Starting phenix.real_space_refine on Wed Sep 25 15:16:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8e_15230/09_2024/8a8e_15230.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8e_15230/09_2024/8a8e_15230.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8e_15230/09_2024/8a8e_15230.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8e_15230/09_2024/8a8e_15230.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8e_15230/09_2024/8a8e_15230.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a8e_15230/09_2024/8a8e_15230.cif" } resolution = 2.9 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= 0.003 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 264 5.16 5 C 35832 2.51 5 N 10032 2.21 5 O 10440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 360 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 56568 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2357 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 17, 'TRANS': 284} Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, U, T, W, V, X Time building chain proxies: 9.91, per 1000 atoms: 0.18 Number of scatterers: 56568 At special positions: 0 Unit cell: (165, 165, 165, 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 264 16.00 O 10440 8.00 N 10032 7.00 C 35832 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.43 Conformation dependent library (CDL) restraints added in 5.8 seconds 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13392 Finding SS restraints... Secondary structure from input PDB file: 408 helices and 24 sheets defined 59.9% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.25 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 Processing helix chain 'A' and resid 36 through 41 Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL A 70 " --> pdb=" O GLY A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'A' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY A 109 " --> pdb=" O PRO A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG A 115 " --> pdb=" O ARG A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU A 123 " --> pdb=" O GLN A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE A 154 " --> pdb=" O HIS A 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL A 164 " --> pdb=" O ILE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 186 Processing helix chain 'A' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 211 Processing helix chain 'A' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU A 222 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR A 223 " --> pdb=" O ALA A 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 219 through 223' Processing helix chain 'A' and resid 227 through 245 Processing helix chain 'A' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER A 256 " --> pdb=" O GLN A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 256' Processing helix chain 'A' and resid 257 through 268 Processing helix chain 'A' and resid 278 through 302 Processing helix chain 'B' and resid 20 through 25 Processing helix chain 'B' and resid 36 through 41 Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU B 59 " --> pdb=" O LYS B 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL B 70 " --> pdb=" O GLY B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY B 109 " --> pdb=" O PRO B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG B 115 " --> pdb=" O ARG B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU B 123 " --> pdb=" O GLN B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE B 154 " --> pdb=" O HIS B 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 186 Processing helix chain 'B' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 211 Processing helix chain 'B' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU B 222 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR B 223 " --> pdb=" O ALA B 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 219 through 223' Processing helix chain 'B' and resid 227 through 245 Processing helix chain 'B' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER B 256 " --> pdb=" O GLN B 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 253 through 256' Processing helix chain 'B' and resid 257 through 268 Processing helix chain 'B' and resid 278 through 302 Processing helix chain 'C' and resid 20 through 25 Processing helix chain 'C' and resid 36 through 41 Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'C' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU C 59 " --> pdb=" O LYS C 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL C 70 " --> pdb=" O GLY C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY C 109 " --> pdb=" O PRO C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG C 115 " --> pdb=" O ARG C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU C 123 " --> pdb=" O GLN C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE C 154 " --> pdb=" O HIS C 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL C 164 " --> pdb=" O ILE C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 186 Processing helix chain 'C' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 211 Processing helix chain 'C' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU C 222 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR C 223 " --> pdb=" O ALA C 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 219 through 223' Processing helix chain 'C' and resid 227 through 245 Processing helix chain 'C' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER C 256 " --> pdb=" O GLN C 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 253 through 256' Processing helix chain 'C' and resid 257 through 268 Processing helix chain 'C' and resid 278 through 302 Processing helix chain 'D' and resid 20 through 25 Processing helix chain 'D' and resid 36 through 41 Processing helix chain 'D' and resid 46 through 54 Processing helix chain 'D' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU D 59 " --> pdb=" O LYS D 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL D 70 " --> pdb=" O GLY D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY D 109 " --> pdb=" O PRO D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG D 115 " --> pdb=" O ARG D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU D 123 " --> pdb=" O GLN D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE D 154 " --> pdb=" O HIS D 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL D 164 " --> pdb=" O ILE D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 186 Processing helix chain 'D' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU D 190 " --> pdb=" O ILE D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 211 Processing helix chain 'D' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU D 222 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR D 223 " --> pdb=" O ALA D 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 219 through 223' Processing helix chain 'D' and resid 227 through 245 Processing helix chain 'D' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER D 256 " --> pdb=" O GLN D 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 253 through 256' Processing helix chain 'D' and resid 257 through 268 Processing helix chain 'D' and resid 278 through 302 Processing helix chain 'E' and resid 20 through 25 Processing helix chain 'E' and resid 36 through 41 Processing helix chain 'E' and resid 46 through 54 Processing helix chain 'E' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU E 59 " --> pdb=" O LYS E 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL E 70 " --> pdb=" O GLY E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY E 109 " --> pdb=" O PRO E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG E 115 " --> pdb=" O ARG E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU E 123 " --> pdb=" O GLN E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE E 154 " --> pdb=" O HIS E 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL E 164 " --> pdb=" O ILE E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 186 Processing helix chain 'E' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU E 190 " --> pdb=" O ILE E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 211 Processing helix chain 'E' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU E 222 " --> pdb=" O VAL E 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR E 223 " --> pdb=" O ALA E 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 219 through 223' Processing helix chain 'E' and resid 227 through 245 Processing helix chain 'E' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER E 256 " --> pdb=" O GLN E 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 253 through 256' Processing helix chain 'E' and resid 257 through 268 Processing helix chain 'E' and resid 278 through 302 Processing helix chain 'F' and resid 20 through 25 Processing helix chain 'F' and resid 36 through 41 Processing helix chain 'F' and resid 46 through 54 Processing helix chain 'F' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU F 59 " --> pdb=" O LYS F 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL F 70 " --> pdb=" O GLY F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'F' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY F 109 " --> pdb=" O PRO F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG F 115 " --> pdb=" O ARG F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU F 123 " --> pdb=" O GLN F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE F 154 " --> pdb=" O HIS F 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL F 164 " --> pdb=" O ILE F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 186 Processing helix chain 'F' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU F 190 " --> pdb=" O ILE F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 211 Processing helix chain 'F' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU F 222 " --> pdb=" O VAL F 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR F 223 " --> pdb=" O ALA F 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 219 through 223' Processing helix chain 'F' and resid 227 through 245 Processing helix chain 'F' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER F 256 " --> pdb=" O GLN F 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 253 through 256' Processing helix chain 'F' and resid 257 through 268 Processing helix chain 'F' and resid 278 through 302 Processing helix chain 'G' and resid 20 through 25 Processing helix chain 'G' and resid 36 through 41 Processing helix chain 'G' and resid 46 through 54 Processing helix chain 'G' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU G 59 " --> pdb=" O LYS G 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL G 70 " --> pdb=" O GLY G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'G' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY G 109 " --> pdb=" O PRO G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG G 115 " --> pdb=" O ARG G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU G 123 " --> pdb=" O GLN G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE G 154 " --> pdb=" O HIS G 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL G 164 " --> pdb=" O ILE G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 186 Processing helix chain 'G' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU G 190 " --> pdb=" O ILE G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 211 Processing helix chain 'G' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU G 222 " --> pdb=" O VAL G 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR G 223 " --> pdb=" O ALA G 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 219 through 223' Processing helix chain 'G' and resid 227 through 245 Processing helix chain 'G' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER G 256 " --> pdb=" O GLN G 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 253 through 256' Processing helix chain 'G' and resid 257 through 268 Processing helix chain 'G' and resid 278 through 302 Processing helix chain 'H' and resid 20 through 25 Processing helix chain 'H' and resid 36 through 41 Processing helix chain 'H' and resid 46 through 54 Processing helix chain 'H' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU H 59 " --> pdb=" O LYS H 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL H 70 " --> pdb=" O GLY H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY H 109 " --> pdb=" O PRO H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG H 115 " --> pdb=" O ARG H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU H 123 " --> pdb=" O GLN H 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE H 154 " --> pdb=" O HIS H 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL H 164 " --> pdb=" O ILE H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 180 through 186 Processing helix chain 'H' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU H 190 " --> pdb=" O ILE H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 211 Processing helix chain 'H' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU H 222 " --> pdb=" O VAL H 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR H 223 " --> pdb=" O ALA H 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 219 through 223' Processing helix chain 'H' and resid 227 through 245 Processing helix chain 'H' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER H 256 " --> pdb=" O GLN H 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 253 through 256' Processing helix chain 'H' and resid 257 through 268 Processing helix chain 'H' and resid 278 through 302 Processing helix chain 'I' and resid 20 through 25 Processing helix chain 'I' and resid 36 through 41 Processing helix chain 'I' and resid 46 through 54 Processing helix chain 'I' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU I 59 " --> pdb=" O LYS I 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL I 70 " --> pdb=" O GLY I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'I' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY I 109 " --> pdb=" O PRO I 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG I 115 " --> pdb=" O ARG I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU I 123 " --> pdb=" O GLN I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE I 154 " --> pdb=" O HIS I 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL I 164 " --> pdb=" O ILE I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 186 Processing helix chain 'I' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU I 190 " --> pdb=" O ILE I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 211 Processing helix chain 'I' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU I 222 " --> pdb=" O VAL I 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR I 223 " --> pdb=" O ALA I 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 219 through 223' Processing helix chain 'I' and resid 227 through 245 Processing helix chain 'I' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER I 256 " --> pdb=" O GLN I 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 253 through 256' Processing helix chain 'I' and resid 257 through 268 Processing helix chain 'I' and resid 278 through 302 Processing helix chain 'J' and resid 20 through 25 Processing helix chain 'J' and resid 36 through 41 Processing helix chain 'J' and resid 46 through 54 Processing helix chain 'J' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU J 59 " --> pdb=" O LYS J 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL J 70 " --> pdb=" O GLY J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'J' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY J 109 " --> pdb=" O PRO J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG J 115 " --> pdb=" O ARG J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU J 123 " --> pdb=" O GLN J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE J 154 " --> pdb=" O HIS J 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL J 164 " --> pdb=" O ILE J 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 186 Processing helix chain 'J' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU J 190 " --> pdb=" O ILE J 186 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 211 Processing helix chain 'J' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU J 222 " --> pdb=" O VAL J 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR J 223 " --> pdb=" O ALA J 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 219 through 223' Processing helix chain 'J' and resid 227 through 245 Processing helix chain 'J' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER J 256 " --> pdb=" O GLN J 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 253 through 256' Processing helix chain 'J' and resid 257 through 268 Processing helix chain 'J' and resid 278 through 302 Processing helix chain 'K' and resid 20 through 25 Processing helix chain 'K' and resid 36 through 41 Processing helix chain 'K' and resid 46 through 54 Processing helix chain 'K' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU K 59 " --> pdb=" O LYS K 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL K 70 " --> pdb=" O GLY K 66 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 91 Processing helix chain 'K' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY K 109 " --> pdb=" O PRO K 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG K 115 " --> pdb=" O ARG K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU K 123 " --> pdb=" O GLN K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE K 154 " --> pdb=" O HIS K 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL K 164 " --> pdb=" O ILE K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 180 through 186 Processing helix chain 'K' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU K 190 " --> pdb=" O ILE K 186 " (cutoff:3.500A) Processing helix chain 'K' and resid 202 through 211 Processing helix chain 'K' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU K 222 " --> pdb=" O VAL K 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR K 223 " --> pdb=" O ALA K 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 219 through 223' Processing helix chain 'K' and resid 227 through 245 Processing helix chain 'K' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER K 256 " --> pdb=" O GLN K 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 253 through 256' Processing helix chain 'K' and resid 257 through 268 Processing helix chain 'K' and resid 278 through 302 Processing helix chain 'L' and resid 20 through 25 Processing helix chain 'L' and resid 36 through 41 Processing helix chain 'L' and resid 46 through 54 Processing helix chain 'L' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU L 59 " --> pdb=" O LYS L 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL L 70 " --> pdb=" O GLY L 66 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 91 Processing helix chain 'L' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY L 109 " --> pdb=" O PRO L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG L 115 " --> pdb=" O ARG L 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU L 123 " --> pdb=" O GLN L 119 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE L 154 " --> pdb=" O HIS L 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL L 164 " --> pdb=" O ILE L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 180 through 186 Processing helix chain 'L' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU L 190 " --> pdb=" O ILE L 186 " (cutoff:3.500A) Processing helix chain 'L' and resid 202 through 211 Processing helix chain 'L' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU L 222 " --> pdb=" O VAL L 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR L 223 " --> pdb=" O ALA L 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 219 through 223' Processing helix chain 'L' and resid 227 through 245 Processing helix chain 'L' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER L 256 " --> pdb=" O GLN L 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 253 through 256' Processing helix chain 'L' and resid 257 through 268 Processing helix chain 'L' and resid 278 through 302 Processing helix chain 'M' and resid 20 through 25 Processing helix chain 'M' and resid 36 through 41 Processing helix chain 'M' and resid 46 through 54 Processing helix chain 'M' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU M 59 " --> pdb=" O LYS M 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL M 70 " --> pdb=" O GLY M 66 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'M' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY M 109 " --> pdb=" O PRO M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG M 115 " --> pdb=" O ARG M 111 " (cutoff:3.500A) Processing helix chain 'M' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU M 123 " --> pdb=" O GLN M 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE M 154 " --> pdb=" O HIS M 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL M 164 " --> pdb=" O ILE M 160 " (cutoff:3.500A) Processing helix chain 'M' and resid 180 through 186 Processing helix chain 'M' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU M 190 " --> pdb=" O ILE M 186 " (cutoff:3.500A) Processing helix chain 'M' and resid 202 through 211 Processing helix chain 'M' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU M 222 " --> pdb=" O VAL M 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR M 223 " --> pdb=" O ALA M 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 219 through 223' Processing helix chain 'M' and resid 227 through 245 Processing helix chain 'M' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER M 256 " --> pdb=" O GLN M 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 253 through 256' Processing helix chain 'M' and resid 257 through 268 Processing helix chain 'M' and resid 278 through 302 Processing helix chain 'N' and resid 20 through 25 Processing helix chain 'N' and resid 36 through 41 Processing helix chain 'N' and resid 46 through 54 Processing helix chain 'N' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU N 59 " --> pdb=" O LYS N 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL N 70 " --> pdb=" O GLY N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'N' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY N 109 " --> pdb=" O PRO N 106 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG N 115 " --> pdb=" O ARG N 111 " (cutoff:3.500A) Processing helix chain 'N' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU N 123 " --> pdb=" O GLN N 119 " (cutoff:3.500A) Processing helix chain 'N' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE N 154 " --> pdb=" O HIS N 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL N 164 " --> pdb=" O ILE N 160 " (cutoff:3.500A) Processing helix chain 'N' and resid 180 through 186 Processing helix chain 'N' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU N 190 " --> pdb=" O ILE N 186 " (cutoff:3.500A) Processing helix chain 'N' and resid 202 through 211 Processing helix chain 'N' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU N 222 " --> pdb=" O VAL N 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR N 223 " --> pdb=" O ALA N 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 219 through 223' Processing helix chain 'N' and resid 227 through 245 Processing helix chain 'N' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER N 256 " --> pdb=" O GLN N 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 253 through 256' Processing helix chain 'N' and resid 257 through 268 Processing helix chain 'N' and resid 278 through 302 Processing helix chain 'O' and resid 20 through 25 Processing helix chain 'O' and resid 36 through 41 Processing helix chain 'O' and resid 46 through 54 Processing helix chain 'O' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU O 59 " --> pdb=" O LYS O 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL O 70 " --> pdb=" O GLY O 66 " (cutoff:3.500A) Processing helix chain 'O' and resid 87 through 91 Processing helix chain 'O' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY O 109 " --> pdb=" O PRO O 106 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG O 115 " --> pdb=" O ARG O 111 " (cutoff:3.500A) Processing helix chain 'O' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU O 123 " --> pdb=" O GLN O 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE O 154 " --> pdb=" O HIS O 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL O 164 " --> pdb=" O ILE O 160 " (cutoff:3.500A) Processing helix chain 'O' and resid 180 through 186 Processing helix chain 'O' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU O 190 " --> pdb=" O ILE O 186 " (cutoff:3.500A) Processing helix chain 'O' and resid 202 through 211 Processing helix chain 'O' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU O 222 " --> pdb=" O VAL O 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR O 223 " --> pdb=" O ALA O 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 219 through 223' Processing helix chain 'O' and resid 227 through 245 Processing helix chain 'O' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER O 256 " --> pdb=" O GLN O 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 253 through 256' Processing helix chain 'O' and resid 257 through 268 Processing helix chain 'O' and resid 278 through 302 Processing helix chain 'P' and resid 20 through 25 Processing helix chain 'P' and resid 36 through 41 Processing helix chain 'P' and resid 46 through 54 Processing helix chain 'P' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU P 59 " --> pdb=" O LYS P 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL P 70 " --> pdb=" O GLY P 66 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 91 Processing helix chain 'P' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY P 109 " --> pdb=" O PRO P 106 " (cutoff:3.500A) Processing helix chain 'P' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG P 115 " --> pdb=" O ARG P 111 " (cutoff:3.500A) Processing helix chain 'P' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU P 123 " --> pdb=" O GLN P 119 " (cutoff:3.500A) Processing helix chain 'P' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE P 154 " --> pdb=" O HIS P 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL P 164 " --> pdb=" O ILE P 160 " (cutoff:3.500A) Processing helix chain 'P' and resid 180 through 186 Processing helix chain 'P' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU P 190 " --> pdb=" O ILE P 186 " (cutoff:3.500A) Processing helix chain 'P' and resid 202 through 211 Processing helix chain 'P' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU P 222 " --> pdb=" O VAL P 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR P 223 " --> pdb=" O ALA P 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 219 through 223' Processing helix chain 'P' and resid 227 through 245 Processing helix chain 'P' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER P 256 " --> pdb=" O GLN P 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 253 through 256' Processing helix chain 'P' and resid 257 through 268 Processing helix chain 'P' and resid 278 through 302 Processing helix chain 'Q' and resid 20 through 25 Processing helix chain 'Q' and resid 36 through 41 Processing helix chain 'Q' and resid 46 through 54 Processing helix chain 'Q' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU Q 59 " --> pdb=" O LYS Q 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL Q 70 " --> pdb=" O GLY Q 66 " (cutoff:3.500A) Processing helix chain 'Q' and resid 87 through 91 Processing helix chain 'Q' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY Q 109 " --> pdb=" O PRO Q 106 " (cutoff:3.500A) Processing helix chain 'Q' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG Q 115 " --> pdb=" O ARG Q 111 " (cutoff:3.500A) Processing helix chain 'Q' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU Q 123 " --> pdb=" O GLN Q 119 " (cutoff:3.500A) Processing helix chain 'Q' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE Q 154 " --> pdb=" O HIS Q 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL Q 164 " --> pdb=" O ILE Q 160 " (cutoff:3.500A) Processing helix chain 'Q' and resid 180 through 186 Processing helix chain 'Q' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU Q 190 " --> pdb=" O ILE Q 186 " (cutoff:3.500A) Processing helix chain 'Q' and resid 202 through 211 Processing helix chain 'Q' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU Q 222 " --> pdb=" O VAL Q 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR Q 223 " --> pdb=" O ALA Q 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 219 through 223' Processing helix chain 'Q' and resid 227 through 245 Processing helix chain 'Q' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER Q 256 " --> pdb=" O GLN Q 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 253 through 256' Processing helix chain 'Q' and resid 257 through 268 Processing helix chain 'Q' and resid 278 through 302 Processing helix chain 'R' and resid 20 through 25 Processing helix chain 'R' and resid 36 through 41 Processing helix chain 'R' and resid 46 through 54 Processing helix chain 'R' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU R 59 " --> pdb=" O LYS R 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL R 70 " --> pdb=" O GLY R 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 91 Processing helix chain 'R' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY R 109 " --> pdb=" O PRO R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG R 115 " --> pdb=" O ARG R 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU R 123 " --> pdb=" O GLN R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE R 154 " --> pdb=" O HIS R 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL R 164 " --> pdb=" O ILE R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 186 Processing helix chain 'R' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU R 190 " --> pdb=" O ILE R 186 " (cutoff:3.500A) Processing helix chain 'R' and resid 202 through 211 Processing helix chain 'R' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU R 222 " --> pdb=" O VAL R 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR R 223 " --> pdb=" O ALA R 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 219 through 223' Processing helix chain 'R' and resid 227 through 245 Processing helix chain 'R' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER R 256 " --> pdb=" O GLN R 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 253 through 256' Processing helix chain 'R' and resid 257 through 268 Processing helix chain 'R' and resid 278 through 302 Processing helix chain 'S' and resid 20 through 25 Processing helix chain 'S' and resid 36 through 41 Processing helix chain 'S' and resid 46 through 54 Processing helix chain 'S' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU S 59 " --> pdb=" O LYS S 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL S 70 " --> pdb=" O GLY S 66 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'S' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY S 109 " --> pdb=" O PRO S 106 " (cutoff:3.500A) Processing helix chain 'S' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG S 115 " --> pdb=" O ARG S 111 " (cutoff:3.500A) Processing helix chain 'S' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU S 123 " --> pdb=" O GLN S 119 " (cutoff:3.500A) Processing helix chain 'S' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE S 154 " --> pdb=" O HIS S 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL S 164 " --> pdb=" O ILE S 160 " (cutoff:3.500A) Processing helix chain 'S' and resid 180 through 186 Processing helix chain 'S' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU S 190 " --> pdb=" O ILE S 186 " (cutoff:3.500A) Processing helix chain 'S' and resid 202 through 211 Processing helix chain 'S' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU S 222 " --> pdb=" O VAL S 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR S 223 " --> pdb=" O ALA S 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 219 through 223' Processing helix chain 'S' and resid 227 through 245 Processing helix chain 'S' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER S 256 " --> pdb=" O GLN S 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 253 through 256' Processing helix chain 'S' and resid 257 through 268 Processing helix chain 'S' and resid 278 through 302 Processing helix chain 'T' and resid 20 through 25 Processing helix chain 'T' and resid 36 through 41 Processing helix chain 'T' and resid 46 through 54 Processing helix chain 'T' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU T 59 " --> pdb=" O LYS T 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL T 70 " --> pdb=" O GLY T 66 " (cutoff:3.500A) Processing helix chain 'T' and resid 87 through 91 Processing helix chain 'T' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY T 109 " --> pdb=" O PRO T 106 " (cutoff:3.500A) Processing helix chain 'T' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG T 115 " --> pdb=" O ARG T 111 " (cutoff:3.500A) Processing helix chain 'T' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU T 123 " --> pdb=" O GLN T 119 " (cutoff:3.500A) Processing helix chain 'T' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE T 154 " --> pdb=" O HIS T 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL T 164 " --> pdb=" O ILE T 160 " (cutoff:3.500A) Processing helix chain 'T' and resid 180 through 186 Processing helix chain 'T' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU T 190 " --> pdb=" O ILE T 186 " (cutoff:3.500A) Processing helix chain 'T' and resid 202 through 211 Processing helix chain 'T' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU T 222 " --> pdb=" O VAL T 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR T 223 " --> pdb=" O ALA T 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 219 through 223' Processing helix chain 'T' and resid 227 through 245 Processing helix chain 'T' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER T 256 " --> pdb=" O GLN T 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 253 through 256' Processing helix chain 'T' and resid 257 through 268 Processing helix chain 'T' and resid 278 through 302 Processing helix chain 'U' and resid 20 through 25 Processing helix chain 'U' and resid 36 through 41 Processing helix chain 'U' and resid 46 through 54 Processing helix chain 'U' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU U 59 " --> pdb=" O LYS U 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL U 70 " --> pdb=" O GLY U 66 " (cutoff:3.500A) Processing helix chain 'U' and resid 87 through 91 Processing helix chain 'U' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY U 109 " --> pdb=" O PRO U 106 " (cutoff:3.500A) Processing helix chain 'U' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG U 115 " --> pdb=" O ARG U 111 " (cutoff:3.500A) Processing helix chain 'U' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU U 123 " --> pdb=" O GLN U 119 " (cutoff:3.500A) Processing helix chain 'U' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE U 154 " --> pdb=" O HIS U 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL U 164 " --> pdb=" O ILE U 160 " (cutoff:3.500A) Processing helix chain 'U' and resid 180 through 186 Processing helix chain 'U' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU U 190 " --> pdb=" O ILE U 186 " (cutoff:3.500A) Processing helix chain 'U' and resid 202 through 211 Processing helix chain 'U' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU U 222 " --> pdb=" O VAL U 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR U 223 " --> pdb=" O ALA U 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 219 through 223' Processing helix chain 'U' and resid 227 through 245 Processing helix chain 'U' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER U 256 " --> pdb=" O GLN U 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 253 through 256' Processing helix chain 'U' and resid 257 through 268 Processing helix chain 'U' and resid 278 through 302 Processing helix chain 'V' and resid 20 through 25 Processing helix chain 'V' and resid 36 through 41 Processing helix chain 'V' and resid 46 through 54 Processing helix chain 'V' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU V 59 " --> pdb=" O LYS V 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL V 70 " --> pdb=" O GLY V 66 " (cutoff:3.500A) Processing helix chain 'V' and resid 87 through 91 Processing helix chain 'V' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY V 109 " --> pdb=" O PRO V 106 " (cutoff:3.500A) Processing helix chain 'V' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG V 115 " --> pdb=" O ARG V 111 " (cutoff:3.500A) Processing helix chain 'V' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU V 123 " --> pdb=" O GLN V 119 " (cutoff:3.500A) Processing helix chain 'V' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE V 154 " --> pdb=" O HIS V 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL V 164 " --> pdb=" O ILE V 160 " (cutoff:3.500A) Processing helix chain 'V' and resid 180 through 186 Processing helix chain 'V' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU V 190 " --> pdb=" O ILE V 186 " (cutoff:3.500A) Processing helix chain 'V' and resid 202 through 211 Processing helix chain 'V' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU V 222 " --> pdb=" O VAL V 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR V 223 " --> pdb=" O ALA V 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 219 through 223' Processing helix chain 'V' and resid 227 through 245 Processing helix chain 'V' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER V 256 " --> pdb=" O GLN V 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 253 through 256' Processing helix chain 'V' and resid 257 through 268 Processing helix chain 'V' and resid 278 through 302 Processing helix chain 'W' and resid 20 through 25 Processing helix chain 'W' and resid 36 through 41 Processing helix chain 'W' and resid 46 through 54 Processing helix chain 'W' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU W 59 " --> pdb=" O LYS W 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL W 70 " --> pdb=" O GLY W 66 " (cutoff:3.500A) Processing helix chain 'W' and resid 87 through 91 Processing helix chain 'W' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY W 109 " --> pdb=" O PRO W 106 " (cutoff:3.500A) Processing helix chain 'W' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG W 115 " --> pdb=" O ARG W 111 " (cutoff:3.500A) Processing helix chain 'W' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU W 123 " --> pdb=" O GLN W 119 " (cutoff:3.500A) Processing helix chain 'W' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE W 154 " --> pdb=" O HIS W 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL W 164 " --> pdb=" O ILE W 160 " (cutoff:3.500A) Processing helix chain 'W' and resid 180 through 186 Processing helix chain 'W' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU W 190 " --> pdb=" O ILE W 186 " (cutoff:3.500A) Processing helix chain 'W' and resid 202 through 211 Processing helix chain 'W' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU W 222 " --> pdb=" O VAL W 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR W 223 " --> pdb=" O ALA W 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 219 through 223' Processing helix chain 'W' and resid 227 through 245 Processing helix chain 'W' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER W 256 " --> pdb=" O GLN W 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 253 through 256' Processing helix chain 'W' and resid 257 through 268 Processing helix chain 'W' and resid 278 through 302 Processing helix chain 'X' and resid 20 through 25 Processing helix chain 'X' and resid 36 through 41 Processing helix chain 'X' and resid 46 through 54 Processing helix chain 'X' and resid 55 through 74 removed outlier: 3.956A pdb=" N LEU X 59 " --> pdb=" O LYS X 55 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL X 70 " --> pdb=" O GLY X 66 " (cutoff:3.500A) Processing helix chain 'X' and resid 87 through 91 Processing helix chain 'X' and resid 105 through 109 removed outlier: 3.823A pdb=" N GLY X 109 " --> pdb=" O PRO X 106 " (cutoff:3.500A) Processing helix chain 'X' and resid 111 through 119 removed outlier: 3.694A pdb=" N ARG X 115 " --> pdb=" O ARG X 111 " (cutoff:3.500A) Processing helix chain 'X' and resid 119 through 135 removed outlier: 4.537A pdb=" N LEU X 123 " --> pdb=" O GLN X 119 " (cutoff:3.500A) Processing helix chain 'X' and resid 150 through 164 removed outlier: 3.944A pdb=" N ILE X 154 " --> pdb=" O HIS X 150 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL X 164 " --> pdb=" O ILE X 160 " (cutoff:3.500A) Processing helix chain 'X' and resid 180 through 186 Processing helix chain 'X' and resid 186 through 192 removed outlier: 3.726A pdb=" N LEU X 190 " --> pdb=" O ILE X 186 " (cutoff:3.500A) Processing helix chain 'X' and resid 202 through 211 Processing helix chain 'X' and resid 219 through 223 removed outlier: 3.517A pdb=" N LEU X 222 " --> pdb=" O VAL X 219 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR X 223 " --> pdb=" O ALA X 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 219 through 223' Processing helix chain 'X' and resid 227 through 245 Processing helix chain 'X' and resid 253 through 256 removed outlier: 3.511A pdb=" N SER X 256 " --> pdb=" O GLN X 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 253 through 256' Processing helix chain 'X' and resid 257 through 268 Processing helix chain 'X' and resid 278 through 302 Processing sheet with id=AA1, first strand: chain 'A' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE A 197 " --> pdb=" O TRP A 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY A 32 " --> pdb=" O TRP A 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG A 82 " --> pdb=" O GLY A 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU A 34 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY A 32 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL A 12 " --> pdb=" O GLY A 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU A 34 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL A 14 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE B 197 " --> pdb=" O TRP B 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY B 32 " --> pdb=" O TRP B 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG B 82 " --> pdb=" O GLY B 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU B 34 " --> pdb=" O ARG B 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY B 32 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL B 12 " --> pdb=" O GLY B 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU B 34 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL B 14 " --> pdb=" O LEU B 34 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE C 197 " --> pdb=" O TRP C 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY C 32 " --> pdb=" O TRP C 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG C 82 " --> pdb=" O GLY C 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU C 34 " --> pdb=" O ARG C 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY C 32 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL C 12 " --> pdb=" O GLY C 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU C 34 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL C 14 " --> pdb=" O LEU C 34 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE D 197 " --> pdb=" O TRP D 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY D 32 " --> pdb=" O TRP D 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG D 82 " --> pdb=" O GLY D 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU D 34 " --> pdb=" O ARG D 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY D 32 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL D 12 " --> pdb=" O GLY D 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU D 34 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL D 14 " --> pdb=" O LEU D 34 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE E 197 " --> pdb=" O TRP E 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY E 32 " --> pdb=" O TRP E 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG E 82 " --> pdb=" O GLY E 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU E 34 " --> pdb=" O ARG E 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY E 32 " --> pdb=" O VAL E 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL E 12 " --> pdb=" O GLY E 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU E 34 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL E 14 " --> pdb=" O LEU E 34 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE F 197 " --> pdb=" O TRP F 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY F 32 " --> pdb=" O TRP F 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG F 82 " --> pdb=" O GLY F 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU F 34 " --> pdb=" O ARG F 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY F 32 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL F 12 " --> pdb=" O GLY F 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU F 34 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL F 14 " --> pdb=" O LEU F 34 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE G 197 " --> pdb=" O TRP G 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY G 32 " --> pdb=" O TRP G 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG G 82 " --> pdb=" O GLY G 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU G 34 " --> pdb=" O ARG G 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY G 32 " --> pdb=" O VAL G 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL G 12 " --> pdb=" O GLY G 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU G 34 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL G 14 " --> pdb=" O LEU G 34 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE H 197 " --> pdb=" O TRP H 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY H 32 " --> pdb=" O TRP H 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG H 82 " --> pdb=" O GLY H 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU H 34 " --> pdb=" O ARG H 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY H 32 " --> pdb=" O VAL H 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL H 12 " --> pdb=" O GLY H 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU H 34 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL H 14 " --> pdb=" O LEU H 34 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE I 197 " --> pdb=" O TRP I 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY I 32 " --> pdb=" O TRP I 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG I 82 " --> pdb=" O GLY I 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU I 34 " --> pdb=" O ARG I 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY I 32 " --> pdb=" O VAL I 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL I 12 " --> pdb=" O GLY I 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU I 34 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL I 14 " --> pdb=" O LEU I 34 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE J 197 " --> pdb=" O TRP J 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY J 32 " --> pdb=" O TRP J 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG J 82 " --> pdb=" O GLY J 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU J 34 " --> pdb=" O ARG J 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY J 32 " --> pdb=" O VAL J 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL J 12 " --> pdb=" O GLY J 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU J 34 " --> pdb=" O VAL J 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL J 14 " --> pdb=" O LEU J 34 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE K 197 " --> pdb=" O TRP K 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY K 32 " --> pdb=" O TRP K 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG K 82 " --> pdb=" O GLY K 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU K 34 " --> pdb=" O ARG K 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY K 32 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL K 12 " --> pdb=" O GLY K 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU K 34 " --> pdb=" O VAL K 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL K 14 " --> pdb=" O LEU K 34 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE L 197 " --> pdb=" O TRP L 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY L 32 " --> pdb=" O TRP L 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG L 82 " --> pdb=" O GLY L 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU L 34 " --> pdb=" O ARG L 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY L 32 " --> pdb=" O VAL L 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL L 12 " --> pdb=" O GLY L 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU L 34 " --> pdb=" O VAL L 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL L 14 " --> pdb=" O LEU L 34 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE M 197 " --> pdb=" O TRP M 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY M 32 " --> pdb=" O TRP M 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG M 82 " --> pdb=" O GLY M 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU M 34 " --> pdb=" O ARG M 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY M 32 " --> pdb=" O VAL M 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL M 12 " --> pdb=" O GLY M 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU M 34 " --> pdb=" O VAL M 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL M 14 " --> pdb=" O LEU M 34 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE N 197 " --> pdb=" O TRP N 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY N 32 " --> pdb=" O TRP N 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG N 82 " --> pdb=" O GLY N 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU N 34 " --> pdb=" O ARG N 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY N 32 " --> pdb=" O VAL N 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL N 12 " --> pdb=" O GLY N 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU N 34 " --> pdb=" O VAL N 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL N 14 " --> pdb=" O LEU N 34 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE O 197 " --> pdb=" O TRP O 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY O 32 " --> pdb=" O TRP O 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG O 82 " --> pdb=" O GLY O 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU O 34 " --> pdb=" O ARG O 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY O 32 " --> pdb=" O VAL O 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL O 12 " --> pdb=" O GLY O 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU O 34 " --> pdb=" O VAL O 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL O 14 " --> pdb=" O LEU O 34 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE P 197 " --> pdb=" O TRP P 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY P 32 " --> pdb=" O TRP P 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG P 82 " --> pdb=" O GLY P 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU P 34 " --> pdb=" O ARG P 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY P 32 " --> pdb=" O VAL P 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL P 12 " --> pdb=" O GLY P 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU P 34 " --> pdb=" O VAL P 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL P 14 " --> pdb=" O LEU P 34 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Q' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE Q 197 " --> pdb=" O TRP Q 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY Q 32 " --> pdb=" O TRP Q 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG Q 82 " --> pdb=" O GLY Q 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU Q 34 " --> pdb=" O ARG Q 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY Q 32 " --> pdb=" O VAL Q 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL Q 12 " --> pdb=" O GLY Q 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU Q 34 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL Q 14 " --> pdb=" O LEU Q 34 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'R' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE R 197 " --> pdb=" O TRP R 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY R 32 " --> pdb=" O TRP R 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG R 82 " --> pdb=" O GLY R 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU R 34 " --> pdb=" O ARG R 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY R 32 " --> pdb=" O VAL R 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL R 12 " --> pdb=" O GLY R 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU R 34 " --> pdb=" O VAL R 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL R 14 " --> pdb=" O LEU R 34 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'S' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE S 197 " --> pdb=" O TRP S 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY S 32 " --> pdb=" O TRP S 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG S 82 " --> pdb=" O GLY S 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU S 34 " --> pdb=" O ARG S 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY S 32 " --> pdb=" O VAL S 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL S 12 " --> pdb=" O GLY S 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU S 34 " --> pdb=" O VAL S 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL S 14 " --> pdb=" O LEU S 34 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'T' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE T 197 " --> pdb=" O TRP T 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY T 32 " --> pdb=" O TRP T 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG T 82 " --> pdb=" O GLY T 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU T 34 " --> pdb=" O ARG T 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY T 32 " --> pdb=" O VAL T 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL T 12 " --> pdb=" O GLY T 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU T 34 " --> pdb=" O VAL T 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL T 14 " --> pdb=" O LEU T 34 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'U' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE U 197 " --> pdb=" O TRP U 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY U 32 " --> pdb=" O TRP U 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG U 82 " --> pdb=" O GLY U 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU U 34 " --> pdb=" O ARG U 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY U 32 " --> pdb=" O VAL U 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL U 12 " --> pdb=" O GLY U 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU U 34 " --> pdb=" O VAL U 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL U 14 " --> pdb=" O LEU U 34 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'V' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE V 197 " --> pdb=" O TRP V 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY V 32 " --> pdb=" O TRP V 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG V 82 " --> pdb=" O GLY V 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU V 34 " --> pdb=" O ARG V 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY V 32 " --> pdb=" O VAL V 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL V 12 " --> pdb=" O GLY V 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU V 34 " --> pdb=" O VAL V 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL V 14 " --> pdb=" O LEU V 34 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'W' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE W 197 " --> pdb=" O TRP W 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY W 32 " --> pdb=" O TRP W 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG W 82 " --> pdb=" O GLY W 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU W 34 " --> pdb=" O ARG W 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY W 32 " --> pdb=" O VAL W 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL W 12 " --> pdb=" O GLY W 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU W 34 " --> pdb=" O VAL W 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL W 14 " --> pdb=" O LEU W 34 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'X' and resid 247 through 251 removed outlier: 3.603A pdb=" N PHE X 197 " --> pdb=" O TRP X 174 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY X 32 " --> pdb=" O TRP X 80 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARG X 82 " --> pdb=" O GLY X 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU X 34 " --> pdb=" O ARG X 82 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLY X 32 " --> pdb=" O VAL X 10 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL X 12 " --> pdb=" O GLY X 32 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU X 34 " --> pdb=" O VAL X 12 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL X 14 " --> pdb=" O LEU X 34 " (cutoff:3.500A) 3024 hydrogen bonds defined for protein. 8784 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: 24.85 Time building geometry restraints manager: 12.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 19200 1.34 - 1.46: 8016 1.46 - 1.58: 29832 1.58 - 1.70: 0 1.70 - 1.81: 480 Bond restraints: 57528 Sorted by residual: bond pdb=" C MET T 94 " pdb=" N PRO T 95 " ideal model delta sigma weight residual 1.332 1.357 -0.025 1.12e-02 7.97e+03 4.87e+00 bond pdb=" C MET W 94 " pdb=" N PRO W 95 " ideal model delta sigma weight residual 1.332 1.357 -0.025 1.12e-02 7.97e+03 4.87e+00 bond pdb=" C MET G 94 " pdb=" N PRO G 95 " ideal model delta sigma weight residual 1.332 1.357 -0.025 1.12e-02 7.97e+03 4.87e+00 bond pdb=" C MET X 94 " pdb=" N PRO X 95 " ideal model delta sigma weight residual 1.332 1.357 -0.025 1.12e-02 7.97e+03 4.87e+00 bond pdb=" C MET H 94 " pdb=" N PRO H 95 " ideal model delta sigma weight residual 1.332 1.357 -0.025 1.12e-02 7.97e+03 4.87e+00 ... (remaining 57523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 75432 1.82 - 3.63: 1800 3.63 - 5.45: 312 5.45 - 7.26: 120 7.26 - 9.08: 48 Bond angle restraints: 77712 Sorted by residual: angle pdb=" C TYR V 75 " pdb=" N PRO V 76 " pdb=" CA PRO V 76 " ideal model delta sigma weight residual 119.84 111.56 8.28 1.25e+00 6.40e-01 4.39e+01 angle pdb=" C TYR J 75 " pdb=" N PRO J 76 " pdb=" CA PRO J 76 " ideal model delta sigma weight residual 119.84 111.56 8.28 1.25e+00 6.40e-01 4.39e+01 angle pdb=" C TYR W 75 " pdb=" N PRO W 76 " pdb=" CA PRO W 76 " ideal model delta sigma weight residual 119.84 111.56 8.28 1.25e+00 6.40e-01 4.39e+01 angle pdb=" C TYR G 75 " pdb=" N PRO G 76 " pdb=" CA PRO G 76 " ideal model delta sigma weight residual 119.84 111.56 8.28 1.25e+00 6.40e-01 4.39e+01 angle pdb=" C TYR I 75 " pdb=" N PRO I 76 " pdb=" CA PRO I 76 " ideal model delta sigma weight residual 119.84 111.56 8.28 1.25e+00 6.40e-01 4.39e+01 ... (remaining 77707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 31464 17.90 - 35.80: 3240 35.80 - 53.70: 768 53.70 - 71.59: 192 71.59 - 89.49: 48 Dihedral angle restraints: 35712 sinusoidal: 14952 harmonic: 20760 Sorted by residual: dihedral pdb=" CB GLU V 37 " pdb=" CG GLU V 37 " pdb=" CD GLU V 37 " pdb=" OE1 GLU V 37 " ideal model delta sinusoidal sigma weight residual 0.00 89.49 -89.49 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU U 37 " pdb=" CG GLU U 37 " pdb=" CD GLU U 37 " pdb=" OE1 GLU U 37 " ideal model delta sinusoidal sigma weight residual 0.00 89.49 -89.49 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU B 37 " pdb=" CG GLU B 37 " pdb=" CD GLU B 37 " pdb=" OE1 GLU B 37 " ideal model delta sinusoidal sigma weight residual 0.00 89.49 -89.49 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 35709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 6696 0.054 - 0.108: 1800 0.108 - 0.162: 264 0.162 - 0.216: 0 0.216 - 0.270: 24 Chirality restraints: 8784 Sorted by residual: chirality pdb=" CA TYR A 75 " pdb=" N TYR A 75 " pdb=" C TYR A 75 " pdb=" CB TYR A 75 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA TYR U 75 " pdb=" N TYR U 75 " pdb=" C TYR U 75 " pdb=" CB TYR U 75 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA TYR M 75 " pdb=" N TYR M 75 " pdb=" C TYR M 75 " pdb=" CB TYR M 75 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 8781 not shown) Planarity restraints: 10152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET H 16 " 0.041 5.00e-02 4.00e+02 6.18e-02 6.11e+00 pdb=" N PRO H 17 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO H 17 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO H 17 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET X 16 " 0.041 5.00e-02 4.00e+02 6.18e-02 6.11e+00 pdb=" N PRO X 17 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO X 17 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO X 17 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET K 16 " 0.041 5.00e-02 4.00e+02 6.18e-02 6.11e+00 pdb=" N PRO K 17 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO K 17 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO K 17 " 0.034 5.00e-02 4.00e+02 ... (remaining 10149 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 18828 2.86 - 3.37: 50352 3.37 - 3.88: 86580 3.88 - 4.39: 100116 4.39 - 4.90: 172368 Nonbonded interactions: 428244 Sorted by model distance: nonbonded pdb=" O ALA K 23 " pdb=" OG1 THR K 26 " model vdw 2.353 3.040 nonbonded pdb=" O ALA Q 23 " pdb=" OG1 THR Q 26 " model vdw 2.353 3.040 nonbonded pdb=" O ALA C 23 " pdb=" OG1 THR C 26 " model vdw 2.353 3.040 nonbonded pdb=" O ALA N 23 " pdb=" OG1 THR N 26 " model vdw 2.353 3.040 nonbonded pdb=" O ALA R 23 " pdb=" OG1 THR R 26 " model vdw 2.353 3.040 ... (remaining 428239 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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 individual isotropic 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 1.830 Check model and map are aligned: 0.340 Set scattering table: 0.450 Process input model: 88.180 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.390 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 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 : 0.005 0.046 57528 Z= 0.349 Angle : 0.790 9.080 77712 Z= 0.500 Chirality : 0.049 0.270 8784 Planarity : 0.007 0.062 10152 Dihedral : 15.948 89.493 22320 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 2.81 % Allowed : 12.45 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.08), residues: 7200 helix: -1.38 (0.07), residues: 3720 sheet: -0.89 (0.17), residues: 720 loop : -2.74 (0.09), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP O 80 HIS 0.005 0.002 HIS G 227 PHE 0.020 0.003 PHE R 74 TYR 0.016 0.002 TYR P 75 ARG 0.003 0.000 ARG O 262 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 5976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 408 time to evaluate : 5.430 Fit side-chains REVERT: A 177 MET cc_start: 0.8456 (mtp) cc_final: 0.8145 (mmm) REVERT: B 177 MET cc_start: 0.8460 (mtp) cc_final: 0.8144 (mmm) REVERT: C 177 MET cc_start: 0.8463 (mtp) cc_final: 0.8147 (mmm) REVERT: D 177 MET cc_start: 0.8462 (mtp) cc_final: 0.8145 (mmm) REVERT: E 177 MET cc_start: 0.8462 (mtp) cc_final: 0.8146 (mmm) REVERT: F 177 MET cc_start: 0.8464 (mtp) cc_final: 0.8145 (mmm) REVERT: G 177 MET cc_start: 0.8469 (mtp) cc_final: 0.8148 (mmm) REVERT: H 177 MET cc_start: 0.8468 (mtp) cc_final: 0.8150 (mmm) REVERT: I 177 MET cc_start: 0.8464 (mtp) cc_final: 0.8145 (mmm) REVERT: J 177 MET cc_start: 0.8469 (mtp) cc_final: 0.8148 (mmm) REVERT: K 177 MET cc_start: 0.8468 (mtp) cc_final: 0.8150 (mmm) REVERT: L 177 MET cc_start: 0.8462 (mtp) cc_final: 0.8146 (mmm) REVERT: M 177 MET cc_start: 0.8460 (mtp) cc_final: 0.8144 (mmm) REVERT: N 177 MET cc_start: 0.8463 (mtp) cc_final: 0.8147 (mmm) REVERT: O 177 MET cc_start: 0.8462 (mtp) cc_final: 0.8145 (mmm) REVERT: P 177 MET cc_start: 0.8456 (mtp) cc_final: 0.8145 (mmm) REVERT: Q 177 MET cc_start: 0.8462 (mtp) cc_final: 0.8145 (mmm) REVERT: R 177 MET cc_start: 0.8456 (mtp) cc_final: 0.8145 (mmm) REVERT: S 177 MET cc_start: 0.8460 (mtp) cc_final: 0.8144 (mmm) REVERT: T 177 MET cc_start: 0.8463 (mtp) cc_final: 0.8147 (mmm) REVERT: U 177 MET cc_start: 0.8462 (mtp) cc_final: 0.8146 (mmm) REVERT: V 177 MET cc_start: 0.8464 (mtp) cc_final: 0.8145 (mmm) REVERT: W 177 MET cc_start: 0.8469 (mtp) cc_final: 0.8148 (mmm) REVERT: X 177 MET cc_start: 0.8468 (mtp) cc_final: 0.8150 (mmm) outliers start: 168 outliers final: 96 residues processed: 576 average time/residue: 1.7680 time to fit residues: 1231.8908 Evaluate side-chains 336 residues out of total 5976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 240 time to evaluate : 5.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 74 PHE Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 74 PHE Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 74 PHE Chi-restraints excluded: chain F residue 163 GLU Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 74 PHE Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 74 PHE Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 74 PHE Chi-restraints excluded: chain I residue 163 GLU Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 74 PHE Chi-restraints excluded: chain J residue 163 GLU Chi-restraints excluded: chain J residue 212 ILE Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 74 PHE Chi-restraints excluded: chain K residue 163 GLU Chi-restraints excluded: chain K residue 212 ILE Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 74 PHE Chi-restraints excluded: chain L residue 163 GLU Chi-restraints excluded: chain L residue 212 ILE Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 74 PHE Chi-restraints excluded: chain M residue 163 GLU Chi-restraints excluded: chain M residue 212 ILE Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 74 PHE Chi-restraints excluded: chain N residue 163 GLU Chi-restraints excluded: chain N residue 212 ILE Chi-restraints excluded: chain O residue 5 VAL Chi-restraints excluded: chain O residue 74 PHE Chi-restraints excluded: chain O residue 163 GLU Chi-restraints excluded: chain O residue 212 ILE Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 74 PHE Chi-restraints excluded: chain P residue 163 GLU Chi-restraints excluded: chain P residue 212 ILE Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain Q residue 74 PHE Chi-restraints excluded: chain Q residue 163 GLU Chi-restraints excluded: chain Q residue 212 ILE Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 163 GLU Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 74 PHE Chi-restraints excluded: chain S residue 163 GLU Chi-restraints excluded: chain S residue 212 ILE Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain T residue 74 PHE Chi-restraints excluded: chain T residue 163 GLU Chi-restraints excluded: chain T residue 212 ILE Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 74 PHE Chi-restraints excluded: chain U residue 163 GLU Chi-restraints excluded: chain U residue 212 ILE Chi-restraints excluded: chain V residue 5 VAL Chi-restraints excluded: chain V residue 74 PHE Chi-restraints excluded: chain V residue 163 GLU Chi-restraints excluded: chain V residue 212 ILE Chi-restraints excluded: chain W residue 5 VAL Chi-restraints excluded: chain W residue 74 PHE Chi-restraints excluded: chain W residue 163 GLU Chi-restraints excluded: chain W residue 212 ILE Chi-restraints excluded: chain X residue 5 VAL Chi-restraints excluded: chain X residue 74 PHE Chi-restraints excluded: chain X residue 163 GLU Chi-restraints excluded: chain X residue 212 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.9907 > 50: distance: 14 - 23: 3.211 distance: 55 - 74: 19.108 distance: 60 - 79: 19.057 distance: 63 - 67: 9.308 distance: 64 - 84: 18.744 distance: 67 - 68: 13.995 distance: 68 - 69: 11.583 distance: 68 - 71: 4.079 distance: 69 - 70: 19.048 distance: 69 - 74: 7.202 distance: 70 - 89: 36.211 distance: 71 - 72: 10.783 distance: 71 - 73: 14.999 distance: 74 - 75: 24.055 distance: 75 - 78: 9.250 distance: 76 - 79: 17.320 distance: 79 - 80: 10.569 distance: 80 - 81: 12.438 distance: 80 - 83: 32.819 distance: 81 - 82: 34.594 distance: 81 - 84: 18.315 distance: 84 - 85: 20.499 distance: 85 - 86: 18.451 distance: 85 - 88: 21.966 distance: 86 - 87: 11.531 distance: 86 - 89: 10.214 distance: 89 - 90: 6.035 distance: 90 - 91: 45.007 distance: 90 - 93: 32.755 distance: 91 - 92: 56.804 distance: 91 - 100: 56.426 distance: 93 - 94: 28.803 distance: 94 - 95: 15.532 distance: 94 - 96: 19.121 distance: 95 - 97: 11.856 distance: 96 - 98: 41.574 distance: 97 - 99: 24.181 distance: 98 - 99: 38.056 distance: 100 - 101: 46.196 distance: 101 - 102: 46.768 distance: 101 - 104: 15.322 distance: 102 - 112: 40.757 distance: 105 - 106: 19.941 distance: 105 - 107: 15.662 distance: 106 - 108: 38.247 distance: 107 - 109: 30.723 distance: 108 - 110: 31.707 distance: 109 - 110: 19.319 distance: 110 - 111: 25.824 distance: 112 - 113: 45.842 distance: 112 - 118: 39.470 distance: 113 - 114: 18.473 distance: 113 - 116: 51.465 distance: 114 - 115: 31.830 distance: 114 - 119: 40.040 distance: 116 - 117: 17.561 distance: 117 - 118: 5.126 distance: 119 - 120: 3.747 distance: 120 - 121: 40.863 distance: 120 - 123: 21.500 distance: 121 - 122: 42.032 distance: 121 - 130: 14.365 distance: 123 - 124: 24.250 distance: 124 - 125: 21.137 distance: 125 - 126: 31.258 distance: 126 - 127: 16.190 distance: 127 - 128: 11.169 distance: 127 - 129: 28.050 distance: 130 - 131: 4.594 distance: 130 - 136: 42.415 distance: 131 - 132: 11.874 distance: 131 - 134: 35.202 distance: 132 - 133: 29.333 distance: 132 - 137: 36.881 distance: 134 - 135: 7.126 distance: 135 - 136: 4.763 distance: 137 - 138: 16.035 distance: 138 - 139: 44.909 distance: 138 - 141: 24.917 distance: 139 - 140: 17.597 distance: 139 - 144: 27.971 distance: 140 - 190: 33.697 distance: 141 - 142: 32.894 distance: 141 - 143: 33.374 distance: 154 - 193: 3.134