Starting phenix.real_space_refine on Sat Nov 18 14:42:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5j8v_8073/11_2023/5j8v_8073.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5j8v_8073/11_2023/5j8v_8073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5j8v_8073/11_2023/5j8v_8073.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5j8v_8073/11_2023/5j8v_8073.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5j8v_8073/11_2023/5j8v_8073.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5j8v_8073/11_2023/5j8v_8073.pdb" } resolution = 4.9 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= 0.001 sd= 0.014 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 28 5.16 5 C 45372 2.51 5 N 14212 2.21 5 O 14004 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 3984": "NH1" <-> "NH2" Residue "A GLU 4182": "OE1" <-> "OE2" Residue "A GLU 4948": "OE1" <-> "OE2" Residue "A GLU 4952": "OE1" <-> "OE2" Residue "B ARG 3984": "NH1" <-> "NH2" Residue "B GLU 4182": "OE1" <-> "OE2" Residue "B GLU 4948": "OE1" <-> "OE2" Residue "B GLU 4952": "OE1" <-> "OE2" Residue "C ARG 3984": "NH1" <-> "NH2" Residue "C GLU 4182": "OE1" <-> "OE2" Residue "C GLU 4948": "OE1" <-> "OE2" Residue "C GLU 4952": "OE1" <-> "OE2" Residue "D ARG 3984": "NH1" <-> "NH2" Residue "D GLU 4182": "OE1" <-> "OE2" Residue "D GLU 4948": "OE1" <-> "OE2" Residue "D GLU 4952": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 73616 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 18404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3453, 18404 Classifications: {'peptide': 3453} Incomplete info: {'backbone_only': 2, 'n_c_alpha_c_only': 6, 'truncation_to_alanine': 2656} Link IDs: {'CIS': 86, 'PCIS': 4, 'PTRANS': 145, 'TRANS': 3217} Unresolved chain links: 1 Chain breaks: 69 Unresolved chain link angles: 187 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 9697 Unresolved non-hydrogen angles: 12351 Unresolved non-hydrogen dihedrals: 7952 Unresolved non-hydrogen chiralities: 886 Planarities with less than four sites: {'GLN:plan1': 142, 'HIS:plan': 86, 'TYR:plan': 73, 'ASN:plan1': 125, 'TRP:plan': 33, 'ASP:plan': 153, 'PHE:plan': 106, 'GLU:plan': 260, 'ARG:plan': 190} Unresolved non-hydrogen planarities: 5266 Chain: "B" Number of atoms: 18404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3453, 18404 Classifications: {'peptide': 3453} Incomplete info: {'backbone_only': 2, 'n_c_alpha_c_only': 6, 'truncation_to_alanine': 2656} Link IDs: {'CIS': 86, 'PCIS': 4, 'PTRANS': 145, 'TRANS': 3217} Unresolved chain links: 1 Chain breaks: 69 Unresolved chain link angles: 187 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 9697 Unresolved non-hydrogen angles: 12351 Unresolved non-hydrogen dihedrals: 7952 Unresolved non-hydrogen chiralities: 886 Planarities with less than four sites: {'GLN:plan1': 142, 'HIS:plan': 86, 'TYR:plan': 73, 'ASN:plan1': 125, 'TRP:plan': 33, 'ASP:plan': 153, 'PHE:plan': 106, 'GLU:plan': 260, 'ARG:plan': 190} Unresolved non-hydrogen planarities: 5266 Chain: "C" Number of atoms: 18404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3453, 18404 Classifications: {'peptide': 3453} Incomplete info: {'backbone_only': 2, 'n_c_alpha_c_only': 6, 'truncation_to_alanine': 2656} Link IDs: {'CIS': 86, 'PCIS': 4, 'PTRANS': 145, 'TRANS': 3217} Unresolved chain links: 1 Chain breaks: 69 Unresolved chain link angles: 187 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 9697 Unresolved non-hydrogen angles: 12351 Unresolved non-hydrogen dihedrals: 7952 Unresolved non-hydrogen chiralities: 886 Planarities with less than four sites: {'GLN:plan1': 142, 'HIS:plan': 86, 'TYR:plan': 73, 'ASN:plan1': 125, 'TRP:plan': 33, 'ASP:plan': 153, 'PHE:plan': 106, 'GLU:plan': 260, 'ARG:plan': 190} Unresolved non-hydrogen planarities: 5266 Chain: "D" Number of atoms: 18404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3453, 18404 Classifications: {'peptide': 3453} Incomplete info: {'backbone_only': 2, 'n_c_alpha_c_only': 6, 'truncation_to_alanine': 2656} Link IDs: {'CIS': 86, 'PCIS': 4, 'PTRANS': 145, 'TRANS': 3217} Unresolved chain links: 1 Chain breaks: 69 Unresolved chain link angles: 187 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 9697 Unresolved non-hydrogen angles: 12351 Unresolved non-hydrogen dihedrals: 7952 Unresolved non-hydrogen chiralities: 886 Planarities with less than four sites: {'GLN:plan1': 142, 'HIS:plan': 86, 'TYR:plan': 73, 'ASN:plan1': 125, 'TRP:plan': 33, 'ASP:plan': 153, 'PHE:plan': 106, 'GLU:plan': 260, 'ARG:plan': 190} Unresolved non-hydrogen planarities: 5266 Time building chain proxies: 31.61, per 1000 atoms: 0.43 Number of scatterers: 73616 At special positions: 0 Unit cell: (361.564, 361.564, 208.004, 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 28 16.00 O 14004 8.00 N 14212 7.00 C 45372 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: 26.27 Conformation dependent library (CDL) restraints added in 13.7 seconds 26480 Ramachandran restraints generated. 13240 Oldfield, 0 Emsley, 13240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 25992 Finding SS restraints... Secondary structure from input PDB file: 540 helices and 52 sheets defined 62.9% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.11 Creating SS restraints... Processing helix chain 'A' and resid 74 through 84 Processing helix chain 'A' and resid 250 through 256 removed outlier: 4.170A pdb=" N THR A 254 " --> pdb=" O GLY A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 311 Processing helix chain 'A' and resid 394 through 421 removed outlier: 4.028A pdb=" N SER A 398 " --> pdb=" O GLN A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 452 Processing helix chain 'A' and resid 462 through 482 removed outlier: 3.613A pdb=" N ARG A 469 " --> pdb=" O GLN A 465 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU A 480 " --> pdb=" O SER A 476 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 498 removed outlier: 3.946A pdb=" N LEU A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG A 493 " --> pdb=" O ASN A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 505 Processing helix chain 'A' and resid 510 through 531 removed outlier: 3.909A pdb=" N TYR A 523 " --> pdb=" O VAL A 519 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLU A 524 " --> pdb=" O ASN A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 552 removed outlier: 3.592A pdb=" N ALA A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N THR A 542 " --> pdb=" O ALA A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 571 removed outlier: 3.821A pdb=" N ILE A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER A 571 " --> pdb=" O VAL A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 577 removed outlier: 3.554A pdb=" N LEU A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 593 Processing helix chain 'A' and resid 598 through 607 Processing helix chain 'A' and resid 614 through 629 Proline residue: A 627 - end of helix Processing helix chain 'A' and resid 699 through 703 Processing helix chain 'A' and resid 865 through 887 removed outlier: 3.738A pdb=" N THR A 885 " --> pdb=" O LEU A 881 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG A 886 " --> pdb=" O TRP A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 936 Processing helix chain 'A' and resid 979 through 1003 Processing helix chain 'A' and resid 1023 through 1028 Processing helix chain 'A' and resid 1028 through 1050 Processing helix chain 'A' and resid 1215 through 1222 Processing helix chain 'A' and resid 1578 through 1585 Processing helix chain 'A' and resid 1649 through 1656 Processing helix chain 'A' and resid 1656 through 1675 Processing helix chain 'A' and resid 1679 through 1687 Processing helix chain 'A' and resid 1690 through 1700 Processing helix chain 'A' and resid 1704 through 1720 removed outlier: 4.435A pdb=" N LEU A1720 " --> pdb=" O ILE A1716 " (cutoff:3.500A) Processing helix chain 'A' and resid 1721 through 1732 Processing helix chain 'A' and resid 1739 through 1745 removed outlier: 3.863A pdb=" N ILE A1745 " --> pdb=" O GLU A1741 " (cutoff:3.500A) Processing helix chain 'A' and resid 1803 through 1822 removed outlier: 3.502A pdb=" N GLY A1816 " --> pdb=" O LEU A1812 " (cutoff:3.500A) Processing helix chain 'A' and resid 1833 through 1852 Proline residue: A1840 - end of helix Processing helix chain 'A' and resid 1855 through 1867 removed outlier: 3.887A pdb=" N GLU A1867 " --> pdb=" O LEU A1863 " (cutoff:3.500A) Processing helix chain 'A' and resid 1932 through 1976 removed outlier: 3.578A pdb=" N GLN A1949 " --> pdb=" O TYR A1945 " (cutoff:3.500A) Processing helix chain 'A' and resid 2034 through 2047 Processing helix chain 'A' and resid 2059 through 2072 Processing helix chain 'A' and resid 2094 through 2108 Processing helix chain 'A' and resid 2113 through 2130 removed outlier: 3.609A pdb=" N VAL A2117 " --> pdb=" O SER A2113 " (cutoff:3.500A) Processing helix chain 'A' and resid 2131 through 2141 Proline residue: A2139 - end of helix Processing helix chain 'A' and resid 2149 through 2168 Processing helix chain 'A' and resid 2173 through 2189 Processing helix chain 'A' and resid 2193 through 2198 Processing helix chain 'A' and resid 2201 through 2216 Processing helix chain 'A' and resid 2227 through 2243 removed outlier: 3.729A pdb=" N ILE A2242 " --> pdb=" O TYR A2238 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER A2243 " --> pdb=" O PHE A2239 " (cutoff:3.500A) Processing helix chain 'A' and resid 2243 through 2262 Processing helix chain 'A' and resid 2283 through 2290 removed outlier: 3.739A pdb=" N ALA A2287 " --> pdb=" O ASN A2283 " (cutoff:3.500A) Processing helix chain 'A' and resid 2291 through 2305 removed outlier: 3.825A pdb=" N LEU A2295 " --> pdb=" O GLN A2291 " (cutoff:3.500A) Processing helix chain 'A' and resid 2326 through 2340 Processing helix chain 'A' and resid 2346 through 2360 Processing helix chain 'A' and resid 2376 through 2386 Processing helix chain 'A' and resid 2426 through 2440 Proline residue: A2438 - end of helix Processing helix chain 'A' and resid 2450 through 2460 Processing helix chain 'A' and resid 2464 through 2476 Proline residue: A2473 - end of helix Processing helix chain 'A' and resid 2499 through 2510 Processing helix chain 'A' and resid 2518 through 2537 removed outlier: 3.577A pdb=" N VAL A2524 " --> pdb=" O HIS A2520 " (cutoff:3.500A) Proline residue: A2528 - end of helix removed outlier: 3.904A pdb=" N ARG A2531 " --> pdb=" O LEU A2527 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA A2532 " --> pdb=" O PRO A2528 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA A2533 " --> pdb=" O ASP A2529 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A2534 " --> pdb=" O MET A2530 " (cutoff:3.500A) Processing helix chain 'A' and resid 2544 through 2562 removed outlier: 3.539A pdb=" N VAL A2558 " --> pdb=" O LEU A2554 " (cutoff:3.500A) Proline residue: A2560 - end of helix Processing helix chain 'A' and resid 2568 through 2586 Processing helix chain 'A' and resid 2592 through 2609 Processing helix chain 'A' and resid 2616 through 2634 Proline residue: A2631 - end of helix Processing helix chain 'A' and resid 2639 through 2656 Processing helix chain 'A' and resid 2668 through 2686 Processing helix chain 'A' and resid 2692 through 2710 Proline residue: A2701 - end of helix Processing helix chain 'A' and resid 2748 through 2773 removed outlier: 3.553A pdb=" N LYS A2757 " --> pdb=" O SER A2753 " (cutoff:3.500A) Processing helix chain 'A' and resid 2798 through 2819 removed outlier: 4.014A pdb=" N ILE A2804 " --> pdb=" O LYS A2800 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TYR A2805 " --> pdb=" O ASP A2801 " (cutoff:3.500A) Proline residue: A2808 - end of helix Processing helix chain 'A' and resid 2861 through 2865 removed outlier: 3.546A pdb=" N VAL A2865 " --> pdb=" O LEU A2862 " (cutoff:3.500A) Processing helix chain 'A' and resid 2868 through 2898 removed outlier: 4.305A pdb=" N GLU A2876 " --> pdb=" O GLN A2872 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN A2877 " --> pdb=" O ALA A2873 " (cutoff:3.500A) Processing helix chain 'A' and resid 2912 through 2933 removed outlier: 3.740A pdb=" N ARG A2918 " --> pdb=" O LYS A2914 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASP A2919 " --> pdb=" O GLU A2915 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU A2925 " --> pdb=" O GLU A2921 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE A2929 " --> pdb=" O GLU A2925 " (cutoff:3.500A) Processing helix chain 'A' and resid 3018 through 3039 removed outlier: 3.636A pdb=" N SER A3032 " --> pdb=" O GLY A3028 " (cutoff:3.500A) Processing helix chain 'A' and resid 3044 through 3061 Processing helix chain 'A' and resid 3071 through 3090 Proline residue: A3085 - end of helix Processing helix chain 'A' and resid 3099 through 3114 Processing helix chain 'A' and resid 3133 through 3152 Proline residue: A3138 - end of helix Processing helix chain 'A' and resid 3159 through 3178 removed outlier: 3.869A pdb=" N CYS A3170 " --> pdb=" O TYR A3166 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER A3171 " --> pdb=" O ARG A3167 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A3172 " --> pdb=" O THR A3168 " (cutoff:3.500A) Processing helix chain 'A' and resid 3185 through 3200 Processing helix chain 'A' and resid 3205 through 3217 Processing helix chain 'A' and resid 3274 through 3288 Proline residue: A3282 - end of helix Processing helix chain 'A' and resid 3294 through 3300 removed outlier: 3.630A pdb=" N ALA A3298 " --> pdb=" O PRO A3294 " (cutoff:3.500A) Processing helix chain 'A' and resid 3300 through 3313 Processing helix chain 'A' and resid 3322 through 3339 Processing helix chain 'A' and resid 3348 through 3363 Proline residue: A3360 - end of helix Processing helix chain 'A' and resid 3368 through 3389 Processing helix chain 'A' and resid 3407 through 3433 Proline residue: A3427 - end of helix Processing helix chain 'A' and resid 3438 through 3454 Processing helix chain 'A' and resid 3455 through 3470 Processing helix chain 'A' and resid 3476 through 3488 Processing helix chain 'A' and resid 3514 through 3526 Proline residue: A3519 - end of helix Processing helix chain 'A' and resid 3553 through 3572 Proline residue: A3567 - end of helix Processing helix chain 'A' and resid 3646 through 3663 Processing helix chain 'A' and resid 3668 through 3679 Processing helix chain 'A' and resid 3699 through 3709 Processing helix chain 'A' and resid 3719 through 3733 Processing helix chain 'A' and resid 3753 through 3773 Processing helix chain 'A' and resid 3774 through 3787 removed outlier: 4.037A pdb=" N LYS A3787 " --> pdb=" O ILE A3783 " (cutoff:3.500A) Processing helix chain 'A' and resid 3791 through 3805 Processing helix chain 'A' and resid 3809 through 3824 Processing helix chain 'A' and resid 3827 through 3837 Processing helix chain 'A' and resid 3843 through 3852 Processing helix chain 'A' and resid 3878 through 3892 removed outlier: 4.119A pdb=" N GLN A3882 " --> pdb=" O ASP A3878 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS A3892 " --> pdb=" O LEU A3888 " (cutoff:3.500A) Processing helix chain 'A' and resid 3896 through 3905 Processing helix chain 'A' and resid 3915 through 3938 Processing helix chain 'A' and resid 3946 through 3971 removed outlier: 3.667A pdb=" N GLY A3971 " --> pdb=" O GLU A3967 " (cutoff:3.500A) Processing helix chain 'A' and resid 3973 through 3984 removed outlier: 4.108A pdb=" N ARG A3984 " --> pdb=" O LEU A3980 " (cutoff:3.500A) Processing helix chain 'A' and resid 3988 through 4003 removed outlier: 3.551A pdb=" N HIS A3998 " --> pdb=" O HIS A3994 " (cutoff:3.500A) Processing helix chain 'A' and resid 4009 through 4032 removed outlier: 3.921A pdb=" N LEU A4031 " --> pdb=" O LEU A4027 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU A4032 " --> pdb=" O LEU A4028 " (cutoff:3.500A) Processing helix chain 'A' and resid 4038 through 4051 Processing helix chain 'A' and resid 4052 through 4074 Processing helix chain 'A' and resid 4074 through 4081 removed outlier: 3.949A pdb=" N VAL A4081 " --> pdb=" O PHE A4077 " (cutoff:3.500A) Processing helix chain 'A' and resid 4088 through 4100 Processing helix chain 'A' and resid 4104 through 4115 Processing helix chain 'A' and resid 4125 through 4154 Proline residue: A4135 - end of helix removed outlier: 3.666A pdb=" N PHE A4141 " --> pdb=" O ARG A4137 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ASN A4142 " --> pdb=" O ASP A4138 " (cutoff:3.500A) Processing helix chain 'A' and resid 4157 through 4167 removed outlier: 3.534A pdb=" N ARG A4161 " --> pdb=" O ASP A4157 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA A4167 " --> pdb=" O PHE A4163 " (cutoff:3.500A) Processing helix chain 'A' and resid 4168 through 4178 removed outlier: 3.663A pdb=" N TYR A4173 " --> pdb=" O SER A4169 " (cutoff:3.500A) Proline residue: A4176 - end of helix Processing helix chain 'A' and resid 4198 through 4206 Processing helix chain 'A' and resid 4207 through 4224 Processing helix chain 'A' and resid 4230 through 4251 Processing helix chain 'A' and resid 4541 through 4579 removed outlier: 4.136A pdb=" N ARG A4557 " --> pdb=" O ASN A4553 " (cutoff:3.500A) Processing helix chain 'A' and resid 4638 through 4684 removed outlier: 3.685A pdb=" N ILE A4659 " --> pdb=" O PHE A4655 " (cutoff:3.500A) Proline residue: A4667 - end of helix removed outlier: 3.772A pdb=" N LYS A4672 " --> pdb=" O LEU A4668 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A4683 " --> pdb=" O ARG A4679 " (cutoff:3.500A) Processing helix chain 'A' and resid 4686 through 4691 Processing helix chain 'A' and resid 4698 through 4706 Processing helix chain 'A' and resid 4718 through 4728 removed outlier: 3.526A pdb=" N HIS A4728 " --> pdb=" O VAL A4724 " (cutoff:3.500A) Processing helix chain 'A' and resid 4732 through 4740 removed outlier: 3.920A pdb=" N ARG A4736 " --> pdb=" O PHE A4732 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE A4737 " --> pdb=" O GLY A4733 " (cutoff:3.500A) Processing helix chain 'A' and resid 4773 through 4786 removed outlier: 3.641A pdb=" N ASP A4786 " --> pdb=" O VAL A4782 " (cutoff:3.500A) Processing helix chain 'A' and resid 4786 through 4805 Processing helix chain 'A' and resid 4805 through 4818 removed outlier: 3.614A pdb=" N PHE A4809 " --> pdb=" O ASN A4805 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N MET A4818 " --> pdb=" O LEU A4814 " (cutoff:3.500A) Processing helix chain 'A' and resid 4820 through 4831 Processing helix chain 'A' and resid 4836 through 4859 Processing helix chain 'A' and resid 4878 through 4892 Processing helix chain 'A' and resid 4896 through 4901 Processing helix chain 'A' and resid 4909 through 4957 removed outlier: 3.643A pdb=" N VAL A4924 " --> pdb=" O PHE A4920 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ILE A4925 " --> pdb=" O PHE A4921 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL A4926 " --> pdb=" O PHE A4922 " (cutoff:3.500A) Processing helix chain 'A' and resid 4965 through 4970 Processing helix chain 'A' and resid 4973 through 4982 Processing helix chain 'A' and resid 4985 through 4997 removed outlier: 3.728A pdb=" N ASN A4997 " --> pdb=" O MET A4993 " (cutoff:3.500A) Processing helix chain 'A' and resid 4998 through 5006 Processing helix chain 'A' and resid 5008 through 5017 removed outlier: 4.269A pdb=" N ARG A5017 " --> pdb=" O MET A5013 " (cutoff:3.500A) Processing helix chain 'A' and resid 5027 through 5032 Processing helix chain 'B' and resid 74 through 84 Processing helix chain 'B' and resid 250 through 256 removed outlier: 4.170A pdb=" N THR B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 311 Processing helix chain 'B' and resid 394 through 421 removed outlier: 4.028A pdb=" N SER B 398 " --> pdb=" O GLN B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 452 Processing helix chain 'B' and resid 462 through 482 removed outlier: 3.613A pdb=" N ARG B 469 " --> pdb=" O GLN B 465 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU B 480 " --> pdb=" O SER B 476 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 498 removed outlier: 3.946A pdb=" N LEU B 488 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG B 493 " --> pdb=" O ASN B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 505 Processing helix chain 'B' and resid 510 through 531 removed outlier: 3.909A pdb=" N TYR B 523 " --> pdb=" O VAL B 519 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLU B 524 " --> pdb=" O ASN B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 552 removed outlier: 3.592A pdb=" N ALA B 538 " --> pdb=" O ARG B 534 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N THR B 542 " --> pdb=" O ALA B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 571 removed outlier: 3.821A pdb=" N ILE B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 577 removed outlier: 3.554A pdb=" N LEU B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 593 Processing helix chain 'B' and resid 598 through 607 Processing helix chain 'B' and resid 614 through 629 Proline residue: B 627 - end of helix Processing helix chain 'B' and resid 699 through 703 Processing helix chain 'B' and resid 865 through 887 removed outlier: 3.737A pdb=" N THR B 885 " --> pdb=" O LEU B 881 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG B 886 " --> pdb=" O TRP B 882 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 936 Processing helix chain 'B' and resid 979 through 1003 Processing helix chain 'B' and resid 1023 through 1028 Processing helix chain 'B' and resid 1028 through 1050 Processing helix chain 'B' and resid 1215 through 1222 Processing helix chain 'B' and resid 1578 through 1585 Processing helix chain 'B' and resid 1649 through 1656 Processing helix chain 'B' and resid 1656 through 1675 Processing helix chain 'B' and resid 1679 through 1687 Processing helix chain 'B' and resid 1690 through 1700 Processing helix chain 'B' and resid 1704 through 1720 removed outlier: 4.435A pdb=" N LEU B1720 " --> pdb=" O ILE B1716 " (cutoff:3.500A) Processing helix chain 'B' and resid 1721 through 1732 Processing helix chain 'B' and resid 1739 through 1745 removed outlier: 3.863A pdb=" N ILE B1745 " --> pdb=" O GLU B1741 " (cutoff:3.500A) Processing helix chain 'B' and resid 1803 through 1822 removed outlier: 3.502A pdb=" N GLY B1816 " --> pdb=" O LEU B1812 " (cutoff:3.500A) Processing helix chain 'B' and resid 1833 through 1852 Proline residue: B1840 - end of helix Processing helix chain 'B' and resid 1855 through 1867 removed outlier: 3.887A pdb=" N GLU B1867 " --> pdb=" O LEU B1863 " (cutoff:3.500A) Processing helix chain 'B' and resid 1932 through 1976 removed outlier: 3.578A pdb=" N GLN B1949 " --> pdb=" O TYR B1945 " (cutoff:3.500A) Processing helix chain 'B' and resid 2034 through 2047 Processing helix chain 'B' and resid 2059 through 2072 Processing helix chain 'B' and resid 2094 through 2108 Processing helix chain 'B' and resid 2113 through 2130 removed outlier: 3.609A pdb=" N VAL B2117 " --> pdb=" O SER B2113 " (cutoff:3.500A) Processing helix chain 'B' and resid 2131 through 2141 Proline residue: B2139 - end of helix Processing helix chain 'B' and resid 2149 through 2168 Processing helix chain 'B' and resid 2173 through 2189 Processing helix chain 'B' and resid 2193 through 2198 Processing helix chain 'B' and resid 2201 through 2216 Processing helix chain 'B' and resid 2227 through 2243 removed outlier: 3.729A pdb=" N ILE B2242 " --> pdb=" O TYR B2238 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER B2243 " --> pdb=" O PHE B2239 " (cutoff:3.500A) Processing helix chain 'B' and resid 2243 through 2262 Processing helix chain 'B' and resid 2283 through 2290 removed outlier: 3.738A pdb=" N ALA B2287 " --> pdb=" O ASN B2283 " (cutoff:3.500A) Processing helix chain 'B' and resid 2291 through 2305 removed outlier: 3.825A pdb=" N LEU B2295 " --> pdb=" O GLN B2291 " (cutoff:3.500A) Processing helix chain 'B' and resid 2326 through 2340 Processing helix chain 'B' and resid 2346 through 2360 Processing helix chain 'B' and resid 2376 through 2386 Processing helix chain 'B' and resid 2426 through 2440 Proline residue: B2438 - end of helix Processing helix chain 'B' and resid 2450 through 2460 Processing helix chain 'B' and resid 2464 through 2476 Proline residue: B2473 - end of helix Processing helix chain 'B' and resid 2499 through 2510 Processing helix chain 'B' and resid 2518 through 2537 removed outlier: 3.577A pdb=" N VAL B2524 " --> pdb=" O HIS B2520 " (cutoff:3.500A) Proline residue: B2528 - end of helix removed outlier: 3.903A pdb=" N ARG B2531 " --> pdb=" O LEU B2527 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA B2532 " --> pdb=" O PRO B2528 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA B2533 " --> pdb=" O ASP B2529 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA B2534 " --> pdb=" O MET B2530 " (cutoff:3.500A) Processing helix chain 'B' and resid 2544 through 2562 removed outlier: 3.539A pdb=" N VAL B2558 " --> pdb=" O LEU B2554 " (cutoff:3.500A) Proline residue: B2560 - end of helix Processing helix chain 'B' and resid 2568 through 2586 Processing helix chain 'B' and resid 2592 through 2609 Processing helix chain 'B' and resid 2616 through 2634 Proline residue: B2631 - end of helix Processing helix chain 'B' and resid 2639 through 2656 Processing helix chain 'B' and resid 2668 through 2686 Processing helix chain 'B' and resid 2692 through 2710 Proline residue: B2701 - end of helix Processing helix chain 'B' and resid 2748 through 2773 removed outlier: 3.553A pdb=" N LYS B2757 " --> pdb=" O SER B2753 " (cutoff:3.500A) Processing helix chain 'B' and resid 2798 through 2819 removed outlier: 4.014A pdb=" N ILE B2804 " --> pdb=" O LYS B2800 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TYR B2805 " --> pdb=" O ASP B2801 " (cutoff:3.500A) Proline residue: B2808 - end of helix Processing helix chain 'B' and resid 2861 through 2865 removed outlier: 3.547A pdb=" N VAL B2865 " --> pdb=" O LEU B2862 " (cutoff:3.500A) Processing helix chain 'B' and resid 2868 through 2898 removed outlier: 4.305A pdb=" N GLU B2876 " --> pdb=" O GLN B2872 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN B2877 " --> pdb=" O ALA B2873 " (cutoff:3.500A) Processing helix chain 'B' and resid 2912 through 2933 removed outlier: 3.741A pdb=" N ARG B2918 " --> pdb=" O LYS B2914 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASP B2919 " --> pdb=" O GLU B2915 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU B2925 " --> pdb=" O GLU B2921 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE B2929 " --> pdb=" O GLU B2925 " (cutoff:3.500A) Processing helix chain 'B' and resid 3018 through 3039 removed outlier: 3.636A pdb=" N SER B3032 " --> pdb=" O GLY B3028 " (cutoff:3.500A) Processing helix chain 'B' and resid 3044 through 3061 Processing helix chain 'B' and resid 3071 through 3090 Proline residue: B3085 - end of helix Processing helix chain 'B' and resid 3099 through 3114 Processing helix chain 'B' and resid 3133 through 3152 Proline residue: B3138 - end of helix Processing helix chain 'B' and resid 3159 through 3178 removed outlier: 3.869A pdb=" N CYS B3170 " --> pdb=" O TYR B3166 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER B3171 " --> pdb=" O ARG B3167 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B3172 " --> pdb=" O THR B3168 " (cutoff:3.500A) Processing helix chain 'B' and resid 3185 through 3200 Processing helix chain 'B' and resid 3205 through 3217 Processing helix chain 'B' and resid 3274 through 3288 Proline residue: B3282 - end of helix Processing helix chain 'B' and resid 3294 through 3300 removed outlier: 3.630A pdb=" N ALA B3298 " --> pdb=" O PRO B3294 " (cutoff:3.500A) Processing helix chain 'B' and resid 3300 through 3313 Processing helix chain 'B' and resid 3322 through 3339 Processing helix chain 'B' and resid 3348 through 3363 Proline residue: B3360 - end of helix Processing helix chain 'B' and resid 3368 through 3389 Processing helix chain 'B' and resid 3407 through 3433 Proline residue: B3427 - end of helix Processing helix chain 'B' and resid 3438 through 3454 Processing helix chain 'B' and resid 3455 through 3470 Processing helix chain 'B' and resid 3476 through 3488 Processing helix chain 'B' and resid 3514 through 3526 Proline residue: B3519 - end of helix Processing helix chain 'B' and resid 3553 through 3572 Proline residue: B3567 - end of helix Processing helix chain 'B' and resid 3646 through 3663 Processing helix chain 'B' and resid 3668 through 3679 Processing helix chain 'B' and resid 3699 through 3709 Processing helix chain 'B' and resid 3719 through 3733 Processing helix chain 'B' and resid 3753 through 3773 Processing helix chain 'B' and resid 3774 through 3787 removed outlier: 4.036A pdb=" N LYS B3787 " --> pdb=" O ILE B3783 " (cutoff:3.500A) Processing helix chain 'B' and resid 3791 through 3805 Processing helix chain 'B' and resid 3809 through 3824 Processing helix chain 'B' and resid 3827 through 3837 Processing helix chain 'B' and resid 3843 through 3852 Processing helix chain 'B' and resid 3878 through 3892 removed outlier: 4.119A pdb=" N GLN B3882 " --> pdb=" O ASP B3878 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS B3892 " --> pdb=" O LEU B3888 " (cutoff:3.500A) Processing helix chain 'B' and resid 3896 through 3905 Processing helix chain 'B' and resid 3915 through 3938 Processing helix chain 'B' and resid 3946 through 3971 removed outlier: 3.668A pdb=" N GLY B3971 " --> pdb=" O GLU B3967 " (cutoff:3.500A) Processing helix chain 'B' and resid 3973 through 3984 removed outlier: 4.108A pdb=" N ARG B3984 " --> pdb=" O LEU B3980 " (cutoff:3.500A) Processing helix chain 'B' and resid 3988 through 4003 removed outlier: 3.551A pdb=" N HIS B3998 " --> pdb=" O HIS B3994 " (cutoff:3.500A) Processing helix chain 'B' and resid 4009 through 4032 removed outlier: 3.920A pdb=" N LEU B4031 " --> pdb=" O LEU B4027 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU B4032 " --> pdb=" O LEU B4028 " (cutoff:3.500A) Processing helix chain 'B' and resid 4038 through 4051 Processing helix chain 'B' and resid 4052 through 4074 Processing helix chain 'B' and resid 4074 through 4081 removed outlier: 3.949A pdb=" N VAL B4081 " --> pdb=" O PHE B4077 " (cutoff:3.500A) Processing helix chain 'B' and resid 4088 through 4100 Processing helix chain 'B' and resid 4104 through 4115 Processing helix chain 'B' and resid 4125 through 4154 Proline residue: B4135 - end of helix removed outlier: 3.666A pdb=" N PHE B4141 " --> pdb=" O ARG B4137 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ASN B4142 " --> pdb=" O ASP B4138 " (cutoff:3.500A) Processing helix chain 'B' and resid 4157 through 4167 removed outlier: 3.534A pdb=" N ARG B4161 " --> pdb=" O ASP B4157 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA B4167 " --> pdb=" O PHE B4163 " (cutoff:3.500A) Processing helix chain 'B' and resid 4168 through 4178 removed outlier: 3.663A pdb=" N TYR B4173 " --> pdb=" O SER B4169 " (cutoff:3.500A) Proline residue: B4176 - end of helix Processing helix chain 'B' and resid 4198 through 4206 Processing helix chain 'B' and resid 4207 through 4224 Processing helix chain 'B' and resid 4230 through 4251 Processing helix chain 'B' and resid 4541 through 4579 removed outlier: 4.136A pdb=" N ARG B4557 " --> pdb=" O ASN B4553 " (cutoff:3.500A) Processing helix chain 'B' and resid 4638 through 4684 removed outlier: 3.684A pdb=" N ILE B4659 " --> pdb=" O PHE B4655 " (cutoff:3.500A) Proline residue: B4667 - end of helix removed outlier: 3.772A pdb=" N LYS B4672 " --> pdb=" O LEU B4668 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE B4683 " --> pdb=" O ARG B4679 " (cutoff:3.500A) Processing helix chain 'B' and resid 4686 through 4691 Processing helix chain 'B' and resid 4698 through 4706 Processing helix chain 'B' and resid 4718 through 4728 removed outlier: 3.527A pdb=" N HIS B4728 " --> pdb=" O VAL B4724 " (cutoff:3.500A) Processing helix chain 'B' and resid 4732 through 4740 removed outlier: 3.921A pdb=" N ARG B4736 " --> pdb=" O PHE B4732 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE B4737 " --> pdb=" O GLY B4733 " (cutoff:3.500A) Processing helix chain 'B' and resid 4773 through 4786 removed outlier: 3.642A pdb=" N ASP B4786 " --> pdb=" O VAL B4782 " (cutoff:3.500A) Processing helix chain 'B' and resid 4786 through 4805 Processing helix chain 'B' and resid 4805 through 4818 removed outlier: 3.613A pdb=" N PHE B4809 " --> pdb=" O ASN B4805 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N MET B4818 " --> pdb=" O LEU B4814 " (cutoff:3.500A) Processing helix chain 'B' and resid 4820 through 4831 Processing helix chain 'B' and resid 4836 through 4859 Processing helix chain 'B' and resid 4878 through 4892 Processing helix chain 'B' and resid 4896 through 4901 Processing helix chain 'B' and resid 4909 through 4957 removed outlier: 3.643A pdb=" N VAL B4924 " --> pdb=" O PHE B4920 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ILE B4925 " --> pdb=" O PHE B4921 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL B4926 " --> pdb=" O PHE B4922 " (cutoff:3.500A) Processing helix chain 'B' and resid 4965 through 4970 Processing helix chain 'B' and resid 4973 through 4982 Processing helix chain 'B' and resid 4985 through 4997 Processing helix chain 'B' and resid 4998 through 5006 Processing helix chain 'B' and resid 5008 through 5017 removed outlier: 4.269A pdb=" N ARG B5017 " --> pdb=" O MET B5013 " (cutoff:3.500A) Processing helix chain 'B' and resid 5027 through 5032 Processing helix chain 'C' and resid 74 through 84 Processing helix chain 'C' and resid 250 through 256 removed outlier: 4.170A pdb=" N THR C 254 " --> pdb=" O GLY C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 311 Processing helix chain 'C' and resid 394 through 421 removed outlier: 4.028A pdb=" N SER C 398 " --> pdb=" O GLN C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 452 Processing helix chain 'C' and resid 462 through 482 removed outlier: 3.613A pdb=" N ARG C 469 " --> pdb=" O GLN C 465 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU C 480 " --> pdb=" O SER C 476 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU C 481 " --> pdb=" O LEU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 498 removed outlier: 3.946A pdb=" N LEU C 488 " --> pdb=" O LEU C 484 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG C 493 " --> pdb=" O ASN C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 505 Processing helix chain 'C' and resid 510 through 531 removed outlier: 3.909A pdb=" N TYR C 523 " --> pdb=" O VAL C 519 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLU C 524 " --> pdb=" O ASN C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 552 removed outlier: 3.592A pdb=" N ALA C 538 " --> pdb=" O ARG C 534 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N THR C 542 " --> pdb=" O ALA C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 571 removed outlier: 3.821A pdb=" N ILE C 560 " --> pdb=" O ALA C 556 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER C 571 " --> pdb=" O VAL C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 577 removed outlier: 3.553A pdb=" N LEU C 575 " --> pdb=" O SER C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 593 Processing helix chain 'C' and resid 598 through 607 Processing helix chain 'C' and resid 614 through 629 Proline residue: C 627 - end of helix Processing helix chain 'C' and resid 699 through 703 Processing helix chain 'C' and resid 865 through 887 removed outlier: 3.738A pdb=" N THR C 885 " --> pdb=" O LEU C 881 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG C 886 " --> pdb=" O TRP C 882 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 936 Processing helix chain 'C' and resid 979 through 1003 Processing helix chain 'C' and resid 1023 through 1028 Processing helix chain 'C' and resid 1028 through 1050 Processing helix chain 'C' and resid 1215 through 1222 Processing helix chain 'C' and resid 1578 through 1585 Processing helix chain 'C' and resid 1649 through 1656 Processing helix chain 'C' and resid 1656 through 1675 Processing helix chain 'C' and resid 1679 through 1687 Processing helix chain 'C' and resid 1690 through 1700 Processing helix chain 'C' and resid 1704 through 1720 removed outlier: 4.435A pdb=" N LEU C1720 " --> pdb=" O ILE C1716 " (cutoff:3.500A) Processing helix chain 'C' and resid 1721 through 1732 Processing helix chain 'C' and resid 1739 through 1745 removed outlier: 3.863A pdb=" N ILE C1745 " --> pdb=" O GLU C1741 " (cutoff:3.500A) Processing helix chain 'C' and resid 1803 through 1822 removed outlier: 3.502A pdb=" N GLY C1816 " --> pdb=" O LEU C1812 " (cutoff:3.500A) Processing helix chain 'C' and resid 1833 through 1852 Proline residue: C1840 - end of helix Processing helix chain 'C' and resid 1855 through 1867 removed outlier: 3.887A pdb=" N GLU C1867 " --> pdb=" O LEU C1863 " (cutoff:3.500A) Processing helix chain 'C' and resid 1932 through 1976 removed outlier: 3.578A pdb=" N GLN C1949 " --> pdb=" O TYR C1945 " (cutoff:3.500A) Processing helix chain 'C' and resid 2034 through 2047 Processing helix chain 'C' and resid 2059 through 2072 Processing helix chain 'C' and resid 2094 through 2108 Processing helix chain 'C' and resid 2113 through 2130 removed outlier: 3.609A pdb=" N VAL C2117 " --> pdb=" O SER C2113 " (cutoff:3.500A) Processing helix chain 'C' and resid 2131 through 2141 Proline residue: C2139 - end of helix Processing helix chain 'C' and resid 2149 through 2168 Processing helix chain 'C' and resid 2173 through 2189 Processing helix chain 'C' and resid 2193 through 2198 Processing helix chain 'C' and resid 2201 through 2216 Processing helix chain 'C' and resid 2227 through 2243 removed outlier: 3.729A pdb=" N ILE C2242 " --> pdb=" O TYR C2238 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER C2243 " --> pdb=" O PHE C2239 " (cutoff:3.500A) Processing helix chain 'C' and resid 2243 through 2262 Processing helix chain 'C' and resid 2283 through 2290 removed outlier: 3.738A pdb=" N ALA C2287 " --> pdb=" O ASN C2283 " (cutoff:3.500A) Processing helix chain 'C' and resid 2291 through 2305 removed outlier: 3.825A pdb=" N LEU C2295 " --> pdb=" O GLN C2291 " (cutoff:3.500A) Processing helix chain 'C' and resid 2326 through 2340 Processing helix chain 'C' and resid 2346 through 2360 Processing helix chain 'C' and resid 2376 through 2386 Processing helix chain 'C' and resid 2426 through 2440 Proline residue: C2438 - end of helix Processing helix chain 'C' and resid 2450 through 2460 Processing helix chain 'C' and resid 2464 through 2476 Proline residue: C2473 - end of helix Processing helix chain 'C' and resid 2499 through 2510 Processing helix chain 'C' and resid 2518 through 2537 removed outlier: 3.577A pdb=" N VAL C2524 " --> pdb=" O HIS C2520 " (cutoff:3.500A) Proline residue: C2528 - end of helix removed outlier: 3.904A pdb=" N ARG C2531 " --> pdb=" O LEU C2527 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA C2532 " --> pdb=" O PRO C2528 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA C2533 " --> pdb=" O ASP C2529 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA C2534 " --> pdb=" O MET C2530 " (cutoff:3.500A) Processing helix chain 'C' and resid 2544 through 2562 removed outlier: 3.538A pdb=" N VAL C2558 " --> pdb=" O LEU C2554 " (cutoff:3.500A) Proline residue: C2560 - end of helix Processing helix chain 'C' and resid 2568 through 2586 Processing helix chain 'C' and resid 2592 through 2609 Processing helix chain 'C' and resid 2616 through 2634 Proline residue: C2631 - end of helix Processing helix chain 'C' and resid 2639 through 2656 Processing helix chain 'C' and resid 2668 through 2686 Processing helix chain 'C' and resid 2692 through 2710 Proline residue: C2701 - end of helix Processing helix chain 'C' and resid 2748 through 2773 removed outlier: 3.554A pdb=" N LYS C2757 " --> pdb=" O SER C2753 " (cutoff:3.500A) Processing helix chain 'C' and resid 2798 through 2819 removed outlier: 4.014A pdb=" N ILE C2804 " --> pdb=" O LYS C2800 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR C2805 " --> pdb=" O ASP C2801 " (cutoff:3.500A) Proline residue: C2808 - end of helix Processing helix chain 'C' and resid 2861 through 2865 removed outlier: 3.546A pdb=" N VAL C2865 " --> pdb=" O LEU C2862 " (cutoff:3.500A) Processing helix chain 'C' and resid 2868 through 2898 removed outlier: 4.305A pdb=" N GLU C2876 " --> pdb=" O GLN C2872 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN C2877 " --> pdb=" O ALA C2873 " (cutoff:3.500A) Processing helix chain 'C' and resid 2912 through 2933 removed outlier: 3.740A pdb=" N ARG C2918 " --> pdb=" O LYS C2914 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASP C2919 " --> pdb=" O GLU C2915 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU C2925 " --> pdb=" O GLU C2921 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE C2929 " --> pdb=" O GLU C2925 " (cutoff:3.500A) Processing helix chain 'C' and resid 3018 through 3039 removed outlier: 3.636A pdb=" N SER C3032 " --> pdb=" O GLY C3028 " (cutoff:3.500A) Processing helix chain 'C' and resid 3044 through 3061 Processing helix chain 'C' and resid 3071 through 3090 Proline residue: C3085 - end of helix Processing helix chain 'C' and resid 3099 through 3114 Processing helix chain 'C' and resid 3133 through 3152 Proline residue: C3138 - end of helix Processing helix chain 'C' and resid 3159 through 3178 removed outlier: 3.868A pdb=" N CYS C3170 " --> pdb=" O TYR C3166 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER C3171 " --> pdb=" O ARG C3167 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE C3172 " --> pdb=" O THR C3168 " (cutoff:3.500A) Processing helix chain 'C' and resid 3185 through 3200 Processing helix chain 'C' and resid 3205 through 3217 Processing helix chain 'C' and resid 3274 through 3288 Proline residue: C3282 - end of helix Processing helix chain 'C' and resid 3294 through 3300 removed outlier: 3.630A pdb=" N ALA C3298 " --> pdb=" O PRO C3294 " (cutoff:3.500A) Processing helix chain 'C' and resid 3300 through 3313 Processing helix chain 'C' and resid 3322 through 3339 Processing helix chain 'C' and resid 3348 through 3363 Proline residue: C3360 - end of helix Processing helix chain 'C' and resid 3368 through 3389 Processing helix chain 'C' and resid 3407 through 3433 Proline residue: C3427 - end of helix Processing helix chain 'C' and resid 3438 through 3454 Processing helix chain 'C' and resid 3455 through 3470 Processing helix chain 'C' and resid 3476 through 3488 Processing helix chain 'C' and resid 3514 through 3526 Proline residue: C3519 - end of helix Processing helix chain 'C' and resid 3553 through 3572 Proline residue: C3567 - end of helix Processing helix chain 'C' and resid 3646 through 3663 Processing helix chain 'C' and resid 3668 through 3679 Processing helix chain 'C' and resid 3699 through 3709 Processing helix chain 'C' and resid 3719 through 3733 Processing helix chain 'C' and resid 3753 through 3773 Processing helix chain 'C' and resid 3774 through 3787 removed outlier: 4.037A pdb=" N LYS C3787 " --> pdb=" O ILE C3783 " (cutoff:3.500A) Processing helix chain 'C' and resid 3791 through 3805 Processing helix chain 'C' and resid 3809 through 3824 Processing helix chain 'C' and resid 3827 through 3837 Processing helix chain 'C' and resid 3843 through 3852 Processing helix chain 'C' and resid 3878 through 3892 removed outlier: 4.120A pdb=" N GLN C3882 " --> pdb=" O ASP C3878 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS C3892 " --> pdb=" O LEU C3888 " (cutoff:3.500A) Processing helix chain 'C' and resid 3896 through 3905 Processing helix chain 'C' and resid 3915 through 3938 Processing helix chain 'C' and resid 3946 through 3971 removed outlier: 3.668A pdb=" N GLY C3971 " --> pdb=" O GLU C3967 " (cutoff:3.500A) Processing helix chain 'C' and resid 3973 through 3984 removed outlier: 4.108A pdb=" N ARG C3984 " --> pdb=" O LEU C3980 " (cutoff:3.500A) Processing helix chain 'C' and resid 3988 through 4003 removed outlier: 3.550A pdb=" N HIS C3998 " --> pdb=" O HIS C3994 " (cutoff:3.500A) Processing helix chain 'C' and resid 4009 through 4032 removed outlier: 3.920A pdb=" N LEU C4031 " --> pdb=" O LEU C4027 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU C4032 " --> pdb=" O LEU C4028 " (cutoff:3.500A) Processing helix chain 'C' and resid 4038 through 4051 Processing helix chain 'C' and resid 4052 through 4074 Processing helix chain 'C' and resid 4074 through 4081 removed outlier: 3.949A pdb=" N VAL C4081 " --> pdb=" O PHE C4077 " (cutoff:3.500A) Processing helix chain 'C' and resid 4088 through 4100 Processing helix chain 'C' and resid 4104 through 4115 Processing helix chain 'C' and resid 4125 through 4154 Proline residue: C4135 - end of helix removed outlier: 3.666A pdb=" N PHE C4141 " --> pdb=" O ARG C4137 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASN C4142 " --> pdb=" O ASP C4138 " (cutoff:3.500A) Processing helix chain 'C' and resid 4157 through 4167 removed outlier: 3.534A pdb=" N ARG C4161 " --> pdb=" O ASP C4157 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA C4167 " --> pdb=" O PHE C4163 " (cutoff:3.500A) Processing helix chain 'C' and resid 4168 through 4178 removed outlier: 3.663A pdb=" N TYR C4173 " --> pdb=" O SER C4169 " (cutoff:3.500A) Proline residue: C4176 - end of helix Processing helix chain 'C' and resid 4198 through 4206 Processing helix chain 'C' and resid 4207 through 4224 Processing helix chain 'C' and resid 4230 through 4251 Processing helix chain 'C' and resid 4541 through 4579 removed outlier: 4.136A pdb=" N ARG C4557 " --> pdb=" O ASN C4553 " (cutoff:3.500A) Processing helix chain 'C' and resid 4638 through 4684 removed outlier: 3.684A pdb=" N ILE C4659 " --> pdb=" O PHE C4655 " (cutoff:3.500A) Proline residue: C4667 - end of helix removed outlier: 3.772A pdb=" N LYS C4672 " --> pdb=" O LEU C4668 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE C4683 " --> pdb=" O ARG C4679 " (cutoff:3.500A) Processing helix chain 'C' and resid 4686 through 4691 Processing helix chain 'C' and resid 4698 through 4706 Processing helix chain 'C' and resid 4718 through 4728 removed outlier: 3.526A pdb=" N HIS C4728 " --> pdb=" O VAL C4724 " (cutoff:3.500A) Processing helix chain 'C' and resid 4732 through 4740 removed outlier: 3.920A pdb=" N ARG C4736 " --> pdb=" O PHE C4732 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE C4737 " --> pdb=" O GLY C4733 " (cutoff:3.500A) Processing helix chain 'C' and resid 4773 through 4786 removed outlier: 3.642A pdb=" N ASP C4786 " --> pdb=" O VAL C4782 " (cutoff:3.500A) Processing helix chain 'C' and resid 4786 through 4805 Processing helix chain 'C' and resid 4805 through 4818 removed outlier: 3.614A pdb=" N PHE C4809 " --> pdb=" O ASN C4805 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N MET C4818 " --> pdb=" O LEU C4814 " (cutoff:3.500A) Processing helix chain 'C' and resid 4820 through 4831 Processing helix chain 'C' and resid 4836 through 4859 Processing helix chain 'C' and resid 4878 through 4892 Processing helix chain 'C' and resid 4896 through 4901 Processing helix chain 'C' and resid 4909 through 4957 removed outlier: 3.643A pdb=" N VAL C4924 " --> pdb=" O PHE C4920 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ILE C4925 " --> pdb=" O PHE C4921 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL C4926 " --> pdb=" O PHE C4922 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU C4955 " --> pdb=" O LYS C4951 " (cutoff:3.500A) Processing helix chain 'C' and resid 4965 through 4970 Processing helix chain 'C' and resid 4973 through 4982 Processing helix chain 'C' and resid 4985 through 4997 Processing helix chain 'C' and resid 4998 through 5006 Processing helix chain 'C' and resid 5008 through 5017 removed outlier: 4.270A pdb=" N ARG C5017 " --> pdb=" O MET C5013 " (cutoff:3.500A) Processing helix chain 'C' and resid 5027 through 5032 Processing helix chain 'D' and resid 74 through 84 Processing helix chain 'D' and resid 250 through 256 removed outlier: 4.170A pdb=" N THR D 254 " --> pdb=" O GLY D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 311 Processing helix chain 'D' and resid 394 through 421 removed outlier: 4.028A pdb=" N SER D 398 " --> pdb=" O GLN D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 452 Processing helix chain 'D' and resid 462 through 482 removed outlier: 3.613A pdb=" N ARG D 469 " --> pdb=" O GLN D 465 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU D 480 " --> pdb=" O SER D 476 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU D 481 " --> pdb=" O LEU D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 498 removed outlier: 3.946A pdb=" N LEU D 488 " --> pdb=" O LEU D 484 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG D 493 " --> pdb=" O ASN D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 505 Processing helix chain 'D' and resid 510 through 531 removed outlier: 3.909A pdb=" N TYR D 523 " --> pdb=" O VAL D 519 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU D 524 " --> pdb=" O ASN D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 552 removed outlier: 3.592A pdb=" N ALA D 538 " --> pdb=" O ARG D 534 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR D 542 " --> pdb=" O ALA D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 571 removed outlier: 3.821A pdb=" N ILE D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER D 571 " --> pdb=" O VAL D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 577 removed outlier: 3.554A pdb=" N LEU D 575 " --> pdb=" O SER D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 593 Processing helix chain 'D' and resid 598 through 607 Processing helix chain 'D' and resid 614 through 629 Proline residue: D 627 - end of helix Processing helix chain 'D' and resid 699 through 703 Processing helix chain 'D' and resid 865 through 887 removed outlier: 3.738A pdb=" N THR D 885 " --> pdb=" O LEU D 881 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG D 886 " --> pdb=" O TRP D 882 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 936 Processing helix chain 'D' and resid 979 through 1003 Processing helix chain 'D' and resid 1023 through 1028 Processing helix chain 'D' and resid 1028 through 1050 Processing helix chain 'D' and resid 1215 through 1222 Processing helix chain 'D' and resid 1578 through 1585 Processing helix chain 'D' and resid 1649 through 1656 Processing helix chain 'D' and resid 1656 through 1675 Processing helix chain 'D' and resid 1679 through 1687 Processing helix chain 'D' and resid 1690 through 1700 Processing helix chain 'D' and resid 1704 through 1720 removed outlier: 4.435A pdb=" N LEU D1720 " --> pdb=" O ILE D1716 " (cutoff:3.500A) Processing helix chain 'D' and resid 1721 through 1732 Processing helix chain 'D' and resid 1739 through 1745 removed outlier: 3.863A pdb=" N ILE D1745 " --> pdb=" O GLU D1741 " (cutoff:3.500A) Processing helix chain 'D' and resid 1803 through 1822 removed outlier: 3.502A pdb=" N GLY D1816 " --> pdb=" O LEU D1812 " (cutoff:3.500A) Processing helix chain 'D' and resid 1833 through 1852 Proline residue: D1840 - end of helix Processing helix chain 'D' and resid 1855 through 1867 removed outlier: 3.887A pdb=" N GLU D1867 " --> pdb=" O LEU D1863 " (cutoff:3.500A) Processing helix chain 'D' and resid 1932 through 1976 removed outlier: 3.578A pdb=" N GLN D1949 " --> pdb=" O TYR D1945 " (cutoff:3.500A) Processing helix chain 'D' and resid 2034 through 2047 Processing helix chain 'D' and resid 2059 through 2072 Processing helix chain 'D' and resid 2094 through 2108 Processing helix chain 'D' and resid 2113 through 2130 removed outlier: 3.609A pdb=" N VAL D2117 " --> pdb=" O SER D2113 " (cutoff:3.500A) Processing helix chain 'D' and resid 2131 through 2141 Proline residue: D2139 - end of helix Processing helix chain 'D' and resid 2149 through 2168 Processing helix chain 'D' and resid 2173 through 2189 Processing helix chain 'D' and resid 2193 through 2198 Processing helix chain 'D' and resid 2201 through 2216 Processing helix chain 'D' and resid 2227 through 2243 removed outlier: 3.729A pdb=" N ILE D2242 " --> pdb=" O TYR D2238 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER D2243 " --> pdb=" O PHE D2239 " (cutoff:3.500A) Processing helix chain 'D' and resid 2243 through 2262 Processing helix chain 'D' and resid 2283 through 2290 removed outlier: 3.739A pdb=" N ALA D2287 " --> pdb=" O ASN D2283 " (cutoff:3.500A) Processing helix chain 'D' and resid 2291 through 2305 removed outlier: 3.825A pdb=" N LEU D2295 " --> pdb=" O GLN D2291 " (cutoff:3.500A) Processing helix chain 'D' and resid 2326 through 2340 Processing helix chain 'D' and resid 2346 through 2360 Processing helix chain 'D' and resid 2376 through 2386 Processing helix chain 'D' and resid 2426 through 2440 Proline residue: D2438 - end of helix Processing helix chain 'D' and resid 2450 through 2460 Processing helix chain 'D' and resid 2464 through 2476 Proline residue: D2473 - end of helix Processing helix chain 'D' and resid 2499 through 2510 Processing helix chain 'D' and resid 2518 through 2537 removed outlier: 3.577A pdb=" N VAL D2524 " --> pdb=" O HIS D2520 " (cutoff:3.500A) Proline residue: D2528 - end of helix removed outlier: 3.904A pdb=" N ARG D2531 " --> pdb=" O LEU D2527 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA D2532 " --> pdb=" O PRO D2528 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA D2533 " --> pdb=" O ASP D2529 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA D2534 " --> pdb=" O MET D2530 " (cutoff:3.500A) Processing helix chain 'D' and resid 2544 through 2562 removed outlier: 3.539A pdb=" N VAL D2558 " --> pdb=" O LEU D2554 " (cutoff:3.500A) Proline residue: D2560 - end of helix Processing helix chain 'D' and resid 2568 through 2586 Processing helix chain 'D' and resid 2592 through 2609 Processing helix chain 'D' and resid 2616 through 2634 Proline residue: D2631 - end of helix Processing helix chain 'D' and resid 2639 through 2656 Processing helix chain 'D' and resid 2668 through 2686 Processing helix chain 'D' and resid 2692 through 2710 Proline residue: D2701 - end of helix Processing helix chain 'D' and resid 2748 through 2773 removed outlier: 3.553A pdb=" N LYS D2757 " --> pdb=" O SER D2753 " (cutoff:3.500A) Processing helix chain 'D' and resid 2798 through 2819 removed outlier: 4.014A pdb=" N ILE D2804 " --> pdb=" O LYS D2800 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TYR D2805 " --> pdb=" O ASP D2801 " (cutoff:3.500A) Proline residue: D2808 - end of helix Processing helix chain 'D' and resid 2861 through 2865 removed outlier: 3.546A pdb=" N VAL D2865 " --> pdb=" O LEU D2862 " (cutoff:3.500A) Processing helix chain 'D' and resid 2868 through 2898 removed outlier: 4.305A pdb=" N GLU D2876 " --> pdb=" O GLN D2872 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN D2877 " --> pdb=" O ALA D2873 " (cutoff:3.500A) Processing helix chain 'D' and resid 2912 through 2933 removed outlier: 3.740A pdb=" N ARG D2918 " --> pdb=" O LYS D2914 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ASP D2919 " --> pdb=" O GLU D2915 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU D2925 " --> pdb=" O GLU D2921 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE D2929 " --> pdb=" O GLU D2925 " (cutoff:3.500A) Processing helix chain 'D' and resid 3018 through 3039 removed outlier: 3.636A pdb=" N SER D3032 " --> pdb=" O GLY D3028 " (cutoff:3.500A) Processing helix chain 'D' and resid 3044 through 3061 Processing helix chain 'D' and resid 3071 through 3090 Proline residue: D3085 - end of helix Processing helix chain 'D' and resid 3099 through 3114 Processing helix chain 'D' and resid 3133 through 3152 Proline residue: D3138 - end of helix Processing helix chain 'D' and resid 3159 through 3178 removed outlier: 3.869A pdb=" N CYS D3170 " --> pdb=" O TYR D3166 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER D3171 " --> pdb=" O ARG D3167 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE D3172 " --> pdb=" O THR D3168 " (cutoff:3.500A) Processing helix chain 'D' and resid 3185 through 3200 Processing helix chain 'D' and resid 3205 through 3217 Processing helix chain 'D' and resid 3274 through 3288 Proline residue: D3282 - end of helix Processing helix chain 'D' and resid 3294 through 3300 removed outlier: 3.630A pdb=" N ALA D3298 " --> pdb=" O PRO D3294 " (cutoff:3.500A) Processing helix chain 'D' and resid 3300 through 3313 Processing helix chain 'D' and resid 3322 through 3339 Processing helix chain 'D' and resid 3348 through 3363 Proline residue: D3360 - end of helix Processing helix chain 'D' and resid 3368 through 3389 Processing helix chain 'D' and resid 3407 through 3433 Proline residue: D3427 - end of helix Processing helix chain 'D' and resid 3438 through 3454 Processing helix chain 'D' and resid 3455 through 3470 Processing helix chain 'D' and resid 3476 through 3488 Processing helix chain 'D' and resid 3514 through 3526 Proline residue: D3519 - end of helix Processing helix chain 'D' and resid 3553 through 3572 Proline residue: D3567 - end of helix Processing helix chain 'D' and resid 3646 through 3663 Processing helix chain 'D' and resid 3668 through 3679 Processing helix chain 'D' and resid 3699 through 3709 Processing helix chain 'D' and resid 3719 through 3733 Processing helix chain 'D' and resid 3753 through 3773 Processing helix chain 'D' and resid 3774 through 3787 removed outlier: 4.037A pdb=" N LYS D3787 " --> pdb=" O ILE D3783 " (cutoff:3.500A) Processing helix chain 'D' and resid 3791 through 3805 Processing helix chain 'D' and resid 3809 through 3824 Processing helix chain 'D' and resid 3827 through 3837 Processing helix chain 'D' and resid 3843 through 3852 Processing helix chain 'D' and resid 3878 through 3892 removed outlier: 4.119A pdb=" N GLN D3882 " --> pdb=" O ASP D3878 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS D3892 " --> pdb=" O LEU D3888 " (cutoff:3.500A) Processing helix chain 'D' and resid 3896 through 3905 Processing helix chain 'D' and resid 3915 through 3938 Processing helix chain 'D' and resid 3946 through 3971 removed outlier: 3.667A pdb=" N GLY D3971 " --> pdb=" O GLU D3967 " (cutoff:3.500A) Processing helix chain 'D' and resid 3973 through 3984 removed outlier: 4.108A pdb=" N ARG D3984 " --> pdb=" O LEU D3980 " (cutoff:3.500A) Processing helix chain 'D' and resid 3988 through 4003 removed outlier: 3.550A pdb=" N HIS D3998 " --> pdb=" O HIS D3994 " (cutoff:3.500A) Processing helix chain 'D' and resid 4009 through 4032 removed outlier: 3.920A pdb=" N LEU D4031 " --> pdb=" O LEU D4027 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU D4032 " --> pdb=" O LEU D4028 " (cutoff:3.500A) Processing helix chain 'D' and resid 4038 through 4051 Processing helix chain 'D' and resid 4052 through 4074 Processing helix chain 'D' and resid 4074 through 4081 removed outlier: 3.949A pdb=" N VAL D4081 " --> pdb=" O PHE D4077 " (cutoff:3.500A) Processing helix chain 'D' and resid 4088 through 4100 Processing helix chain 'D' and resid 4104 through 4115 Processing helix chain 'D' and resid 4125 through 4154 Proline residue: D4135 - end of helix removed outlier: 3.666A pdb=" N PHE D4141 " --> pdb=" O ARG D4137 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASN D4142 " --> pdb=" O ASP D4138 " (cutoff:3.500A) Processing helix chain 'D' and resid 4157 through 4167 removed outlier: 3.535A pdb=" N ARG D4161 " --> pdb=" O ASP D4157 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA D4167 " --> pdb=" O PHE D4163 " (cutoff:3.500A) Processing helix chain 'D' and resid 4168 through 4178 removed outlier: 3.663A pdb=" N TYR D4173 " --> pdb=" O SER D4169 " (cutoff:3.500A) Proline residue: D4176 - end of helix Processing helix chain 'D' and resid 4198 through 4206 Processing helix chain 'D' and resid 4207 through 4224 Processing helix chain 'D' and resid 4230 through 4251 Processing helix chain 'D' and resid 4541 through 4579 removed outlier: 4.136A pdb=" N ARG D4557 " --> pdb=" O ASN D4553 " (cutoff:3.500A) Processing helix chain 'D' and resid 4638 through 4684 removed outlier: 3.685A pdb=" N ILE D4659 " --> pdb=" O PHE D4655 " (cutoff:3.500A) Proline residue: D4667 - end of helix removed outlier: 3.772A pdb=" N LYS D4672 " --> pdb=" O LEU D4668 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE D4683 " --> pdb=" O ARG D4679 " (cutoff:3.500A) Processing helix chain 'D' and resid 4686 through 4691 Processing helix chain 'D' and resid 4698 through 4706 Processing helix chain 'D' and resid 4718 through 4728 removed outlier: 3.526A pdb=" N HIS D4728 " --> pdb=" O VAL D4724 " (cutoff:3.500A) Processing helix chain 'D' and resid 4732 through 4740 removed outlier: 3.920A pdb=" N ARG D4736 " --> pdb=" O PHE D4732 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE D4737 " --> pdb=" O GLY D4733 " (cutoff:3.500A) Processing helix chain 'D' and resid 4773 through 4786 removed outlier: 3.642A pdb=" N ASP D4786 " --> pdb=" O VAL D4782 " (cutoff:3.500A) Processing helix chain 'D' and resid 4786 through 4805 Processing helix chain 'D' and resid 4805 through 4818 removed outlier: 3.614A pdb=" N PHE D4809 " --> pdb=" O ASN D4805 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N MET D4818 " --> pdb=" O LEU D4814 " (cutoff:3.500A) Processing helix chain 'D' and resid 4820 through 4831 Processing helix chain 'D' and resid 4836 through 4859 Processing helix chain 'D' and resid 4878 through 4892 Processing helix chain 'D' and resid 4896 through 4901 Processing helix chain 'D' and resid 4909 through 4957 removed outlier: 3.643A pdb=" N VAL D4924 " --> pdb=" O PHE D4920 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ILE D4925 " --> pdb=" O PHE D4921 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL D4926 " --> pdb=" O PHE D4922 " (cutoff:3.500A) Processing helix chain 'D' and resid 4965 through 4970 Processing helix chain 'D' and resid 4973 through 4982 Processing helix chain 'D' and resid 4985 through 4997 Processing helix chain 'D' and resid 4998 through 5006 Processing helix chain 'D' and resid 5008 through 5017 removed outlier: 4.269A pdb=" N ARG D5017 " --> pdb=" O MET D5013 " (cutoff:3.500A) Processing helix chain 'D' and resid 5027 through 5032 Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 51 removed outlier: 3.735A pdb=" N GLU A 50 " --> pdb=" O CYS A 36 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N CYS A 36 " --> pdb=" O GLU A 50 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASN A 201 " --> pdb=" O GLN A 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 28 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 removed outlier: 4.750A pdb=" N ALA A 39 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU A 46 " --> pdb=" O ALA A 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA5, first strand: chain 'A' and resid 260 through 262 removed outlier: 3.585A pdb=" N ARG A 261 " --> pdb=" O ARG A 283 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 762 through 763 removed outlier: 3.650A pdb=" N CYS A 747 " --> pdb=" O SER A 756 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASP A 742 " --> pdb=" O VAL A 668 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 666 " --> pdb=" O VAL A 744 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 711 through 714 Processing sheet with id=AA8, first strand: chain 'A' and resid 1073 through 1075 Processing sheet with id=AA9, first strand: chain 'A' and resid 1167 through 1168 removed outlier: 3.889A pdb=" N GLU A1167 " --> pdb=" O LEU A1164 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL A1149 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE A1092 " --> pdb=" O VAL A1149 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS A1151 " --> pdb=" O PHE A1090 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A1090 " --> pdb=" O CYS A1151 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1117 through 1118 removed outlier: 4.311A pdb=" N ASP A1118 " --> pdb=" O ALA A1121 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN A1130 " --> pdb=" O ASN A1125 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1237 through 1238 Processing sheet with id=AB3, first strand: chain 'A' and resid 1735 through 1736 Processing sheet with id=AB4, first strand: chain 'A' and resid 2821 through 2823 Processing sheet with id=AB5, first strand: chain 'B' and resid 50 through 51 removed outlier: 3.735A pdb=" N GLU B 50 " --> pdb=" O CYS B 36 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N CYS B 36 " --> pdb=" O GLU B 50 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASN B 201 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 27 through 28 Processing sheet with id=AB7, first strand: chain 'B' and resid 39 through 41 removed outlier: 4.750A pdb=" N ALA B 39 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU B 46 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 119 through 120 Processing sheet with id=AB9, first strand: chain 'B' and resid 260 through 262 removed outlier: 3.585A pdb=" N ARG B 261 " --> pdb=" O ARG B 283 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 762 through 763 removed outlier: 3.650A pdb=" N CYS B 747 " --> pdb=" O SER B 756 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ASP B 742 " --> pdb=" O VAL B 668 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL B 666 " --> pdb=" O VAL B 744 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 711 through 714 Processing sheet with id=AC3, first strand: chain 'B' and resid 1073 through 1075 Processing sheet with id=AC4, first strand: chain 'B' and resid 1167 through 1168 removed outlier: 3.889A pdb=" N GLU B1167 " --> pdb=" O LEU B1164 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL B1149 " --> pdb=" O PHE B1092 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE B1092 " --> pdb=" O VAL B1149 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N CYS B1151 " --> pdb=" O PHE B1090 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE B1090 " --> pdb=" O CYS B1151 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 1117 through 1118 removed outlier: 4.311A pdb=" N ASP B1118 " --> pdb=" O ALA B1121 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN B1130 " --> pdb=" O ASN B1125 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1237 through 1238 Processing sheet with id=AC7, first strand: chain 'B' and resid 1735 through 1736 Processing sheet with id=AC8, first strand: chain 'B' and resid 2821 through 2823 Processing sheet with id=AC9, first strand: chain 'C' and resid 50 through 51 removed outlier: 3.735A pdb=" N GLU C 50 " --> pdb=" O CYS C 36 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N CYS C 36 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASN C 201 " --> pdb=" O GLN C 23 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 27 through 28 Processing sheet with id=AD2, first strand: chain 'C' and resid 39 through 41 removed outlier: 4.749A pdb=" N ALA C 39 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU C 46 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 119 through 120 Processing sheet with id=AD4, first strand: chain 'C' and resid 260 through 262 removed outlier: 3.585A pdb=" N ARG C 261 " --> pdb=" O ARG C 283 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 762 through 763 removed outlier: 3.650A pdb=" N CYS C 747 " --> pdb=" O SER C 756 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASP C 742 " --> pdb=" O VAL C 668 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL C 666 " --> pdb=" O VAL C 744 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 711 through 714 Processing sheet with id=AD7, first strand: chain 'C' and resid 1073 through 1075 Processing sheet with id=AD8, first strand: chain 'C' and resid 1167 through 1168 removed outlier: 3.889A pdb=" N GLU C1167 " --> pdb=" O LEU C1164 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL C1149 " --> pdb=" O PHE C1092 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE C1092 " --> pdb=" O VAL C1149 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N CYS C1151 " --> pdb=" O PHE C1090 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE C1090 " --> pdb=" O CYS C1151 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 1117 through 1118 removed outlier: 4.311A pdb=" N ASP C1118 " --> pdb=" O ALA C1121 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN C1130 " --> pdb=" O ASN C1125 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 1237 through 1238 Processing sheet with id=AE2, first strand: chain 'C' and resid 1735 through 1736 Processing sheet with id=AE3, first strand: chain 'C' and resid 2821 through 2823 Processing sheet with id=AE4, first strand: chain 'D' and resid 50 through 51 removed outlier: 3.735A pdb=" N GLU D 50 " --> pdb=" O CYS D 36 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N CYS D 36 " --> pdb=" O GLU D 50 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN D 201 " --> pdb=" O GLN D 23 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 27 through 28 Processing sheet with id=AE6, first strand: chain 'D' and resid 39 through 41 removed outlier: 4.750A pdb=" N ALA D 39 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU D 46 " --> pdb=" O ALA D 39 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 119 through 120 Processing sheet with id=AE8, first strand: chain 'D' and resid 260 through 262 removed outlier: 3.585A pdb=" N ARG D 261 " --> pdb=" O ARG D 283 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 762 through 763 removed outlier: 3.650A pdb=" N CYS D 747 " --> pdb=" O SER D 756 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASP D 742 " --> pdb=" O VAL D 668 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL D 666 " --> pdb=" O VAL D 744 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 711 through 714 Processing sheet with id=AF2, first strand: chain 'D' and resid 1073 through 1075 Processing sheet with id=AF3, first strand: chain 'D' and resid 1167 through 1168 removed outlier: 3.889A pdb=" N GLU D1167 " --> pdb=" O LEU D1164 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL D1149 " --> pdb=" O PHE D1092 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE D1092 " --> pdb=" O VAL D1149 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS D1151 " --> pdb=" O PHE D1090 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE D1090 " --> pdb=" O CYS D1151 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 1117 through 1118 removed outlier: 4.311A pdb=" N ASP D1118 " --> pdb=" O ALA D1121 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN D1130 " --> pdb=" O ASN D1125 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 1237 through 1238 Processing sheet with id=AF6, first strand: chain 'D' and resid 1735 through 1736 Processing sheet with id=AF7, first strand: chain 'D' and resid 2821 through 2823 6226 hydrogen bonds defined for protein. 18426 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: 44.24 Time building geometry restraints manager: 28.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.58 - 0.85: 24 0.85 - 1.12: 36 1.12 - 1.39: 30790 1.39 - 1.65: 43138 1.65 - 1.92: 44 Bond restraints: 74032 Sorted by residual: bond pdb=" CA PHE B4859 " pdb=" CB PHE B4859 " ideal model delta sigma weight residual 1.527 0.578 0.948 1.39e-02 5.18e+03 4.65e+03 bond pdb=" CA PHE D4859 " pdb=" CB PHE D4859 " ideal model delta sigma weight residual 1.527 0.578 0.948 1.39e-02 5.18e+03 4.65e+03 bond pdb=" CA PHE A4859 " pdb=" CB PHE A4859 " ideal model delta sigma weight residual 1.527 0.578 0.948 1.39e-02 5.18e+03 4.65e+03 bond pdb=" CA PHE C4859 " pdb=" CB PHE C4859 " ideal model delta sigma weight residual 1.527 0.578 0.948 1.39e-02 5.18e+03 4.65e+03 bond pdb=" CA GLN A4691 " pdb=" CB GLN A4691 " ideal model delta sigma weight residual 1.530 0.634 0.896 1.58e-02 4.01e+03 3.21e+03 ... (remaining 74027 not shown) Histogram of bond angle deviations from ideal: 41.78 - 66.40: 12 66.40 - 91.01: 136 91.01 - 115.63: 45716 115.63 - 140.25: 56496 140.25 - 164.86: 44 Bond angle restraints: 102404 Sorted by residual: angle pdb=" N GLU A2047 " pdb=" CA GLU A2047 " pdb=" CB GLU A2047 " ideal model delta sigma weight residual 110.50 41.78 68.72 1.70e+00 3.46e-01 1.63e+03 angle pdb=" N GLU D2047 " pdb=" CA GLU D2047 " pdb=" CB GLU D2047 " ideal model delta sigma weight residual 110.50 41.78 68.72 1.70e+00 3.46e-01 1.63e+03 angle pdb=" N GLU C2047 " pdb=" CA GLU C2047 " pdb=" CB GLU C2047 " ideal model delta sigma weight residual 110.50 41.78 68.72 1.70e+00 3.46e-01 1.63e+03 angle pdb=" N GLU B2047 " pdb=" CA GLU B2047 " pdb=" CB GLU B2047 " ideal model delta sigma weight residual 110.50 41.80 68.70 1.70e+00 3.46e-01 1.63e+03 angle pdb=" C PRO B1750 " pdb=" N GLY B1751 " pdb=" CA GLY B1751 " ideal model delta sigma weight residual 121.61 91.21 30.40 7.70e-01 1.69e+00 1.56e+03 ... (remaining 102399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.40: 41358 23.40 - 46.79: 741 46.79 - 70.19: 129 70.19 - 93.58: 12 93.58 - 116.98: 12 Dihedral angle restraints: 42252 sinusoidal: 2572 harmonic: 39680 Sorted by residual: dihedral pdb=" N GLU C2047 " pdb=" C GLU C2047 " pdb=" CA GLU C2047 " pdb=" CB GLU C2047 " ideal model delta harmonic sigma weight residual 122.80 25.78 97.02 0 2.50e+00 1.60e-01 1.51e+03 dihedral pdb=" N GLU D2047 " pdb=" C GLU D2047 " pdb=" CA GLU D2047 " pdb=" CB GLU D2047 " ideal model delta harmonic sigma weight residual 122.80 25.78 97.02 0 2.50e+00 1.60e-01 1.51e+03 dihedral pdb=" N GLU A2047 " pdb=" C GLU A2047 " pdb=" CA GLU A2047 " pdb=" CB GLU A2047 " ideal model delta harmonic sigma weight residual 122.80 25.78 97.02 0 2.50e+00 1.60e-01 1.51e+03 ... (remaining 42249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.463: 13197 0.463 - 0.926: 159 0.926 - 1.389: 36 1.389 - 1.852: 16 1.852 - 2.314: 4 Chirality restraints: 13412 Sorted by residual: chirality pdb=" CA GLN C4691 " pdb=" N GLN C4691 " pdb=" C GLN C4691 " pdb=" CB GLN C4691 " both_signs ideal model delta sigma weight residual False 2.51 0.20 2.31 2.00e-01 2.50e+01 1.34e+02 chirality pdb=" CA GLN B4691 " pdb=" N GLN B4691 " pdb=" C GLN B4691 " pdb=" CB GLN B4691 " both_signs ideal model delta sigma weight residual False 2.51 0.20 2.31 2.00e-01 2.50e+01 1.34e+02 chirality pdb=" CA GLN A4691 " pdb=" N GLN A4691 " pdb=" C GLN A4691 " pdb=" CB GLN A4691 " both_signs ideal model delta sigma weight residual False 2.51 0.20 2.31 2.00e-01 2.50e+01 1.34e+02 ... (remaining 13409 not shown) Planarity restraints: 14240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A2192 " -0.040 2.00e-02 2.50e+03 8.32e-02 6.92e+01 pdb=" C TYR A2192 " 0.144 2.00e-02 2.50e+03 pdb=" O TYR A2192 " -0.057 2.00e-02 2.50e+03 pdb=" N GLN A2193 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C2192 " 0.040 2.00e-02 2.50e+03 8.32e-02 6.92e+01 pdb=" C TYR C2192 " -0.144 2.00e-02 2.50e+03 pdb=" O TYR C2192 " 0.057 2.00e-02 2.50e+03 pdb=" N GLN C2193 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B2192 " 0.040 2.00e-02 2.50e+03 8.30e-02 6.88e+01 pdb=" C TYR B2192 " -0.143 2.00e-02 2.50e+03 pdb=" O TYR B2192 " 0.057 2.00e-02 2.50e+03 pdb=" N GLN B2193 " 0.047 2.00e-02 2.50e+03 ... (remaining 14237 not shown) Histogram of nonbonded interaction distances: 1.14 - 1.90: 183 1.90 - 2.65: 5299 2.65 - 3.40: 122385 3.40 - 4.15: 148185 4.15 - 4.90: 241515 Nonbonded interactions: 517567 Sorted by model distance: nonbonded pdb=" ND2 ASN A4574 " pdb=" OH TYR D4849 " model vdw 1.145 2.520 nonbonded pdb=" OH TYR C4849 " pdb=" ND2 ASN D4574 " model vdw 1.152 2.520 nonbonded pdb=" OH TYR A4849 " pdb=" ND2 ASN B4574 " model vdw 1.153 2.520 nonbonded pdb=" OH TYR B4849 " pdb=" ND2 ASN C4574 " model vdw 1.154 2.520 nonbonded pdb=" O LEU A 102 " pdb=" O GLY A 104 " model vdw 1.230 3.040 ... (remaining 517562 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 3.240 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: 0.060 Extract box with map and model: 13.880 Check model and map are aligned: 0.900 Set scattering table: 0.550 Process input model: 181.610 Find NCS groups from input model: 4.490 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.020 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 207.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 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 : 0.024 0.948 74032 Z= 1.726 Angle : 2.670 68.720 102404 Z= 1.844 Chirality : 0.161 2.314 13412 Planarity : 0.008 0.125 14240 Dihedral : 10.167 116.977 16260 Min Nonbonded Distance : 1.145 Molprobity Statistics. All-atom Clashscore : 73.68 Ramachandran Plot: Outliers : 7.33 % Allowed : 6.16 % Favored : 86.52 % Rotamer: Outliers : 28.71 % Allowed : 20.98 % Favored : 50.32 % Cbeta Deviations : 1.65 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 2.65 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 2.50 (0.08), residues: 13240 helix: 4.09 (0.06), residues: 8004 sheet: -0.66 (0.27), residues: 416 loop : -2.77 (0.08), residues: 4820 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26480 Ramachandran restraints generated. 13240 Oldfield, 0 Emsley, 13240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26480 Ramachandran restraints generated. 13240 Oldfield, 0 Emsley, 13240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 169 time to evaluate : 1.580 Fit side-chains revert: symmetry clash outliers start: 92 outliers final: 48 residues processed: 240 average time/residue: 0.1766 time to fit residues: 73.6103 Evaluate side-chains 204 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 156 time to evaluate : 1.598 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 2 residues processed: 48 average time/residue: 0.1369 time to fit residues: 14.2581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1380 random chunks: chunk 1165 optimal weight: 0.2980 chunk 1045 optimal weight: 0.0670 chunk 580 optimal weight: 8.9990 chunk 357 optimal weight: 8.9990 chunk 705 optimal weight: 0.6980 chunk 558 optimal weight: 9.9990 chunk 1081 optimal weight: 8.9990 chunk 418 optimal weight: 0.6980 chunk 657 optimal weight: 3.9990 chunk 805 optimal weight: 20.0000 chunk 1253 optimal weight: 20.0000 overall best weight: 1.1520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1702 HIS ** A4662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4803 HIS A4806 ASN A4886 HIS ** A4983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 74032 Z= 0.284 Angle : 1.117 18.210 102404 Z= 0.624 Chirality : 0.046 0.407 13412 Planarity : 0.005 0.051 14240 Dihedral : 6.833 52.402 13732 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 3.02 % Allowed : 7.49 % Favored : 89.49 % Rotamer: Outliers : 1.89 % Allowed : 7.26 % Favored : 90.85 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 2.44 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: 1.22 (0.08), residues: 13240 helix: 2.83 (0.06), residues: 8200 sheet: -0.53 (0.25), residues: 472 loop : -3.15 (0.08), residues: 4568 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26480 Ramachandran restraints generated. 13240 Oldfield, 0 Emsley, 13240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26480 Ramachandran restraints generated. 13240 Oldfield, 0 Emsley, 13240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 207 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 210 average time/residue: 0.1686 time to fit residues: 64.4488 Evaluate side-chains 164 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 1.592 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1367 time to fit residues: 2.3354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1380 random chunks: chunk 696 optimal weight: 9.9990 chunk 388 optimal weight: 10.0000 chunk 1043 optimal weight: 6.9990 chunk 853 optimal weight: 9.9990 chunk 345 optimal weight: 20.0000 chunk 1255 optimal weight: 20.0000 chunk 1356 optimal weight: 6.9990 chunk 1118 optimal weight: 6.9990 chunk 1244 optimal weight: 6.9990 chunk 428 optimal weight: 6.9990 chunk 1007 optimal weight: 0.9980 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2161 GLN ** A4833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4978 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4983 HIS ** 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: 0.6811 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 74032 Z= 0.394 Angle : 1.084 21.379 102404 Z= 0.619 Chirality : 0.046 0.478 13412 Planarity : 0.005 0.046 14240 Dihedral : 6.598 61.368 13732 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 2.63 % Allowed : 9.52 % Favored : 87.85 % Rotamer: Outliers : 0.95 % Allowed : 8.83 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 2.41 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: 0.10 (0.07), residues: 13240 helix: 1.81 (0.06), residues: 8284 sheet: -0.79 (0.22), residues: 560 loop : -3.49 (0.08), residues: 4396 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26480 Ramachandran restraints generated. 13240 Oldfield, 0 Emsley, 13240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26480 Ramachandran restraints generated. 13240 Oldfield, 0 Emsley, 13240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 169 time to evaluate : 1.881 Fit side-chains TARDY: cannot create tardy model for: "TYR A2510 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 172 average time/residue: 0.1653 time to fit residues: 52.7034 Evaluate side-chains 152 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 150 time to evaluate : 1.600 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "TYR A2510 " (corrupted residue). Skipping it. outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.1495 time to fit residues: 2.6301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1380 random chunks: chunk 1240 optimal weight: 8.9990 chunk 943 optimal weight: 4.9990 chunk 651 optimal weight: 8.9990 chunk 138 optimal weight: 0.9990 chunk 599 optimal weight: 10.0000 chunk 843 optimal weight: 20.0000 chunk 1259 optimal weight: 20.0000 chunk 1333 optimal weight: 4.9990 chunk 658 optimal weight: 5.9990 chunk 1194 optimal weight: 5.9990 chunk 359 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 74032 Z= 0.321 Angle : 0.983 20.156 102404 Z= 0.556 Chirality : 0.043 0.322 13412 Planarity : 0.004 0.040 14240 Dihedral : 6.204 67.304 13732 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 2.30 % Allowed : 8.97 % Favored : 88.73 % Rotamer: Outliers : 0.95 % Allowed : 7.89 % Favored : 91.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: 0.36 (0.08), residues: 13240 helix: 2.13 (0.06), residues: 8228 sheet: -0.82 (0.22), residues: 508 loop : -3.51 (0.08), residues: 4504 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26480 Ramachandran restraints generated. 13240 Oldfield, 0 Emsley, 13240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26480 Ramachandran restraints generated. 13240 Oldfield, 0 Emsley, 13240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 176 time to evaluate : 1.602 Fit side-chains TARDY: cannot create tardy model for: "TYR A2510 " (corrupted residue). Skipping it. outliers start: 3 outliers final: 2 residues processed: 179 average time/residue: 0.1527 time to fit residues: 51.2427 Evaluate side-chains 150 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 148 time to evaluate : 1.594 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "TYR A2510 " (corrupted residue). Skipping it. outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.1419 time to fit residues: 2.6205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1380 random chunks: chunk 1110 optimal weight: 0.1980 chunk 757 optimal weight: 30.0000 chunk 19 optimal weight: 20.0000 chunk 993 optimal weight: 10.0000 chunk 550 optimal weight: 9.9990 chunk 1138 optimal weight: 8.9990 chunk 922 optimal weight: 9.9990 chunk 1 optimal weight: 0.0470 chunk 681 optimal weight: 3.9990 chunk 1197 optimal weight: 1.9990 chunk 336 optimal weight: 3.9990 overall best weight: 2.0484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4886 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 74032 Z= 0.231 Angle : 0.912 19.877 102404 Z= 0.510 Chirality : 0.042 0.346 13412 Planarity : 0.003 0.041 14240 Dihedral : 5.664 69.262 13732 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 2.02 % Allowed : 8.82 % Favored : 89.15 % Rotamer: Outliers : 0.95 % Allowed : 2.21 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 2.53 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: 0.94 (0.08), residues: 13240 helix: 2.69 (0.06), residues: 8212 sheet: -0.76 (0.23), residues: 528 loop : -3.48 (0.08), residues: 4500 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26480 Ramachandran restraints generated. 13240 Oldfield, 0 Emsley, 13240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26480 Ramachandran restraints generated. 13240 Oldfield, 0 Emsley, 13240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 178 time to evaluate : 1.629 Fit side-chains TARDY: cannot create tardy model for: "TYR A2510 " (corrupted residue). Skipping it. outliers start: 3 outliers final: 3 residues processed: 181 average time/residue: 0.1501 time to fit residues: 50.6721 Evaluate side-chains 161 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 158 time to evaluate : 1.595 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "TYR A2510 " (corrupted residue). Skipping it. outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.1422 time to fit residues: 2.8762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1380 random chunks: chunk 448 optimal weight: 9.9990 chunk 1201 optimal weight: 4.9990 chunk 263 optimal weight: 5.9990 chunk 783 optimal weight: 20.0000 chunk 329 optimal weight: 4.9990 chunk 1335 optimal weight: 5.9990 chunk 1108 optimal weight: 0.1980 chunk 618 optimal weight: 7.9990 chunk 111 optimal weight: 30.0000 chunk 441 optimal weight: 7.9990 chunk 700 optimal weight: 9.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D4978 HIS ** 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: 0.6819 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 74032 Z= 0.311 Angle : 0.930 20.207 102404 Z= 0.527 Chirality : 0.042 0.323 13412 Planarity : 0.004 0.039 14240 Dihedral : 5.916 72.526 13732 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 1.84 % Allowed : 10.45 % Favored : 87.70 % Rotamer: Outliers : 0.63 % Allowed : 4.10 % Favored : 95.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 2.50 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: 0.55 (0.08), residues: 13240 helix: 2.36 (0.06), residues: 8172 sheet: -0.96 (0.23), residues: 528 loop : -3.52 (0.08), residues: 4540 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19860 Ramachandran restraints generated. 9930 Oldfield, 0 Emsley, 9930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19860 Ramachandran restraints generated. 9930 Oldfield, 0 Emsley, 9930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 171 time to evaluate : 1.692 Fit side-chains TARDY: cannot create tardy model for: "TYR D2510 " (corrupted residue). Skipping it. outliers start: 2 outliers final: 2 residues processed: 173 average time/residue: 0.1560 time to fit residues: 50.8703 Evaluate side-chains 155 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 153 time to evaluate : 1.704 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "TYR D2510 " (corrupted residue). Skipping it. outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.1510 time to fit residues: 3.0611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1380 random chunks: chunk 1287 optimal weight: 10.0000 chunk 150 optimal weight: 4.9990 chunk 760 optimal weight: 10.0000 chunk 975 optimal weight: 3.9990 chunk 755 optimal weight: 30.0000 chunk 1123 optimal weight: 4.9990 chunk 745 optimal weight: 20.0000 chunk 1330 optimal weight: 7.9990 chunk 832 optimal weight: 1.9990 chunk 810 optimal weight: 8.9990 chunk 614 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4886 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.5392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 74032 Z= 0.260 Angle : 0.889 20.163 102404 Z= 0.499 Chirality : 0.041 0.323 13412 Planarity : 0.003 0.041 14240 Dihedral : 5.645 73.681 13732 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 1.87 % Allowed : 10.73 % Favored : 87.40 % Rotamer: Outliers : 0.32 % Allowed : 4.10 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 2.50 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: 0.36 (0.08), residues: 13240 helix: 2.25 (0.06), residues: 8180 sheet: -1.36 (0.23), residues: 504 loop : -3.65 (0.08), residues: 4556 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19860 Ramachandran restraints generated. 9930 Oldfield, 0 Emsley, 9930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19860 Ramachandran restraints generated. 9930 Oldfield, 0 Emsley, 9930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 172 time to evaluate : 1.584 Fit side-chains TARDY: cannot create tardy model for: "TYR A2510 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 173 average time/residue: 0.1511 time to fit residues: 49.1694 Evaluate side-chains 159 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 1.620 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "TYR A2510 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1558 time to fit residues: 2.4060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1380 random chunks: chunk 822 optimal weight: 7.9990 chunk 531 optimal weight: 8.9990 chunk 794 optimal weight: 20.0000 chunk 400 optimal weight: 8.9990 chunk 261 optimal weight: 5.9990 chunk 257 optimal weight: 3.9990 chunk 845 optimal weight: 5.9990 chunk 906 optimal weight: 6.9990 chunk 657 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 1045 optimal weight: 0.0270 overall best weight: 4.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.5663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 74032 Z= 0.286 Angle : 0.896 21.363 102404 Z= 0.505 Chirality : 0.042 0.317 13412 Planarity : 0.003 0.036 14240 Dihedral : 5.786 74.906 13732 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 1.78 % Allowed : 11.33 % Favored : 86.89 % Rotamer: Outliers : 0.32 % Allowed : 0.95 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 2.50 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: 0.07 (0.08), residues: 13240 helix: 2.01 (0.06), residues: 8172 sheet: -1.55 (0.24), residues: 456 loop : -3.71 (0.08), residues: 4612 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19860 Ramachandran restraints generated. 9930 Oldfield, 0 Emsley, 9930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19860 Ramachandran restraints generated. 9930 Oldfield, 0 Emsley, 9930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 169 time to evaluate : 1.727 Fit side-chains TARDY: cannot create tardy model for: "TYR A2510 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 170 average time/residue: 0.1516 time to fit residues: 48.3713 Evaluate side-chains 158 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 1.669 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "TYR A2510 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1630 time to fit residues: 2.4164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1380 random chunks: chunk 1209 optimal weight: 8.9990 chunk 1274 optimal weight: 1.9990 chunk 1162 optimal weight: 20.0000 chunk 1239 optimal weight: 40.0000 chunk 1273 optimal weight: 5.9990 chunk 746 optimal weight: 20.0000 chunk 539 optimal weight: 10.0000 chunk 973 optimal weight: 3.9990 chunk 380 optimal weight: 2.9990 chunk 1120 optimal weight: 10.0000 chunk 1172 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4662 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: 0.6846 moved from start: 0.5870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 74032 Z= 0.299 Angle : 0.888 19.430 102404 Z= 0.500 Chirality : 0.042 0.314 13412 Planarity : 0.004 0.039 14240 Dihedral : 5.878 75.924 13732 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 1.78 % Allowed : 11.36 % Favored : 86.86 % Rotamer: Outliers : 0.32 % Allowed : 1.26 % Favored : 98.42 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 2.50 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -0.16 (0.08), residues: 13240 helix: 1.81 (0.06), residues: 8184 sheet: -1.64 (0.24), residues: 456 loop : -3.79 (0.08), residues: 4600 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19860 Ramachandran restraints generated. 9930 Oldfield, 0 Emsley, 9930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19860 Ramachandran restraints generated. 9930 Oldfield, 0 Emsley, 9930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 160 time to evaluate : 1.631 Fit side-chains TARDY: cannot create tardy model for: "TYR A2510 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 161 average time/residue: 0.1490 time to fit residues: 45.5500 Evaluate side-chains 149 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 148 time to evaluate : 1.595 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "TYR A2510 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1516 time to fit residues: 2.3652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1380 random chunks: chunk 1235 optimal weight: 30.0000 chunk 813 optimal weight: 6.9990 chunk 1310 optimal weight: 4.9990 chunk 799 optimal weight: 9.9990 chunk 621 optimal weight: 5.9990 chunk 911 optimal weight: 20.0000 chunk 1374 optimal weight: 3.9990 chunk 1265 optimal weight: 7.9990 chunk 1094 optimal weight: 40.0000 chunk 113 optimal weight: 30.0000 chunk 845 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D4662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4886 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.6175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 74032 Z= 0.361 Angle : 0.931 19.487 102404 Z= 0.530 Chirality : 0.043 0.307 13412 Planarity : 0.004 0.041 14240 Dihedral : 6.309 77.449 13732 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 1.75 % Allowed : 12.81 % Favored : 85.44 % Rotamer: Outliers : 0.32 % Allowed : 1.26 % Favored : 98.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 2.50 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -0.92 (0.07), residues: 13240 helix: 1.21 (0.06), residues: 8160 sheet: -1.94 (0.24), residues: 456 loop : -4.05 (0.08), residues: 4624 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19860 Ramachandran restraints generated. 9930 Oldfield, 0 Emsley, 9930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19860 Ramachandran restraints generated. 9930 Oldfield, 0 Emsley, 9930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 1.686 Fit side-chains TARDY: cannot create tardy model for: "TYR D2510 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 160 average time/residue: 0.1547 time to fit residues: 47.4627 Evaluate side-chains 147 residues out of total 3018 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 146 time to evaluate : 1.601 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "TYR D2510 " (corrupted residue). Skipping it. outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1569 time to fit residues: 2.4368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1380 random chunks: chunk 671 optimal weight: 0.0370 chunk 869 optimal weight: 10.0000 chunk 1166 optimal weight: 0.0050 chunk 335 optimal weight: 0.2980 chunk 1009 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 304 optimal weight: 2.9990 chunk 1096 optimal weight: 0.7980 chunk 458 optimal weight: 30.0000 chunk 1125 optimal weight: 9.9990 chunk 138 optimal weight: 6.9990 overall best weight: 0.8274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.094857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.093328 restraints weight = 94245.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.093053 restraints weight = 170875.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.087639 restraints weight = 226878.382| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.6317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 74032 Z= 0.200 Angle : 0.829 18.050 102404 Z= 0.459 Chirality : 0.041 0.343 13412 Planarity : 0.003 0.038 14240 Dihedral : 5.561 75.583 13732 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 1.66 % Allowed : 9.55 % Favored : 88.79 % Rotamer: Outliers : 0.32 % Allowed : 0.63 % Favored : 99.05 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 2.47 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: 0.19 (0.08), residues: 13240 helix: 2.22 (0.06), residues: 8196 sheet: -1.92 (0.22), residues: 532 loop : -3.91 (0.08), residues: 4512 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5858.85 seconds wall clock time: 105 minutes 10.56 seconds (6310.56 seconds total)