : angle 0.76200 (17640) hydrogen bonds : bond 0.04296 ( 496) hydrogen bonds : angle 5.23214 ( 1380) metal coordination : bond 0.01308 ( 42) metal coordination : angle 11.74048 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5475.51 seconds wall clock time: 93 minutes 52.01 seconds (5632.01 seconds total)