Starting phenix.real_space_refine on Thu Mar 5 15:57:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t7s_10371/03_2026/6t7s_10371.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t7s_10371/03_2026/6t7s_10371.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6t7s_10371/03_2026/6t7s_10371.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t7s_10371/03_2026/6t7s_10371.map" model { file = "/net/cci-nas-00/data/ceres_data/6t7s_10371/03_2026/6t7s_10371.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t7s_10371/03_2026/6t7s_10371.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 15081 2.51 5 N 3894 2.21 5 O 4341 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23436 Number of models: 1 Model: "" Number of chains: 3 Chain: "J" Number of atoms: 7812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 7812 Classifications: {'peptide': 1030} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 978} Chain: "K" Number of atoms: 7812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 7812 Classifications: {'peptide': 1030} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 978} Chain: "L" Number of atoms: 7812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 7812 Classifications: {'peptide': 1030} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 978} Time building chain proxies: 4.96, per 1000 atoms: 0.21 Number of scatterers: 23436 At special positions: 0 Unit cell: (149.6, 138.72, 131.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 4341 8.00 N 3894 7.00 C 15081 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: 1.88 Conformation dependent library (CDL) restraints added in 975.9 milliseconds 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5640 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 31 sheets defined 51.4% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'J' and resid 9 through 29 removed outlier: 3.941A pdb=" N ILE J 15 " --> pdb=" O PHE J 11 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU J 28 " --> pdb=" O GLY J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 59 Processing helix chain 'J' and resid 61 through 66 Processing helix chain 'J' and resid 99 through 110 removed outlier: 3.994A pdb=" N LYS J 110 " --> pdb=" O GLN J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 119 through 124 Processing helix chain 'J' and resid 150 through 162 removed outlier: 3.659A pdb=" N LEU J 154 " --> pdb=" O THR J 150 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL J 159 " --> pdb=" O SER J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 169 removed outlier: 3.850A pdb=" N ARG J 168 " --> pdb=" O PRO J 165 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR J 169 " --> pdb=" O LEU J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 189 through 197 Processing helix chain 'J' and resid 199 through 211 removed outlier: 3.820A pdb=" N VAL J 203 " --> pdb=" O THR J 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 242 through 248 removed outlier: 3.952A pdb=" N PHE J 246 " --> pdb=" O THR J 242 " (cutoff:3.500A) Processing helix chain 'J' and resid 300 through 314 removed outlier: 3.895A pdb=" N LYS J 304 " --> pdb=" O LEU J 300 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE J 306 " --> pdb=" O THR J 302 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE J 310 " --> pdb=" O ILE J 306 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ALA J 311 " --> pdb=" O ARG J 307 " (cutoff:3.500A) Processing helix chain 'J' and resid 329 through 343 removed outlier: 3.785A pdb=" N VAL J 333 " --> pdb=" O THR J 329 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS J 342 " --> pdb=" O HIS J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 343 through 349 Processing helix chain 'J' and resid 350 through 360 removed outlier: 4.072A pdb=" N VAL J 354 " --> pdb=" O LEU J 350 " (cutoff:3.500A) Processing helix chain 'J' and resid 362 through 366 removed outlier: 3.579A pdb=" N THR J 365 " --> pdb=" O PHE J 362 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU J 366 " --> pdb=" O ARG J 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 362 through 366' Processing helix chain 'J' and resid 371 through 378 removed outlier: 3.897A pdb=" N VAL J 375 " --> pdb=" O ALA J 371 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU J 377 " --> pdb=" O PRO J 373 " (cutoff:3.500A) Processing helix chain 'J' and resid 380 through 386 removed outlier: 4.217A pdb=" N ALA J 384 " --> pdb=" O PHE J 380 " (cutoff:3.500A) Processing helix chain 'J' and resid 401 through 412 removed outlier: 3.978A pdb=" N VAL J 412 " --> pdb=" O ASP J 408 " (cutoff:3.500A) Processing helix chain 'J' and resid 413 through 423 removed outlier: 4.316A pdb=" N GLU J 417 " --> pdb=" O VAL J 413 " (cutoff:3.500A) Processing helix chain 'J' and resid 426 through 434 Processing helix chain 'J' and resid 434 through 452 removed outlier: 4.253A pdb=" N ILE J 438 " --> pdb=" O SER J 434 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN J 439 " --> pdb=" O MET J 435 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY J 444 " --> pdb=" O GLY J 440 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET J 447 " --> pdb=" O VAL J 443 " (cutoff:3.500A) Processing helix chain 'J' and resid 454 through 459 removed outlier: 3.641A pdb=" N PHE J 458 " --> pdb=" O PRO J 455 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE J 459 " --> pdb=" O MET J 456 " (cutoff:3.500A) Processing helix chain 'J' and resid 461 through 468 removed outlier: 4.230A pdb=" N VAL J 465 " --> pdb=" O GLY J 461 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE J 466 " --> pdb=" O SER J 462 " (cutoff:3.500A) Processing helix chain 'J' and resid 474 through 493 removed outlier: 4.477A pdb=" N VAL J 482 " --> pdb=" O MET J 478 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE J 483 " --> pdb=" O ALA J 479 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE J 487 " --> pdb=" O ILE J 483 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N THR J 489 " --> pdb=" O ALA J 485 " (cutoff:3.500A) Proline residue: J 490 - end of helix removed outlier: 3.547A pdb=" N CYS J 493 " --> pdb=" O THR J 489 " (cutoff:3.500A) Processing helix chain 'J' and resid 514 through 537 removed outlier: 4.205A pdb=" N ARG J 518 " --> pdb=" O GLY J 514 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU J 535 " --> pdb=" O VAL J 531 " (cutoff:3.500A) Processing helix chain 'J' and resid 545 through 550 removed outlier: 3.690A pdb=" N ALA J 550 " --> pdb=" O VAL J 546 " (cutoff:3.500A) Processing helix chain 'J' and resid 550 through 559 removed outlier: 4.489A pdb=" N PHE J 556 " --> pdb=" O MET J 552 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N THR J 557 " --> pdb=" O ILE J 553 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE J 559 " --> pdb=" O MET J 555 " (cutoff:3.500A) Processing helix chain 'J' and resid 583 through 600 removed outlier: 3.569A pdb=" N VAL J 590 " --> pdb=" O ARG J 586 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N SER J 593 " --> pdb=" O VAL J 589 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N MET J 594 " --> pdb=" O VAL J 590 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG J 595 " --> pdb=" O VAL J 591 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLU J 596 " --> pdb=" O ASP J 592 " (cutoff:3.500A) Processing helix chain 'J' and resid 639 through 642 removed outlier: 3.670A pdb=" N ASN J 642 " --> pdb=" O GLY J 639 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 639 through 642' Processing helix chain 'J' and resid 643 through 651 removed outlier: 3.508A pdb=" N LEU J 647 " --> pdb=" O SER J 643 " (cutoff:3.500A) Processing helix chain 'J' and resid 691 through 708 removed outlier: 3.880A pdb=" N LEU J 695 " --> pdb=" O GLY J 691 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET J 704 " --> pdb=" O ASN J 700 " (cutoff:3.500A) Processing helix chain 'J' and resid 731 through 738 Processing helix chain 'J' and resid 742 through 754 removed outlier: 3.576A pdb=" N VAL J 749 " --> pdb=" O ILE J 745 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER J 750 " --> pdb=" O ASN J 746 " (cutoff:3.500A) Processing helix chain 'J' and resid 776 through 779 Processing helix chain 'J' and resid 782 through 787 Processing helix chain 'J' and resid 836 through 842 Processing helix chain 'J' and resid 843 through 844 No H-bonds generated for 'chain 'J' and resid 843 through 844' Processing helix chain 'J' and resid 845 through 849 removed outlier: 3.777A pdb=" N LYS J 848 " --> pdb=" O GLU J 845 " (cutoff:3.500A) Processing helix chain 'J' and resid 860 through 868 removed outlier: 4.198A pdb=" N GLU J 864 " --> pdb=" O GLY J 860 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU J 865 " --> pdb=" O LEU J 861 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ARG J 866 " --> pdb=" O SER J 862 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU J 867 " --> pdb=" O TYR J 863 " (cutoff:3.500A) Processing helix chain 'J' and resid 878 through 887 removed outlier: 3.797A pdb=" N VAL J 883 " --> pdb=" O SER J 879 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU J 887 " --> pdb=" O VAL J 883 " (cutoff:3.500A) Processing helix chain 'J' and resid 887 through 892 Processing helix chain 'J' and resid 895 through 900 Processing helix chain 'J' and resid 904 through 918 removed outlier: 3.661A pdb=" N VAL J 908 " --> pdb=" O VAL J 904 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N GLY J 910 " --> pdb=" O LEU J 906 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ALA J 911 " --> pdb=" O GLY J 907 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR J 915 " --> pdb=" O ALA J 911 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER J 916 " --> pdb=" O LEU J 912 " (cutoff:3.500A) Processing helix chain 'J' and resid 925 through 953 removed outlier: 4.090A pdb=" N THR J 933 " --> pdb=" O GLY J 929 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA J 938 " --> pdb=" O ILE J 934 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS J 939 " --> pdb=" O GLY J 935 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA J 941 " --> pdb=" O SER J 937 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU J 943 " --> pdb=" O LYS J 939 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ILE J 944 " --> pdb=" O ASN J 940 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE J 947 " --> pdb=" O LEU J 943 " (cutoff:3.500A) Processing helix chain 'J' and resid 958 through 969 Processing helix chain 'J' and resid 969 through 980 removed outlier: 4.428A pdb=" N ILE J 973 " --> pdb=" O ARG J 969 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET J 975 " --> pdb=" O ARG J 971 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU J 978 " --> pdb=" O VAL J 974 " (cutoff:3.500A) Processing helix chain 'J' and resid 984 through 989 removed outlier: 4.080A pdb=" N ILE J 989 " --> pdb=" O VAL J 985 " (cutoff:3.500A) Processing helix chain 'J' and resid 994 through 1011 removed outlier: 4.105A pdb=" N HIS J 999 " --> pdb=" O SER J 995 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ALA J1000 " --> pdb=" O GLY J 996 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLY J1004 " --> pdb=" O ALA J1000 " (cutoff:3.500A) Processing helix chain 'J' and resid 1015 through 1018 Processing helix chain 'J' and resid 1019 through 1024 Processing helix chain 'K' and resid 8 through 29 removed outlier: 4.229A pdb=" N ILE K 15 " --> pdb=" O PHE K 11 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA K 16 " --> pdb=" O ALA K 12 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU K 28 " --> pdb=" O GLY K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 60 Processing helix chain 'K' and resid 65 through 69 removed outlier: 3.578A pdb=" N GLN K 68 " --> pdb=" O ILE K 65 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N MET K 69 " --> pdb=" O GLU K 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 65 through 69' Processing helix chain 'K' and resid 99 through 104 Processing helix chain 'K' and resid 104 through 111 removed outlier: 3.684A pdb=" N LEU K 111 " --> pdb=" O VAL K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 119 through 124 Processing helix chain 'K' and resid 152 through 162 Processing helix chain 'K' and resid 189 through 197 Processing helix chain 'K' and resid 199 through 211 removed outlier: 3.511A pdb=" N VAL K 203 " --> pdb=" O THR K 199 " (cutoff:3.500A) Processing helix chain 'K' and resid 242 through 248 removed outlier: 3.529A pdb=" N PHE K 246 " --> pdb=" O THR K 242 " (cutoff:3.500A) Processing helix chain 'K' and resid 298 through 312 removed outlier: 3.903A pdb=" N THR K 302 " --> pdb=" O ASN K 298 " (cutoff:3.500A) Processing helix chain 'K' and resid 313 through 317 Processing helix chain 'K' and resid 329 through 360 removed outlier: 4.277A pdb=" N VAL K 333 " --> pdb=" O THR K 329 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER K 334 " --> pdb=" O THR K 330 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR K 343 " --> pdb=" O GLU K 339 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU K 344 " --> pdb=" O VAL K 340 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY K 345 " --> pdb=" O VAL K 341 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU K 346 " --> pdb=" O LYS K 342 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ALA K 347 " --> pdb=" O THR K 343 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU K 349 " --> pdb=" O GLY K 345 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LEU K 350 " --> pdb=" O GLU K 346 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL K 351 " --> pdb=" O ALA K 347 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N MET K 355 " --> pdb=" O VAL K 351 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR K 356 " --> pdb=" O PHE K 352 " (cutoff:3.500A) Processing helix chain 'K' and resid 366 through 369 Processing helix chain 'K' and resid 370 through 387 removed outlier: 3.730A pdb=" N VAL K 374 " --> pdb=" O ILE K 370 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE K 380 " --> pdb=" O LEU K 376 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY K 381 " --> pdb=" O LEU K 377 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL K 382 " --> pdb=" O GLY K 378 " (cutoff:3.500A) Processing helix chain 'K' and resid 391 through 402 removed outlier: 3.782A pdb=" N MET K 395 " --> pdb=" O ASN K 391 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU K 400 " --> pdb=" O PHE K 396 " (cutoff:3.500A) Processing helix chain 'K' and resid 406 through 423 removed outlier: 3.632A pdb=" N VAL K 413 " --> pdb=" O ALA K 409 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL K 416 " --> pdb=" O VAL K 412 " (cutoff:3.500A) Processing helix chain 'K' and resid 426 through 436 removed outlier: 3.816A pdb=" N ARG K 432 " --> pdb=" O ARG K 428 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLY K 436 " --> pdb=" O ARG K 432 " (cutoff:3.500A) Processing helix chain 'K' and resid 438 through 451 removed outlier: 3.573A pdb=" N LEU K 442 " --> pdb=" O ILE K 438 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL K 443 " --> pdb=" O GLN K 439 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY K 444 " --> pdb=" O GLY K 440 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU K 449 " --> pdb=" O ILE K 445 " (cutoff:3.500A) Processing helix chain 'K' and resid 453 through 459 Processing helix chain 'K' and resid 461 through 465 removed outlier: 3.814A pdb=" N GLY K 464 " --> pdb=" O GLY K 461 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL K 465 " --> pdb=" O SER K 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 461 through 465' Processing helix chain 'K' and resid 471 through 480 removed outlier: 3.643A pdb=" N VAL K 475 " --> pdb=" O SER K 471 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA K 477 " --> pdb=" O THR K 473 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N MET K 478 " --> pdb=" O ILE K 474 " (cutoff:3.500A) Processing helix chain 'K' and resid 481 through 488 Processing helix chain 'K' and resid 490 through 495 Processing helix chain 'K' and resid 513 through 538 removed outlier: 3.700A pdb=" N ASN K 517 " --> pdb=" O PHE K 513 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER K 522 " --> pdb=" O ARG K 518 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS K 536 " --> pdb=" O ALA K 532 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N HIS K 537 " --> pdb=" O SER K 533 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG K 538 " --> pdb=" O ILE K 534 " (cutoff:3.500A) Processing helix chain 'K' and resid 539 through 559 removed outlier: 4.200A pdb=" N LEU K 543 " --> pdb=" O ALA K 539 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N TYR K 545 " --> pdb=" O TYR K 541 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE K 548 " --> pdb=" O ILE K 544 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE K 553 " --> pdb=" O VAL K 549 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TRP K 554 " --> pdb=" O ALA K 550 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE K 559 " --> pdb=" O MET K 555 " (cutoff:3.500A) Processing helix chain 'K' and resid 583 through 602 removed outlier: 3.713A pdb=" N THR K 587 " --> pdb=" O SER K 583 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER K 593 " --> pdb=" O VAL K 589 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU K 600 " --> pdb=" O GLU K 596 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU K 602 " --> pdb=" O LEU K 598 " (cutoff:3.500A) Processing helix chain 'K' and resid 633 through 637 removed outlier: 3.738A pdb=" N ARG K 637 " --> pdb=" O TRP K 634 " (cutoff:3.500A) Processing helix chain 'K' and resid 639 through 642 Processing helix chain 'K' and resid 643 through 656 removed outlier: 3.831A pdb=" N ARG K 650 " --> pdb=" O GLU K 646 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N MET K 653 " --> pdb=" O LYS K 649 " (cutoff:3.500A) Processing helix chain 'K' and resid 692 through 705 removed outlier: 3.723A pdb=" N GLN K 697 " --> pdb=" O GLU K 693 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA K 698 " --> pdb=" O VAL K 694 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N MET K 704 " --> pdb=" O ASN K 700 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU K 705 " --> pdb=" O LYS K 701 " (cutoff:3.500A) Processing helix chain 'K' and resid 731 through 737 Processing helix chain 'K' and resid 742 through 754 Processing helix chain 'K' and resid 776 through 779 removed outlier: 3.904A pdb=" N ARG K 779 " --> pdb=" O PRO K 776 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 776 through 779' Processing helix chain 'K' and resid 783 through 787 Processing helix chain 'K' and resid 801 through 804 removed outlier: 3.963A pdb=" N ALA K 804 " --> pdb=" O ASN K 801 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 801 through 804' Processing helix chain 'K' and resid 838 through 843 Processing helix chain 'K' and resid 843 through 848 Processing helix chain 'K' and resid 860 through 869 removed outlier: 3.506A pdb=" N GLU K 864 " --> pdb=" O GLY K 860 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU K 865 " --> pdb=" O LEU K 861 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG K 866 " --> pdb=" O SER K 862 " (cutoff:3.500A) Processing helix chain 'K' and resid 871 through 892 removed outlier: 5.763A pdb=" N LEU K 880 " --> pdb=" O TYR K 876 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU K 881 " --> pdb=" O ALA K 877 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL K 883 " --> pdb=" O SER K 879 " (cutoff:3.500A) Processing helix chain 'K' and resid 894 through 901 removed outlier: 3.948A pdb=" N PHE K 898 " --> pdb=" O TRP K 894 " (cutoff:3.500A) Processing helix chain 'K' and resid 904 through 919 removed outlier: 4.058A pdb=" N VAL K 908 " --> pdb=" O VAL K 904 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N GLY K 910 " --> pdb=" O LEU K 906 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR K 915 " --> pdb=" O ALA K 911 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER K 916 " --> pdb=" O LEU K 912 " (cutoff:3.500A) Processing helix chain 'K' and resid 923 through 955 removed outlier: 3.692A pdb=" N LEU K 931 " --> pdb=" O GLN K 927 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY K 935 " --> pdb=" O LEU K 931 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU K 936 " --> pdb=" O THR K 932 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN K 940 " --> pdb=" O LEU K 936 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA K 941 " --> pdb=" O SER K 937 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE K 944 " --> pdb=" O ASN K 940 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU K 946 " --> pdb=" O ILE K 942 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N PHE K 947 " --> pdb=" O LEU K 943 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY K 955 " --> pdb=" O LEU K 951 " (cutoff:3.500A) Processing helix chain 'K' and resid 959 through 968 removed outlier: 4.005A pdb=" N ILE K 963 " --> pdb=" O VAL K 959 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU K 964 " --> pdb=" O GLU K 960 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ALA K 965 " --> pdb=" O ALA K 961 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET K 968 " --> pdb=" O GLU K 964 " (cutoff:3.500A) Processing helix chain 'K' and resid 970 through 989 removed outlier: 4.538A pdb=" N VAL K 974 " --> pdb=" O LEU K 970 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N MET K 975 " --> pdb=" O ARG K 971 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL K 985 " --> pdb=" O ILE K 981 " (cutoff:3.500A) Proline residue: K 986 - end of helix Processing helix chain 'K' and resid 994 through 1014 removed outlier: 3.517A pdb=" N THR K1003 " --> pdb=" O HIS K 999 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLY K1004 " --> pdb=" O ALA K1000 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL K1005 " --> pdb=" O ILE K1001 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE K1006 " --> pdb=" O GLY K1002 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY K1007 " --> pdb=" O THR K1003 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLY K1008 " --> pdb=" O GLY K1004 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL K1010 " --> pdb=" O ILE K1006 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR K1011 " --> pdb=" O GLY K1007 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA K1012 " --> pdb=" O GLY K1008 " (cutoff:3.500A) Processing helix chain 'K' and resid 1015 through 1018 Processing helix chain 'K' and resid 1019 through 1024 Processing helix chain 'L' and resid 8 through 28 removed outlier: 3.514A pdb=" N ALA L 12 " --> pdb=" O ARG L 8 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE L 15 " --> pdb=" O PHE L 11 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA L 16 " --> pdb=" O ALA L 12 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE L 19 " --> pdb=" O ILE L 15 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER L 26 " --> pdb=" O ALA L 22 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE L 27 " --> pdb=" O GLY L 23 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU L 28 " --> pdb=" O GLY L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 61 removed outlier: 3.761A pdb=" N VAL L 61 " --> pdb=" O VAL L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 112 removed outlier: 4.044A pdb=" N ALA L 103 " --> pdb=" O ASP L 99 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL L 107 " --> pdb=" O ALA L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 119 through 124 removed outlier: 3.754A pdb=" N ARG L 124 " --> pdb=" O GLN L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 162 removed outlier: 3.743A pdb=" N LEU L 154 " --> pdb=" O THR L 150 " (cutoff:3.500A) Processing helix chain 'L' and resid 189 through 196 Processing helix chain 'L' and resid 200 through 211 Processing helix chain 'L' and resid 242 through 248 Processing helix chain 'L' and resid 298 through 307 removed outlier: 4.132A pdb=" N THR L 302 " --> pdb=" O ASN L 298 " (cutoff:3.500A) Processing helix chain 'L' and resid 310 through 314 removed outlier: 3.523A pdb=" N LEU L 313 " --> pdb=" O ILE L 310 " (cutoff:3.500A) Processing helix chain 'L' and resid 330 through 360 removed outlier: 4.573A pdb=" N SER L 336 " --> pdb=" O VAL L 332 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE L 337 " --> pdb=" O VAL L 333 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS L 342 " --> pdb=" O HIS L 338 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU L 350 " --> pdb=" O GLU L 346 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL L 351 " --> pdb=" O ALA L 347 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N PHE L 352 " --> pdb=" O ILE L 348 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LEU L 353 " --> pdb=" O LEU L 349 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET L 355 " --> pdb=" O VAL L 351 " (cutoff:3.500A) Processing helix chain 'L' and resid 371 through 387 removed outlier: 3.954A pdb=" N LEU L 376 " --> pdb=" O VAL L 372 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LEU L 377 " --> pdb=" O PRO L 373 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY L 378 " --> pdb=" O VAL L 374 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR L 379 " --> pdb=" O VAL L 375 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE L 380 " --> pdb=" O LEU L 376 " (cutoff:3.500A) Processing helix chain 'L' and resid 391 through 405 removed outlier: 3.733A pdb=" N MET L 395 " --> pdb=" O ASN L 391 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU L 400 " --> pdb=" O PHE L 396 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N GLY L 403 " --> pdb=" O VAL L 399 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU L 404 " --> pdb=" O LEU L 400 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 421 removed outlier: 3.811A pdb=" N VAL L 419 " --> pdb=" O ASN L 415 " (cutoff:3.500A) Processing helix chain 'L' and resid 426 through 443 removed outlier: 4.650A pdb=" N ARG L 432 " --> pdb=" O ARG L 428 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LYS L 433 " --> pdb=" O GLU L 429 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN L 437 " --> pdb=" O LYS L 433 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN L 439 " --> pdb=" O MET L 435 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLY L 440 " --> pdb=" O GLY L 436 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA L 441 " --> pdb=" O GLN L 437 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL L 443 " --> pdb=" O GLN L 439 " (cutoff:3.500A) Processing helix chain 'L' and resid 444 through 451 removed outlier: 3.821A pdb=" N VAL L 448 " --> pdb=" O GLY L 444 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA L 451 " --> pdb=" O MET L 447 " (cutoff:3.500A) Processing helix chain 'L' and resid 474 through 488 removed outlier: 4.084A pdb=" N MET L 478 " --> pdb=" O ILE L 474 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE L 483 " --> pdb=" O ALA L 479 " (cutoff:3.500A) Processing helix chain 'L' and resid 488 through 493 removed outlier: 4.090A pdb=" N LEU L 492 " --> pdb=" O LEU L 488 " (cutoff:3.500A) Processing helix chain 'L' and resid 516 through 535 removed outlier: 3.542A pdb=" N ALA L 532 " --> pdb=" O GLU L 528 " (cutoff:3.500A) Processing helix chain 'L' and resid 539 through 559 removed outlier: 3.756A pdb=" N TYR L 545 " --> pdb=" O TYR L 541 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL L 547 " --> pdb=" O LEU L 543 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE L 548 " --> pdb=" O ILE L 544 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE L 553 " --> pdb=" O VAL L 549 " (cutoff:3.500A) Processing helix chain 'L' and resid 583 through 601 removed outlier: 4.813A pdb=" N VAL L 590 " --> pdb=" O ARG L 586 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL L 591 " --> pdb=" O THR L 587 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP L 592 " --> pdb=" O GLN L 588 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER L 593 " --> pdb=" O VAL L 589 " (cutoff:3.500A) Processing helix chain 'L' and resid 639 through 642 Processing helix chain 'L' and resid 643 through 656 Processing helix chain 'L' and resid 691 through 705 removed outlier: 3.828A pdb=" N LEU L 695 " --> pdb=" O GLY L 691 " (cutoff:3.500A) Processing helix chain 'L' and resid 731 through 739 Processing helix chain 'L' and resid 742 through 754 Processing helix chain 'L' and resid 775 through 779 removed outlier: 3.512A pdb=" N ALA L 778 " --> pdb=" O ARG L 775 " (cutoff:3.500A) Processing helix chain 'L' and resid 782 through 787 Processing helix chain 'L' and resid 836 through 842 Processing helix chain 'L' and resid 845 through 849 removed outlier: 3.777A pdb=" N LYS L 848 " --> pdb=" O GLU L 845 " (cutoff:3.500A) Processing helix chain 'L' and resid 860 through 869 removed outlier: 4.301A pdb=" N GLU L 864 " --> pdb=" O GLY L 860 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU L 865 " --> pdb=" O LEU L 861 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY L 869 " --> pdb=" O GLU L 865 " (cutoff:3.500A) Processing helix chain 'L' and resid 877 through 887 removed outlier: 3.568A pdb=" N VAL L 883 " --> pdb=" O SER L 879 " (cutoff:3.500A) Processing helix chain 'L' and resid 887 through 892 removed outlier: 4.328A pdb=" N TYR L 891 " --> pdb=" O LEU L 887 " (cutoff:3.500A) Processing helix chain 'L' and resid 894 through 901 Processing helix chain 'L' and resid 903 through 919 removed outlier: 3.643A pdb=" N GLY L 907 " --> pdb=" O VAL L 903 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL L 908 " --> pdb=" O VAL L 904 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE L 909 " --> pdb=" O PRO L 905 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLY L 910 " --> pdb=" O LEU L 906 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA L 911 " --> pdb=" O GLY L 907 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU L 912 " --> pdb=" O VAL L 908 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU L 913 " --> pdb=" O ILE L 909 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR L 915 " --> pdb=" O ALA L 911 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER L 916 " --> pdb=" O LEU L 912 " (cutoff:3.500A) Processing helix chain 'L' and resid 923 through 953 removed outlier: 4.005A pdb=" N LEU L 931 " --> pdb=" O GLN L 927 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU L 943 " --> pdb=" O LYS L 939 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ILE L 944 " --> pdb=" O ASN L 940 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL L 945 " --> pdb=" O ALA L 941 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU L 946 " --> pdb=" O ILE L 942 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N PHE L 947 " --> pdb=" O LEU L 943 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA L 948 " --> pdb=" O ILE L 944 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU L 953 " --> pdb=" O LYS L 949 " (cutoff:3.500A) Processing helix chain 'L' and resid 959 through 969 removed outlier: 4.042A pdb=" N ILE L 963 " --> pdb=" O VAL L 959 " (cutoff:3.500A) Processing helix chain 'L' and resid 970 through 982 removed outlier: 3.612A pdb=" N VAL L 974 " --> pdb=" O LEU L 970 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER L 977 " --> pdb=" O ILE L 973 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU L 978 " --> pdb=" O VAL L 974 " (cutoff:3.500A) Processing helix chain 'L' and resid 984 through 989 Processing helix chain 'L' and resid 994 through 1014 removed outlier: 3.762A pdb=" N ILE L1001 " --> pdb=" O SER L 997 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR L1003 " --> pdb=" O HIS L 999 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N GLY L1004 " --> pdb=" O ALA L1000 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL L1005 " --> pdb=" O ILE L1001 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE L1006 " --> pdb=" O GLY L1002 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLY L1007 " --> pdb=" O THR L1003 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR L1011 " --> pdb=" O GLY L1007 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA L1012 " --> pdb=" O GLY L1008 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL L1014 " --> pdb=" O VAL L1010 " (cutoff:3.500A) Processing helix chain 'L' and resid 1019 through 1025 Processing sheet with id=AA1, first strand: chain 'J' and resid 42 through 43 removed outlier: 3.667A pdb=" N THR J 91 " --> pdb=" O SER J 79 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR J 77 " --> pdb=" O THR J 93 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 45 through 46 Processing sheet with id=AA3, first strand: chain 'J' and resid 136 through 139 removed outlier: 7.314A pdb=" N ILE J 291 " --> pdb=" O LEU J 137 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL J 139 " --> pdb=" O ILE J 289 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE J 289 " --> pdb=" O VAL J 139 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 141 through 143 Processing sheet with id=AA5, first strand: chain 'J' and resid 266 through 272 removed outlier: 8.522A pdb=" N TYR J 182 " --> pdb=" O VAL J 767 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ARG J 769 " --> pdb=" O TYR J 182 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ARG J 766 " --> pdb=" O ILE J 762 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ILE J 762 " --> pdb=" O ARG J 766 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LYS J 768 " --> pdb=" O ASP J 760 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ASP J 760 " --> pdb=" O LYS J 768 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL J 770 " --> pdb=" O VAL J 758 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 234 through 235 removed outlier: 6.080A pdb=" N ILE J 235 " --> pdb=" O LEU K 728 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 252 through 253 removed outlier: 3.590A pdb=" N LYS J 252 " --> pdb=" O VAL J 260 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 284 through 285 removed outlier: 3.975A pdb=" N PHE J 610 " --> pdb=" O PHE J 628 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY J 614 " --> pdb=" O SER J 624 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N SER J 624 " --> pdb=" O GLY J 614 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 712 through 716 removed outlier: 5.103A pdb=" N ARG J 714 " --> pdb=" O GLU J 829 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU J 829 " --> pdb=" O ARG J 714 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLU J 816 " --> pdb=" O ALA J 823 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 712 through 716 removed outlier: 5.103A pdb=" N ARG J 714 " --> pdb=" O GLU J 829 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU J 829 " --> pdb=" O ARG J 714 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 804 through 811 Processing sheet with id=AB3, first strand: chain 'J' and resid 789 through 791 Processing sheet with id=AB4, first strand: chain 'K' and resid 75 through 82 removed outlier: 4.273A pdb=" N TYR K 77 " --> pdb=" O THR K 93 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE K 90 " --> pdb=" O VAL K 45 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N VAL K 45 " --> pdb=" O ILE K 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 138 through 140 removed outlier: 3.948A pdb=" N MET K 138 " --> pdb=" O ILE K 291 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL K 140 " --> pdb=" O ILE K 289 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE K 289 " --> pdb=" O VAL K 140 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 142 through 143 removed outlier: 3.621A pdb=" N VAL K 142 " --> pdb=" O LYS K 322 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS K 322 " --> pdb=" O VAL K 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'K' and resid 266 through 272 removed outlier: 3.641A pdb=" N ASP K 267 " --> pdb=" O TRP K 187 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TRP K 187 " --> pdb=" O ASP K 267 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N TYR K 182 " --> pdb=" O VAL K 767 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ARG K 769 " --> pdb=" O TYR K 182 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 217 through 218 removed outlier: 4.219A pdb=" N GLY K 217 " --> pdb=" O ILE K 234 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N THR K 233 " --> pdb=" O TYR L 726 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LEU L 728 " --> pdb=" O THR K 233 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE K 235 " --> pdb=" O LEU L 728 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ILE L 730 " --> pdb=" O ILE K 235 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 250 through 253 removed outlier: 6.885A pdb=" N VAL K 260 " --> pdb=" O LEU K 251 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 284 through 285 removed outlier: 6.892A pdb=" N MET K 630 " --> pdb=" O SER K 607 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N VAL K 609 " --> pdb=" O PHE K 628 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N PHE K 628 " --> pdb=" O VAL K 609 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N THR K 611 " --> pdb=" O MET K 626 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N MET K 626 " --> pdb=" O THR K 611 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N THR K 613 " --> pdb=" O SER K 624 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N SER K 624 " --> pdb=" O THR K 613 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N PHE K 615 " --> pdb=" O GLN K 622 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N GLN K 622 " --> pdb=" O PHE K 615 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY K 625 " --> pdb=" O VAL K 576 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 712 through 717 removed outlier: 4.984A pdb=" N ARG K 714 " --> pdb=" O GLU K 829 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU K 829 " --> pdb=" O ARG K 714 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N MET K 824 " --> pdb=" O LEU K 684 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE K 826 " --> pdb=" O LEU K 682 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU K 682 " --> pdb=" O ILE K 826 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 789 through 791 Processing sheet with id=AC4, first strand: chain 'L' and resid 75 through 82 removed outlier: 3.683A pdb=" N TYR L 77 " --> pdb=" O THR L 93 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR L 89 " --> pdb=" O GLU L 81 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N MET L 88 " --> pdb=" O VAL L 47 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL L 47 " --> pdb=" O MET L 88 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N VAL L 45 " --> pdb=" O ILE L 90 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 136 through 140 removed outlier: 7.018A pdb=" N ILE L 291 " --> pdb=" O LEU L 137 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL L 139 " --> pdb=" O ILE L 289 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE L 289 " --> pdb=" O VAL L 139 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 142 through 143 Processing sheet with id=AC7, first strand: chain 'L' and resid 266 through 272 removed outlier: 8.066A pdb=" N TYR L 182 " --> pdb=" O VAL L 767 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ARG L 769 " --> pdb=" O TYR L 182 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE L 186 " --> pdb=" O TYR L 771 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN L 759 " --> pdb=" O VAL L 770 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU L 772 " --> pdb=" O TYR L 757 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N TYR L 757 " --> pdb=" O LEU L 772 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 250 through 253 removed outlier: 3.644A pdb=" N LYS L 252 " --> pdb=" O VAL L 260 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 284 through 286 removed outlier: 3.832A pdb=" N SER L 284 " --> pdb=" O PHE L 281 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN L 278 " --> pdb=" O THR L 613 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET L 626 " --> pdb=" O VAL L 612 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 615 through 616 removed outlier: 3.974A pdb=" N GLY L 619 " --> pdb=" O ASN L 616 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 712 through 717 removed outlier: 5.105A pdb=" N ARG L 714 " --> pdb=" O GLU L 829 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLU L 829 " --> pdb=" O ARG L 714 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET L 824 " --> pdb=" O LEU L 684 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE L 826 " --> pdb=" O LEU L 682 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 789 through 791 Processing sheet with id=AD4, first strand: chain 'L' and resid 817 through 818 989 hydrogen bonds defined for protein. 2817 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.57 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7552 1.34 - 1.46: 4924 1.46 - 1.58: 11206 1.58 - 1.70: 0 1.70 - 1.82: 231 Bond restraints: 23913 Sorted by residual: bond pdb=" C VAL L 904 " pdb=" N PRO L 905 " ideal model delta sigma weight residual 1.336 1.390 -0.054 1.25e-02 6.40e+03 1.86e+01 bond pdb=" C ALA L 872 " pdb=" N PRO L 873 " ideal model delta sigma weight residual 1.335 1.368 -0.033 1.30e-02 5.92e+03 6.31e+00 bond pdb=" C THR L 115 " pdb=" N PRO L 116 " ideal model delta sigma weight residual 1.337 1.366 -0.029 1.24e-02 6.50e+03 5.55e+00 bond pdb=" C ASP J 164 " pdb=" N PRO J 165 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.28e+00 bond pdb=" C VAL K 372 " pdb=" N PRO K 373 " ideal model delta sigma weight residual 1.336 1.358 -0.023 1.23e-02 6.61e+03 3.40e+00 ... (remaining 23908 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 31635 2.39 - 4.78: 660 4.78 - 7.16: 130 7.16 - 9.55: 64 9.55 - 11.94: 10 Bond angle restraints: 32499 Sorted by residual: angle pdb=" C ALA L 371 " pdb=" N VAL L 372 " pdb=" CA VAL L 372 " ideal model delta sigma weight residual 120.24 124.15 -3.91 6.30e-01 2.52e+00 3.86e+01 angle pdb=" C VAL L 984 " pdb=" N VAL L 985 " pdb=" CA VAL L 985 " ideal model delta sigma weight residual 120.24 123.77 -3.53 6.30e-01 2.52e+00 3.14e+01 angle pdb=" N ILE L 370 " pdb=" CA ILE L 370 " pdb=" C ILE L 370 " ideal model delta sigma weight residual 112.96 107.52 5.44 1.00e+00 1.00e+00 2.96e+01 angle pdb=" N ILE J 370 " pdb=" CA ILE J 370 " pdb=" C ILE J 370 " ideal model delta sigma weight residual 113.43 108.21 5.22 1.09e+00 8.42e-01 2.29e+01 angle pdb=" C GLN K 176 " pdb=" N VAL K 177 " pdb=" CA VAL K 177 " ideal model delta sigma weight residual 120.49 126.65 -6.16 1.38e+00 5.25e-01 2.00e+01 ... (remaining 32494 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 12888 17.88 - 35.77: 1148 35.77 - 53.65: 182 53.65 - 71.53: 49 71.53 - 89.41: 10 Dihedral angle restraints: 14277 sinusoidal: 5472 harmonic: 8805 Sorted by residual: dihedral pdb=" CA GLN L 469 " pdb=" C GLN L 469 " pdb=" N PHE L 470 " pdb=" CA PHE L 470 " ideal model delta harmonic sigma weight residual 180.00 150.09 29.91 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA GLN K 469 " pdb=" C GLN K 469 " pdb=" N PHE K 470 " pdb=" CA PHE K 470 " ideal model delta harmonic sigma weight residual 180.00 155.55 24.45 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA TYR K 876 " pdb=" C TYR K 876 " pdb=" N ALA K 877 " pdb=" CA ALA K 877 " ideal model delta harmonic sigma weight residual 180.00 156.46 23.54 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 14274 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2866 0.058 - 0.115: 743 0.115 - 0.173: 141 0.173 - 0.231: 30 0.231 - 0.288: 12 Chirality restraints: 3792 Sorted by residual: chirality pdb=" CB VAL K1025 " pdb=" CA VAL K1025 " pdb=" CG1 VAL K1025 " pdb=" CG2 VAL K1025 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CB ILE L 289 " pdb=" CA ILE L 289 " pdb=" CG1 ILE L 289 " pdb=" CG2 ILE L 289 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CB ILE L 989 " pdb=" CA ILE L 989 " pdb=" CG1 ILE L 989 " pdb=" CG2 ILE L 989 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 3789 not shown) Planarity restraints: 4173 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR J 578 " -0.049 5.00e-02 4.00e+02 7.38e-02 8.71e+00 pdb=" N PRO J 579 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO J 579 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO J 579 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR L 199 " -0.049 5.00e-02 4.00e+02 7.37e-02 8.68e+00 pdb=" N PRO L 200 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO L 200 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO L 200 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE K 90 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.01e+00 pdb=" C ILE K 90 " 0.049 2.00e-02 2.50e+03 pdb=" O ILE K 90 " -0.019 2.00e-02 2.50e+03 pdb=" N THR K 91 " -0.016 2.00e-02 2.50e+03 ... (remaining 4170 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 6878 2.80 - 3.33: 21405 3.33 - 3.85: 40136 3.85 - 4.38: 44200 4.38 - 4.90: 74252 Nonbonded interactions: 186871 Sorted by model distance: nonbonded pdb=" O ASN K 361 " pdb=" OG1 THR K 365 " model vdw 2.278 3.040 nonbonded pdb=" O ALA L 305 " pdb=" OG1 THR L 309 " model vdw 2.283 3.040 nonbonded pdb=" OG SER L 79 " pdb=" OG1 THR L 91 " model vdw 2.294 3.040 nonbonded pdb=" OD1 ASN K 278 " pdb=" OG1 THR K 613 " model vdw 2.296 3.040 nonbonded pdb=" O LYS L 170 " pdb=" OG1 THR L 302 " model vdw 2.298 3.040 ... (remaining 186866 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: 0.03 Found NCS groups: ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 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: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 20.900 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 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 : 0.004 0.067 23913 Z= 0.187 Angle : 0.926 11.938 32499 Z= 0.478 Chirality : 0.056 0.288 3792 Planarity : 0.007 0.074 4173 Dihedral : 14.162 89.414 8637 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.28 % Allowed : 10.42 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.74 (0.12), residues: 3084 helix: -3.75 (0.08), residues: 1328 sheet: -2.67 (0.24), residues: 362 loop : -2.48 (0.15), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 769 TYR 0.017 0.001 TYR K 856 PHE 0.018 0.001 PHE L 470 TRP 0.010 0.001 TRP K 894 HIS 0.006 0.001 HIS L 952 Details of bonding type rmsd covalent geometry : bond 0.00370 (23913) covalent geometry : angle 0.92599 (32499) hydrogen bonds : bond 0.12584 ( 987) hydrogen bonds : angle 6.87789 ( 2817) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 113 LEU cc_start: 0.9063 (mt) cc_final: 0.8754 (mt) REVERT: J 134 LYS cc_start: 0.9024 (mptt) cc_final: 0.8712 (mmmm) REVERT: J 149 MET cc_start: 0.6913 (mtt) cc_final: 0.6611 (mpp) REVERT: J 244 GLU cc_start: 0.9467 (mp0) cc_final: 0.9198 (mp0) REVERT: J 352 PHE cc_start: 0.7953 (p90) cc_final: 0.7624 (t80) REVERT: J 386 PHE cc_start: 0.8844 (m-10) cc_final: 0.8588 (m-80) REVERT: J 456 MET cc_start: 0.8656 (ptm) cc_final: 0.7856 (ptm) REVERT: J 516 PHE cc_start: 0.9499 (t80) cc_final: 0.9234 (t80) REVERT: J 662 MET cc_start: 0.7938 (ttp) cc_final: 0.6928 (mpp) REVERT: J 666 PHE cc_start: 0.8558 (p90) cc_final: 0.8114 (p90) REVERT: J 723 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8067 (mp0) REVERT: J 780 MET cc_start: 0.8932 (mmp) cc_final: 0.8495 (mmt) REVERT: J 891 TYR cc_start: 0.7960 (t80) cc_final: 0.7725 (t80) REVERT: J 925 PHE cc_start: 0.8768 (m-80) cc_final: 0.8524 (m-80) REVERT: J 968 MET cc_start: 0.9287 (ttt) cc_final: 0.8999 (tmm) REVERT: J 1024 TYR cc_start: 0.7979 (t80) cc_final: 0.7768 (t80) outliers start: 1 outliers final: 1 residues processed: 176 average time/residue: 0.0827 time to fit residues: 19.8145 Evaluate side-chains 130 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.3980 chunk 298 optimal weight: 0.6980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 67 GLN J 104 GLN J 123 GLN ** J 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 282 ASN ** J 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 469 GLN J 517 ASN J 642 ASN J 676 ASN J 692 HIS J 700 ASN J 725 GLN ** J 940 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.077925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.067209 restraints weight = 43177.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.068566 restraints weight = 26426.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.069508 restraints weight = 18370.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.070170 restraints weight = 13909.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.070586 restraints weight = 11320.983| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 1.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 23913 Z= 0.238 Angle : 0.971 10.504 32499 Z= 0.544 Chirality : 0.052 0.340 3792 Planarity : 0.007 0.060 4173 Dihedral : 5.704 27.479 3279 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.78 % Allowed : 4.86 % Favored : 94.36 % Rotamer: Outliers : 0.59 % Allowed : 8.44 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.44 (0.13), residues: 3084 helix: -2.25 (0.11), residues: 1599 sheet: -1.92 (0.24), residues: 420 loop : -2.13 (0.17), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 586 TYR 0.014 0.002 TYR K 810 PHE 0.022 0.002 PHE K 512 TRP 0.017 0.003 TRP L1019 HIS 0.004 0.001 HIS L 692 Details of bonding type rmsd covalent geometry : bond 0.00454 (23913) covalent geometry : angle 0.97096 (32499) hydrogen bonds : bond 0.13820 ( 987) hydrogen bonds : angle 7.22563 ( 2817) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 155 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 208 GLN cc_start: 0.9208 (tp-100) cc_final: 0.8939 (tp-100) REVERT: J 317 MET cc_start: 0.8336 (ptt) cc_final: 0.7574 (ptm) REVERT: J 334 SER cc_start: 0.9380 (t) cc_final: 0.8979 (p) REVERT: J 395 MET cc_start: 0.8398 (ptm) cc_final: 0.7996 (ptt) REVERT: J 470 PHE cc_start: 0.8835 (m-80) cc_final: 0.8590 (m-80) REVERT: J 597 TYR cc_start: 0.8097 (m-80) cc_final: 0.7317 (m-80) REVERT: J 662 MET cc_start: 0.8152 (ttp) cc_final: 0.7419 (mpp) REVERT: J 666 PHE cc_start: 0.8649 (p90) cc_final: 0.8267 (p90) REVERT: J 676 ASN cc_start: 0.6912 (m-40) cc_final: 0.6631 (m110) REVERT: J 723 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8326 (mp0) REVERT: J 891 TYR cc_start: 0.7926 (t80) cc_final: 0.7505 (t80) REVERT: J 913 LEU cc_start: 0.9703 (tp) cc_final: 0.9255 (pp) REVERT: J 968 MET cc_start: 0.9150 (ttt) cc_final: 0.8733 (tmm) outliers start: 5 outliers final: 1 residues processed: 159 average time/residue: 0.0780 time to fit residues: 17.4785 Evaluate side-chains 120 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 53 optimal weight: 0.7980 chunk 25 optimal weight: 0.0050 chunk 45 optimal weight: 0.9990 chunk 112 optimal weight: 8.9990 chunk 181 optimal weight: 2.9990 chunk 306 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 274 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 139 optimal weight: 0.0980 chunk 102 optimal weight: 0.0770 overall best weight: 0.3954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 58 GLN J 469 GLN J 849 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.079604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.069069 restraints weight = 44880.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.070473 restraints weight = 27590.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.071416 restraints weight = 19041.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.072091 restraints weight = 14306.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.072558 restraints weight = 11539.412| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 1.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23913 Z= 0.177 Angle : 0.860 10.476 32499 Z= 0.470 Chirality : 0.047 0.252 3792 Planarity : 0.005 0.056 4173 Dihedral : 5.446 32.951 3279 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.06 % Favored : 94.75 % Rotamer: Outliers : 0.24 % Allowed : 5.71 % Favored : 94.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.14), residues: 3084 helix: -1.52 (0.12), residues: 1572 sheet: -1.66 (0.25), residues: 384 loop : -1.83 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 432 TYR 0.016 0.001 TYR K 810 PHE 0.031 0.002 PHE L 702 TRP 0.015 0.001 TRP K 515 HIS 0.004 0.001 HIS K 654 Details of bonding type rmsd covalent geometry : bond 0.00338 (23913) covalent geometry : angle 0.86028 (32499) hydrogen bonds : bond 0.10385 ( 987) hydrogen bonds : angle 6.55896 ( 2817) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 145 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 99 ASP cc_start: 0.8928 (t0) cc_final: 0.8728 (t70) REVERT: J 108 GLN cc_start: 0.9096 (tt0) cc_final: 0.8559 (tm-30) REVERT: J 137 LEU cc_start: 0.8863 (mp) cc_final: 0.8304 (mp) REVERT: J 175 PHE cc_start: 0.5309 (p90) cc_final: 0.5094 (p90) REVERT: J 208 GLN cc_start: 0.9201 (tp-100) cc_final: 0.8700 (tp40) REVERT: J 293 LEU cc_start: 0.8639 (tp) cc_final: 0.7883 (mp) REVERT: J 317 MET cc_start: 0.8084 (ptt) cc_final: 0.7242 (ptm) REVERT: J 334 SER cc_start: 0.9349 (t) cc_final: 0.8974 (p) REVERT: J 353 LEU cc_start: 0.8525 (pp) cc_final: 0.8235 (mm) REVERT: J 453 PHE cc_start: 0.9252 (m-10) cc_final: 0.8720 (m-10) REVERT: J 470 PHE cc_start: 0.8798 (m-80) cc_final: 0.8487 (m-80) REVERT: J 496 MET cc_start: 0.7256 (tpp) cc_final: 0.7015 (tpp) REVERT: J 552 MET cc_start: 0.8292 (tmm) cc_final: 0.8075 (tmm) REVERT: J 662 MET cc_start: 0.7964 (ttp) cc_final: 0.7165 (mpp) REVERT: J 666 PHE cc_start: 0.8588 (p90) cc_final: 0.8219 (p90) REVERT: J 723 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8291 (mp0) REVERT: J 913 LEU cc_start: 0.9745 (tp) cc_final: 0.9306 (pp) REVERT: J 980 PHE cc_start: 0.8920 (t80) cc_final: 0.8594 (t80) REVERT: J 1001 ILE cc_start: 0.9464 (mm) cc_final: 0.9159 (pt) REVERT: J 1009 MET cc_start: 0.8965 (ttt) cc_final: 0.8176 (tpt) outliers start: 2 outliers final: 1 residues processed: 147 average time/residue: 0.0719 time to fit residues: 15.3438 Evaluate side-chains 119 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 149 optimal weight: 0.7980 chunk 240 optimal weight: 0.0370 chunk 107 optimal weight: 0.0980 chunk 3 optimal weight: 9.9990 chunk 289 optimal weight: 0.0000 chunk 140 optimal weight: 0.5980 chunk 207 optimal weight: 3.9990 chunk 274 optimal weight: 0.9990 chunk 219 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 160 optimal weight: 5.9990 overall best weight: 0.3062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 211 ASN J 654 HIS J 676 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.080359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.069877 restraints weight = 44507.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.071217 restraints weight = 27796.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.072160 restraints weight = 19315.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.072797 restraints weight = 14694.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.073215 restraints weight = 12023.469| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 1.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23913 Z= 0.157 Angle : 0.824 11.224 32499 Z= 0.448 Chirality : 0.046 0.246 3792 Planarity : 0.005 0.055 4173 Dihedral : 5.104 32.715 3279 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.86 % Favored : 94.94 % Rotamer: Outliers : 0.12 % Allowed : 4.40 % Favored : 95.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.14), residues: 3084 helix: -1.10 (0.12), residues: 1563 sheet: -1.55 (0.25), residues: 375 loop : -1.64 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 969 TYR 0.017 0.001 TYR K 810 PHE 0.018 0.001 PHE L 884 TRP 0.017 0.001 TRP L 515 HIS 0.021 0.002 HIS K 654 Details of bonding type rmsd covalent geometry : bond 0.00300 (23913) covalent geometry : angle 0.82427 (32499) hydrogen bonds : bond 0.08387 ( 987) hydrogen bonds : angle 6.19456 ( 2817) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 99 ASP cc_start: 0.8993 (t0) cc_final: 0.8762 (t0) REVERT: J 137 LEU cc_start: 0.8924 (mp) cc_final: 0.8518 (mp) REVERT: J 175 PHE cc_start: 0.5199 (p90) cc_final: 0.4831 (p90) REVERT: J 177 VAL cc_start: 0.8971 (p) cc_final: 0.8727 (p) REVERT: J 211 ASN cc_start: 0.8408 (OUTLIER) cc_final: 0.7803 (t0) REVERT: J 244 GLU cc_start: 0.9116 (mp0) cc_final: 0.8915 (mp0) REVERT: J 293 LEU cc_start: 0.8674 (tp) cc_final: 0.7916 (mp) REVERT: J 317 MET cc_start: 0.8118 (ptt) cc_final: 0.7280 (ptm) REVERT: J 334 SER cc_start: 0.9345 (t) cc_final: 0.8957 (p) REVERT: J 416 VAL cc_start: 0.9051 (t) cc_final: 0.8805 (t) REVERT: J 449 LEU cc_start: 0.9310 (tp) cc_final: 0.9047 (tp) REVERT: J 453 PHE cc_start: 0.8874 (m-10) cc_final: 0.8308 (m-10) REVERT: J 597 TYR cc_start: 0.8325 (m-80) cc_final: 0.7858 (m-80) REVERT: J 662 MET cc_start: 0.7953 (ttp) cc_final: 0.7133 (mpp) REVERT: J 666 PHE cc_start: 0.8520 (p90) cc_final: 0.8166 (p90) REVERT: J 866 ARG cc_start: 0.8011 (ttp-110) cc_final: 0.7540 (ttp80) REVERT: J 913 LEU cc_start: 0.9738 (tp) cc_final: 0.9294 (pp) REVERT: J 968 MET cc_start: 0.9056 (tmm) cc_final: 0.8739 (tmm) REVERT: J 1001 ILE cc_start: 0.9465 (mm) cc_final: 0.9200 (pt) REVERT: J 1009 MET cc_start: 0.9094 (ttt) cc_final: 0.8199 (tpt) REVERT: J 1013 THR cc_start: 0.8034 (p) cc_final: 0.7615 (p) REVERT: J 1019 TRP cc_start: 0.8151 (m-90) cc_final: 0.7918 (m-90) outliers start: 1 outliers final: 0 residues processed: 149 average time/residue: 0.0602 time to fit residues: 13.3153 Evaluate side-chains 118 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 96 optimal weight: 3.9990 chunk 282 optimal weight: 4.9990 chunk 247 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 112 optimal weight: 0.0370 chunk 48 optimal weight: 3.9990 chunk 87 optimal weight: 0.0170 chunk 62 optimal weight: 0.0470 chunk 229 optimal weight: 0.0010 overall best weight: 0.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 46 GLN J 108 GLN J 654 HIS J 692 HIS ** J 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.080773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.070161 restraints weight = 44604.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.071517 restraints weight = 27091.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.072441 restraints weight = 18747.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.073101 restraints weight = 14178.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.073504 restraints weight = 11491.578| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 1.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23913 Z= 0.151 Angle : 0.817 10.016 32499 Z= 0.437 Chirality : 0.045 0.190 3792 Planarity : 0.005 0.053 4173 Dihedral : 4.970 34.338 3279 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.96 % Favored : 94.84 % Rotamer: Outliers : 0.24 % Allowed : 3.09 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.14), residues: 3084 helix: -0.90 (0.13), residues: 1566 sheet: -1.64 (0.25), residues: 390 loop : -1.49 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 969 TYR 0.016 0.001 TYR K 49 PHE 0.019 0.001 PHE L 884 TRP 0.015 0.001 TRP L 515 HIS 0.019 0.002 HIS K 654 Details of bonding type rmsd covalent geometry : bond 0.00292 (23913) covalent geometry : angle 0.81734 (32499) hydrogen bonds : bond 0.07710 ( 987) hydrogen bonds : angle 6.04091 ( 2817) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 139 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 137 LEU cc_start: 0.8955 (mp) cc_final: 0.8677 (mp) REVERT: J 138 MET cc_start: 0.8233 (ptm) cc_final: 0.7948 (ptm) REVERT: J 175 PHE cc_start: 0.5140 (p90) cc_final: 0.4824 (p90) REVERT: J 208 GLN cc_start: 0.9084 (tp-100) cc_final: 0.8883 (tp-100) REVERT: J 293 LEU cc_start: 0.8604 (tp) cc_final: 0.7777 (mp) REVERT: J 317 MET cc_start: 0.8078 (ptt) cc_final: 0.6985 (ptm) REVERT: J 330 THR cc_start: 0.9385 (p) cc_final: 0.9029 (p) REVERT: J 334 SER cc_start: 0.9427 (t) cc_final: 0.9082 (p) REVERT: J 414 GLU cc_start: 0.9087 (tp30) cc_final: 0.8642 (tm-30) REVERT: J 449 LEU cc_start: 0.9326 (tp) cc_final: 0.9113 (tp) REVERT: J 453 PHE cc_start: 0.8850 (m-10) cc_final: 0.8344 (m-10) REVERT: J 596 GLU cc_start: 0.9168 (tm-30) cc_final: 0.8882 (tm-30) REVERT: J 662 MET cc_start: 0.7971 (ttp) cc_final: 0.7090 (mpp) REVERT: J 666 PHE cc_start: 0.8418 (p90) cc_final: 0.8132 (p90) REVERT: J 686 ASP cc_start: 0.7787 (t0) cc_final: 0.7529 (t0) REVERT: J 913 LEU cc_start: 0.9743 (tp) cc_final: 0.9266 (pp) REVERT: J 968 MET cc_start: 0.8996 (tmm) cc_final: 0.8688 (tmm) REVERT: J 1001 ILE cc_start: 0.9432 (mm) cc_final: 0.9144 (pt) outliers start: 2 outliers final: 0 residues processed: 141 average time/residue: 0.0634 time to fit residues: 13.2889 Evaluate side-chains 114 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 109 optimal weight: 0.0470 chunk 236 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 308 optimal weight: 6.9990 chunk 54 optimal weight: 0.0020 chunk 201 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 131 optimal weight: 0.0070 chunk 31 optimal weight: 4.9990 chunk 260 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 overall best weight: 0.7306 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 654 HIS J 692 HIS ** J 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.080300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.069518 restraints weight = 44170.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.070936 restraints weight = 27177.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.071849 restraints weight = 18931.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.072438 restraints weight = 14249.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.072948 restraints weight = 11667.377| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 1.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23913 Z= 0.149 Angle : 0.804 9.603 32499 Z= 0.433 Chirality : 0.045 0.222 3792 Planarity : 0.005 0.052 4173 Dihedral : 4.886 33.866 3279 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.45 % Favored : 94.46 % Rotamer: Outliers : 0.12 % Allowed : 2.38 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.14), residues: 3084 helix: -0.77 (0.13), residues: 1575 sheet: -1.67 (0.24), residues: 417 loop : -1.31 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 168 TYR 0.025 0.001 TYR L 891 PHE 0.032 0.001 PHE K 702 TRP 0.018 0.001 TRP L 515 HIS 0.018 0.002 HIS K 654 Details of bonding type rmsd covalent geometry : bond 0.00295 (23913) covalent geometry : angle 0.80411 (32499) hydrogen bonds : bond 0.07337 ( 987) hydrogen bonds : angle 5.99897 ( 2817) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 137 LEU cc_start: 0.8909 (mp) cc_final: 0.8672 (mp) REVERT: J 138 MET cc_start: 0.8208 (ptm) cc_final: 0.7811 (ptm) REVERT: J 175 PHE cc_start: 0.5191 (p90) cc_final: 0.4849 (p90) REVERT: J 177 VAL cc_start: 0.8982 (p) cc_final: 0.8770 (p) REVERT: J 293 LEU cc_start: 0.8642 (tp) cc_final: 0.7765 (mp) REVERT: J 317 MET cc_start: 0.8196 (ptt) cc_final: 0.7943 (ptm) REVERT: J 330 THR cc_start: 0.9412 (p) cc_final: 0.9093 (p) REVERT: J 334 SER cc_start: 0.9434 (t) cc_final: 0.9107 (p) REVERT: J 377 LEU cc_start: 0.9060 (pt) cc_final: 0.8760 (pt) REVERT: J 414 GLU cc_start: 0.9078 (tp30) cc_final: 0.8603 (tm-30) REVERT: J 442 LEU cc_start: 0.8031 (tp) cc_final: 0.7811 (tp) REVERT: J 449 LEU cc_start: 0.9234 (tp) cc_final: 0.8917 (tp) REVERT: J 453 PHE cc_start: 0.8814 (m-10) cc_final: 0.8129 (m-10) REVERT: J 662 MET cc_start: 0.8011 (ttp) cc_final: 0.7101 (mpp) REVERT: J 666 PHE cc_start: 0.8405 (p90) cc_final: 0.8153 (p90) REVERT: J 686 ASP cc_start: 0.7810 (t0) cc_final: 0.7542 (t0) REVERT: J 1001 ILE cc_start: 0.9478 (mm) cc_final: 0.9216 (pt) outliers start: 1 outliers final: 0 residues processed: 138 average time/residue: 0.0606 time to fit residues: 12.6700 Evaluate side-chains 113 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 222 optimal weight: 20.0000 chunk 14 optimal weight: 7.9990 chunk 301 optimal weight: 1.9990 chunk 69 optimal weight: 0.1980 chunk 196 optimal weight: 0.0060 chunk 201 optimal weight: 2.9990 chunk 300 optimal weight: 0.0020 chunk 250 optimal weight: 3.9990 chunk 246 optimal weight: 0.7980 chunk 178 optimal weight: 0.1980 chunk 183 optimal weight: 0.2980 overall best weight: 0.1404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 692 HIS J 849 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.081434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.070475 restraints weight = 44055.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.071940 restraints weight = 27291.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.072817 restraints weight = 19128.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.073473 restraints weight = 14530.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.073889 restraints weight = 11780.655| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 1.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23913 Z= 0.147 Angle : 0.810 9.477 32499 Z= 0.431 Chirality : 0.044 0.175 3792 Planarity : 0.004 0.049 4173 Dihedral : 4.799 33.287 3279 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.45 % Favored : 94.46 % Rotamer: Outliers : 0.24 % Allowed : 2.02 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.15), residues: 3084 helix: -0.69 (0.13), residues: 1566 sheet: -1.49 (0.24), residues: 429 loop : -1.24 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 969 TYR 0.017 0.001 TYR K 891 PHE 0.020 0.001 PHE L 884 TRP 0.017 0.001 TRP J 515 HIS 0.017 0.002 HIS J 654 Details of bonding type rmsd covalent geometry : bond 0.00283 (23913) covalent geometry : angle 0.80963 (32499) hydrogen bonds : bond 0.06955 ( 987) hydrogen bonds : angle 5.93028 ( 2817) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 138 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 137 LEU cc_start: 0.8897 (mp) cc_final: 0.8642 (mp) REVERT: J 138 MET cc_start: 0.8434 (ptm) cc_final: 0.8169 (ptm) REVERT: J 175 PHE cc_start: 0.5169 (p90) cc_final: 0.4831 (p90) REVERT: J 293 LEU cc_start: 0.8519 (tp) cc_final: 0.7771 (mp) REVERT: J 330 THR cc_start: 0.9402 (p) cc_final: 0.9076 (p) REVERT: J 334 SER cc_start: 0.9436 (t) cc_final: 0.9098 (p) REVERT: J 414 GLU cc_start: 0.9226 (tp30) cc_final: 0.8628 (tm-30) REVERT: J 442 LEU cc_start: 0.7979 (tp) cc_final: 0.7761 (tp) REVERT: J 449 LEU cc_start: 0.9230 (tp) cc_final: 0.8918 (tp) REVERT: J 453 PHE cc_start: 0.8766 (m-10) cc_final: 0.7867 (m-10) REVERT: J 519 MET cc_start: 0.9315 (ptp) cc_final: 0.8982 (ptp) REVERT: J 662 MET cc_start: 0.7977 (ttp) cc_final: 0.7064 (mpp) REVERT: J 666 PHE cc_start: 0.8456 (p90) cc_final: 0.8241 (p90) REVERT: J 686 ASP cc_start: 0.7810 (t0) cc_final: 0.7524 (t0) REVERT: J 898 PHE cc_start: 0.8887 (t80) cc_final: 0.8583 (t80) REVERT: J 1001 ILE cc_start: 0.9460 (mm) cc_final: 0.9198 (pt) outliers start: 2 outliers final: 0 residues processed: 140 average time/residue: 0.0606 time to fit residues: 12.9358 Evaluate side-chains 116 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 135 optimal weight: 0.0570 chunk 154 optimal weight: 0.3980 chunk 213 optimal weight: 8.9990 chunk 305 optimal weight: 10.0000 chunk 252 optimal weight: 8.9990 chunk 142 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 140 optimal weight: 0.4980 chunk 226 optimal weight: 0.9990 chunk 247 optimal weight: 0.9980 chunk 294 optimal weight: 4.9990 overall best weight: 0.5900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 58 GLN J 692 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.081322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.070311 restraints weight = 43991.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.071710 restraints weight = 26896.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.072611 restraints weight = 18718.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.073251 restraints weight = 14197.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.073734 restraints weight = 11615.621| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 1.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23913 Z= 0.144 Angle : 0.799 9.741 32499 Z= 0.428 Chirality : 0.044 0.169 3792 Planarity : 0.004 0.049 4173 Dihedral : 4.755 33.112 3279 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.86 % Favored : 95.04 % Rotamer: Outliers : 0.12 % Allowed : 1.55 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.15), residues: 3084 helix: -0.63 (0.13), residues: 1575 sheet: -1.49 (0.24), residues: 423 loop : -1.19 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 432 TYR 0.011 0.001 TYR K 49 PHE 0.029 0.001 PHE L 702 TRP 0.015 0.001 TRP J 515 HIS 0.018 0.002 HIS K 654 Details of bonding type rmsd covalent geometry : bond 0.00289 (23913) covalent geometry : angle 0.79908 (32499) hydrogen bonds : bond 0.06703 ( 987) hydrogen bonds : angle 5.88778 ( 2817) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 65 ILE cc_start: 0.9267 (mt) cc_final: 0.8908 (tp) REVERT: J 124 ARG cc_start: 0.9259 (mtm110) cc_final: 0.7556 (tpm170) REVERT: J 137 LEU cc_start: 0.8849 (mp) cc_final: 0.8622 (mp) REVERT: J 138 MET cc_start: 0.8531 (ptm) cc_final: 0.8245 (ptm) REVERT: J 293 LEU cc_start: 0.8537 (tp) cc_final: 0.7750 (mp) REVERT: J 317 MET cc_start: 0.7715 (ptm) cc_final: 0.7415 (ppp) REVERT: J 330 THR cc_start: 0.9404 (p) cc_final: 0.9088 (p) REVERT: J 334 SER cc_start: 0.9400 (t) cc_final: 0.9083 (p) REVERT: J 395 MET cc_start: 0.7410 (ptt) cc_final: 0.6946 (tpt) REVERT: J 414 GLU cc_start: 0.9149 (tp30) cc_final: 0.8579 (tm-30) REVERT: J 442 LEU cc_start: 0.8016 (tp) cc_final: 0.7798 (tp) REVERT: J 449 LEU cc_start: 0.9321 (tp) cc_final: 0.9026 (tp) REVERT: J 453 PHE cc_start: 0.8833 (m-10) cc_final: 0.8027 (m-10) REVERT: J 470 PHE cc_start: 0.8690 (m-80) cc_final: 0.8467 (m-80) REVERT: J 519 MET cc_start: 0.9305 (ptp) cc_final: 0.8971 (ptp) REVERT: J 662 MET cc_start: 0.8053 (ttp) cc_final: 0.7102 (mpp) REVERT: J 666 PHE cc_start: 0.8469 (p90) cc_final: 0.8237 (p90) REVERT: J 686 ASP cc_start: 0.7905 (t0) cc_final: 0.7546 (t0) REVERT: J 780 MET cc_start: 0.8517 (mmm) cc_final: 0.8285 (mmt) REVERT: J 1001 ILE cc_start: 0.9475 (mm) cc_final: 0.9216 (pt) outliers start: 1 outliers final: 0 residues processed: 137 average time/residue: 0.0651 time to fit residues: 12.9289 Evaluate side-chains 114 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 68 optimal weight: 0.6980 chunk 180 optimal weight: 7.9990 chunk 115 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 271 optimal weight: 5.9990 chunk 163 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 152 optimal weight: 0.0070 chunk 97 optimal weight: 0.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 58 GLN J 692 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.080956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.069769 restraints weight = 43097.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.071012 restraints weight = 26865.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.071976 restraints weight = 19434.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.072664 restraints weight = 14814.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.073119 restraints weight = 11963.482| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 1.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23913 Z= 0.145 Angle : 0.815 9.853 32499 Z= 0.433 Chirality : 0.045 0.177 3792 Planarity : 0.004 0.049 4173 Dihedral : 4.737 33.171 3279 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.25 % Favored : 94.65 % Rotamer: Outliers : 0.12 % Allowed : 0.95 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.15), residues: 3084 helix: -0.57 (0.13), residues: 1578 sheet: -1.43 (0.24), residues: 435 loop : -1.12 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 128 TYR 0.010 0.001 TYR K 863 PHE 0.022 0.001 PHE J 884 TRP 0.016 0.001 TRP K 515 HIS 0.017 0.002 HIS J 654 Details of bonding type rmsd covalent geometry : bond 0.00291 (23913) covalent geometry : angle 0.81533 (32499) hydrogen bonds : bond 0.06497 ( 987) hydrogen bonds : angle 5.83014 ( 2817) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 65 ILE cc_start: 0.9277 (mt) cc_final: 0.8912 (tp) REVERT: J 124 ARG cc_start: 0.9079 (mtm110) cc_final: 0.7256 (tpm170) REVERT: J 293 LEU cc_start: 0.8505 (tp) cc_final: 0.7697 (mp) REVERT: J 330 THR cc_start: 0.9381 (p) cc_final: 0.9060 (p) REVERT: J 334 SER cc_start: 0.9414 (t) cc_final: 0.9028 (p) REVERT: J 395 MET cc_start: 0.7361 (ptt) cc_final: 0.7063 (tpt) REVERT: J 414 GLU cc_start: 0.9264 (tp30) cc_final: 0.8610 (tm-30) REVERT: J 442 LEU cc_start: 0.8048 (tp) cc_final: 0.7840 (tp) REVERT: J 449 LEU cc_start: 0.9324 (tp) cc_final: 0.9025 (tp) REVERT: J 453 PHE cc_start: 0.8838 (m-10) cc_final: 0.8029 (m-10) REVERT: J 519 MET cc_start: 0.9287 (ptp) cc_final: 0.8965 (ptp) REVERT: J 596 GLU cc_start: 0.9075 (tm-30) cc_final: 0.8805 (tm-30) REVERT: J 662 MET cc_start: 0.8009 (ttp) cc_final: 0.7091 (mpp) REVERT: J 666 PHE cc_start: 0.8525 (p90) cc_final: 0.8318 (p90) REVERT: J 686 ASP cc_start: 0.7798 (t0) cc_final: 0.7411 (t0) REVERT: J 898 PHE cc_start: 0.8648 (t80) cc_final: 0.8419 (t80) REVERT: J 902 LEU cc_start: 0.8160 (mt) cc_final: 0.7939 (mt) REVERT: J 1001 ILE cc_start: 0.9456 (mm) cc_final: 0.9187 (pt) outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 0.0674 time to fit residues: 13.8539 Evaluate side-chains 119 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 186 optimal weight: 7.9990 chunk 233 optimal weight: 0.0570 chunk 129 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 107 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 180 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 42 optimal weight: 0.0570 chunk 244 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.9818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 58 GLN J 120 GLN J 692 HIS ** J 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.080657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.069502 restraints weight = 43206.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.070903 restraints weight = 27305.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.071797 restraints weight = 19236.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.072351 restraints weight = 14694.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.072588 restraints weight = 12262.935| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 1.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23913 Z= 0.148 Angle : 0.820 9.787 32499 Z= 0.437 Chirality : 0.044 0.181 3792 Planarity : 0.004 0.048 4173 Dihedral : 4.791 33.341 3279 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.25 % Favored : 94.65 % Rotamer: Outliers : 0.12 % Allowed : 0.48 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.15), residues: 3084 helix: -0.56 (0.13), residues: 1572 sheet: -1.43 (0.23), residues: 435 loop : -1.20 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 128 TYR 0.011 0.001 TYR J 891 PHE 0.024 0.001 PHE J 702 TRP 0.015 0.001 TRP J 515 HIS 0.004 0.001 HIS K 692 Details of bonding type rmsd covalent geometry : bond 0.00301 (23913) covalent geometry : angle 0.81990 (32499) hydrogen bonds : bond 0.06296 ( 987) hydrogen bonds : angle 5.86989 ( 2817) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 65 ILE cc_start: 0.9272 (mt) cc_final: 0.8904 (tp) REVERT: J 124 ARG cc_start: 0.9099 (mtm110) cc_final: 0.7204 (tpm170) REVERT: J 293 LEU cc_start: 0.8482 (tp) cc_final: 0.7589 (mp) REVERT: J 330 THR cc_start: 0.9347 (p) cc_final: 0.9052 (p) REVERT: J 334 SER cc_start: 0.9419 (t) cc_final: 0.9035 (p) REVERT: J 395 MET cc_start: 0.7410 (ptt) cc_final: 0.7088 (tpt) REVERT: J 442 LEU cc_start: 0.8134 (tp) cc_final: 0.7911 (tp) REVERT: J 449 LEU cc_start: 0.9326 (tp) cc_final: 0.9014 (tp) REVERT: J 453 PHE cc_start: 0.8828 (m-10) cc_final: 0.7993 (m-10) REVERT: J 519 MET cc_start: 0.9284 (ptp) cc_final: 0.8959 (ptp) REVERT: J 662 MET cc_start: 0.8018 (ttp) cc_final: 0.7088 (mpp) REVERT: J 686 ASP cc_start: 0.8102 (t0) cc_final: 0.7555 (t0) REVERT: J 891 TYR cc_start: 0.7940 (t80) cc_final: 0.7714 (t80) REVERT: J 1001 ILE cc_start: 0.9482 (mm) cc_final: 0.9211 (pt) outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 0.0613 time to fit residues: 12.0830 Evaluate side-chains 112 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 103 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 225 optimal weight: 6.9990 chunk 167 optimal weight: 0.6980 chunk 179 optimal weight: 4.9990 chunk 306 optimal weight: 0.0060 chunk 216 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 26 optimal weight: 0.2980 chunk 138 optimal weight: 0.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 692 HIS ** J 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.081178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.070041 restraints weight = 43020.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.071432 restraints weight = 27084.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.072361 restraints weight = 19064.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.073043 restraints weight = 14609.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.073502 restraints weight = 11956.865| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 1.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23913 Z= 0.146 Angle : 0.815 9.951 32499 Z= 0.434 Chirality : 0.045 0.173 3792 Planarity : 0.004 0.049 4173 Dihedral : 4.721 31.868 3279 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.25 % Favored : 94.65 % Rotamer: Outliers : 0.12 % Allowed : 0.48 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.15), residues: 3084 helix: -0.52 (0.13), residues: 1572 sheet: -1.38 (0.24), residues: 429 loop : -1.24 (0.18), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 969 TYR 0.012 0.001 TYR L 541 PHE 0.022 0.001 PHE J 898 TRP 0.014 0.001 TRP K 515 HIS 0.016 0.002 HIS L 654 Details of bonding type rmsd covalent geometry : bond 0.00292 (23913) covalent geometry : angle 0.81509 (32499) hydrogen bonds : bond 0.06285 ( 987) hydrogen bonds : angle 5.80533 ( 2817) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1874.41 seconds wall clock time: 33 minutes 52.42 seconds (2032.42 seconds total)