Starting phenix.real_space_refine on Fri May 23 01:54:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t7s_10371/05_2025/6t7s_10371.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t7s_10371/05_2025/6t7s_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_10371/05_2025/6t7s_10371.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t7s_10371/05_2025/6t7s_10371.map" model { file = "/net/cci-nas-00/data/ceres_data/6t7s_10371/05_2025/6t7s_10371.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t7s_10371/05_2025/6t7s_10371.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 12.60, per 1000 atoms: 0.54 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: 5.20 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 2.83 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: 9.36 Time building geometry restraints manager: 6.14 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: 0.08 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: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.990 Check model and map are aligned: 0.160 Set scattering table: 0.180 Process input model: 50.490 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.260 ------------------------------------------------------------------------------- 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 : 7.26 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.010 0.001 TRP K 894 HIS 0.006 0.001 HIS L 952 PHE 0.018 0.001 PHE L 470 TYR 0.017 0.001 TYR K 856 ARG 0.003 0.000 ARG J 769 Details of bonding type rmsd hydrogen bonds : bond 0.12584 ( 987) hydrogen bonds : angle 6.87789 ( 2817) covalent geometry : bond 0.00370 (23913) covalent geometry : angle 0.92599 (32499) *********************** 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 : 0.770 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: 0.8559 (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: 0.7978 (t80) cc_final: 0.7768 (t80) outliers start: 1 outliers final: 1 residues processed: 176 average time/residue: 0.1845 time to fit residues: 44.6260 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 : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 4.9990 chunk 234 optimal weight: 0.8980 chunk 129 optimal weight: 0.0980 chunk 80 optimal weight: 5.9990 chunk 157 optimal weight: 0.4980 chunk 125 optimal weight: 0.0370 chunk 242 optimal weight: 0.2980 chunk 93 optimal weight: 0.3980 chunk 147 optimal weight: 9.9990 chunk 180 optimal weight: 6.9990 chunk 280 optimal weight: 2.9990 overall best weight: 0.2658 ------------------------------------------------------------------------------- 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 63 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 517 ASN J 642 ASN J 676 ASN J 692 HIS J 700 ASN J 725 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.079738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.068881 restraints weight = 41952.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.070272 restraints weight = 26039.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.071301 restraints weight = 18016.182| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 1.2090 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= 0.229 Angle : 0.963 11.638 32499 Z= 0.531 Chirality : 0.050 0.279 3792 Planarity : 0.008 0.116 4173 Dihedral : 5.614 27.539 3279 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.68 % Allowed : 4.77 % Favored : 94.55 % Rotamer: Outliers : 0.71 % Allowed : 7.97 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.13), residues: 3084 helix: -2.38 (0.11), residues: 1578 sheet: -1.74 (0.24), residues: 423 loop : -2.19 (0.16), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 894 HIS 0.005 0.001 HIS L 692 PHE 0.023 0.002 PHE L 352 TYR 0.029 0.002 TYR K 876 ARG 0.025 0.001 ARG J 586 Details of bonding type rmsd hydrogen bonds : bond 0.14789 ( 987) hydrogen bonds : angle 7.26729 ( 2817) covalent geometry : bond 0.00426 (23913) covalent geometry : angle 0.96279 (32499) *********************** 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 165 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 159 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 208 GLN cc_start: 0.9210 (tp-100) cc_final: 0.8943 (tp-100) REVERT: J 317 MET cc_start: 0.8350 (ptt) cc_final: 0.7683 (ptm) REVERT: J 334 SER cc_start: 0.9361 (t) cc_final: 0.8960 (p) REVERT: J 453 PHE cc_start: 0.9292 (m-10) cc_final: 0.8799 (m-10) REVERT: J 470 PHE cc_start: 0.8934 (m-80) cc_final: 0.8680 (m-80) REVERT: J 597 TYR cc_start: 0.8090 (m-80) cc_final: 0.7242 (m-80) REVERT: J 662 MET cc_start: 0.8117 (ttp) cc_final: 0.7346 (mpp) REVERT: J 666 PHE cc_start: 0.8657 (p90) cc_final: 0.8300 (p90) REVERT: J 723 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8263 (mp0) REVERT: J 891 TYR cc_start: 0.7996 (t80) cc_final: 0.7553 (t80) REVERT: J 913 LEU cc_start: 0.9709 (tp) cc_final: 0.9279 (pp) REVERT: J 968 MET cc_start: 0.9170 (ttt) cc_final: 0.8773 (tmm) outliers start: 6 outliers final: 1 residues processed: 163 average time/residue: 0.1786 time to fit residues: 40.4282 Evaluate side-chains 116 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 288 optimal weight: 9.9990 chunk 220 optimal weight: 0.0030 chunk 194 optimal weight: 0.0370 chunk 135 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 240 optimal weight: 7.9990 chunk 249 optimal weight: 0.2980 chunk 168 optimal weight: 4.9990 chunk 169 optimal weight: 8.9990 chunk 183 optimal weight: 4.9990 overall best weight: 0.8470 ------------------------------------------------------------------------------- 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 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 849 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.079646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.069247 restraints weight = 45274.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.070616 restraints weight = 28554.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.071536 restraints weight = 19972.736| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 1.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 23913 Z= 0.179 Angle : 0.859 10.155 32499 Z= 0.471 Chirality : 0.046 0.249 3792 Planarity : 0.005 0.052 4173 Dihedral : 5.469 32.446 3279 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.06 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.14), residues: 3084 helix: -1.58 (0.12), residues: 1566 sheet: -1.58 (0.25), residues: 381 loop : -1.84 (0.17), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 515 HIS 0.003 0.001 HIS K 692 PHE 0.032 0.002 PHE J 702 TYR 0.012 0.001 TYR K 541 ARG 0.008 0.001 ARG L 586 Details of bonding type rmsd hydrogen bonds : bond 0.10422 ( 987) hydrogen bonds : angle 6.57166 ( 2817) covalent geometry : bond 0.00355 (23913) covalent geometry : angle 0.85924 (32499) *********************** 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 145 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 108 GLN cc_start: 0.9089 (tt0) cc_final: 0.8578 (tm-30) REVERT: J 137 LEU cc_start: 0.8821 (mp) cc_final: 0.8355 (mp) REVERT: J 175 PHE cc_start: 0.5359 (p90) cc_final: 0.5129 (p90) REVERT: J 208 GLN cc_start: 0.9164 (tp-100) cc_final: 0.8608 (tp40) REVERT: J 293 LEU cc_start: 0.8628 (tp) cc_final: 0.7871 (mp) REVERT: J 301 ASP cc_start: 0.8455 (m-30) cc_final: 0.8172 (m-30) REVERT: J 317 MET cc_start: 0.8167 (ptt) cc_final: 0.7356 (ptm) REVERT: J 334 SER cc_start: 0.9367 (t) cc_final: 0.8997 (p) REVERT: J 353 LEU cc_start: 0.8501 (pp) cc_final: 0.8170 (mm) REVERT: J 415 ASN cc_start: 0.8984 (p0) cc_final: 0.8692 (m110) REVERT: J 453 PHE cc_start: 0.9250 (m-10) cc_final: 0.8721 (m-10) REVERT: J 496 MET cc_start: 0.7272 (tpp) cc_final: 0.7026 (tpp) REVERT: J 662 MET cc_start: 0.8003 (ttp) cc_final: 0.7261 (mpp) REVERT: J 666 PHE cc_start: 0.8541 (p90) cc_final: 0.8171 (p90) REVERT: J 913 LEU cc_start: 0.9706 (tp) cc_final: 0.9293 (pp) REVERT: J 968 MET cc_start: 0.9142 (ttt) cc_final: 0.8752 (tmm) REVERT: J 1009 MET cc_start: 0.8978 (ttt) cc_final: 0.8244 (tpt) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.1597 time to fit residues: 33.4676 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 : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 296 optimal weight: 0.4980 chunk 170 optimal weight: 8.9990 chunk 237 optimal weight: 0.9990 chunk 64 optimal weight: 8.9990 chunk 190 optimal weight: 0.8980 chunk 193 optimal weight: 10.0000 chunk 276 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 29 optimal weight: 0.6980 chunk 242 optimal weight: 0.0670 chunk 260 optimal weight: 0.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 58 GLN ** J 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 229 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 = 0.3578 r_free = 0.3578 target = 0.080298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.069740 restraints weight = 44168.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.071088 restraints weight = 27704.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.071961 restraints weight = 19503.586| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 1.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23913 Z= 0.157 Angle : 0.825 10.956 32499 Z= 0.447 Chirality : 0.045 0.252 3792 Planarity : 0.005 0.054 4173 Dihedral : 5.118 31.075 3279 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.67 % Favored : 95.14 % 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 : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.14), residues: 3084 helix: -1.12 (0.12), residues: 1581 sheet: -1.60 (0.24), residues: 420 loop : -1.58 (0.18), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 515 HIS 0.021 0.002 HIS J 654 PHE 0.018 0.001 PHE L 884 TYR 0.010 0.001 TYR L 891 ARG 0.007 0.000 ARG K 866 Details of bonding type rmsd hydrogen bonds : bond 0.08479 ( 987) hydrogen bonds : angle 6.24456 ( 2817) covalent geometry : bond 0.00303 (23913) covalent geometry : angle 0.82482 (32499) *********************** 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 148 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 147 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 137 LEU cc_start: 0.8895 (mp) cc_final: 0.8503 (mp) REVERT: J 175 PHE cc_start: 0.5245 (p90) cc_final: 0.4892 (p90) REVERT: J 208 GLN cc_start: 0.9082 (tp-100) cc_final: 0.8584 (tp40) REVERT: J 244 GLU cc_start: 0.9172 (mp0) cc_final: 0.8932 (mp0) REVERT: J 293 LEU cc_start: 0.8739 (tp) cc_final: 0.7938 (mp) REVERT: J 317 MET cc_start: 0.8138 (ptt) cc_final: 0.7306 (ptm) REVERT: J 330 THR cc_start: 0.9490 (p) cc_final: 0.9189 (p) REVERT: J 334 SER cc_start: 0.9437 (t) cc_final: 0.9089 (p) REVERT: J 353 LEU cc_start: 0.8628 (pp) cc_final: 0.8240 (mm) REVERT: J 415 ASN cc_start: 0.8929 (p0) cc_final: 0.8681 (m110) REVERT: J 453 PHE cc_start: 0.8865 (m-10) cc_final: 0.8389 (m-10) REVERT: J 597 TYR cc_start: 0.8367 (m-80) cc_final: 0.7900 (m-80) REVERT: J 662 MET cc_start: 0.7989 (ttp) cc_final: 0.7130 (mpp) REVERT: J 666 PHE cc_start: 0.8489 (p90) cc_final: 0.8139 (p90) REVERT: J 866 ARG cc_start: 0.7993 (ttp-110) cc_final: 0.7525 (ttp80) REVERT: J 968 MET cc_start: 0.9157 (ttt) cc_final: 0.8938 (tmm) REVERT: J 980 PHE cc_start: 0.8820 (t80) cc_final: 0.8587 (t80) REVERT: J 1009 MET cc_start: 0.9154 (ttt) cc_final: 0.8284 (tpt) REVERT: J 1013 THR cc_start: 0.8115 (p) cc_final: 0.7903 (p) outliers start: 1 outliers final: 0 residues processed: 148 average time/residue: 0.1580 time to fit residues: 33.9283 Evaluate side-chains 118 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 92 optimal weight: 0.0970 chunk 54 optimal weight: 0.7980 chunk 306 optimal weight: 5.9990 chunk 302 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 239 optimal weight: 0.0270 chunk 69 optimal weight: 3.9990 chunk 34 optimal weight: 0.3980 chunk 81 optimal weight: 0.7980 chunk 266 optimal weight: 0.1980 chunk 193 optimal weight: 8.9990 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 46 GLN ** J 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 211 ASN J 654 HIS ** J 849 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 = 0.3588 r_free = 0.3588 target = 0.080796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.070384 restraints weight = 44063.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.071692 restraints weight = 27450.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.072609 restraints weight = 18976.230| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 1.2546 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= 0.151 Angle : 0.819 10.206 32499 Z= 0.440 Chirality : 0.045 0.191 3792 Planarity : 0.005 0.051 4173 Dihedral : 4.994 33.214 3279 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.25 % Favored : 94.55 % Rotamer: Outliers : 0.24 % Allowed : 3.21 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.14), residues: 3084 helix: -0.92 (0.13), residues: 1563 sheet: -1.52 (0.24), residues: 384 loop : -1.50 (0.17), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 515 HIS 0.019 0.002 HIS K 654 PHE 0.020 0.001 PHE L 884 TYR 0.017 0.001 TYR J 49 ARG 0.003 0.000 ARG J 239 Details of bonding type rmsd hydrogen bonds : bond 0.07717 ( 987) hydrogen bonds : angle 6.08517 ( 2817) covalent geometry : bond 0.00288 (23913) covalent geometry : angle 0.81945 (32499) *********************** 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 143 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 141 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 137 LEU cc_start: 0.8924 (mp) cc_final: 0.8646 (mp) REVERT: J 175 PHE cc_start: 0.5189 (p90) cc_final: 0.4857 (p90) REVERT: J 177 VAL cc_start: 0.8817 (p) cc_final: 0.8562 (p) REVERT: J 208 GLN cc_start: 0.9104 (tp-100) cc_final: 0.8878 (tp-100) REVERT: J 211 ASN cc_start: 0.8382 (OUTLIER) cc_final: 0.7824 (t0) REVERT: J 244 GLU cc_start: 0.9157 (mp0) cc_final: 0.8934 (mp0) REVERT: J 293 LEU cc_start: 0.8660 (tp) cc_final: 0.7779 (mp) REVERT: J 317 MET cc_start: 0.8073 (ptt) cc_final: 0.7000 (ptm) REVERT: J 330 THR cc_start: 0.9481 (p) cc_final: 0.9194 (p) REVERT: J 334 SER cc_start: 0.9441 (t) cc_final: 0.9108 (p) REVERT: J 377 LEU cc_start: 0.9183 (pt) cc_final: 0.8934 (pt) REVERT: J 414 GLU cc_start: 0.9082 (tp30) cc_final: 0.8666 (tp30) REVERT: J 415 ASN cc_start: 0.8845 (p0) cc_final: 0.8621 (m110) REVERT: J 416 VAL cc_start: 0.9058 (t) cc_final: 0.8795 (t) REVERT: J 417 GLU cc_start: 0.9101 (pp20) cc_final: 0.8819 (tp30) REVERT: J 420 MET cc_start: 0.6964 (mmm) cc_final: 0.6475 (tpt) REVERT: J 453 PHE cc_start: 0.8899 (m-10) cc_final: 0.8377 (m-10) REVERT: J 662 MET cc_start: 0.8045 (ttp) cc_final: 0.7222 (mpp) REVERT: J 666 PHE cc_start: 0.8441 (p90) cc_final: 0.8147 (p90) REVERT: J 866 ARG cc_start: 0.8016 (ttp-110) cc_final: 0.7569 (ttp80) REVERT: J 1001 ILE cc_start: 0.9474 (mm) cc_final: 0.9203 (pt) outliers start: 2 outliers final: 0 residues processed: 143 average time/residue: 0.1652 time to fit residues: 34.3958 Evaluate side-chains 124 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 285 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 158 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 300 optimal weight: 7.9990 chunk 202 optimal weight: 9.9990 chunk 225 optimal weight: 6.9990 chunk 81 optimal weight: 0.0170 overall best weight: 2.4026 ------------------------------------------------------------------------------- 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 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 = 0.3540 r_free = 0.3540 target = 0.077993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.067384 restraints weight = 44881.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.068630 restraints weight = 27250.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.069542 restraints weight = 18842.054| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 1.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23913 Z= 0.174 Angle : 0.815 9.040 32499 Z= 0.444 Chirality : 0.044 0.205 3792 Planarity : 0.005 0.051 4173 Dihedral : 4.913 33.404 3279 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.25 % Favored : 94.55 % Rotamer: Outliers : 0.12 % Allowed : 2.50 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.14), residues: 3084 helix: -0.78 (0.13), residues: 1575 sheet: -1.61 (0.25), residues: 375 loop : -1.32 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 515 HIS 0.018 0.002 HIS J 654 PHE 0.034 0.002 PHE K 702 TYR 0.012 0.001 TYR K 863 ARG 0.009 0.001 ARG K 168 Details of bonding type rmsd hydrogen bonds : bond 0.07174 ( 987) hydrogen bonds : angle 6.14731 ( 2817) covalent geometry : bond 0.00354 (23913) covalent geometry : angle 0.81522 (32499) *********************** 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 137 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 137 LEU cc_start: 0.8935 (mp) cc_final: 0.8595 (mp) REVERT: J 175 PHE cc_start: 0.5459 (p90) cc_final: 0.5035 (p90) REVERT: J 293 LEU cc_start: 0.8875 (tp) cc_final: 0.7935 (mp) REVERT: J 317 MET cc_start: 0.8305 (ptt) cc_final: 0.8051 (ptm) REVERT: J 330 THR cc_start: 0.9444 (p) cc_final: 0.9203 (p) REVERT: J 334 SER cc_start: 0.9422 (t) cc_final: 0.9072 (p) REVERT: J 377 LEU cc_start: 0.9064 (pt) cc_final: 0.8666 (pt) REVERT: J 414 GLU cc_start: 0.9061 (tp30) cc_final: 0.8628 (tp30) REVERT: J 415 ASN cc_start: 0.8863 (p0) cc_final: 0.8647 (m110) REVERT: J 416 VAL cc_start: 0.9225 (t) cc_final: 0.9004 (t) REVERT: J 453 PHE cc_start: 0.8783 (m-10) cc_final: 0.8111 (m-10) REVERT: J 662 MET cc_start: 0.7962 (ttp) cc_final: 0.7189 (mpp) REVERT: J 666 PHE cc_start: 0.8492 (p90) cc_final: 0.8211 (p90) REVERT: J 968 MET cc_start: 0.9192 (tmm) cc_final: 0.8879 (tmm) REVERT: J 1001 ILE cc_start: 0.9477 (mm) cc_final: 0.9182 (pt) outliers start: 1 outliers final: 0 residues processed: 137 average time/residue: 0.1712 time to fit residues: 33.4424 Evaluate side-chains 111 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 307 optimal weight: 10.0000 chunk 308 optimal weight: 0.4980 chunk 67 optimal weight: 6.9990 chunk 166 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 chunk 203 optimal weight: 4.9990 chunk 137 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 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 = 0.3561 r_free = 0.3561 target = 0.079139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.068336 restraints weight = 44875.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.069732 restraints weight = 27546.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.070676 restraints weight = 19008.604| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 1.2534 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 : 0.814 9.333 32499 Z= 0.434 Chirality : 0.044 0.168 3792 Planarity : 0.005 0.052 4173 Dihedral : 4.850 32.681 3279 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.25 % Favored : 94.55 % Rotamer: Outliers : 0.24 % Allowed : 2.26 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.15), residues: 3084 helix: -0.62 (0.13), residues: 1569 sheet: -1.60 (0.24), residues: 381 loop : -1.23 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 515 HIS 0.017 0.002 HIS L 654 PHE 0.021 0.001 PHE L 884 TYR 0.021 0.001 TYR J 891 ARG 0.007 0.000 ARG K 866 Details of bonding type rmsd hydrogen bonds : bond 0.06884 ( 987) hydrogen bonds : angle 6.03259 ( 2817) covalent geometry : bond 0.00294 (23913) covalent geometry : angle 0.81430 (32499) *********************** 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 138 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 136 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 124 ARG cc_start: 0.9277 (mtm110) cc_final: 0.7413 (tpm170) REVERT: J 137 LEU cc_start: 0.8938 (mp) cc_final: 0.8600 (mp) REVERT: J 244 GLU cc_start: 0.9156 (mp0) cc_final: 0.8933 (mp0) REVERT: J 293 LEU cc_start: 0.8852 (tp) cc_final: 0.7941 (mp) REVERT: J 330 THR cc_start: 0.9430 (p) cc_final: 0.9169 (p) REVERT: J 334 SER cc_start: 0.9362 (t) cc_final: 0.8953 (p) REVERT: J 377 LEU cc_start: 0.9180 (pt) cc_final: 0.8808 (pt) REVERT: J 453 PHE cc_start: 0.8895 (m-10) cc_final: 0.8308 (m-10) REVERT: J 597 TYR cc_start: 0.8470 (m-80) cc_final: 0.8090 (m-80) REVERT: J 662 MET cc_start: 0.7992 (ttp) cc_final: 0.7225 (mpp) REVERT: J 849 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.7083 (pm20) REVERT: J 1001 ILE cc_start: 0.9491 (mm) cc_final: 0.9191 (pt) REVERT: J 1019 TRP cc_start: 0.8342 (m-90) cc_final: 0.8039 (m-90) outliers start: 2 outliers final: 0 residues processed: 138 average time/residue: 0.1810 time to fit residues: 35.3288 Evaluate side-chains 113 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 59 optimal weight: 0.9990 chunk 266 optimal weight: 0.0020 chunk 138 optimal weight: 1.9990 chunk 180 optimal weight: 0.0570 chunk 142 optimal weight: 3.9990 chunk 281 optimal weight: 8.9990 chunk 211 optimal weight: 0.9990 chunk 287 optimal weight: 0.0980 chunk 64 optimal weight: 6.9990 chunk 274 optimal weight: 0.1980 chunk 68 optimal weight: 0.8980 overall best weight: 0.2506 ------------------------------------------------------------------------------- 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 692 HIS ** J 759 ASN ** 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 = 0.3592 r_free = 0.3592 target = 0.080796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.069871 restraints weight = 44689.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.071251 restraints weight = 27332.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.072225 restraints weight = 18974.585| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 1.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23913 Z= 0.147 Angle : 0.821 9.630 32499 Z= 0.434 Chirality : 0.044 0.187 3792 Planarity : 0.004 0.050 4173 Dihedral : 4.784 32.493 3279 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.35 % Favored : 94.55 % Rotamer: Outliers : 0.12 % Allowed : 1.07 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.15), residues: 3084 helix: -0.59 (0.13), residues: 1575 sheet: -1.53 (0.23), residues: 420 loop : -1.22 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP K 515 HIS 0.018 0.002 HIS L 654 PHE 0.030 0.001 PHE L 702 TYR 0.012 0.001 TYR L 49 ARG 0.011 0.001 ARG L 432 Details of bonding type rmsd hydrogen bonds : bond 0.06687 ( 987) hydrogen bonds : angle 5.93913 ( 2817) covalent geometry : bond 0.00285 (23913) covalent geometry : angle 0.82058 (32499) *********************** 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 139 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 65 ILE cc_start: 0.9379 (mt) cc_final: 0.9129 (tp) REVERT: J 124 ARG cc_start: 0.9068 (mtm110) cc_final: 0.7316 (tpm170) REVERT: J 137 LEU cc_start: 0.8951 (mp) cc_final: 0.8556 (mp) REVERT: J 138 MET cc_start: 0.8291 (ptm) cc_final: 0.8085 (ptm) REVERT: J 293 LEU cc_start: 0.8747 (tp) cc_final: 0.7869 (mp) REVERT: J 330 THR cc_start: 0.9425 (p) cc_final: 0.9143 (p) REVERT: J 334 SER cc_start: 0.9346 (t) cc_final: 0.8943 (p) REVERT: J 442 LEU cc_start: 0.8121 (tp) cc_final: 0.7881 (tp) REVERT: J 453 PHE cc_start: 0.8873 (m-10) cc_final: 0.8243 (m-10) REVERT: J 662 MET cc_start: 0.7977 (ttp) cc_final: 0.7192 (mpp) REVERT: J 686 ASP cc_start: 0.8087 (t0) cc_final: 0.7641 (t0) REVERT: J 1001 ILE cc_start: 0.9537 (mm) cc_final: 0.9288 (pt) outliers start: 1 outliers final: 0 residues processed: 139 average time/residue: 0.1652 time to fit residues: 32.7786 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 : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 231 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 252 optimal weight: 8.9990 chunk 267 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 204 optimal weight: 0.1980 chunk 196 optimal weight: 5.9990 chunk 232 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 692 HIS ** J 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3585 r_free = 0.3585 target = 0.080359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.069556 restraints weight = 44955.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.070934 restraints weight = 27890.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.071901 restraints weight = 19481.838| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 1.2626 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= 0.147 Angle : 0.823 9.666 32499 Z= 0.436 Chirality : 0.045 0.233 3792 Planarity : 0.004 0.051 4173 Dihedral : 4.759 32.854 3279 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.77 % Favored : 95.14 % Rotamer: Outliers : 0.12 % Allowed : 1.07 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.15), residues: 3084 helix: -0.54 (0.13), residues: 1575 sheet: -1.55 (0.23), residues: 420 loop : -1.14 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP K 515 HIS 0.018 0.002 HIS L 654 PHE 0.022 0.001 PHE L 884 TYR 0.010 0.001 TYR K 49 ARG 0.006 0.000 ARG L 128 Details of bonding type rmsd hydrogen bonds : bond 0.06522 ( 987) hydrogen bonds : angle 5.92650 ( 2817) covalent geometry : bond 0.00297 (23913) covalent geometry : angle 0.82301 (32499) *********************** 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 135 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 65 ILE cc_start: 0.9419 (mt) cc_final: 0.9103 (tp) REVERT: J 124 ARG cc_start: 0.9094 (mtm110) cc_final: 0.7279 (tpm170) REVERT: J 137 LEU cc_start: 0.8883 (mp) cc_final: 0.8478 (mp) REVERT: J 293 LEU cc_start: 0.8723 (tp) cc_final: 0.7840 (mp) REVERT: J 330 THR cc_start: 0.9405 (p) cc_final: 0.9148 (p) REVERT: J 334 SER cc_start: 0.9407 (t) cc_final: 0.9030 (p) REVERT: J 453 PHE cc_start: 0.8920 (m-80) cc_final: 0.8286 (m-10) REVERT: J 662 MET cc_start: 0.8127 (ttp) cc_final: 0.7281 (mpp) REVERT: J 686 ASP cc_start: 0.8141 (t0) cc_final: 0.7659 (t0) REVERT: J 902 LEU cc_start: 0.8030 (mt) cc_final: 0.7747 (mt) REVERT: J 1001 ILE cc_start: 0.9550 (mm) cc_final: 0.9288 (pt) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.1762 time to fit residues: 34.0654 Evaluate side-chains 115 residues out of total 841 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 801, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.7205 > 50: distance: 0 - 1: 6.893 distance: 1 - 2: 4.288 distance: 2 - 3: 16.062 distance: 2 - 6: 10.276 distance: 4 - 5: 8.193 distance: 6 - 7: 9.897 distance: 7 - 8: 14.323 distance: 7 - 10: 8.513 distance: 8 - 9: 11.928 distance: 8 - 14: 7.709 distance: 10 - 11: 15.876 distance: 11 - 12: 14.030 distance: 11 - 13: 19.242 distance: 14 - 15: 29.530 distance: 15 - 16: 5.550 distance: 15 - 18: 18.191 distance: 16 - 17: 12.326 distance: 16 - 22: 13.163 distance: 18 - 19: 15.325 distance: 18 - 20: 6.273 distance: 19 - 21: 18.929 distance: 22 - 23: 13.410 distance: 23 - 24: 13.780 distance: 23 - 26: 13.190 distance: 24 - 25: 14.454 distance: 24 - 31: 17.501 distance: 26 - 27: 6.631 distance: 27 - 28: 9.451 distance: 28 - 29: 8.005 distance: 28 - 30: 24.634 distance: 31 - 32: 6.657 distance: 32 - 33: 22.349 distance: 32 - 35: 7.814 distance: 33 - 34: 35.495 distance: 33 - 39: 29.650 distance: 35 - 36: 10.902 distance: 36 - 37: 6.293 distance: 36 - 38: 3.289 distance: 39 - 40: 8.529 distance: 39 - 45: 8.343 distance: 40 - 41: 8.518 distance: 40 - 43: 11.917 distance: 41 - 42: 24.772 distance: 41 - 46: 11.428 distance: 43 - 44: 10.638 distance: 44 - 45: 6.739 distance: 46 - 47: 21.225 distance: 47 - 48: 26.563 distance: 47 - 50: 17.737 distance: 48 - 49: 19.115 distance: 48 - 54: 8.419 distance: 50 - 51: 15.474 distance: 51 - 52: 10.562 distance: 51 - 53: 33.097 distance: 55 - 56: 16.138 distance: 55 - 58: 14.973 distance: 56 - 57: 35.610 distance: 56 - 60: 20.839 distance: 58 - 59: 21.363 distance: 60 - 61: 7.648 distance: 61 - 62: 8.808 distance: 61 - 64: 3.240 distance: 62 - 63: 10.189 distance: 62 - 71: 9.544 distance: 64 - 65: 4.765 distance: 65 - 66: 7.852 distance: 67 - 68: 3.313 distance: 71 - 72: 5.461 distance: 72 - 73: 6.977 distance: 72 - 75: 3.762 distance: 73 - 74: 6.083 distance: 75 - 76: 7.730