Starting phenix.real_space_refine on Wed Dec 13 01:51:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t7s_10371/12_2023/6t7s_10371.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t7s_10371/12_2023/6t7s_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_2023/6t7s_10371.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t7s_10371/12_2023/6t7s_10371.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t7s_10371/12_2023/6t7s_10371.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t7s_10371/12_2023/6t7s_10371.pdb" } 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 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 12.78, per 1000 atoms: 0.55 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: 9.96 Conformation dependent library (CDL) restraints added in 5.0 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: 3.37 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: 9.41 Time building geometry restraints manager: 10.66 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. 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: 1.320 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: 7.340 Check model and map are aligned: 0.350 Set scattering table: 0.230 Process input model: 66.470 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.750 ------------------------------------------------------------------------------- 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= 0.238 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 % 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 *********************** 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 : 0.931 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: 0.1986 time to fit residues: 47.7392 Evaluate side-chains 126 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 0.950 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0723 time to fit residues: 1.4165 ------------------------------------------------------------------------------- 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: 0.7411 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 0.081 23913 Z= 0.280 Angle : 0.963 11.884 32499 Z= 0.535 Chirality : 0.050 0.262 3792 Planarity : 0.007 0.057 4173 Dihedral : 5.570 25.928 3279 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.78 % Allowed : 4.38 % Favored : 94.84 % Rotamer: Outliers : 0.59 % Allowed : 9.39 % Favored : 90.01 % 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: -2.24 (0.11), residues: 1557 sheet: -1.80 (0.24), residues: 426 loop : -2.02 (0.17), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 515 HIS 0.004 0.001 HIS J 692 PHE 0.016 0.002 PHE L 512 TYR 0.016 0.001 TYR K 810 ARG 0.007 0.001 ARG L 586 *********************** 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 161 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 156 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 160 average time/residue: 0.1859 time to fit residues: 41.3876 Evaluate side-chains 113 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.941 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3109 ------------------------------------------------------------------------------- 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: 6.9990 chunk 87 optimal weight: 0.0170 chunk 233 optimal weight: 0.1980 chunk 191 optimal weight: 5.9990 chunk 77 optimal weight: 0.0000 chunk 281 optimal weight: 7.9990 chunk 303 optimal weight: 2.9990 chunk 250 optimal weight: 0.0670 chunk 278 optimal weight: 0.5980 chunk 95 optimal weight: 0.0980 chunk 225 optimal weight: 0.6980 overall best weight: 0.0760 ------------------------------------------------------------------------------- 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 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: 0.7389 moved from start: 1.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23913 Z= 0.217 Angle : 0.853 9.608 32499 Z= 0.464 Chirality : 0.046 0.261 3792 Planarity : 0.005 0.047 4173 Dihedral : 5.408 33.609 3279 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.16 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % 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: -2.66 (0.14), residues: 3084 helix: -1.56 (0.12), residues: 1584 sheet: -1.61 (0.25), residues: 396 loop : -1.84 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 515 HIS 0.002 0.001 HIS K 692 PHE 0.033 0.001 PHE K 702 TYR 0.021 0.001 TYR L 891 ARG 0.007 0.000 ARG K 586 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.1574 time to fit residues: 33.7450 Evaluate side-chains 116 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.836 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1258 ------------------------------------------------------------------------------- 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: 5.9990 chunk 211 optimal weight: 0.8980 chunk 145 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 134 optimal weight: 0.0000 chunk 188 optimal weight: 4.9990 chunk 282 optimal weight: 3.9990 chunk 298 optimal weight: 0.0570 chunk 147 optimal weight: 2.9990 chunk 267 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 overall best weight: 0.7304 ------------------------------------------------------------------------------- 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: 0.7396 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 : 0.003 0.030 23913 Z= 0.186 Angle : 0.808 9.645 32499 Z= 0.438 Chirality : 0.045 0.259 3792 Planarity : 0.005 0.051 4173 Dihedral : 5.072 30.498 3279 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.16 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % 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: -2.11 (0.14), residues: 3084 helix: -1.00 (0.13), residues: 1572 sheet: -1.57 (0.25), residues: 384 loop : -1.68 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 515 HIS 0.006 0.001 HIS K 692 PHE 0.020 0.001 PHE L 884 TYR 0.024 0.001 TYR K 891 ARG 0.008 0.000 ARG K 432 *********************** 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 142 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1642 time to fit residues: 33.8027 Evaluate side-chains 116 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.882 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 248 optimal weight: 5.9990 chunk 169 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 222 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 254 optimal weight: 2.9990 chunk 206 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 152 optimal weight: 0.6980 chunk 268 optimal weight: 0.7980 chunk 75 optimal weight: 9.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 940 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 1.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23913 Z= 0.199 Angle : 0.811 9.864 32499 Z= 0.435 Chirality : 0.044 0.176 3792 Planarity : 0.005 0.052 4173 Dihedral : 4.977 32.191 3279 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.35 % Favored : 94.46 % Rotamer: Outliers : 0.12 % Allowed : 2.97 % Favored : 96.91 % 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: -1.83 (0.15), residues: 3084 helix: -0.79 (0.13), residues: 1566 sheet: -1.52 (0.25), residues: 399 loop : -1.48 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 515 HIS 0.002 0.001 HIS L 654 PHE 0.034 0.001 PHE J 702 TYR 0.026 0.001 TYR L 891 ARG 0.007 0.000 ARG L 432 *********************** 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 137 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 137 average time/residue: 0.1685 time to fit residues: 33.1425 Evaluate side-chains 116 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.929 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 100 optimal weight: 1.9990 chunk 268 optimal weight: 0.0030 chunk 59 optimal weight: 0.5980 chunk 175 optimal weight: 0.1980 chunk 73 optimal weight: 3.9990 chunk 298 optimal weight: 0.8980 chunk 248 optimal weight: 0.1980 chunk 138 optimal weight: 4.9990 chunk 24 optimal weight: 0.0980 chunk 98 optimal weight: 8.9990 chunk 156 optimal weight: 0.2980 overall best weight: 0.1590 ------------------------------------------------------------------------------- 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 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 940 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 1.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23913 Z= 0.186 Angle : 0.800 9.803 32499 Z= 0.426 Chirality : 0.044 0.228 3792 Planarity : 0.005 0.050 4173 Dihedral : 4.851 33.361 3279 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.84 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % 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: -1.72 (0.15), residues: 3084 helix: -0.75 (0.13), residues: 1575 sheet: -1.55 (0.24), residues: 417 loop : -1.29 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 515 HIS 0.002 0.000 HIS J 654 PHE 0.021 0.001 PHE L 898 TYR 0.018 0.001 TYR J 891 ARG 0.011 0.000 ARG K 168 *********************** 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 141 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.882 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: 141 average time/residue: 0.1764 time to fit residues: 35.2537 Evaluate side-chains 110 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.857 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 288 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 218 optimal weight: 0.8980 chunk 169 optimal weight: 5.9990 chunk 251 optimal weight: 0.0170 chunk 166 optimal weight: 0.0040 chunk 297 optimal weight: 0.8980 chunk 186 optimal weight: 0.0770 chunk 181 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 overall best weight: 0.3788 ------------------------------------------------------------------------------- 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 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: 0.7385 moved from start: 1.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23913 Z= 0.197 Angle : 0.819 9.473 32499 Z= 0.433 Chirality : 0.044 0.171 3792 Planarity : 0.005 0.079 4173 Dihedral : 4.870 34.089 3279 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.64 % Favored : 94.26 % Rotamer: Outliers : 0.12 % Allowed : 2.02 % Favored : 97.86 % 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: -1.64 (0.15), residues: 3084 helix: -0.69 (0.13), residues: 1569 sheet: -1.46 (0.24), residues: 423 loop : -1.27 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 515 HIS 0.002 0.000 HIS J 654 PHE 0.016 0.001 PHE K 898 TYR 0.036 0.001 TYR L 597 ARG 0.009 0.000 ARG K 124 *********************** 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 137 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 137 average time/residue: 0.1648 time to fit residues: 33.1450 Evaluate side-chains 111 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.039 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 184 optimal weight: 0.0870 chunk 118 optimal weight: 0.6980 chunk 177 optimal weight: 0.8980 chunk 89 optimal weight: 0.0670 chunk 58 optimal weight: 0.5980 chunk 57 optimal weight: 7.9990 chunk 189 optimal weight: 3.9990 chunk 202 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 234 optimal weight: 0.0030 overall best weight: 0.2906 ------------------------------------------------------------------------------- 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 940 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 1.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23913 Z= 0.187 Angle : 0.816 10.002 32499 Z= 0.430 Chirality : 0.044 0.181 3792 Planarity : 0.005 0.052 4173 Dihedral : 4.786 33.665 3279 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.74 % Favored : 94.16 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % 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: -1.52 (0.15), residues: 3084 helix: -0.58 (0.13), residues: 1569 sheet: -1.44 (0.24), residues: 429 loop : -1.20 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 515 HIS 0.002 0.000 HIS K 654 PHE 0.035 0.001 PHE L 702 TYR 0.015 0.001 TYR L 49 ARG 0.008 0.000 ARG L 124 *********************** 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 138 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.945 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: 138 average time/residue: 0.1636 time to fit residues: 32.7997 Evaluate side-chains 115 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.902 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 270 optimal weight: 0.2980 chunk 285 optimal weight: 0.0270 chunk 260 optimal weight: 0.4980 chunk 277 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 217 optimal weight: 2.9990 chunk 85 optimal weight: 0.4980 chunk 250 optimal weight: 0.5980 chunk 262 optimal weight: 7.9990 chunk 276 optimal weight: 5.9990 overall best weight: 0.3838 ------------------------------------------------------------------------------- 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 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 940 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 1.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23913 Z= 0.188 Angle : 0.824 10.408 32499 Z= 0.432 Chirality : 0.044 0.176 3792 Planarity : 0.004 0.047 4173 Dihedral : 4.782 32.991 3279 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.35 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (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: -1.41 (0.15), residues: 3084 helix: -0.52 (0.13), residues: 1566 sheet: -1.39 (0.25), residues: 429 loop : -1.08 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 515 HIS 0.016 0.002 HIS J 654 PHE 0.024 0.001 PHE L 898 TYR 0.013 0.001 TYR J 49 ARG 0.011 0.001 ARG L 432 *********************** 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 142 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1594 time to fit residues: 33.1402 Evaluate side-chains 116 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.908 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 182 optimal weight: 10.0000 chunk 293 optimal weight: 9.9990 chunk 179 optimal weight: 0.0470 chunk 139 optimal weight: 4.9990 chunk 204 optimal weight: 0.5980 chunk 307 optimal weight: 0.5980 chunk 283 optimal weight: 0.9980 chunk 245 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 189 optimal weight: 3.9990 chunk 150 optimal weight: 0.2980 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 940 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 1.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23913 Z= 0.187 Angle : 0.818 10.116 32499 Z= 0.430 Chirality : 0.044 0.178 3792 Planarity : 0.004 0.047 4173 Dihedral : 4.767 31.466 3279 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.64 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: -1.33 (0.15), residues: 3084 helix: -0.45 (0.13), residues: 1560 sheet: -1.34 (0.25), residues: 429 loop : -1.07 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 515 HIS 0.018 0.002 HIS L 654 PHE 0.009 0.001 PHE K 925 TYR 0.012 0.001 TYR J 49 ARG 0.006 0.000 ARG L 124 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6168 Ramachandran restraints generated. 3084 Oldfield, 0 Emsley, 3084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1546 time to fit residues: 32.1946 Evaluate side-chains 122 residues out of total 841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.881 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 194 optimal weight: 0.8980 chunk 261 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 226 optimal weight: 0.9980 chunk 36 optimal weight: 8.9990 chunk 68 optimal weight: 9.9990 chunk 245 optimal weight: 0.0770 chunk 102 optimal weight: 3.9990 chunk 252 optimal weight: 10.0000 chunk 31 optimal weight: 0.0470 chunk 45 optimal weight: 6.9990 overall best weight: 1.2038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 254 ASN ** J 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 940 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 = 0.3589 r_free = 0.3589 target = 0.080814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.070159 restraints weight = 43212.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.071495 restraints weight = 27126.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.072425 restraints weight = 18952.840| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 1.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23913 Z= 0.194 Angle : 0.805 10.079 32499 Z= 0.425 Chirality : 0.044 0.177 3792 Planarity : 0.004 0.047 4173 Dihedral : 4.670 30.270 3279 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.03 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % 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: -1.26 (0.15), residues: 3084 helix: -0.40 (0.13), residues: 1563 sheet: -1.30 (0.25), residues: 420 loop : -1.03 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 515 HIS 0.017 0.002 HIS L 654 PHE 0.019 0.001 PHE J 898 TYR 0.010 0.001 TYR K 49 ARG 0.006 0.000 ARG L 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2999.65 seconds wall clock time: 56 minutes 39.08 seconds (3399.08 seconds total)