Starting phenix.real_space_refine on Thu Jan 18 06:23:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bnp_7116/01_2024/6bnp_7116_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bnp_7116/01_2024/6bnp_7116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bnp_7116/01_2024/6bnp_7116.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bnp_7116/01_2024/6bnp_7116.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bnp_7116/01_2024/6bnp_7116_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bnp_7116/01_2024/6bnp_7116_updated.pdb" } resolution = 4.6 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 8 5.21 5 S 310 5.16 5 C 35822 2.51 5 N 9738 2.21 5 O 10898 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I ASP 3": "OD1" <-> "OD2" Residue "I ASP 14": "OD1" <-> "OD2" Residue "I ASP 23": "OD1" <-> "OD2" Residue "I PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 54": "OD1" <-> "OD2" Residue "I GLU 60": "OE1" <-> "OE2" Residue "I TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 132": "OD1" <-> "OD2" Residue "I GLU 152": "OE1" <-> "OE2" Residue "I GLU 159": "OE1" <-> "OE2" Residue "I ASP 177": "OD1" <-> "OD2" Residue "I ASP 179": "OD1" <-> "OD2" Residue "I GLU 190": "OE1" <-> "OE2" Residue "I GLU 211": "OE1" <-> "OE2" Residue "I PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 216": "OE1" <-> "OE2" Residue "I TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 241": "OE1" <-> "OE2" Residue "I GLU 242": "OE1" <-> "OE2" Residue "I GLU 261": "OE1" <-> "OE2" Residue "I ASP 269": "OD1" <-> "OD2" Residue "I GLU 286": "OE1" <-> "OE2" Residue "I ASP 288": "OD1" <-> "OD2" Residue "I TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 308": "OD1" <-> "OD2" Residue "I ASP 331": "OD1" <-> "OD2" Residue "I ASP 351": "OD1" <-> "OD2" Residue "I GLU 353": "OE1" <-> "OE2" Residue "I GLU 354": "OE1" <-> "OE2" Residue "I GLU 373": "OE1" <-> "OE2" Residue "I TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 384": "OD1" <-> "OD2" Residue "I GLU 414": "OE1" <-> "OE2" Residue "I PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 464": "OE1" <-> "OE2" Residue "I GLU 494": "OE1" <-> "OE2" Residue "I ASP 513": "OD1" <-> "OD2" Residue "I GLU 519": "OE1" <-> "OE2" Residue "I ASP 527": "OD1" <-> "OD2" Residue "I GLU 531": "OE1" <-> "OE2" Residue "I ASP 540": "OD1" <-> "OD2" Residue "I ASP 574": "OD1" <-> "OD2" Residue "I PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 595": "OE1" <-> "OE2" Residue "I ASP 599": "OD1" <-> "OD2" Residue "I ASP 614": "OD1" <-> "OD2" Residue "I GLU 619": "OE1" <-> "OE2" Residue "I PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 656": "OD1" <-> "OD2" Residue "I PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 3": "OD1" <-> "OD2" Residue "J ASP 27": "OD1" <-> "OD2" Residue "J GLU 32": "OE1" <-> "OE2" Residue "J PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 61": "OD1" <-> "OD2" Residue "J GLU 70": "OE1" <-> "OE2" Residue "J ASP 102": "OD1" <-> "OD2" Residue "J TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 132": "OD1" <-> "OD2" Residue "J GLU 152": "OE1" <-> "OE2" Residue "J ASP 177": "OD1" <-> "OD2" Residue "J GLU 190": "OE1" <-> "OE2" Residue "J PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 211": "OE1" <-> "OE2" Residue "J PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 241": "OE1" <-> "OE2" Residue "J GLU 242": "OE1" <-> "OE2" Residue "J ASP 258": "OD1" <-> "OD2" Residue "J ASP 269": "OD1" <-> "OD2" Residue "J GLU 286": "OE1" <-> "OE2" Residue "J GLU 299": "OE1" <-> "OE2" Residue "J TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 308": "OD1" <-> "OD2" Residue "J ASP 330": "OD1" <-> "OD2" Residue "J GLU 332": "OE1" <-> "OE2" Residue "J GLU 333": "OE1" <-> "OE2" Residue "J ASP 351": "OD1" <-> "OD2" Residue "J GLU 354": "OE1" <-> "OE2" Residue "J TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 385": "OD1" <-> "OD2" Residue "J PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 433": "OD1" <-> "OD2" Residue "J PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 456": "OD1" <-> "OD2" Residue "J GLU 461": "OE1" <-> "OE2" Residue "J GLU 486": "OE1" <-> "OE2" Residue "J GLU 491": "OE1" <-> "OE2" Residue "J GLU 499": "OE1" <-> "OE2" Residue "J GLU 505": "OE1" <-> "OE2" Residue "J ASP 527": "OD1" <-> "OD2" Residue "J PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 606": "OE1" <-> "OE2" Residue "J ASP 614": "OD1" <-> "OD2" Residue "J ASP 630": "OD1" <-> "OD2" Residue "J PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 681": "OE1" <-> "OE2" Residue "K ASP 3": "OD1" <-> "OD2" Residue "K ASP 23": "OD1" <-> "OD2" Residue "K PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 53": "OE1" <-> "OE2" Residue "K ASP 54": "OD1" <-> "OD2" Residue "K ASP 61": "OD1" <-> "OD2" Residue "K GLU 70": "OE1" <-> "OE2" Residue "K PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 102": "OD1" <-> "OD2" Residue "K TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 152": "OE1" <-> "OE2" Residue "K ASP 177": "OD1" <-> "OD2" Residue "K ASP 180": "OD1" <-> "OD2" Residue "K GLU 184": "OE1" <-> "OE2" Residue "K GLU 190": "OE1" <-> "OE2" Residue "K PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 211": "OE1" <-> "OE2" Residue "K PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 216": "OE1" <-> "OE2" Residue "K GLU 241": "OE1" <-> "OE2" Residue "K GLU 242": "OE1" <-> "OE2" Residue "K TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 258": "OD1" <-> "OD2" Residue "K GLU 261": "OE1" <-> "OE2" Residue "K ASP 269": "OD1" <-> "OD2" Residue "K GLU 286": "OE1" <-> "OE2" Residue "K GLU 299": "OE1" <-> "OE2" Residue "K TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 308": "OD1" <-> "OD2" Residue "K GLU 333": "OE1" <-> "OE2" Residue "K ASP 351": "OD1" <-> "OD2" Residue "K PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 373": "OE1" <-> "OE2" Residue "K ASP 382": "OD1" <-> "OD2" Residue "K ASP 385": "OD1" <-> "OD2" Residue "K GLU 414": "OE1" <-> "OE2" Residue "K PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 446": "OE1" <-> "OE2" Residue "K PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 456": "OD1" <-> "OD2" Residue "K GLU 486": "OE1" <-> "OE2" Residue "K GLU 492": "OE1" <-> "OE2" Residue "K GLU 494": "OE1" <-> "OE2" Residue "K GLU 499": "OE1" <-> "OE2" Residue "K GLU 505": "OE1" <-> "OE2" Residue "K ASP 513": "OD1" <-> "OD2" Residue "K ASP 540": "OD1" <-> "OD2" Residue "K ASP 574": "OD1" <-> "OD2" Residue "K PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 589": "OE1" <-> "OE2" Residue "K PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 595": "OE1" <-> "OE2" Residue "K ASP 599": "OD1" <-> "OD2" Residue "K GLU 606": "OE1" <-> "OE2" Residue "K ASP 614": "OD1" <-> "OD2" Residue "K ASP 630": "OD1" <-> "OD2" Residue "K PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 656": "OD1" <-> "OD2" Residue "K PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 681": "OE1" <-> "OE2" Residue "L ASP 14": "OD1" <-> "OD2" Residue "L PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 53": "OE1" <-> "OE2" Residue "L ASP 61": "OD1" <-> "OD2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "L ASP 102": "OD1" <-> "OD2" Residue "L TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 132": "OD1" <-> "OD2" Residue "L GLU 159": "OE1" <-> "OE2" Residue "L ASP 179": "OD1" <-> "OD2" Residue "L ASP 180": "OD1" <-> "OD2" Residue "L GLU 184": "OE1" <-> "OE2" Residue "L GLU 190": "OE1" <-> "OE2" Residue "L PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 211": "OE1" <-> "OE2" Residue "L PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 241": "OE1" <-> "OE2" Residue "L GLU 242": "OE1" <-> "OE2" Residue "L TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 257": "OE1" <-> "OE2" Residue "L ASP 258": "OD1" <-> "OD2" Residue "L ASP 269": "OD1" <-> "OD2" Residue "L GLU 286": "OE1" <-> "OE2" Residue "L ASP 288": "OD1" <-> "OD2" Residue "L ASP 316": "OD1" <-> "OD2" Residue "L ASP 331": "OD1" <-> "OD2" Residue "L ASP 351": "OD1" <-> "OD2" Residue "L PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 353": "OE1" <-> "OE2" Residue "L GLU 354": "OE1" <-> "OE2" Residue "L TYR 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 377": "OE1" <-> "OE2" Residue "L ASP 382": "OD1" <-> "OD2" Residue "L ASP 384": "OD1" <-> "OD2" Residue "L ASP 385": "OD1" <-> "OD2" Residue "L GLU 414": "OE1" <-> "OE2" Residue "L TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 446": "OE1" <-> "OE2" Residue "L PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 456": "OD1" <-> "OD2" Residue "L GLU 461": "OE1" <-> "OE2" Residue "L GLU 499": "OE1" <-> "OE2" Residue "L GLU 505": "OE1" <-> "OE2" Residue "L ASP 527": "OD1" <-> "OD2" Residue "L GLU 531": "OE1" <-> "OE2" Residue "L PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 606": "OE1" <-> "OE2" Residue "L GLU 611": "OE1" <-> "OE2" Residue "L PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 656": "OD1" <-> "OD2" Residue "L PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 3": "OD1" <-> "OD2" Residue "M ASP 23": "OD1" <-> "OD2" Residue "M ASP 27": "OD1" <-> "OD2" Residue "M PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 52": "OE1" <-> "OE2" Residue "M ASP 54": "OD1" <-> "OD2" Residue "M GLU 60": "OE1" <-> "OE2" Residue "M ASP 61": "OD1" <-> "OD2" Residue "M GLU 110": "OE1" <-> "OE2" Residue "M ASP 132": "OD1" <-> "OD2" Residue "M GLU 152": "OE1" <-> "OE2" Residue "M GLU 159": "OE1" <-> "OE2" Residue "M ASP 177": "OD1" <-> "OD2" Residue "M ASP 179": "OD1" <-> "OD2" Residue "M ASP 180": "OD1" <-> "OD2" Residue "M GLU 190": "OE1" <-> "OE2" Residue "M PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 216": "OE1" <-> "OE2" Residue "M GLU 241": "OE1" <-> "OE2" Residue "M GLU 242": "OE1" <-> "OE2" Residue "M TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 261": "OE1" <-> "OE2" Residue "M ASP 269": "OD1" <-> "OD2" Residue "M PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 299": "OE1" <-> "OE2" Residue "M TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 308": "OD1" <-> "OD2" Residue "M ASP 330": "OD1" <-> "OD2" Residue "M GLU 332": "OE1" <-> "OE2" Residue "M GLU 353": "OE1" <-> "OE2" Residue "M GLU 377": "OE1" <-> "OE2" Residue "M ASP 382": "OD1" <-> "OD2" Residue "M GLU 414": "OE1" <-> "OE2" Residue "M GLU 446": "OE1" <-> "OE2" Residue "M ASP 456": "OD1" <-> "OD2" Residue "M PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 486": "OE1" <-> "OE2" Residue "M GLU 494": "OE1" <-> "OE2" Residue "M GLU 499": "OE1" <-> "OE2" Residue "M GLU 505": "OE1" <-> "OE2" Residue "M ASP 516": "OD1" <-> "OD2" Residue "M GLU 519": "OE1" <-> "OE2" Residue "M ASP 527": "OD1" <-> "OD2" Residue "M ASP 530": "OD1" <-> "OD2" Residue "M GLU 531": "OE1" <-> "OE2" Residue "M ASP 573": "OD1" <-> "OD2" Residue "M ASP 574": "OD1" <-> "OD2" Residue "M PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 589": "OE1" <-> "OE2" Residue "M PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 630": "OD1" <-> "OD2" Residue "M PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 656": "OD1" <-> "OD2" Residue "M PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 3": "OD1" <-> "OD2" Residue "N PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 52": "OE1" <-> "OE2" Residue "N ASP 102": "OD1" <-> "OD2" Residue "N TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 159": "OE1" <-> "OE2" Residue "N GLU 170": "OE1" <-> "OE2" Residue "N GLU 190": "OE1" <-> "OE2" Residue "N GLU 211": "OE1" <-> "OE2" Residue "N PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 242": "OE1" <-> "OE2" Residue "N ASP 269": "OD1" <-> "OD2" Residue "N GLU 286": "OE1" <-> "OE2" Residue "N GLU 299": "OE1" <-> "OE2" Residue "N TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 308": "OD1" <-> "OD2" Residue "N ASP 330": "OD1" <-> "OD2" Residue "N GLU 333": "OE1" <-> "OE2" Residue "N ASP 351": "OD1" <-> "OD2" Residue "N GLU 354": "OE1" <-> "OE2" Residue "N GLU 373": "OE1" <-> "OE2" Residue "N ASP 382": "OD1" <-> "OD2" Residue "N ASP 384": "OD1" <-> "OD2" Residue "N ASP 385": "OD1" <-> "OD2" Residue "N ASP 433": "OD1" <-> "OD2" Residue "N PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 456": "OD1" <-> "OD2" Residue "N GLU 461": "OE1" <-> "OE2" Residue "N GLU 491": "OE1" <-> "OE2" Residue "N GLU 494": "OE1" <-> "OE2" Residue "N GLU 499": "OE1" <-> "OE2" Residue "N ASP 513": "OD1" <-> "OD2" Residue "N ASP 516": "OD1" <-> "OD2" Residue "N GLU 519": "OE1" <-> "OE2" Residue "N ASP 527": "OD1" <-> "OD2" Residue "N ASP 540": "OD1" <-> "OD2" Residue "N PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 589": "OE1" <-> "OE2" Residue "N PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 614": "OD1" <-> "OD2" Residue "N PHE 680": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 681": "OE1" <-> "OE2" Residue "A PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 51": "OD1" <-> "OD2" Residue "A TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 56": "OD1" <-> "OD2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 72": "OE1" <-> "OE2" Residue "A GLU 99": "OE1" <-> "OE2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 157": "OD1" <-> "OD2" Residue "A TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 184": "OD1" <-> "OD2" Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 222": "OD1" <-> "OD2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A GLU 241": "OE1" <-> "OE2" Residue "A GLU 253": "OE1" <-> "OE2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 270": "OE1" <-> "OE2" Residue "A ASP 292": "OD1" <-> "OD2" Residue "A ASP 311": "OD1" <-> "OD2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 361": "OE1" <-> "OE2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 51": "OD1" <-> "OD2" Residue "B ASP 56": "OD1" <-> "OD2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B ASP 81": "OD1" <-> "OD2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 93": "OE1" <-> "OE2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B GLU 117": "OE1" <-> "OE2" Residue "B ASP 157": "OD1" <-> "OD2" Residue "B ASP 184": "OD1" <-> "OD2" Residue "B GLU 195": "OE1" <-> "OE2" Residue "B TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 211": "OD1" <-> "OD2" Residue "B ASP 222": "OD1" <-> "OD2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B GLU 237": "OE1" <-> "OE2" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 259": "OE1" <-> "OE2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 276": "OE1" <-> "OE2" Residue "B ASP 286": "OD1" <-> "OD2" Residue "B ASP 288": "OD1" <-> "OD2" Residue "B GLU 316": "OE1" <-> "OE2" Residue "B PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 363": "OD1" <-> "OD2" Residue "B GLU 364": "OE1" <-> "OE2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 51": "OD1" <-> "OD2" Residue "C ASP 56": "OD1" <-> "OD2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C GLU 93": "OE1" <-> "OE2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "C GLU 107": "OE1" <-> "OE2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "C ASP 157": "OD1" <-> "OD2" Residue "C GLU 167": "OE1" <-> "OE2" Residue "C ASP 179": "OD1" <-> "OD2" Residue "C ASP 187": "OD1" <-> "OD2" Residue "C GLU 195": "OE1" <-> "OE2" Residue "C TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C GLU 237": "OE1" <-> "OE2" Residue "C GLU 241": "OE1" <-> "OE2" Residue "C GLU 259": "OE1" <-> "OE2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 334": "OE1" <-> "OE2" Residue "C PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 361": "OE1" <-> "OE2" Residue "C ASP 363": "OD1" <-> "OD2" Residue "D PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 25": "OD1" <-> "OD2" Residue "D PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 51": "OD1" <-> "OD2" Residue "D ASP 56": "OD1" <-> "OD2" Residue "D GLU 72": "OE1" <-> "OE2" Residue "D ASP 80": "OD1" <-> "OD2" Residue "D GLU 83": "OE1" <-> "OE2" Residue "D PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D GLU 125": "OE1" <-> "OE2" Residue "D TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 157": "OD1" <-> "OD2" Residue "D ASP 179": "OD1" <-> "OD2" Residue "D ASP 184": "OD1" <-> "OD2" Residue "D ASP 187": "OD1" <-> "OD2" Residue "D GLU 195": "OE1" <-> "OE2" Residue "D TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 211": "OD1" <-> "OD2" Residue "D ASP 222": "OD1" <-> "OD2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D GLU 226": "OE1" <-> "OE2" Residue "D GLU 237": "OE1" <-> "OE2" Residue "D GLU 259": "OE1" <-> "OE2" Residue "D GLU 276": "OE1" <-> "OE2" Residue "D ASP 286": "OD1" <-> "OD2" Residue "D ASP 288": "OD1" <-> "OD2" Residue "D GLU 316": "OE1" <-> "OE2" Residue "D GLU 334": "OE1" <-> "OE2" Residue "D PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 363": "OD1" <-> "OD2" Residue "D GLU 364": "OE1" <-> "OE2" Residue "E ASP 51": "OD1" <-> "OD2" Residue "E ASP 56": "OD1" <-> "OD2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "E TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 72": "OE1" <-> "OE2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E GLU 93": "OE1" <-> "OE2" Residue "E GLU 117": "OE1" <-> "OE2" Residue "E PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 157": "OD1" <-> "OD2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E ASP 179": "OD1" <-> "OD2" Residue "E TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 214": "OE1" <-> "OE2" Residue "E GLU 224": "OE1" <-> "OE2" Residue "E GLU 237": "OE1" <-> "OE2" Residue "E PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 286": "OD1" <-> "OD2" Residue "E ASP 292": "OD1" <-> "OD2" Residue "E ASP 311": "OD1" <-> "OD2" Residue "E PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 361": "OE1" <-> "OE2" Residue "E ASP 363": "OD1" <-> "OD2" Residue "E GLU 364": "OE1" <-> "OE2" Residue "F PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 51": "OD1" <-> "OD2" Residue "F ASP 56": "OD1" <-> "OD2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "F TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 100": "OE1" <-> "OE2" Residue "F TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 157": "OD1" <-> "OD2" Residue "F TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 167": "OE1" <-> "OE2" Residue "F TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 179": "OD1" <-> "OD2" Residue "F ASP 187": "OD1" <-> "OD2" Residue "F TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 207": "OE1" <-> "OE2" Residue "F ASP 222": "OD1" <-> "OD2" Residue "F GLU 226": "OE1" <-> "OE2" Residue "F GLU 237": "OE1" <-> "OE2" Residue "F PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 276": "OE1" <-> "OE2" Residue "F ASP 288": "OD1" <-> "OD2" Residue "F ASP 292": "OD1" <-> "OD2" Residue "F GLU 334": "OE1" <-> "OE2" Residue "F PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 361": "OE1" <-> "OE2" Residue "F ASP 363": "OD1" <-> "OD2" Residue "F GLU 364": "OE1" <-> "OE2" Residue "G PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 24": "OD1" <-> "OD2" Residue "G PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 51": "OD1" <-> "OD2" Residue "G TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 56": "OD1" <-> "OD2" Residue "G GLU 72": "OE1" <-> "OE2" Residue "G ASP 81": "OD1" <-> "OD2" Residue "G PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 99": "OE1" <-> "OE2" Residue "G GLU 125": "OE1" <-> "OE2" Residue "G ASP 157": "OD1" <-> "OD2" Residue "G GLU 167": "OE1" <-> "OE2" Residue "G ASP 179": "OD1" <-> "OD2" Residue "G GLU 195": "OE1" <-> "OE2" Residue "G TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 205": "OE1" <-> "OE2" Residue "G ASP 211": "OD1" <-> "OD2" Residue "G GLU 224": "OE1" <-> "OE2" Residue "G GLU 241": "OE1" <-> "OE2" Residue "G ASP 244": "OD1" <-> "OD2" Residue "G PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 276": "OE1" <-> "OE2" Residue "G ASP 288": "OD1" <-> "OD2" Residue "G PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 361": "OE1" <-> "OE2" Residue "G ASP 363": "OD1" <-> "OD2" Residue "H ASP 25": "OD1" <-> "OD2" Residue "H PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 51": "OD1" <-> "OD2" Residue "H TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 56": "OD1" <-> "OD2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "H TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 81": "OD1" <-> "OD2" Residue "H GLU 93": "OE1" <-> "OE2" Residue "H GLU 99": "OE1" <-> "OE2" Residue "H GLU 117": "OE1" <-> "OE2" Residue "H TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 157": "OD1" <-> "OD2" Residue "H GLU 167": "OE1" <-> "OE2" Residue "H ASP 184": "OD1" <-> "OD2" Residue "H GLU 195": "OE1" <-> "OE2" Residue "H TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 214": "OE1" <-> "OE2" Residue "H GLU 224": "OE1" <-> "OE2" Residue "H GLU 237": "OE1" <-> "OE2" Residue "H GLU 241": "OE1" <-> "OE2" Residue "H ASP 244": "OD1" <-> "OD2" Residue "H GLU 259": "OE1" <-> "OE2" Residue "H PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 288": "OD1" <-> "OD2" Residue "H ASP 311": "OD1" <-> "OD2" Residue "H GLU 316": "OE1" <-> "OE2" Residue "H PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 363": "OD1" <-> "OD2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 56792 Number of models: 1 Model: "" Number of chains: 22 Chain: "I" Number of atoms: 5612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5612 Classifications: {'peptide': 704} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 20, 'TRANS': 681} Chain: "J" Number of atoms: 5612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5612 Classifications: {'peptide': 704} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 20, 'TRANS': 681} Chain: "K" Number of atoms: 5612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5612 Classifications: {'peptide': 704} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 20, 'TRANS': 681} Chain: "L" Number of atoms: 5612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5612 Classifications: {'peptide': 704} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 20, 'TRANS': 681} Chain: "M" Number of atoms: 5612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5612 Classifications: {'peptide': 704} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 20, 'TRANS': 681} Chain: "N" Number of atoms: 5612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 704, 5612 Classifications: {'peptide': 704} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 20, 'TRANS': 681} Chain: "A" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} Chain: "B" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} Chain: "C" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} Chain: "D" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} Chain: "E" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} Chain: "F" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} Chain: "G" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} Chain: "H" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2862 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'CIS': 10, 'PTRANS': 19, 'TRANS': 337} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 21.42, per 1000 atoms: 0.38 Number of scatterers: 56792 At special positions: 0 Unit cell: (194.31, 213.36, 280.67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 310 16.00 P 16 15.00 Mg 8 11.99 O 10898 8.00 N 9738 7.00 C 35822 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: 16.07 Conformation dependent library (CDL) restraints added in 7.6 seconds 14264 Ramachandran restraints generated. 7132 Oldfield, 0 Emsley, 7132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13332 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 341 helices and 68 sheets defined 40.4% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.37 Creating SS restraints... Processing helix chain 'I' and resid 45 through 47 No H-bonds generated for 'chain 'I' and resid 45 through 47' Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'I' and resid 70 through 82 Processing helix chain 'I' and resid 109 through 115 Processing helix chain 'I' and resid 127 through 136 removed outlier: 4.035A pdb=" N ALA I 131 " --> pdb=" O PHE I 128 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ASP I 132 " --> pdb=" O ALA I 129 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE I 135 " --> pdb=" O ASP I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 170 removed outlier: 3.623A pdb=" N THR I 161 " --> pdb=" O LYS I 157 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 184 removed outlier: 3.967A pdb=" N VAL I 183 " --> pdb=" O ASP I 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 192 removed outlier: 3.502A pdb=" N GLU I 190 " --> pdb=" O ASN I 186 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA I 191 " --> pdb=" O PRO I 187 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE I 192 " --> pdb=" O LEU I 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 186 through 192' Processing helix chain 'I' and resid 232 through 236 removed outlier: 4.291A pdb=" N CYS I 236 " --> pdb=" O LYS I 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 232 through 236' Processing helix chain 'I' and resid 246 through 254 removed outlier: 4.092A pdb=" N ARG I 250 " --> pdb=" O ILE I 247 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LEU I 251 " --> pdb=" O PHE I 248 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA I 253 " --> pdb=" O ARG I 250 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY I 254 " --> pdb=" O LEU I 251 " (cutoff:3.500A) Processing helix chain 'I' and resid 257 through 263 removed outlier: 3.924A pdb=" N GLU I 261 " --> pdb=" O GLU I 257 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ARG I 262 " --> pdb=" O ASP I 258 " (cutoff:3.500A) Processing helix chain 'I' and resid 268 through 270 No H-bonds generated for 'chain 'I' and resid 268 through 270' Processing helix chain 'I' and resid 272 through 275 No H-bonds generated for 'chain 'I' and resid 272 through 275' Processing helix chain 'I' and resid 285 through 290 removed outlier: 3.760A pdb=" N LYS I 289 " --> pdb=" O LYS I 285 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN I 290 " --> pdb=" O GLU I 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 285 through 290' Processing helix chain 'I' and resid 293 through 295 No H-bonds generated for 'chain 'I' and resid 293 through 295' Processing helix chain 'I' and resid 298 through 303 Processing helix chain 'I' and resid 313 through 327 removed outlier: 3.672A pdb=" N PHE I 317 " --> pdb=" O ASP I 313 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE I 318 " --> pdb=" O HIS I 314 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS I 325 " --> pdb=" O CYS I 321 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS I 326 " --> pdb=" O THR I 322 " (cutoff:3.500A) Processing helix chain 'I' and resid 331 through 345 removed outlier: 4.320A pdb=" N VAL I 341 " --> pdb=" O LEU I 337 " (cutoff:3.500A) Processing helix chain 'I' and resid 366 through 368 No H-bonds generated for 'chain 'I' and resid 366 through 368' Processing helix chain 'I' and resid 370 through 379 removed outlier: 3.984A pdb=" N CYS I 375 " --> pdb=" O ALA I 371 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU I 377 " --> pdb=" O GLU I 373 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LEU I 378 " --> pdb=" O TYR I 374 " (cutoff:3.500A) Processing helix chain 'I' and resid 383 through 389 removed outlier: 3.550A pdb=" N ARG I 387 " --> pdb=" O GLN I 383 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL I 388 " --> pdb=" O ASP I 384 " (cutoff:3.500A) Processing helix chain 'I' and resid 413 through 441 removed outlier: 3.532A pdb=" N ALA I 424 " --> pdb=" O ARG I 420 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N SER I 429 " --> pdb=" O LYS I 425 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP I 433 " --> pdb=" O SER I 429 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS I 434 " --> pdb=" O HIS I 430 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN I 441 " --> pdb=" O ASN I 437 " (cutoff:3.500A) Processing helix chain 'I' and resid 468 through 493 removed outlier: 3.608A pdb=" N LYS I 479 " --> pdb=" O TYR I 475 " (cutoff:3.500A) Processing helix chain 'I' and resid 512 through 518 removed outlier: 3.601A pdb=" N LEU I 517 " --> pdb=" O ASP I 513 " (cutoff:3.500A) Processing helix chain 'I' and resid 525 through 534 removed outlier: 3.559A pdb=" N GLU I 531 " --> pdb=" O ASP I 527 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN I 533 " --> pdb=" O LEU I 529 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG I 534 " --> pdb=" O ASP I 530 " (cutoff:3.500A) Processing helix chain 'I' and resid 541 through 550 Processing helix chain 'I' and resid 560 through 562 No H-bonds generated for 'chain 'I' and resid 560 through 562' Processing helix chain 'I' and resid 566 through 570 removed outlier: 3.858A pdb=" N ASN I 570 " --> pdb=" O ILE I 567 " (cutoff:3.500A) Processing helix chain 'I' and resid 573 through 575 No H-bonds generated for 'chain 'I' and resid 573 through 575' Processing helix chain 'I' and resid 593 through 597 Processing helix chain 'I' and resid 603 through 609 removed outlier: 4.978A pdb=" N LEU I 608 " --> pdb=" O SER I 604 " (cutoff:3.500A) Processing helix chain 'I' and resid 615 through 621 removed outlier: 3.579A pdb=" N GLU I 619 " --> pdb=" O LYS I 615 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU I 620 " --> pdb=" O PHE I 616 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N PHE I 621 " --> pdb=" O ILE I 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 615 through 621' Processing helix chain 'I' and resid 633 through 635 No H-bonds generated for 'chain 'I' and resid 633 through 635' Processing helix chain 'I' and resid 646 through 660 removed outlier: 4.033A pdb=" N LEU I 651 " --> pdb=" O PHE I 647 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU I 654 " --> pdb=" O GLN I 650 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS I 657 " --> pdb=" O LEU I 653 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER I 660 " --> pdb=" O ASP I 656 " (cutoff:3.500A) Processing helix chain 'I' and resid 682 through 689 removed outlier: 3.594A pdb=" N LEU I 686 " --> pdb=" O GLY I 682 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N SER I 687 " --> pdb=" O ALA I 683 " (cutoff:3.500A) Processing helix chain 'I' and resid 694 through 698 Processing helix chain 'J' and resid 37 through 39 No H-bonds generated for 'chain 'J' and resid 37 through 39' Processing helix chain 'J' and resid 45 through 47 No H-bonds generated for 'chain 'J' and resid 45 through 47' Processing helix chain 'J' and resid 62 through 64 No H-bonds generated for 'chain 'J' and resid 62 through 64' Processing helix chain 'J' and resid 70 through 83 removed outlier: 3.563A pdb=" N LYS J 78 " --> pdb=" O LEU J 74 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR J 81 " --> pdb=" O ILE J 77 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER J 82 " --> pdb=" O LYS J 78 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS J 83 " --> pdb=" O VAL J 79 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 115 removed outlier: 3.523A pdb=" N TYR J 115 " --> pdb=" O THR J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 139 removed outlier: 3.741A pdb=" N ALA J 131 " --> pdb=" O PHE J 128 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP J 132 " --> pdb=" O ALA J 129 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP J 137 " --> pdb=" O ALA J 134 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LYS J 139 " --> pdb=" O ARG J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 157 through 170 removed outlier: 3.767A pdb=" N THR J 161 " --> pdb=" O LYS J 157 " (cutoff:3.500A) Processing helix chain 'J' and resid 179 through 184 removed outlier: 4.333A pdb=" N VAL J 183 " --> pdb=" O ASP J 179 " (cutoff:3.500A) Processing helix chain 'J' and resid 186 through 193 removed outlier: 4.154A pdb=" N PHE J 192 " --> pdb=" O LEU J 188 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY J 193 " --> pdb=" O LEU J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 235 No H-bonds generated for 'chain 'J' and resid 233 through 235' Processing helix chain 'J' and resid 246 through 254 removed outlier: 3.955A pdb=" N ARG J 250 " --> pdb=" O ILE J 247 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N LEU J 251 " --> pdb=" O PHE J 248 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA J 253 " --> pdb=" O ARG J 250 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY J 254 " --> pdb=" O LEU J 251 " (cutoff:3.500A) Processing helix chain 'J' and resid 257 through 263 removed outlier: 3.713A pdb=" N GLU J 261 " --> pdb=" O GLU J 257 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ARG J 262 " --> pdb=" O ASP J 258 " (cutoff:3.500A) Processing helix chain 'J' and resid 268 through 270 No H-bonds generated for 'chain 'J' and resid 268 through 270' Processing helix chain 'J' and resid 287 through 289 No H-bonds generated for 'chain 'J' and resid 287 through 289' Processing helix chain 'J' and resid 298 through 303 Processing helix chain 'J' and resid 313 through 327 removed outlier: 4.057A pdb=" N PHE J 317 " --> pdb=" O ASP J 313 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE J 318 " --> pdb=" O HIS J 314 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS J 325 " --> pdb=" O CYS J 321 " (cutoff:3.500A) Processing helix chain 'J' and resid 331 through 345 removed outlier: 3.960A pdb=" N LEU J 335 " --> pdb=" O ASP J 331 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP J 336 " --> pdb=" O GLU J 332 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL J 340 " --> pdb=" O ASP J 336 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL J 341 " --> pdb=" O LEU J 337 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU J 345 " --> pdb=" O VAL J 341 " (cutoff:3.500A) Processing helix chain 'J' and resid 366 through 368 No H-bonds generated for 'chain 'J' and resid 366 through 368' Processing helix chain 'J' and resid 370 through 379 removed outlier: 4.007A pdb=" N CYS J 375 " --> pdb=" O ALA J 371 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU J 377 " --> pdb=" O GLU J 373 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LEU J 378 " --> pdb=" O TYR J 374 " (cutoff:3.500A) Processing helix chain 'J' and resid 385 through 389 removed outlier: 3.558A pdb=" N SER J 389 " --> pdb=" O ASP J 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 385 through 389' Processing helix chain 'J' and resid 413 through 442 removed outlier: 3.511A pdb=" N ALA J 424 " --> pdb=" O ARG J 420 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N SER J 429 " --> pdb=" O LYS J 425 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP J 433 " --> pdb=" O SER J 429 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N CYS J 442 " --> pdb=" O ARG J 438 " (cutoff:3.500A) Processing helix chain 'J' and resid 468 through 493 Processing helix chain 'J' and resid 512 through 518 Processing helix chain 'J' and resid 525 through 534 removed outlier: 3.848A pdb=" N ARG J 534 " --> pdb=" O ASP J 530 " (cutoff:3.500A) Processing helix chain 'J' and resid 541 through 550 removed outlier: 3.734A pdb=" N VAL J 547 " --> pdb=" O PHE J 543 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N HIS J 548 " --> pdb=" O THR J 544 " (cutoff:3.500A) Processing helix chain 'J' and resid 560 through 562 No H-bonds generated for 'chain 'J' and resid 560 through 562' Processing helix chain 'J' and resid 566 through 569 Processing helix chain 'J' and resid 573 through 575 No H-bonds generated for 'chain 'J' and resid 573 through 575' Processing helix chain 'J' and resid 593 through 597 Processing helix chain 'J' and resid 603 through 609 removed outlier: 4.472A pdb=" N LEU J 608 " --> pdb=" O SER J 604 " (cutoff:3.500A) Processing helix chain 'J' and resid 615 through 621 removed outlier: 3.636A pdb=" N GLU J 619 " --> pdb=" O LYS J 615 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU J 620 " --> pdb=" O PHE J 616 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE J 621 " --> pdb=" O ILE J 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 615 through 621' Processing helix chain 'J' and resid 646 through 660 removed outlier: 3.603A pdb=" N LEU J 651 " --> pdb=" O PHE J 647 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU J 654 " --> pdb=" O GLN J 650 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS J 657 " --> pdb=" O LEU J 653 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER J 660 " --> pdb=" O ASP J 656 " (cutoff:3.500A) Processing helix chain 'J' and resid 685 through 689 Processing helix chain 'J' and resid 694 through 698 Processing helix chain 'K' and resid 45 through 47 No H-bonds generated for 'chain 'K' and resid 45 through 47' Processing helix chain 'K' and resid 62 through 64 No H-bonds generated for 'chain 'K' and resid 62 through 64' Processing helix chain 'K' and resid 70 through 82 removed outlier: 3.569A pdb=" N TYR K 81 " --> pdb=" O ILE K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 115 Processing helix chain 'K' and resid 127 through 139 removed outlier: 4.005A pdb=" N ALA K 131 " --> pdb=" O PHE K 128 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASP K 132 " --> pdb=" O ALA K 129 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA K 134 " --> pdb=" O ALA K 131 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE K 135 " --> pdb=" O ASP K 132 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP K 137 " --> pdb=" O ALA K 134 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS K 139 " --> pdb=" O ARG K 136 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 168 removed outlier: 3.809A pdb=" N THR K 161 " --> pdb=" O LYS K 157 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 184 removed outlier: 4.104A pdb=" N VAL K 183 " --> pdb=" O ASP K 179 " (cutoff:3.500A) Processing helix chain 'K' and resid 186 through 192 Processing helix chain 'K' and resid 232 through 236 removed outlier: 4.017A pdb=" N CYS K 236 " --> pdb=" O LYS K 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 232 through 236' Processing helix chain 'K' and resid 246 through 254 removed outlier: 4.080A pdb=" N ARG K 250 " --> pdb=" O ILE K 247 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LEU K 251 " --> pdb=" O PHE K 248 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA K 253 " --> pdb=" O ARG K 250 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY K 254 " --> pdb=" O LEU K 251 " (cutoff:3.500A) Processing helix chain 'K' and resid 257 through 263 removed outlier: 4.925A pdb=" N ARG K 262 " --> pdb=" O ASP K 258 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU K 263 " --> pdb=" O ILE K 259 " (cutoff:3.500A) Processing helix chain 'K' and resid 272 through 275 No H-bonds generated for 'chain 'K' and resid 272 through 275' Processing helix chain 'K' and resid 285 through 289 removed outlier: 3.810A pdb=" N LYS K 289 " --> pdb=" O LYS K 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 285 through 289' Processing helix chain 'K' and resid 293 through 295 No H-bonds generated for 'chain 'K' and resid 293 through 295' Processing helix chain 'K' and resid 298 through 303 Processing helix chain 'K' and resid 316 through 327 removed outlier: 3.526A pdb=" N CYS K 321 " --> pdb=" O PHE K 317 " (cutoff:3.500A) Processing helix chain 'K' and resid 331 through 345 removed outlier: 3.682A pdb=" N VAL K 340 " --> pdb=" O ASP K 336 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL K 341 " --> pdb=" O LEU K 337 " (cutoff:3.500A) Processing helix chain 'K' and resid 366 through 368 No H-bonds generated for 'chain 'K' and resid 366 through 368' Processing helix chain 'K' and resid 370 through 376 removed outlier: 3.864A pdb=" N CYS K 375 " --> pdb=" O ALA K 371 " (cutoff:3.500A) Processing helix chain 'K' and resid 383 through 389 removed outlier: 3.625A pdb=" N ARG K 387 " --> pdb=" O GLN K 383 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL K 388 " --> pdb=" O ASP K 384 " (cutoff:3.500A) Processing helix chain 'K' and resid 413 through 441 removed outlier: 3.515A pdb=" N ASP K 421 " --> pdb=" O ASN K 417 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU K 423 " --> pdb=" O ALA K 419 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA K 424 " --> pdb=" O ARG K 420 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR K 426 " --> pdb=" O ALA K 422 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR K 428 " --> pdb=" O ALA K 424 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER K 429 " --> pdb=" O LYS K 425 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP K 433 " --> pdb=" O SER K 429 " (cutoff:3.500A) Processing helix chain 'K' and resid 468 through 493 removed outlier: 3.533A pdb=" N CYS K 472 " --> pdb=" O PHE K 468 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE K 473 " --> pdb=" O GLU K 469 " (cutoff:3.500A) Processing helix chain 'K' and resid 512 through 519 Processing helix chain 'K' and resid 525 through 534 removed outlier: 3.583A pdb=" N GLU K 531 " --> pdb=" O ASP K 527 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN K 533 " --> pdb=" O LEU K 529 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG K 534 " --> pdb=" O ASP K 530 " (cutoff:3.500A) Processing helix chain 'K' and resid 541 through 550 removed outlier: 3.589A pdb=" N ALA K 546 " --> pdb=" O HIS K 542 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N HIS K 548 " --> pdb=" O THR K 544 " (cutoff:3.500A) Processing helix chain 'K' and resid 560 through 562 No H-bonds generated for 'chain 'K' and resid 560 through 562' Processing helix chain 'K' and resid 566 through 570 removed outlier: 3.998A pdb=" N ASN K 570 " --> pdb=" O ILE K 567 " (cutoff:3.500A) Processing helix chain 'K' and resid 573 through 575 No H-bonds generated for 'chain 'K' and resid 573 through 575' Processing helix chain 'K' and resid 593 through 597 removed outlier: 3.580A pdb=" N ASN K 597 " --> pdb=" O PHE K 593 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 593 through 597' Processing helix chain 'K' and resid 603 through 609 removed outlier: 4.689A pdb=" N LEU K 608 " --> pdb=" O SER K 604 " (cutoff:3.500A) Processing helix chain 'K' and resid 615 through 618 No H-bonds generated for 'chain 'K' and resid 615 through 618' Processing helix chain 'K' and resid 646 through 659 removed outlier: 3.756A pdb=" N LEU K 651 " --> pdb=" O PHE K 647 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU K 654 " --> pdb=" O GLN K 650 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS K 657 " --> pdb=" O LEU K 653 " (cutoff:3.500A) Processing helix chain 'K' and resid 685 through 689 Processing helix chain 'K' and resid 694 through 700 Processing helix chain 'L' and resid 45 through 47 No H-bonds generated for 'chain 'L' and resid 45 through 47' Processing helix chain 'L' and resid 62 through 64 No H-bonds generated for 'chain 'L' and resid 62 through 64' Processing helix chain 'L' and resid 70 through 83 removed outlier: 3.533A pdb=" N TYR L 81 " --> pdb=" O ILE L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 109 through 115 Processing helix chain 'L' and resid 127 through 139 removed outlier: 3.774A pdb=" N ALA L 131 " --> pdb=" O PHE L 128 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ASP L 132 " --> pdb=" O ALA L 129 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP L 137 " --> pdb=" O ALA L 134 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET L 138 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS L 139 " --> pdb=" O ARG L 136 " (cutoff:3.500A) Processing helix chain 'L' and resid 157 through 170 removed outlier: 3.755A pdb=" N THR L 161 " --> pdb=" O LYS L 157 " (cutoff:3.500A) Processing helix chain 'L' and resid 179 through 184 removed outlier: 4.404A pdb=" N VAL L 183 " --> pdb=" O ASP L 179 " (cutoff:3.500A) Processing helix chain 'L' and resid 186 through 193 removed outlier: 3.675A pdb=" N ALA L 191 " --> pdb=" O PRO L 187 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE L 192 " --> pdb=" O LEU L 188 " (cutoff:3.500A) Processing helix chain 'L' and resid 232 through 236 Processing helix chain 'L' and resid 246 through 254 removed outlier: 4.020A pdb=" N ARG L 250 " --> pdb=" O ILE L 247 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N LEU L 251 " --> pdb=" O PHE L 248 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA L 253 " --> pdb=" O ARG L 250 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY L 254 " --> pdb=" O LEU L 251 " (cutoff:3.500A) Processing helix chain 'L' and resid 257 through 263 removed outlier: 4.811A pdb=" N ARG L 262 " --> pdb=" O ASP L 258 " (cutoff:3.500A) Processing helix chain 'L' and resid 268 through 270 No H-bonds generated for 'chain 'L' and resid 268 through 270' Processing helix chain 'L' and resid 285 through 290 removed outlier: 3.769A pdb=" N LYS L 289 " --> pdb=" O LYS L 285 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLN L 290 " --> pdb=" O GLU L 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 285 through 290' Processing helix chain 'L' and resid 293 through 295 No H-bonds generated for 'chain 'L' and resid 293 through 295' Processing helix chain 'L' and resid 298 through 303 Processing helix chain 'L' and resid 315 through 327 removed outlier: 3.754A pdb=" N LYS L 325 " --> pdb=" O CYS L 321 " (cutoff:3.500A) Processing helix chain 'L' and resid 331 through 345 removed outlier: 4.113A pdb=" N VAL L 341 " --> pdb=" O LEU L 337 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL L 344 " --> pdb=" O VAL L 340 " (cutoff:3.500A) Processing helix chain 'L' and resid 366 through 368 No H-bonds generated for 'chain 'L' and resid 366 through 368' Processing helix chain 'L' and resid 370 through 379 removed outlier: 3.716A pdb=" N CYS L 375 " --> pdb=" O ALA L 371 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU L 377 " --> pdb=" O GLU L 373 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LEU L 378 " --> pdb=" O TYR L 374 " (cutoff:3.500A) Processing helix chain 'L' and resid 383 through 389 removed outlier: 3.709A pdb=" N ARG L 387 " --> pdb=" O GLN L 383 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL L 388 " --> pdb=" O ASP L 384 " (cutoff:3.500A) Processing helix chain 'L' and resid 413 through 441 removed outlier: 3.633A pdb=" N ALA L 424 " --> pdb=" O ARG L 420 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR L 428 " --> pdb=" O ALA L 424 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N SER L 429 " --> pdb=" O LYS L 425 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP L 433 " --> pdb=" O SER L 429 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS L 434 " --> pdb=" O HIS L 430 " (cutoff:3.500A) Processing helix chain 'L' and resid 468 through 496 Processing helix chain 'L' and resid 512 through 518 Processing helix chain 'L' and resid 525 through 534 removed outlier: 4.025A pdb=" N ARG L 534 " --> pdb=" O ASP L 530 " (cutoff:3.500A) Processing helix chain 'L' and resid 541 through 550 removed outlier: 3.530A pdb=" N VAL L 547 " --> pdb=" O PHE L 543 " (cutoff:3.500A) Processing helix chain 'L' and resid 560 through 562 No H-bonds generated for 'chain 'L' and resid 560 through 562' Processing helix chain 'L' and resid 566 through 569 Processing helix chain 'L' and resid 573 through 575 No H-bonds generated for 'chain 'L' and resid 573 through 575' Processing helix chain 'L' and resid 593 through 597 Processing helix chain 'L' and resid 603 through 609 removed outlier: 4.888A pdb=" N LEU L 608 " --> pdb=" O SER L 604 " (cutoff:3.500A) Processing helix chain 'L' and resid 615 through 618 No H-bonds generated for 'chain 'L' and resid 615 through 618' Processing helix chain 'L' and resid 633 through 635 No H-bonds generated for 'chain 'L' and resid 633 through 635' Processing helix chain 'L' and resid 646 through 660 removed outlier: 3.503A pdb=" N LEU L 651 " --> pdb=" O PHE L 647 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU L 654 " --> pdb=" O GLN L 650 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS L 657 " --> pdb=" O LEU L 653 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER L 660 " --> pdb=" O ASP L 656 " (cutoff:3.500A) Processing helix chain 'L' and resid 682 through 689 removed outlier: 3.678A pdb=" N LEU L 686 " --> pdb=" O GLY L 682 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N SER L 687 " --> pdb=" O ALA L 683 " (cutoff:3.500A) Processing helix chain 'L' and resid 694 through 698 Processing helix chain 'M' and resid 45 through 47 No H-bonds generated for 'chain 'M' and resid 45 through 47' Processing helix chain 'M' and resid 62 through 64 No H-bonds generated for 'chain 'M' and resid 62 through 64' Processing helix chain 'M' and resid 70 through 82 Processing helix chain 'M' and resid 109 through 115 Processing helix chain 'M' and resid 127 through 139 removed outlier: 3.780A pdb=" N ALA M 131 " --> pdb=" O PHE M 128 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASP M 132 " --> pdb=" O ALA M 129 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA M 134 " --> pdb=" O ALA M 131 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE M 135 " --> pdb=" O ASP M 132 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP M 137 " --> pdb=" O ALA M 134 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET M 138 " --> pdb=" O PHE M 135 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS M 139 " --> pdb=" O ARG M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 157 through 170 removed outlier: 3.837A pdb=" N THR M 161 " --> pdb=" O LYS M 157 " (cutoff:3.500A) Processing helix chain 'M' and resid 179 through 184 removed outlier: 3.666A pdb=" N VAL M 183 " --> pdb=" O ASP M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 186 through 192 Processing helix chain 'M' and resid 246 through 254 removed outlier: 4.014A pdb=" N ARG M 250 " --> pdb=" O ILE M 247 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LEU M 251 " --> pdb=" O PHE M 248 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA M 253 " --> pdb=" O ARG M 250 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY M 254 " --> pdb=" O LEU M 251 " (cutoff:3.500A) Processing helix chain 'M' and resid 257 through 263 removed outlier: 3.771A pdb=" N GLU M 261 " --> pdb=" O GLU M 257 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ARG M 262 " --> pdb=" O ASP M 258 " (cutoff:3.500A) Processing helix chain 'M' and resid 268 through 270 No H-bonds generated for 'chain 'M' and resid 268 through 270' Processing helix chain 'M' and resid 272 through 275 No H-bonds generated for 'chain 'M' and resid 272 through 275' Processing helix chain 'M' and resid 285 through 288 No H-bonds generated for 'chain 'M' and resid 285 through 288' Processing helix chain 'M' and resid 293 through 295 No H-bonds generated for 'chain 'M' and resid 293 through 295' Processing helix chain 'M' and resid 298 through 303 Processing helix chain 'M' and resid 316 through 327 removed outlier: 3.890A pdb=" N LYS M 325 " --> pdb=" O CYS M 321 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS M 326 " --> pdb=" O THR M 322 " (cutoff:3.500A) Processing helix chain 'M' and resid 331 through 345 removed outlier: 3.547A pdb=" N ASP M 336 " --> pdb=" O GLU M 332 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL M 341 " --> pdb=" O LEU M 337 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU M 345 " --> pdb=" O VAL M 341 " (cutoff:3.500A) Processing helix chain 'M' and resid 366 through 368 No H-bonds generated for 'chain 'M' and resid 366 through 368' Processing helix chain 'M' and resid 370 through 376 removed outlier: 3.938A pdb=" N CYS M 375 " --> pdb=" O ALA M 371 " (cutoff:3.500A) Processing helix chain 'M' and resid 383 through 389 removed outlier: 3.784A pdb=" N ARG M 387 " --> pdb=" O GLN M 383 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL M 388 " --> pdb=" O ASP M 384 " (cutoff:3.500A) Processing helix chain 'M' and resid 413 through 441 removed outlier: 3.677A pdb=" N ALA M 424 " --> pdb=" O ARG M 420 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER M 429 " --> pdb=" O LYS M 425 " (cutoff:3.500A) Processing helix chain 'M' and resid 468 through 493 removed outlier: 3.575A pdb=" N ILE M 473 " --> pdb=" O GLU M 469 " (cutoff:3.500A) Processing helix chain 'M' and resid 512 through 518 Processing helix chain 'M' and resid 525 through 534 removed outlier: 3.775A pdb=" N ARG M 534 " --> pdb=" O ASP M 530 " (cutoff:3.500A) Processing helix chain 'M' and resid 541 through 550 Processing helix chain 'M' and resid 560 through 562 No H-bonds generated for 'chain 'M' and resid 560 through 562' Processing helix chain 'M' and resid 566 through 568 No H-bonds generated for 'chain 'M' and resid 566 through 568' Processing helix chain 'M' and resid 573 through 575 No H-bonds generated for 'chain 'M' and resid 573 through 575' Processing helix chain 'M' and resid 593 through 597 removed outlier: 3.808A pdb=" N ASN M 597 " --> pdb=" O PHE M 593 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 593 through 597' Processing helix chain 'M' and resid 603 through 609 removed outlier: 4.656A pdb=" N LEU M 608 " --> pdb=" O SER M 604 " (cutoff:3.500A) Processing helix chain 'M' and resid 615 through 621 removed outlier: 3.863A pdb=" N GLU M 619 " --> pdb=" O LYS M 615 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU M 620 " --> pdb=" O PHE M 616 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE M 621 " --> pdb=" O ILE M 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 615 through 621' Processing helix chain 'M' and resid 643 through 660 removed outlier: 4.212A pdb=" N LYS M 648 " --> pdb=" O GLY M 644 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU M 651 " --> pdb=" O PHE M 647 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU M 654 " --> pdb=" O GLN M 650 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS M 657 " --> pdb=" O LEU M 653 " (cutoff:3.500A) Processing helix chain 'M' and resid 685 through 689 Processing helix chain 'M' and resid 694 through 703 removed outlier: 3.867A pdb=" N GLN M 702 " --> pdb=" O LEU M 698 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N GLY M 703 " --> pdb=" O ASP M 699 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 79 Processing helix chain 'N' and resid 81 through 83 No H-bonds generated for 'chain 'N' and resid 81 through 83' Processing helix chain 'N' and resid 109 through 115 removed outlier: 3.510A pdb=" N TYR N 115 " --> pdb=" O THR N 111 " (cutoff:3.500A) Processing helix chain 'N' and resid 127 through 139 removed outlier: 3.754A pdb=" N LYS N 133 " --> pdb=" O ALA N 129 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N MET N 138 " --> pdb=" O ALA N 134 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS N 139 " --> pdb=" O PHE N 135 " (cutoff:3.500A) Processing helix chain 'N' and resid 157 through 170 removed outlier: 3.826A pdb=" N THR N 161 " --> pdb=" O LYS N 157 " (cutoff:3.500A) Processing helix chain 'N' and resid 178 through 184 removed outlier: 4.393A pdb=" N VAL N 183 " --> pdb=" O ASP N 179 " (cutoff:3.500A) Processing helix chain 'N' and resid 186 through 193 removed outlier: 3.919A pdb=" N PHE N 192 " --> pdb=" O LEU N 188 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY N 193 " --> pdb=" O LEU N 189 " (cutoff:3.500A) Processing helix chain 'N' and resid 232 through 236 removed outlier: 4.099A pdb=" N CYS N 236 " --> pdb=" O LYS N 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 232 through 236' Processing helix chain 'N' and resid 246 through 254 removed outlier: 4.050A pdb=" N ARG N 250 " --> pdb=" O ILE N 247 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N LEU N 251 " --> pdb=" O PHE N 248 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA N 253 " --> pdb=" O ARG N 250 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY N 254 " --> pdb=" O LEU N 251 " (cutoff:3.500A) Processing helix chain 'N' and resid 257 through 263 removed outlier: 3.680A pdb=" N GLU N 261 " --> pdb=" O GLU N 257 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ARG N 262 " --> pdb=" O ASP N 258 " (cutoff:3.500A) Processing helix chain 'N' and resid 268 through 270 No H-bonds generated for 'chain 'N' and resid 268 through 270' Processing helix chain 'N' and resid 285 through 290 removed outlier: 4.030A pdb=" N GLN N 290 " --> pdb=" O GLU N 286 " (cutoff:3.500A) Processing helix chain 'N' and resid 293 through 295 No H-bonds generated for 'chain 'N' and resid 293 through 295' Processing helix chain 'N' and resid 298 through 303 Processing helix chain 'N' and resid 313 through 327 removed outlier: 3.541A pdb=" N PHE N 317 " --> pdb=" O ASP N 313 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE N 318 " --> pdb=" O HIS N 314 " (cutoff:3.500A) Processing helix chain 'N' and resid 331 through 345 removed outlier: 4.142A pdb=" N VAL N 341 " --> pdb=" O LEU N 337 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU N 345 " --> pdb=" O VAL N 341 " (cutoff:3.500A) Processing helix chain 'N' and resid 366 through 368 No H-bonds generated for 'chain 'N' and resid 366 through 368' Processing helix chain 'N' and resid 370 through 379 removed outlier: 3.797A pdb=" N CYS N 375 " --> pdb=" O ALA N 371 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLU N 377 " --> pdb=" O GLU N 373 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LEU N 378 " --> pdb=" O TYR N 374 " (cutoff:3.500A) Processing helix chain 'N' and resid 383 through 389 removed outlier: 4.136A pdb=" N ARG N 387 " --> pdb=" O GLN N 383 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL N 388 " --> pdb=" O ASP N 384 " (cutoff:3.500A) Processing helix chain 'N' and resid 413 through 442 removed outlier: 3.685A pdb=" N ALA N 424 " --> pdb=" O ARG N 420 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR N 428 " --> pdb=" O ALA N 424 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N SER N 429 " --> pdb=" O LYS N 425 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP N 433 " --> pdb=" O SER N 429 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N CYS N 442 " --> pdb=" O ARG N 438 " (cutoff:3.500A) Processing helix chain 'N' and resid 468 through 493 Processing helix chain 'N' and resid 512 through 518 removed outlier: 3.556A pdb=" N LEU N 517 " --> pdb=" O ASP N 513 " (cutoff:3.500A) Processing helix chain 'N' and resid 525 through 534 removed outlier: 3.505A pdb=" N GLU N 531 " --> pdb=" O ASP N 527 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN N 533 " --> pdb=" O LEU N 529 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG N 534 " --> pdb=" O ASP N 530 " (cutoff:3.500A) Processing helix chain 'N' and resid 541 through 550 removed outlier: 3.641A pdb=" N HIS N 548 " --> pdb=" O THR N 544 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS N 550 " --> pdb=" O ALA N 546 " (cutoff:3.500A) Processing helix chain 'N' and resid 566 through 570 removed outlier: 3.732A pdb=" N ASN N 570 " --> pdb=" O ILE N 567 " (cutoff:3.500A) Processing helix chain 'N' and resid 573 through 575 No H-bonds generated for 'chain 'N' and resid 573 through 575' Processing helix chain 'N' and resid 603 through 609 removed outlier: 4.870A pdb=" N LEU N 608 " --> pdb=" O SER N 604 " (cutoff:3.500A) Processing helix chain 'N' and resid 615 through 621 removed outlier: 3.593A pdb=" N GLU N 619 " --> pdb=" O LYS N 615 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU N 620 " --> pdb=" O PHE N 616 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE N 621 " --> pdb=" O ILE N 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 615 through 621' Processing helix chain 'N' and resid 646 through 659 removed outlier: 3.604A pdb=" N LEU N 651 " --> pdb=" O PHE N 647 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU N 654 " --> pdb=" O GLN N 650 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS N 657 " --> pdb=" O LEU N 653 " (cutoff:3.500A) Processing helix chain 'N' and resid 685 through 689 Processing helix chain 'N' and resid 694 through 698 Processing helix chain 'A' and resid 57 through 59 No H-bonds generated for 'chain 'A' and resid 57 through 59' Processing helix chain 'A' and resid 79 through 92 removed outlier: 4.078A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 127 Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.967A pdb=" N SER A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 183 through 196 removed outlier: 3.778A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 215 removed outlier: 3.628A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 231 removed outlier: 3.663A pdb=" N THR A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 261 Proline residue: A 258 - end of helix removed outlier: 4.538A pdb=" N LEU A 261 " --> pdb=" O CYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 284 removed outlier: 3.594A pdb=" N TYR A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A 282 " --> pdb=" O THR A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 293 removed outlier: 4.058A pdb=" N LYS A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 311 through 320 removed outlier: 3.741A pdb=" N ALA A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 348 removed outlier: 5.374A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER A 344 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A 348 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 355 Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'B' and resid 79 through 92 removed outlier: 4.287A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 117 through 127 Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.946A pdb=" N SER B 141 " --> pdb=" O GLN B 137 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 183 through 196 removed outlier: 3.750A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 215 removed outlier: 3.642A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 231 removed outlier: 3.635A pdb=" N THR B 229 " --> pdb=" O ASN B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 261 Proline residue: B 258 - end of helix removed outlier: 4.769A pdb=" N LEU B 261 " --> pdb=" O CYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 266 No H-bonds generated for 'chain 'B' and resid 264 through 266' Processing helix chain 'B' and resid 274 through 284 Processing helix chain 'B' and resid 287 through 293 removed outlier: 3.697A pdb=" N LYS B 291 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 311 through 320 Processing helix chain 'B' and resid 335 through 348 removed outlier: 5.477A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER B 344 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER B 348 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 354 No H-bonds generated for 'chain 'B' and resid 352 through 354' Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'C' and resid 79 through 92 removed outlier: 4.184A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 115 through 127 removed outlier: 3.528A pdb=" N MET C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.984A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 137 through 145' Processing helix chain 'C' and resid 183 through 196 removed outlier: 3.715A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 215 removed outlier: 4.110A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 231 Processing helix chain 'C' and resid 252 through 259 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'C' and resid 274 through 284 removed outlier: 3.557A pdb=" N LYS C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.792A pdb=" N LYS C 291 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 311 through 320 removed outlier: 3.692A pdb=" N ALA C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 348 removed outlier: 5.370A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER C 344 " --> pdb=" O ILE C 341 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER C 348 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 355 Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'D' and resid 57 through 60 No H-bonds generated for 'chain 'D' and resid 57 through 60' Processing helix chain 'D' and resid 79 through 92 removed outlier: 4.051A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 127 Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.639A pdb=" N SER D 141 " --> pdb=" O GLN D 137 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 137 through 145' Processing helix chain 'D' and resid 183 through 196 removed outlier: 3.802A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 215 removed outlier: 3.831A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 231 removed outlier: 3.595A pdb=" N THR D 229 " --> pdb=" O ASN D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 261 Proline residue: D 258 - end of helix removed outlier: 4.552A pdb=" N LEU D 261 " --> pdb=" O CYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 266 No H-bonds generated for 'chain 'D' and resid 264 through 266' Processing helix chain 'D' and resid 274 through 284 Processing helix chain 'D' and resid 287 through 293 removed outlier: 4.371A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 304 No H-bonds generated for 'chain 'D' and resid 302 through 304' Processing helix chain 'D' and resid 311 through 320 removed outlier: 3.629A pdb=" N ALA D 319 " --> pdb=" O LYS D 315 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 348 removed outlier: 5.210A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER D 344 " --> pdb=" O ILE D 341 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER D 348 " --> pdb=" O ILE D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 354 No H-bonds generated for 'chain 'D' and resid 352 through 354' Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'E' and resid 57 through 60 No H-bonds generated for 'chain 'E' and resid 57 through 60' Processing helix chain 'E' and resid 79 through 92 removed outlier: 4.017A pdb=" N LYS E 84 " --> pdb=" O ASP E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 117 through 127 Processing helix chain 'E' and resid 137 through 145 removed outlier: 4.048A pdb=" N SER E 141 " --> pdb=" O GLN E 137 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU E 142 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TYR E 143 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 196 removed outlier: 3.571A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 removed outlier: 4.256A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL E 209 " --> pdb=" O GLU E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 231 removed outlier: 3.510A pdb=" N ALA E 231 " --> pdb=" O MET E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 261 removed outlier: 4.657A pdb=" N CYS E 257 " --> pdb=" O ARG E 254 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 264 through 266 No H-bonds generated for 'chain 'E' and resid 264 through 266' Processing helix chain 'E' and resid 274 through 284 removed outlier: 3.595A pdb=" N TYR E 279 " --> pdb=" O HIS E 275 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS E 284 " --> pdb=" O ASN E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 293 removed outlier: 3.747A pdb=" N LYS E 291 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 320 removed outlier: 3.507A pdb=" N ALA E 319 " --> pdb=" O LYS E 315 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU E 320 " --> pdb=" O GLU E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 348 removed outlier: 5.312A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER E 344 " --> pdb=" O ILE E 341 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA E 347 " --> pdb=" O SER E 344 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER E 348 " --> pdb=" O ILE E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 354 No H-bonds generated for 'chain 'E' and resid 352 through 354' Processing helix chain 'E' and resid 359 through 365 Processing helix chain 'E' and resid 367 through 370 Processing helix chain 'F' and resid 57 through 59 No H-bonds generated for 'chain 'F' and resid 57 through 59' Processing helix chain 'F' and resid 79 through 92 removed outlier: 3.815A pdb=" N LYS F 84 " --> pdb=" O ASP F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 127 Processing helix chain 'F' and resid 137 through 145 removed outlier: 3.926A pdb=" N SER F 141 " --> pdb=" O GLN F 137 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU F 142 " --> pdb=" O ALA F 138 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N TYR F 143 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA F 144 " --> pdb=" O LEU F 140 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER F 145 " --> pdb=" O SER F 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 137 through 145' Processing helix chain 'F' and resid 183 through 196 removed outlier: 3.506A pdb=" N THR F 194 " --> pdb=" O MET F 190 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU F 195 " --> pdb=" O LYS F 191 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG F 196 " --> pdb=" O ILE F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 215 removed outlier: 3.943A pdb=" N GLU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL F 209 " --> pdb=" O GLU F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 231 Processing helix chain 'F' and resid 252 through 261 Proline residue: F 258 - end of helix removed outlier: 4.569A pdb=" N LEU F 261 " --> pdb=" O CYS F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 284 removed outlier: 3.535A pdb=" N LYS F 284 " --> pdb=" O ASN F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 293 removed outlier: 4.385A pdb=" N LYS F 291 " --> pdb=" O ILE F 287 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ASP F 292 " --> pdb=" O ASP F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 304 No H-bonds generated for 'chain 'F' and resid 302 through 304' Processing helix chain 'F' and resid 311 through 320 removed outlier: 3.657A pdb=" N ALA F 319 " --> pdb=" O LYS F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 348 removed outlier: 5.407A pdb=" N VAL F 339 " --> pdb=" O LYS F 336 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER F 344 " --> pdb=" O ILE F 341 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA F 347 " --> pdb=" O SER F 344 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER F 348 " --> pdb=" O ILE F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 354 No H-bonds generated for 'chain 'F' and resid 352 through 354' Processing helix chain 'F' and resid 359 through 365 Processing helix chain 'G' and resid 57 through 59 No H-bonds generated for 'chain 'G' and resid 57 through 59' Processing helix chain 'G' and resid 79 through 92 removed outlier: 3.935A pdb=" N LYS G 84 " --> pdb=" O ASP G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 100 No H-bonds generated for 'chain 'G' and resid 98 through 100' Processing helix chain 'G' and resid 117 through 127 Processing helix chain 'G' and resid 137 through 145 removed outlier: 4.023A pdb=" N SER G 141 " --> pdb=" O GLN G 137 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU G 142 " --> pdb=" O ALA G 138 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N TYR G 143 " --> pdb=" O VAL G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 174 No H-bonds generated for 'chain 'G' and resid 172 through 174' Processing helix chain 'G' and resid 183 through 196 removed outlier: 3.572A pdb=" N THR G 194 " --> pdb=" O MET G 190 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU G 195 " --> pdb=" O LYS G 191 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ARG G 196 " --> pdb=" O ILE G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 215 removed outlier: 3.684A pdb=" N GLU G 207 " --> pdb=" O THR G 203 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE G 208 " --> pdb=" O ALA G 204 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL G 209 " --> pdb=" O GLU G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 231 Processing helix chain 'G' and resid 252 through 256 Processing helix chain 'G' and resid 258 through 260 No H-bonds generated for 'chain 'G' and resid 258 through 260' Processing helix chain 'G' and resid 264 through 267 Processing helix chain 'G' and resid 274 through 284 removed outlier: 3.670A pdb=" N TYR G 279 " --> pdb=" O HIS G 275 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS G 284 " --> pdb=" O ASN G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 293 removed outlier: 4.370A pdb=" N LYS G 291 " --> pdb=" O ILE G 287 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ASP G 292 " --> pdb=" O ASP G 288 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU G 293 " --> pdb=" O ILE G 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 287 through 293' Processing helix chain 'G' and resid 302 through 304 No H-bonds generated for 'chain 'G' and resid 302 through 304' Processing helix chain 'G' and resid 311 through 320 removed outlier: 3.721A pdb=" N ALA G 319 " --> pdb=" O LYS G 315 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU G 320 " --> pdb=" O GLU G 316 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 348 removed outlier: 5.136A pdb=" N VAL G 339 " --> pdb=" O LYS G 336 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER G 344 " --> pdb=" O ILE G 341 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA G 347 " --> pdb=" O SER G 344 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER G 348 " --> pdb=" O ILE G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 352 through 354 No H-bonds generated for 'chain 'G' and resid 352 through 354' Processing helix chain 'G' and resid 359 through 365 Processing helix chain 'H' and resid 57 through 60 No H-bonds generated for 'chain 'H' and resid 57 through 60' Processing helix chain 'H' and resid 79 through 92 removed outlier: 3.891A pdb=" N LYS H 84 " --> pdb=" O ASP H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 100 No H-bonds generated for 'chain 'H' and resid 98 through 100' Processing helix chain 'H' and resid 115 through 127 removed outlier: 3.515A pdb=" N MET H 119 " --> pdb=" O ASN H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 144 removed outlier: 3.885A pdb=" N SER H 141 " --> pdb=" O GLN H 137 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU H 142 " --> pdb=" O ALA H 138 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR H 143 " --> pdb=" O VAL H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 174 No H-bonds generated for 'chain 'H' and resid 172 through 174' Processing helix chain 'H' and resid 183 through 196 removed outlier: 3.806A pdb=" N THR H 194 " --> pdb=" O MET H 190 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU H 195 " --> pdb=" O LYS H 191 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG H 196 " --> pdb=" O ILE H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 215 removed outlier: 3.605A pdb=" N GLU H 207 " --> pdb=" O THR H 203 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE H 208 " --> pdb=" O ALA H 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 223 through 231 removed outlier: 3.817A pdb=" N THR H 229 " --> pdb=" O ASN H 225 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 261 Proline residue: H 258 - end of helix removed outlier: 4.764A pdb=" N LEU H 261 " --> pdb=" O CYS H 257 " (cutoff:3.500A) Processing helix chain 'H' and resid 264 through 267 Processing helix chain 'H' and resid 274 through 284 removed outlier: 3.692A pdb=" N TYR H 279 " --> pdb=" O HIS H 275 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS H 284 " --> pdb=" O ASN H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 287 through 293 removed outlier: 4.350A pdb=" N LYS H 291 " --> pdb=" O ILE H 287 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ASP H 292 " --> pdb=" O ASP H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 311 through 320 removed outlier: 3.654A pdb=" N ALA H 319 " --> pdb=" O LYS H 315 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU H 320 " --> pdb=" O GLU H 316 " (cutoff:3.500A) Processing helix chain 'H' and resid 335 through 348 removed outlier: 5.293A pdb=" N VAL H 339 " --> pdb=" O LYS H 336 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER H 344 " --> pdb=" O ILE H 341 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA H 347 " --> pdb=" O SER H 344 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER H 348 " --> pdb=" O ILE H 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 352 through 354 No H-bonds generated for 'chain 'H' and resid 352 through 354' Processing helix chain 'H' and resid 359 through 365 Processing helix chain 'H' and resid 367 through 369 No H-bonds generated for 'chain 'H' and resid 367 through 369' Processing sheet with id= A, first strand: chain 'I' and resid 7 through 11 removed outlier: 7.143A pdb=" N THR I 30 " --> pdb=" O VAL I 22 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ILE I 24 " --> pdb=" O SER I 28 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N SER I 28 " --> pdb=" O ILE I 24 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'I' and resid 87 through 90 removed outlier: 7.094A pdb=" N PHE I 665 " --> pdb=" O LEU I 94 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ALA I 96 " --> pdb=" O PHE I 665 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG I 667 " --> pdb=" O ALA I 96 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ASN I 98 " --> pdb=" O ARG I 667 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ILE I 669 " --> pdb=" O ASN I 98 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS I 668 " --> pdb=" O SER I 150 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL I 210 " --> pdb=" O VAL I 454 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY I 222 " --> pdb=" O HIS I 213 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'I' and resid 352 through 354 removed outlier: 3.508A pdb=" N ASN I 363 " --> pdb=" O GLU I 353 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'I' and resid 392 through 396 Processing sheet with id= E, first strand: chain 'I' and resid 576 through 580 Processing sheet with id= F, first strand: chain 'J' and resid 7 through 11 removed outlier: 6.960A pdb=" N THR J 30 " --> pdb=" O VAL J 22 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ILE J 24 " --> pdb=" O SER J 28 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N SER J 28 " --> pdb=" O ILE J 24 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 87 through 90 removed outlier: 3.608A pdb=" N ASN J 98 " --> pdb=" O ILE J 669 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL J 210 " --> pdb=" O VAL J 454 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY J 222 " --> pdb=" O HIS J 213 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 392 through 396 Processing sheet with id= I, first strand: chain 'J' and resid 557 through 559 removed outlier: 3.594A pdb=" N SER J 558 " --> pdb=" O ILE J 578 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE J 578 " --> pdb=" O SER J 558 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'K' and resid 7 through 11 removed outlier: 7.247A pdb=" N THR K 30 " --> pdb=" O VAL K 22 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'K' and resid 87 through 90 removed outlier: 7.123A pdb=" N PHE K 665 " --> pdb=" O LEU K 94 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ALA K 96 " --> pdb=" O PHE K 665 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG K 667 " --> pdb=" O ALA K 96 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ASN K 98 " --> pdb=" O ARG K 667 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE K 669 " --> pdb=" O ASN K 98 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL K 210 " --> pdb=" O VAL K 454 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY K 222 " --> pdb=" O HIS K 213 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'K' and resid 352 through 354 Processing sheet with id= M, first strand: chain 'K' and resid 392 through 396 Processing sheet with id= N, first strand: chain 'K' and resid 557 through 559 Processing sheet with id= O, first strand: chain 'L' and resid 7 through 11 removed outlier: 7.071A pdb=" N THR L 30 " --> pdb=" O VAL L 22 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ILE L 24 " --> pdb=" O SER L 28 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N SER L 28 " --> pdb=" O ILE L 24 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'L' and resid 87 through 90 removed outlier: 3.587A pdb=" N LEU L 94 " --> pdb=" O PHE L 665 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY L 222 " --> pdb=" O HIS L 213 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'L' and resid 392 through 396 Processing sheet with id= R, first strand: chain 'L' and resid 557 through 559 removed outlier: 3.682A pdb=" N SER L 558 " --> pdb=" O ILE L 578 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE L 578 " --> pdb=" O SER L 558 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'M' and resid 7 through 11 removed outlier: 7.360A pdb=" N THR M 30 " --> pdb=" O VAL M 22 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'M' and resid 87 through 90 removed outlier: 3.528A pdb=" N GLY M 453 " --> pdb=" O GLN M 145 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY M 222 " --> pdb=" O HIS M 213 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'M' and resid 392 through 396 Processing sheet with id= V, first strand: chain 'M' and resid 576 through 581 Processing sheet with id= W, first strand: chain 'N' and resid 7 through 11 removed outlier: 7.071A pdb=" N THR N 30 " --> pdb=" O VAL N 22 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'N' and resid 87 through 90 removed outlier: 3.571A pdb=" N VAL N 210 " --> pdb=" O VAL N 454 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY N 222 " --> pdb=" O HIS N 213 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'N' and resid 352 through 354 Processing sheet with id= Z, first strand: chain 'N' and resid 392 through 396 Processing sheet with id= AA, first strand: chain 'N' and resid 557 through 559 Processing sheet with id= AB, first strand: chain 'A' and resid 8 through 11 removed outlier: 3.517A pdb=" N VAL A 17 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 31 " --> pdb=" O VAL A 17 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'A' and resid 34 through 38 removed outlier: 3.697A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'A' and resid 105 through 107 Processing sheet with id= AE, first strand: chain 'A' and resid 298 through 300 removed outlier: 3.524A pdb=" N SER A 155 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY A 156 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'A' and resid 238 through 241 removed outlier: 3.588A pdb=" N ILE A 250 " --> pdb=" O LYS A 238 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'B' and resid 8 through 11 removed outlier: 3.578A pdb=" N PHE B 31 " --> pdb=" O VAL B 17 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'B' and resid 35 through 38 removed outlier: 3.921A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'B' and resid 105 through 107 Processing sheet with id= AJ, first strand: chain 'B' and resid 149 through 156 removed outlier: 3.631A pdb=" N ASP B 154 " --> pdb=" O HIS B 161 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY B 156 " --> pdb=" O VAL B 159 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'B' and resid 238 through 241 removed outlier: 3.521A pdb=" N ILE B 250 " --> pdb=" O LYS B 238 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'B' and resid 297 through 299 Processing sheet with id= AM, first strand: chain 'C' and resid 134 through 136 removed outlier: 8.337A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL C 17 " --> pdb=" O PHE C 31 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE C 31 " --> pdb=" O VAL C 17 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'C' and resid 35 through 38 removed outlier: 3.507A pdb=" N VAL C 35 " --> pdb=" O LYS C 68 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'C' and resid 150 through 152 Processing sheet with id= AP, first strand: chain 'C' and resid 160 through 162 Processing sheet with id= AQ, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= AR, first strand: chain 'D' and resid 132 through 136 removed outlier: 6.830A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE D 31 " --> pdb=" O VAL D 17 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'D' and resid 35 through 38 removed outlier: 3.737A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'D' and resid 298 through 300 removed outlier: 3.719A pdb=" N GLY D 156 " --> pdb=" O VAL D 159 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'D' and resid 238 through 241 removed outlier: 3.557A pdb=" N ILE D 250 " --> pdb=" O LYS D 238 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'E' and resid 8 through 11 removed outlier: 3.533A pdb=" N PHE E 31 " --> pdb=" O VAL E 17 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'E' and resid 35 through 38 removed outlier: 4.258A pdb=" N ARG E 37 " --> pdb=" O THR E 66 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'E' and resid 102 through 107 removed outlier: 6.583A pdb=" N ALA E 131 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N LEU E 105 " --> pdb=" O ALA E 131 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N TYR E 133 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N GLU E 107 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA E 135 " --> pdb=" O GLU E 107 " (cutoff:3.500A) No H-bonds generated for sheet with id= AX Processing sheet with id= AY, first strand: chain 'E' and resid 149 through 152 Processing sheet with id= AZ, first strand: chain 'E' and resid 160 through 162 Processing sheet with id= BA, first strand: chain 'E' and resid 238 through 241 Processing sheet with id= BB, first strand: chain 'F' and resid 8 through 11 removed outlier: 3.523A pdb=" N VAL F 17 " --> pdb=" O PHE F 31 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'F' and resid 34 through 38 removed outlier: 3.527A pdb=" N VAL F 35 " --> pdb=" O LYS F 68 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG F 37 " --> pdb=" O THR F 66 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'F' and resid 105 through 107 Processing sheet with id= BE, first strand: chain 'F' and resid 149 through 152 Processing sheet with id= BF, first strand: chain 'F' and resid 160 through 162 Processing sheet with id= BG, first strand: chain 'F' and resid 238 through 241 Processing sheet with id= BH, first strand: chain 'G' and resid 134 through 136 removed outlier: 8.179A pdb=" N ALA G 135 " --> pdb=" O THR G 103 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU G 105 " --> pdb=" O ALA G 135 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU G 8 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N THR G 106 " --> pdb=" O LEU G 8 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N CYS G 10 " --> pdb=" O THR G 106 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'G' and resid 35 through 38 removed outlier: 3.577A pdb=" N VAL G 35 " --> pdb=" O LYS G 68 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG G 37 " --> pdb=" O THR G 66 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'G' and resid 150 through 156 removed outlier: 3.562A pdb=" N ASP G 154 " --> pdb=" O HIS G 161 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'G' and resid 238 through 241 removed outlier: 3.757A pdb=" N ILE G 250 " --> pdb=" O LYS G 238 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'H' and resid 134 through 136 removed outlier: 8.188A pdb=" N ALA H 135 " --> pdb=" O THR H 103 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU H 105 " --> pdb=" O ALA H 135 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU H 8 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N THR H 106 " --> pdb=" O LEU H 8 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N CYS H 10 " --> pdb=" O THR H 106 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE H 31 " --> pdb=" O VAL H 17 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'H' and resid 35 through 38 removed outlier: 4.038A pdb=" N ARG H 37 " --> pdb=" O THR H 66 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'H' and resid 150 through 152 Processing sheet with id= BO, first strand: chain 'H' and resid 160 through 162 Processing sheet with id= BP, first strand: chain 'H' and resid 238 through 241 removed outlier: 3.794A pdb=" N ILE H 250 " --> pdb=" O LYS H 238 " (cutoff:3.500A) 1711 hydrogen bonds defined for protein. 4473 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: 18.66 Time building geometry restraints manager: 17.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.28: 9663 1.28 - 1.43: 14836 1.43 - 1.59: 32895 1.59 - 1.74: 39 1.74 - 1.89: 499 Bond restraints: 57932 Sorted by residual: bond pdb=" CA THR C 260 " pdb=" C THR C 260 " ideal model delta sigma weight residual 1.523 1.819 -0.296 1.34e-02 5.57e+03 4.88e+02 bond pdb=" C PRO G 258 " pdb=" O PRO G 258 " ideal model delta sigma weight residual 1.237 1.459 -0.222 1.16e-02 7.43e+03 3.67e+02 bond pdb=" C GLU C 259 " pdb=" N THR C 260 " ideal model delta sigma weight residual 1.332 1.591 -0.259 1.40e-02 5.10e+03 3.41e+02 bond pdb=" CA CYS C 257 " pdb=" C CYS C 257 " ideal model delta sigma weight residual 1.521 1.685 -0.164 1.17e-02 7.31e+03 1.96e+02 bond pdb=" C THR C 260 " pdb=" N LEU C 261 " ideal model delta sigma weight residual 1.332 1.488 -0.156 1.40e-02 5.10e+03 1.24e+02 ... (remaining 57927 not shown) Histogram of bond angle deviations from ideal: 75.73 - 91.90: 9 91.90 - 108.07: 4918 108.07 - 124.24: 70415 124.24 - 140.41: 2978 140.41 - 156.58: 2 Bond angle restraints: 78322 Sorted by residual: angle pdb=" O GLU C 259 " pdb=" C GLU C 259 " pdb=" N THR C 260 " ideal model delta sigma weight residual 122.12 141.80 -19.68 1.06e+00 8.90e-01 3.45e+02 angle pdb=" C THR C 260 " pdb=" N LEU C 261 " pdb=" CA LEU C 261 " ideal model delta sigma weight residual 121.54 156.58 -35.04 1.91e+00 2.74e-01 3.37e+02 angle pdb=" C THR C 260 " pdb=" CA THR C 260 " pdb=" CB THR C 260 " ideal model delta sigma weight residual 110.42 75.73 34.69 1.99e+00 2.53e-01 3.04e+02 angle pdb=" C GLU C 259 " pdb=" N THR C 260 " pdb=" CA THR C 260 " ideal model delta sigma weight residual 121.54 89.54 32.00 1.91e+00 2.74e-01 2.81e+02 angle pdb=" N THR C 260 " pdb=" CA THR C 260 " pdb=" CB THR C 260 " ideal model delta sigma weight residual 110.49 136.71 -26.22 1.69e+00 3.50e-01 2.41e+02 ... (remaining 78317 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.54: 32575 20.54 - 41.08: 1624 41.08 - 61.62: 443 61.62 - 82.16: 272 82.16 - 102.70: 78 Dihedral angle restraints: 34992 sinusoidal: 14248 harmonic: 20744 Sorted by residual: dihedral pdb=" CA GLY I 636 " pdb=" C GLY I 636 " pdb=" N LYS I 637 " pdb=" CA LYS I 637 " ideal model delta harmonic sigma weight residual -180.00 -77.30 -102.70 0 5.00e+00 4.00e-02 4.22e+02 dihedral pdb=" CA GLY M 636 " pdb=" C GLY M 636 " pdb=" N LYS M 637 " pdb=" CA LYS M 637 " ideal model delta harmonic sigma weight residual -180.00 -78.76 -101.24 0 5.00e+00 4.00e-02 4.10e+02 dihedral pdb=" CA GLY L 636 " pdb=" C GLY L 636 " pdb=" N LYS L 637 " pdb=" CA LYS L 637 " ideal model delta harmonic sigma weight residual -180.00 -81.84 -98.16 0 5.00e+00 4.00e-02 3.85e+02 ... (remaining 34989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.218: 8296 0.218 - 0.436: 347 0.436 - 0.653: 13 0.653 - 0.871: 1 0.871 - 1.089: 1 Chirality restraints: 8658 Sorted by residual: chirality pdb=" CA THR C 260 " pdb=" N THR C 260 " pdb=" C THR C 260 " pdb=" CB THR C 260 " both_signs ideal model delta sigma weight residual False 2.53 1.44 1.09 2.00e-01 2.50e+01 2.96e+01 chirality pdb=" CA PRO C 258 " pdb=" N PRO C 258 " pdb=" C PRO C 258 " pdb=" CB PRO C 258 " both_signs ideal model delta sigma weight residual False 2.72 3.44 -0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" CA CYS C 257 " pdb=" N CYS C 257 " pdb=" C CYS C 257 " pdb=" CB CYS C 257 " both_signs ideal model delta sigma weight residual False 2.51 3.15 -0.64 2.00e-01 2.50e+01 1.03e+01 ... (remaining 8655 not shown) Planarity restraints: 10170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 362 " -0.190 2.00e-02 2.50e+03 1.07e-01 2.29e+02 pdb=" CG TYR E 362 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR E 362 " 0.079 2.00e-02 2.50e+03 pdb=" CD2 TYR E 362 " 0.088 2.00e-02 2.50e+03 pdb=" CE1 TYR E 362 " 0.069 2.00e-02 2.50e+03 pdb=" CE2 TYR E 362 " 0.063 2.00e-02 2.50e+03 pdb=" CZ TYR E 362 " 0.019 2.00e-02 2.50e+03 pdb=" OH TYR E 362 " -0.175 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 362 " 0.187 2.00e-02 2.50e+03 1.07e-01 2.28e+02 pdb=" CG TYR A 362 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR A 362 " -0.078 2.00e-02 2.50e+03 pdb=" CD2 TYR A 362 " -0.078 2.00e-02 2.50e+03 pdb=" CE1 TYR A 362 " -0.069 2.00e-02 2.50e+03 pdb=" CE2 TYR A 362 " -0.068 2.00e-02 2.50e+03 pdb=" CZ TYR A 362 " -0.025 2.00e-02 2.50e+03 pdb=" OH TYR A 362 " 0.178 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 362 " 0.183 2.00e-02 2.50e+03 1.03e-01 2.13e+02 pdb=" CG TYR G 362 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR G 362 " -0.072 2.00e-02 2.50e+03 pdb=" CD2 TYR G 362 " -0.079 2.00e-02 2.50e+03 pdb=" CE1 TYR G 362 " -0.069 2.00e-02 2.50e+03 pdb=" CE2 TYR G 362 " -0.061 2.00e-02 2.50e+03 pdb=" CZ TYR G 362 " -0.021 2.00e-02 2.50e+03 pdb=" OH TYR G 362 " 0.169 2.00e-02 2.50e+03 ... (remaining 10167 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 37 2.43 - 3.05: 29707 3.05 - 3.67: 82646 3.67 - 4.28: 124809 4.28 - 4.90: 202282 Nonbonded interactions: 439481 Sorted by model distance: nonbonded pdb=" OE1 GLN G 137 " pdb="MG MG G 401 " model vdw 1.814 2.170 nonbonded pdb=" OE1 GLN H 137 " pdb="MG MG H 401 " model vdw 1.817 2.170 nonbonded pdb=" OE1 GLN A 137 " pdb="MG MG A 401 " model vdw 1.817 2.170 nonbonded pdb=" OE1 GLN B 137 " pdb="MG MG B 401 " model vdw 1.819 2.170 nonbonded pdb=" OE1 GLN E 137 " pdb="MG MG E 401 " model vdw 1.819 2.170 ... (remaining 439476 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' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.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' } pdb_interpretation.ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 8.160 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: 0.030 Extract box with map and model: 26.730 Check model and map are aligned: 0.610 Set scattering table: 0.420 Process input model: 111.060 Find NCS groups from input model: 3.020 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:2.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 152.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4758 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 : 0.015 0.296 57932 Z= 0.990 Angle : 2.104 35.040 78322 Z= 1.431 Chirality : 0.107 1.089 8658 Planarity : 0.024 0.328 10170 Dihedral : 16.183 102.705 21660 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 0.55 Ramachandran Plot: Outliers : 1.33 % Allowed : 8.33 % Favored : 90.34 % Rotamer: Outliers : 1.80 % Allowed : 6.03 % Favored : 92.17 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.34 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.08), residues: 7132 helix: -3.58 (0.06), residues: 2726 sheet: -1.80 (0.16), residues: 942 loop : -1.89 (0.09), residues: 3464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.113 0.022 TRP A 340 HIS 0.015 0.003 HIS N 246 PHE 0.082 0.013 PHE H 127 TYR 0.190 0.026 TYR E 362 ARG 0.023 0.003 ARG L 556 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14264 Ramachandran restraints generated. 7132 Oldfield, 0 Emsley, 7132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14264 Ramachandran restraints generated. 7132 Oldfield, 0 Emsley, 7132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 50 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.5638 (OUTLIER) cc_final: 0.5212 (mp0) REVERT: A 283 MET cc_start: 0.6701 (mmm) cc_final: 0.6206 (mmm) outliers start: 11 outliers final: 0 residues processed: 59 average time/residue: 0.1365 time to fit residues: 9.5902 Evaluate side-chains 26 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 25 time to evaluate : 0.263 Evaluate side-chains 98 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 34 LEU cc_start: 0.4403 (OUTLIER) cc_final: 0.4076 (tm) REVERT: I 182 ILE cc_start: 0.6197 (mt) cc_final: 0.5648 (tp) REVERT: I 216 GLU cc_start: 0.6518 (OUTLIER) cc_final: 0.4740 (tp30) outliers start: 7 outliers final: 0 residues processed: 96 average time/residue: 0.2090 time to fit residues: 24.4879 Evaluate side-chains 41 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 597 optimal weight: 3.9990 chunk 536 optimal weight: 8.9990 chunk 297 optimal weight: 0.0770 chunk 183 optimal weight: 3.9990 chunk 361 optimal weight: 0.4980 chunk 286 optimal weight: 9.9990 chunk 554 optimal weight: 0.0670 chunk 214 optimal weight: 9.9990 chunk 337 optimal weight: 7.9990 chunk 413 optimal weight: 10.0000 chunk 642 optimal weight: 0.9990 overall best weight: 1.1280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS ** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5053 moved from start: 0.8364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 57932 Z= 0.218 Angle : 0.795 8.928 78322 Z= 0.442 Chirality : 0.046 0.180 8658 Planarity : 0.007 0.080 10170 Dihedral : 7.821 83.821 7854 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 1.23 % Allowed : 5.27 % Favored : 93.49 % Rotamer: Outliers : 0.10 % Allowed : 2.58 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.34 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.54 (0.09), residues: 7132 helix: -1.67 (0.09), residues: 2732 sheet: -1.06 (0.16), residues: 1030 loop : -1.80 (0.09), residues: 3370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 8 HIS 0.007 0.001 HIS B 87 PHE 0.032 0.002 PHE M 209 TYR 0.014 0.001 TYR N 115 ARG 0.009 0.001 ARG E 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12856 Ramachandran restraints generated. 6428 Oldfield, 0 Emsley, 6428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12856 Ramachandran restraints generated. 6428 Oldfield, 0 Emsley, 6428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8777 (tp) cc_final: 0.8552 (tp) REVERT: A 283 MET cc_start: 0.6721 (mmm) cc_final: 0.6357 (mmm) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0937 time to fit residues: 3.8895 Evaluate side-chains 21 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.260 Evaluate side-chains 63 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 324 MET cc_start: 0.5829 (mtp) cc_final: 0.5537 (mtm) outliers start: 1 outliers final: 0 residues processed: 62 average time/residue: 0.1972 time to fit residues: 15.2842 Evaluate side-chains 24 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 357 optimal weight: 10.0000 chunk 199 optimal weight: 6.9990 chunk 535 optimal weight: 4.9990 chunk 437 optimal weight: 0.0170 chunk 177 optimal weight: 0.0010 chunk 644 optimal weight: 3.9990 chunk 695 optimal weight: 8.9990 chunk 573 optimal weight: 4.9990 chunk 638 optimal weight: 0.9990 chunk 219 optimal weight: 0.2980 chunk 516 optimal weight: 5.9990 overall best weight: 1.0628 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 ASN ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 36 GLN ** K 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 477 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5133 moved from start: 0.8824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 57932 Z= 0.171 Angle : 0.729 9.412 78322 Z= 0.394 Chirality : 0.044 0.159 8658 Planarity : 0.006 0.061 10170 Dihedral : 6.963 83.618 7854 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.85 % Favored : 94.70 % Rotamer: Outliers : 0.10 % Allowed : 3.48 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.34 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.87 (0.09), residues: 7132 helix: -0.84 (0.10), residues: 2690 sheet: -0.94 (0.16), residues: 990 loop : -1.59 (0.10), residues: 3452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP L 8 HIS 0.020 0.001 HIS N 227 PHE 0.037 0.002 PHE L 163 TYR 0.042 0.002 TYR N 107 ARG 0.026 0.001 ARG K 534 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12126 Ramachandran restraints generated. 6063 Oldfield, 0 Emsley, 6063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12126 Ramachandran restraints generated. 6063 Oldfield, 0 Emsley, 6063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.262 Fit side-chains REVERT: C 189 LEU cc_start: 0.8848 (tp) cc_final: 0.8391 (tp) REVERT: C 325 MET cc_start: 0.6316 (tpp) cc_final: 0.6031 (tpt) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0858 time to fit residues: 3.2391 Evaluate side-chains 19 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.258 Evaluate side-chains 36 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: K 324 MET cc_start: 0.6296 (mtp) cc_final: 0.5926 (ttm) outliers start: 1 outliers final: 0 residues processed: 36 average time/residue: 0.1555 time to fit residues: 7.7127 Evaluate side-chains 18 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 636 optimal weight: 0.4980 chunk 484 optimal weight: 10.0000 chunk 334 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 307 optimal weight: 0.0060 chunk 432 optimal weight: 1.9990 chunk 646 optimal weight: 0.8980 chunk 684 optimal weight: 6.9990 chunk 337 optimal weight: 4.9990 chunk 612 optimal weight: 10.0000 chunk 184 optimal weight: 2.9990 overall best weight: 1.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 270 ASN ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 481 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5189 moved from start: 0.9137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 57932 Z= 0.165 Angle : 0.674 12.549 78322 Z= 0.366 Chirality : 0.043 0.224 8658 Planarity : 0.005 0.052 10170 Dihedral : 6.494 85.472 7854 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.63 % Favored : 95.01 % Rotamer: Outliers : 0.10 % Allowed : 2.35 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.34 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.09), residues: 7132 helix: -0.28 (0.10), residues: 2630 sheet: -0.85 (0.16), residues: 966 loop : -1.54 (0.10), residues: 3536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP J 8 HIS 0.020 0.001 HIS M 227 PHE 0.033 0.002 PHE N 163 TYR 0.040 0.002 TYR J 107 ARG 0.017 0.001 ARG L 243 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12126 Ramachandran restraints generated. 6063 Oldfield, 0 Emsley, 6063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12126 Ramachandran restraints generated. 6063 Oldfield, 0 Emsley, 6063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.260 Fit side-chains REVERT: C 123 MET cc_start: 0.6382 (ppp) cc_final: 0.6138 (ppp) REVERT: C 189 LEU cc_start: 0.8881 (tp) cc_final: 0.8501 (tp) REVERT: C 283 MET cc_start: 0.7141 (mmm) cc_final: 0.6618 (mtp) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.0876 time to fit residues: 2.7543 Evaluate side-chains 20 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.255 Evaluate side-chains 30 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 29 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: K 103 ILE cc_start: 0.4414 (mm) cc_final: 0.4189 (mm) REVERT: K 138 MET cc_start: 0.6684 (tpp) cc_final: 0.6468 (tpp) REVERT: K 659 ARG cc_start: 0.7752 (mpt90) cc_final: 0.7017 (mtp85) outliers start: 1 outliers final: 1 residues processed: 29 average time/residue: 0.1701 time to fit residues: 6.7920 Evaluate side-chains 23 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 708 random chunks: chunk 569 optimal weight: 10.0000 chunk 388 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 509 optimal weight: 0.0000 chunk 282 optimal weight: 10.0000 chunk 583 optimal weight: 8.9990 chunk 473 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 349 optimal weight: 2.9990 chunk 614 optimal weight: 0.0770 chunk 172 optimal weight: 1.9990 overall best weight: 1.8148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 HIS ** C 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 116 GLN ** K 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 314 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5289 moved from start: 0.9401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 57932 Z= 0.152 Angle : 0.637 7.550 78322 Z= 0.346 Chirality : 0.042 0.206 8658 Planarity : 0.005 0.044 10170 Dihedral : 6.232 89.829 7854 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.08 % Favored : 94.56 % Rotamer: Outliers : 0.10 % Allowed : 2.09 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.34 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.24 (0.10), residues: 7132 helix: 0.07 (0.10), residues: 2702 sheet: -0.84 (0.15), residues: 986 loop : -1.51 (0.10), residues: 3444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP M 8 HIS 0.020 0.001 HIS L 227 PHE 0.033 0.002 PHE N 163 TYR 0.038 0.002 TYR J 107 ARG 0.015 0.001 ARG N 243 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12126 Ramachandran restraints generated. 6063 Oldfield, 0 Emsley, 6063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12126 Ramachandran restraints generated. 6063 Oldfield, 0 Emsley, 6063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.287 Fit side-chains REVERT: C 123 MET cc_start: 0.6520 (ppp) cc_final: 0.6260 (ppp) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0963 time to fit residues: 2.6181 Evaluate side-chains 18 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.261 Evaluate side-chains 26 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 25 time to evaluate : 0.516 Fit side-chains revert: symmetry clash REVERT: K 103 ILE cc_start: 0.4777 (mm) cc_final: 0.4474 (mm) REVERT: K 138 MET cc_start: 0.6825 (tpp) cc_final: 0.6320 (tpp) REVERT: K 659 ARG cc_start: 0.7591 (mpt90) cc_final: 0.7385 (mmt90) outliers start: 1 outliers final: 1 residues processed: 26 average time/residue: 0.1385 time to fit residues: 5.3991 Evaluate side-chains 15 residues out of total 621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 14 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 798, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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: 67.3084 > 50: distance: 0 - 1: 7.336 distance: 1 - 2: 9.911 distance: 1 - 4: 4.893 distance: 2 - 3: 18.309 distance: 2 - 12: 11.922 distance: 4 - 5: 4.699 distance: 5 - 6: 5.382 distance: 5 - 7: 7.048 distance: 6 - 8: 6.792 distance: 7 - 9: 5.762 distance: 8 - 10: 8.256 distance: 9 - 10: 7.007 distance: 10 - 11: 6.869 distance: 12 - 13: 11.056 distance: 13 - 14: 19.743 distance: 13 - 16: 5.451 distance: 14 - 15: 10.597 distance: 14 - 23: 35.671 distance: 16 - 17: 13.804 distance: 17 - 18: 10.575 distance: 17 - 19: 4.521 distance: 19 - 21: 6.129 distance: 20 - 22: 5.554 distance: 21 - 22: 6.160 distance: 23 - 24: 13.620 distance: 24 - 25: 28.532 distance: 24 - 27: 25.974 distance: 25 - 26: 8.264 distance: 25 - 28: 45.918 distance: 28 - 29: 21.513 distance: 29 - 30: 26.322 distance: 29 - 32: 34.560 distance: 30 - 31: 38.459 distance: 30 - 36: 40.923 distance: 32 - 33: 32.043 distance: 33 - 34: 15.977 distance: 33 - 35: 40.507 distance: 36 - 37: 42.481 distance: 37 - 38: 39.753 distance: 37 - 40: 22.312 distance: 38 - 39: 29.330 distance: 38 - 45: 15.024 distance: 40 - 41: 44.002 distance: 41 - 42: 7.067 distance: 42 - 43: 21.977 distance: 43 - 44: 10.684 distance: 45 - 46: 23.546 distance: 46 - 47: 21.636 distance: 47 - 48: 32.724 distance: 47 - 54: 42.044 distance: 49 - 50: 31.834 distance: 50 - 51: 21.840 distance: 51 - 52: 38.902 distance: 51 - 53: 26.657 distance: 54 - 55: 4.738 distance: 55 - 56: 45.144 distance: 55 - 58: 16.366 distance: 56 - 57: 14.781 distance: 56 - 61: 7.728 distance: 58 - 59: 12.254 distance: 58 - 60: 20.653 distance: 61 - 62: 6.191 distance: 62 - 63: 21.934 distance: 62 - 65: 24.238 distance: 63 - 64: 9.231 distance: 63 - 69: 15.180 distance: 65 - 66: 8.656 distance: 66 - 67: 13.087 distance: 66 - 68: 13.380 distance: 69 - 70: 24.579 distance: 70 - 71: 31.275 distance: 70 - 73: 19.683 distance: 71 - 72: 42.548 distance: 71 - 78: 20.219 distance: 73 - 74: 16.640 distance: 74 - 75: 26.796 distance: 75 - 76: 24.512 distance: 76 - 77: 26.924 distance: 78 - 79: 34.134 distance: 79 - 80: 45.825 distance: 79 - 82: 31.547 distance: 80 - 81: 15.952 distance: 82 - 83: 39.217 distance: 83 - 84: 10.906 distance: 84 - 85: 29.992 distance: 84 - 86: 22.557