Starting phenix.real_space_refine (version: dev) on Sun Dec 18 14:00:31 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t7s_10371/12_2022/6t7s_10371.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t7s_10371/12_2022/6t7s_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t7s_10371/12_2022/6t7s_10371.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t7s_10371/12_2022/6t7s_10371.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t7s_10371/12_2022/6t7s_10371.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t7s_10371/12_2022/6t7s_10371.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "J PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 59": "OD1" <-> "OD2" Residue "J GLU 66": "OE1" <-> "OE2" Residue "J ASP 101": "OD1" <-> "OD2" Residue "J GLU 121": "OE1" <-> "OE2" Residue "J ARG 124": "NH1" <-> "NH2" Residue "J ASP 164": "OD1" <-> "OD2" Residue "J PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 407": "OD1" <-> "OD2" Residue "J ASP 408": "OD1" <-> "OD2" Residue "J PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 673": "OE1" <-> "OE2" Residue "J TYR 726": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 760": "OD1" <-> "OD2" Residue "J ARG 769": "NH1" <-> "NH2" Residue "J PHE 803": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 59": "OD1" <-> "OD2" Residue "K TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 301": "OD1" <-> "OD2" Residue "K TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 363": "NH1" <-> "NH2" Residue "K PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 568": "OD1" <-> "OD2" Residue "K GLU 585": "OE1" <-> "OE2" Residue "K PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 693": "OE1" <-> "OE2" Residue "K GLU 723": "OE1" <-> "OE2" Residue "K TYR 818": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 864": "OE1" <-> "OE2" Residue "K GLU 865": "OE1" <-> "OE2" Residue "K ARG 866": "NH1" <-> "NH2" Residue "K TYR 891": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 59": "OD1" <-> "OD2" Residue "L TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 85": "OD1" <-> "OD2" Residue "L GLU 121": "OE1" <-> "OE2" Residue "L ASP 164": "OD1" <-> "OD2" Residue "L ASP 174": "OD1" <-> "OD2" Residue "L PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 568": "OD1" <-> "OD2" Residue "L TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 13.14, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 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: 9.35 Conformation dependent library (CDL) restraints added in 3.5 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: 1.97 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: 9.38 Time building geometry restraints manager: 10.18 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: 99.38 - 106.71: 774 106.71 - 114.04: 13596 114.04 - 121.37: 12216 121.37 - 128.70: 5768 128.70 - 136.03: 145 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 2.440 nonbonded pdb=" O ALA L 305 " pdb=" OG1 THR L 309 " model vdw 2.283 2.440 nonbonded pdb=" OG SER L 79 " pdb=" OG1 THR L 91 " model vdw 2.294 2.440 nonbonded pdb=" OD1 ASN K 278 " pdb=" OG1 THR K 613 " model vdw 2.296 2.440 nonbonded pdb=" O LYS L 170 " pdb=" OG1 THR L 302 " model vdw 2.298 2.440 ... (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 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. 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. 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: 1.310 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: 8.510 Check model and map are aligned: 0.380 Convert atoms to be neutral: 0.210 Process input model: 61.510 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 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= 0.238 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 % 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 *********************** 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 fitting. rotamer outliers: 1 poor density : 175 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 176 average time/residue: 0.1846 time to fit residues: 44.5860 Evaluate side-chains 126 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 0.887 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0694 time to fit residues: 1.3561 ------------------------------------------------------------------------------- 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: 6.9990 chunk 234 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 157 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 242 optimal weight: 0.8980 chunk 93 optimal weight: 0.2980 chunk 147 optimal weight: 8.9990 chunk 180 optimal weight: 5.9990 chunk 280 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 67 GLN J 104 GLN J 123 GLN J 254 ASN J 282 ASN ** J 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 642 ASN J 676 ASN J 692 HIS J 700 ASN J 725 GLN ** J 759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 940 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 1.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.083 23913 Z= 0.285 Angle : 0.965 11.964 32499 Z= 0.537 Chirality : 0.050 0.262 3792 Planarity : 0.007 0.056 4173 Dihedral : 5.572 25.986 3279 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.78 % Allowed : 4.38 % Favored : 94.84 % Rotamer Outliers : 0.59 % 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: -3.35 (0.13), residues: 3084 helix: -2.25 (0.11), residues: 1557 sheet: -1.80 (0.24), residues: 426 loop : -2.02 (0.17), residues: 1101 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 155 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 159 average time/residue: 0.1743 time to fit residues: 39.0331 Evaluate side-chains 114 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.811 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 155 optimal weight: 9.9990 chunk 87 optimal weight: 0.0020 chunk 233 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 281 optimal weight: 5.9990 chunk 303 optimal weight: 0.0370 chunk 250 optimal weight: 0.9980 chunk 278 optimal weight: 10.0000 chunk 95 optimal weight: 0.0010 chunk 225 optimal weight: 1.9990 overall best weight: 0.6074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 676 ASN J 849 GLN ** J 940 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 1.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 23913 Z= 0.215 Angle : 0.849 9.503 32499 Z= 0.463 Chirality : 0.046 0.255 3792 Planarity : 0.005 0.049 4173 Dihedral : 5.436 35.085 3279 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.16 % Favored : 94.65 % Rotamer Outliers : 0.00 % 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: -2.64 (0.14), residues: 3084 helix: -1.53 (0.12), residues: 1587 sheet: -1.64 (0.24), residues: 423 loop : -1.83 (0.17), residues: 1074 *********************** 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 146 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1588 time to fit residues: 33.5419 Evaluate side-chains 109 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.946 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 277 optimal weight: 0.9990 chunk 211 optimal weight: 0.8980 chunk 145 optimal weight: 5.9990 chunk 31 optimal weight: 0.0670 chunk 134 optimal weight: 0.0470 chunk 188 optimal weight: 5.9990 chunk 282 optimal weight: 3.9990 chunk 298 optimal weight: 6.9990 chunk 147 optimal weight: 2.9990 chunk 267 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 overall best weight: 1.0020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 692 HIS ** J 940 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 1.2425 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= 0.201 Angle : 0.806 9.610 32499 Z= 0.439 Chirality : 0.045 0.256 3792 Planarity : 0.005 0.052 4173 Dihedral : 5.111 29.610 3279 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.77 % Favored : 95.04 % Rotamer Outliers : 0.00 % 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: -2.10 (0.14), residues: 3084 helix: -1.04 (0.13), residues: 1575 sheet: -1.55 (0.27), residues: 351 loop : -1.61 (0.17), residues: 1158 *********************** 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 139 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.1574 time to fit residues: 31.9566 Evaluate side-chains 111 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.937 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 675, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 770, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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-4807/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-4807/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-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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-4807/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-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.225 > 50: distance: 0 - 1: 19.896 distance: 1 - 2: 13.500 distance: 1 - 4: 26.335 distance: 2 - 3: 19.233 distance: 2 - 6: 40.340 distance: 4 - 5: 26.021 distance: 6 - 7: 37.528 distance: 7 - 8: 18.222 distance: 7 - 10: 52.808 distance: 8 - 9: 36.619 distance: 8 - 14: 48.882 distance: 10 - 11: 32.270 distance: 11 - 12: 17.140 distance: 11 - 13: 15.275 distance: 14 - 15: 14.505 distance: 15 - 16: 33.190 distance: 15 - 18: 40.404 distance: 16 - 17: 10.904 distance: 16 - 22: 60.533 distance: 18 - 19: 55.476 distance: 18 - 20: 57.349 distance: 19 - 21: 40.248 distance: 22 - 23: 43.432 distance: 23 - 24: 42.860 distance: 23 - 26: 28.467 distance: 24 - 31: 69.610 distance: 26 - 27: 40.824 distance: 27 - 28: 20.416 distance: 28 - 29: 18.031 distance: 28 - 30: 26.594 distance: 32 - 33: 40.257 distance: 32 - 35: 41.860 distance: 33 - 34: 5.713 distance: 33 - 39: 40.232 distance: 35 - 36: 24.505 distance: 36 - 37: 10.957 distance: 36 - 38: 29.658 distance: 39 - 45: 57.246 distance: 41 - 42: 39.671 distance: 41 - 46: 11.423 distance: 43 - 44: 41.418 distance: 44 - 45: 40.659 distance: 46 - 47: 55.094 distance: 47 - 48: 41.471 distance: 47 - 50: 69.359 distance: 48 - 49: 40.770 distance: 48 - 54: 28.296 distance: 50 - 51: 69.334 distance: 51 - 52: 39.202 distance: 51 - 53: 16.445 distance: 55 - 56: 54.582 distance: 55 - 58: 20.271 distance: 56 - 57: 24.314 distance: 56 - 60: 46.195 distance: 58 - 59: 20.449 distance: 60 - 61: 23.547 distance: 61 - 62: 27.259 distance: 61 - 64: 18.339 distance: 62 - 63: 25.537 distance: 62 - 71: 28.151 distance: 64 - 65: 36.938 distance: 65 - 66: 24.715 distance: 66 - 67: 12.329 distance: 67 - 68: 10.070 distance: 68 - 69: 7.328 distance: 68 - 70: 3.850 distance: 71 - 72: 6.579 distance: 72 - 73: 21.164 distance: 73 - 74: 31.822 distance: 75 - 76: 30.731 distance: 75 - 77: 16.939