Starting phenix.real_space_refine (version: 1.21rc1) on Wed Oct 18 11:08:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz5_20589/10_2023/6tz5_20589_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz5_20589/10_2023/6tz5_20589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz5_20589/10_2023/6tz5_20589.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz5_20589/10_2023/6tz5_20589.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz5_20589/10_2023/6tz5_20589_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tz5_20589/10_2023/6tz5_20589_neut.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 612 5.16 5 C 58582 2.51 5 N 16592 2.21 5 O 17714 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "AA GLU 5": "OE1" <-> "OE2" Residue "AA GLU 17": "OE1" <-> "OE2" Residue "AA GLU 37": "OE1" <-> "OE2" Residue "AA GLU 46": "OE1" <-> "OE2" Residue "AA ARG 49": "NH1" <-> "NH2" Residue "AA GLU 109": "OE1" <-> "OE2" Residue "AA GLU 155": "OE1" <-> "OE2" Residue "AA GLU 159": "OE1" <-> "OE2" Residue "AB GLU 5": "OE1" <-> "OE2" Residue "AB GLU 17": "OE1" <-> "OE2" Residue "AB GLU 37": "OE1" <-> "OE2" Residue "AB GLU 46": "OE1" <-> "OE2" Residue "AB ARG 49": "NH1" <-> "NH2" Residue "AB GLU 109": "OE1" <-> "OE2" Residue "AB GLU 155": "OE1" <-> "OE2" Residue "AB GLU 159": "OE1" <-> "OE2" Residue "BB GLU 73": "OE1" <-> "OE2" Residue "BB ARG 164": "NH1" <-> "NH2" Residue "BB GLU 178": "OE1" <-> "OE2" Residue "CB GLU 5": "OE1" <-> "OE2" Residue "CB GLU 17": "OE1" <-> "OE2" Residue "CB GLU 37": "OE1" <-> "OE2" Residue "CB GLU 46": "OE1" <-> "OE2" Residue "CB ARG 49": "NH1" <-> "NH2" Residue "CB GLU 109": "OE1" <-> "OE2" Residue "CB GLU 155": "OE1" <-> "OE2" Residue "CB GLU 159": "OE1" <-> "OE2" Residue "DB GLU 73": "OE1" <-> "OE2" Residue "DB ARG 164": "NH1" <-> "NH2" Residue "DB GLU 178": "OE1" <-> "OE2" Residue "EB GLU 5": "OE1" <-> "OE2" Residue "EB GLU 17": "OE1" <-> "OE2" Residue "EB GLU 37": "OE1" <-> "OE2" Residue "EB GLU 46": "OE1" <-> "OE2" Residue "EB ARG 49": "NH1" <-> "NH2" Residue "EB GLU 109": "OE1" <-> "OE2" Residue "EB GLU 155": "OE1" <-> "OE2" Residue "EB GLU 159": "OE1" <-> "OE2" Residue "FB GLU 73": "OE1" <-> "OE2" Residue "FB ARG 164": "NH1" <-> "NH2" Residue "FB GLU 178": "OE1" <-> "OE2" Residue "GB GLU 5": "OE1" <-> "OE2" Residue "GB GLU 17": "OE1" <-> "OE2" Residue "GB GLU 37": "OE1" <-> "OE2" Residue "GB GLU 46": "OE1" <-> "OE2" Residue "GB ARG 49": "NH1" <-> "NH2" Residue "GB GLU 109": "OE1" <-> "OE2" Residue "GB GLU 155": "OE1" <-> "OE2" Residue "GB GLU 159": "OE1" <-> "OE2" Residue "HB GLU 73": "OE1" <-> "OE2" Residue "HB ARG 164": "NH1" <-> "NH2" Residue "HB GLU 178": "OE1" <-> "OE2" Residue "IB GLU 5": "OE1" <-> "OE2" Residue "IB GLU 17": "OE1" <-> "OE2" Residue "IB GLU 37": "OE1" <-> "OE2" Residue "IB GLU 46": "OE1" <-> "OE2" Residue "IB ARG 49": "NH1" <-> "NH2" Residue "IB GLU 109": "OE1" <-> "OE2" Residue "IB GLU 155": "OE1" <-> "OE2" Residue "IB GLU 159": "OE1" <-> "OE2" Residue "JB GLU 73": "OE1" <-> "OE2" Residue "JB ARG 164": "NH1" <-> "NH2" Residue "JB GLU 178": "OE1" <-> "OE2" Residue "KB GLU 5": "OE1" <-> "OE2" Residue "KB GLU 17": "OE1" <-> "OE2" Residue "KB GLU 37": "OE1" <-> "OE2" Residue "KB GLU 46": "OE1" <-> "OE2" Residue "KB ARG 49": "NH1" <-> "NH2" Residue "KB GLU 109": "OE1" <-> "OE2" Residue "KB GLU 155": "OE1" <-> "OE2" Residue "KB GLU 159": "OE1" <-> "OE2" Residue "LB GLU 73": "OE1" <-> "OE2" Residue "LB ARG 164": "NH1" <-> "NH2" Residue "LB GLU 178": "OE1" <-> "OE2" Residue "MB GLU 5": "OE1" <-> "OE2" Residue "MB GLU 17": "OE1" <-> "OE2" Residue "MB GLU 37": "OE1" <-> "OE2" Residue "MB GLU 46": "OE1" <-> "OE2" Residue "MB ARG 49": "NH1" <-> "NH2" Residue "MB GLU 109": "OE1" <-> "OE2" Residue "MB GLU 155": "OE1" <-> "OE2" Residue "MB GLU 159": "OE1" <-> "OE2" Residue "NB GLU 73": "OE1" <-> "OE2" Residue "NB ARG 164": "NH1" <-> "NH2" Residue "NB GLU 178": "OE1" <-> "OE2" Residue "OB GLU 5": "OE1" <-> "OE2" Residue "OB GLU 17": "OE1" <-> "OE2" Residue "OB GLU 37": "OE1" <-> "OE2" Residue "OB GLU 46": "OE1" <-> "OE2" Residue "OB ARG 49": "NH1" <-> "NH2" Residue "OB GLU 109": "OE1" <-> "OE2" Residue "OB GLU 155": "OE1" <-> "OE2" Residue "OB GLU 159": "OE1" <-> "OE2" Residue "PB GLU 73": "OE1" <-> "OE2" Residue "PB ARG 164": "NH1" <-> "NH2" Residue "PB GLU 178": "OE1" <-> "OE2" Residue "QB GLU 5": "OE1" <-> "OE2" Residue "QB GLU 17": "OE1" <-> "OE2" Residue "QB GLU 37": "OE1" <-> "OE2" Residue "QB GLU 46": "OE1" <-> "OE2" Residue "QB ARG 49": "NH1" <-> "NH2" Residue "QB GLU 109": "OE1" <-> "OE2" Residue "QB GLU 155": "OE1" <-> "OE2" Residue "QB GLU 159": "OE1" <-> "OE2" Residue "TA GLU 73": "OE1" <-> "OE2" Residue "TA ARG 164": "NH1" <-> "NH2" Residue "TA GLU 178": "OE1" <-> "OE2" Residue "SA GLU 5": "OE1" <-> "OE2" Residue "SA GLU 17": "OE1" <-> "OE2" Residue "SA GLU 37": "OE1" <-> "OE2" Residue "SA GLU 46": "OE1" <-> "OE2" Residue "SA ARG 49": "NH1" <-> "NH2" Residue "SA GLU 109": "OE1" <-> "OE2" Residue "SA GLU 155": "OE1" <-> "OE2" Residue "SA GLU 159": "OE1" <-> "OE2" Residue "VA GLU 73": "OE1" <-> "OE2" Residue "VA ARG 164": "NH1" <-> "NH2" Residue "VA GLU 178": "OE1" <-> "OE2" Residue "UA GLU 5": "OE1" <-> "OE2" Residue "UA GLU 17": "OE1" <-> "OE2" Residue "UA GLU 37": "OE1" <-> "OE2" Residue "UA GLU 46": "OE1" <-> "OE2" Residue "UA ARG 49": "NH1" <-> "NH2" Residue "UA GLU 109": "OE1" <-> "OE2" Residue "UA GLU 155": "OE1" <-> "OE2" Residue "UA GLU 159": "OE1" <-> "OE2" Residue "XA GLU 73": "OE1" <-> "OE2" Residue "XA ARG 164": "NH1" <-> "NH2" Residue "XA GLU 178": "OE1" <-> "OE2" Residue "WA GLU 5": "OE1" <-> "OE2" Residue "WA GLU 17": "OE1" <-> "OE2" Residue "WA GLU 37": "OE1" <-> "OE2" Residue "WA GLU 46": "OE1" <-> "OE2" Residue "WA ARG 49": "NH1" <-> "NH2" Residue "WA GLU 109": "OE1" <-> "OE2" Residue "WA GLU 155": "OE1" <-> "OE2" Residue "WA GLU 159": "OE1" <-> "OE2" Residue "ZA GLU 73": "OE1" <-> "OE2" Residue "ZA ARG 164": "NH1" <-> "NH2" Residue "ZA GLU 178": "OE1" <-> "OE2" Residue "YA GLU 5": "OE1" <-> "OE2" Residue "YA GLU 17": "OE1" <-> "OE2" Residue "YA GLU 37": "OE1" <-> "OE2" Residue "YA GLU 46": "OE1" <-> "OE2" Residue "YA ARG 49": "NH1" <-> "NH2" Residue "YA GLU 109": "OE1" <-> "OE2" Residue "YA GLU 155": "OE1" <-> "OE2" Residue "YA GLU 159": "OE1" <-> "OE2" Residue "BA GLU 73": "OE1" <-> "OE2" Residue "BA ARG 164": "NH1" <-> "NH2" Residue "BA GLU 178": "OE1" <-> "OE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A GLU 178": "OE1" <-> "OE2" Residue "CA GLU 5": "OE1" <-> "OE2" Residue "CA GLU 17": "OE1" <-> "OE2" Residue "CA GLU 37": "OE1" <-> "OE2" Residue "CA GLU 46": "OE1" <-> "OE2" Residue "CA ARG 49": "NH1" <-> "NH2" Residue "CA GLU 109": "OE1" <-> "OE2" Residue "CA GLU 155": "OE1" <-> "OE2" Residue "CA GLU 159": "OE1" <-> "OE2" Residue "DA GLU 73": "OE1" <-> "OE2" Residue "DA ARG 164": "NH1" <-> "NH2" Residue "DA GLU 178": "OE1" <-> "OE2" Residue "EA GLU 5": "OE1" <-> "OE2" Residue "EA GLU 17": "OE1" <-> "OE2" Residue "EA GLU 37": "OE1" <-> "OE2" Residue "EA GLU 46": "OE1" <-> "OE2" Residue "EA ARG 49": "NH1" <-> "NH2" Residue "EA GLU 109": "OE1" <-> "OE2" Residue "EA GLU 155": "OE1" <-> "OE2" Residue "EA GLU 159": "OE1" <-> "OE2" Residue "FA GLU 73": "OE1" <-> "OE2" Residue "FA ARG 164": "NH1" <-> "NH2" Residue "FA GLU 178": "OE1" <-> "OE2" Residue "GA GLU 5": "OE1" <-> "OE2" Residue "GA GLU 17": "OE1" <-> "OE2" Residue "GA GLU 37": "OE1" <-> "OE2" Residue "GA GLU 46": "OE1" <-> "OE2" Residue "GA ARG 49": "NH1" <-> "NH2" Residue "GA GLU 109": "OE1" <-> "OE2" Residue "GA GLU 155": "OE1" <-> "OE2" Residue "GA GLU 159": "OE1" <-> "OE2" Residue "HA GLU 73": "OE1" <-> "OE2" Residue "HA ARG 164": "NH1" <-> "NH2" Residue "HA GLU 178": "OE1" <-> "OE2" Residue "IA GLU 5": "OE1" <-> "OE2" Residue "IA GLU 17": "OE1" <-> "OE2" Residue "IA GLU 37": "OE1" <-> "OE2" Residue "IA GLU 46": "OE1" <-> "OE2" Residue "IA ARG 49": "NH1" <-> "NH2" Residue "IA GLU 109": "OE1" <-> "OE2" Residue "IA GLU 155": "OE1" <-> "OE2" Residue "IA GLU 159": "OE1" <-> "OE2" Residue "JA GLU 73": "OE1" <-> "OE2" Residue "JA ARG 164": "NH1" <-> "NH2" Residue "JA GLU 178": "OE1" <-> "OE2" Residue "KA GLU 5": "OE1" <-> "OE2" Residue "KA GLU 17": "OE1" <-> "OE2" Residue "KA GLU 37": "OE1" <-> "OE2" Residue "KA GLU 46": "OE1" <-> "OE2" Residue "KA ARG 49": "NH1" <-> "NH2" Residue "KA GLU 109": "OE1" <-> "OE2" Residue "KA GLU 155": "OE1" <-> "OE2" Residue "KA GLU 159": "OE1" <-> "OE2" Residue "LA GLU 73": "OE1" <-> "OE2" Residue "LA ARG 164": "NH1" <-> "NH2" Residue "LA GLU 178": "OE1" <-> "OE2" Residue "MA GLU 5": "OE1" <-> "OE2" Residue "MA GLU 17": "OE1" <-> "OE2" Residue "MA GLU 37": "OE1" <-> "OE2" Residue "MA GLU 46": "OE1" <-> "OE2" Residue "MA ARG 49": "NH1" <-> "NH2" Residue "MA GLU 109": "OE1" <-> "OE2" Residue "MA GLU 155": "OE1" <-> "OE2" Residue "MA GLU 159": "OE1" <-> "OE2" Residue "NA GLU 73": "OE1" <-> "OE2" Residue "NA ARG 164": "NH1" <-> "NH2" Residue "NA GLU 178": "OE1" <-> "OE2" Residue "OA GLU 5": "OE1" <-> "OE2" Residue "OA GLU 17": "OE1" <-> "OE2" Residue "OA GLU 37": "OE1" <-> "OE2" Residue "OA GLU 46": "OE1" <-> "OE2" Residue "OA ARG 49": "NH1" <-> "NH2" Residue "OA GLU 109": "OE1" <-> "OE2" Residue "OA GLU 155": "OE1" <-> "OE2" Residue "OA GLU 159": "OE1" <-> "OE2" Residue "PA GLU 73": "OE1" <-> "OE2" Residue "PA ARG 164": "NH1" <-> "NH2" Residue "PA GLU 178": "OE1" <-> "OE2" Residue "QA GLU 5": "OE1" <-> "OE2" Residue "QA GLU 17": "OE1" <-> "OE2" Residue "QA GLU 37": "OE1" <-> "OE2" Residue "QA GLU 46": "OE1" <-> "OE2" Residue "QA ARG 49": "NH1" <-> "NH2" Residue "QA GLU 109": "OE1" <-> "OE2" Residue "QA GLU 155": "OE1" <-> "OE2" Residue "QA GLU 159": "OE1" <-> "OE2" Residue "RA GLU 73": "OE1" <-> "OE2" Residue "RA ARG 164": "NH1" <-> "NH2" Residue "RA GLU 178": "OE1" <-> "OE2" Residue "B GLU 5": "OE1" <-> "OE2" Residue "B GLU 17": "OE1" <-> "OE2" Residue "B GLU 37": "OE1" <-> "OE2" Residue "B GLU 46": "OE1" <-> "OE2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "B GLU 159": "OE1" <-> "OE2" Residue "C GLU 73": "OE1" <-> "OE2" Residue "C ARG 164": "NH1" <-> "NH2" Residue "C GLU 178": "OE1" <-> "OE2" Residue "D GLU 5": "OE1" <-> "OE2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D GLU 37": "OE1" <-> "OE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D GLU 109": "OE1" <-> "OE2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "D GLU 159": "OE1" <-> "OE2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E ARG 164": "NH1" <-> "NH2" Residue "E GLU 178": "OE1" <-> "OE2" Residue "F GLU 5": "OE1" <-> "OE2" Residue "F GLU 17": "OE1" <-> "OE2" Residue "F GLU 37": "OE1" <-> "OE2" Residue "F GLU 46": "OE1" <-> "OE2" Residue "F ARG 49": "NH1" <-> "NH2" Residue "F GLU 109": "OE1" <-> "OE2" Residue "F GLU 155": "OE1" <-> "OE2" Residue "F GLU 159": "OE1" <-> "OE2" Residue "G GLU 73": "OE1" <-> "OE2" Residue "G ARG 164": "NH1" <-> "NH2" Residue "G GLU 178": "OE1" <-> "OE2" Residue "H GLU 5": "OE1" <-> "OE2" Residue "H GLU 17": "OE1" <-> "OE2" Residue "H GLU 37": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H ARG 49": "NH1" <-> "NH2" Residue "H GLU 109": "OE1" <-> "OE2" Residue "H GLU 155": "OE1" <-> "OE2" Residue "H GLU 159": "OE1" <-> "OE2" Residue "I GLU 73": "OE1" <-> "OE2" Residue "I ARG 164": "NH1" <-> "NH2" Residue "I GLU 178": "OE1" <-> "OE2" Residue "J GLU 5": "OE1" <-> "OE2" Residue "J GLU 17": "OE1" <-> "OE2" Residue "J GLU 37": "OE1" <-> "OE2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "J ARG 49": "NH1" <-> "NH2" Residue "J GLU 109": "OE1" <-> "OE2" Residue "J GLU 155": "OE1" <-> "OE2" Residue "J GLU 159": "OE1" <-> "OE2" Residue "K GLU 73": "OE1" <-> "OE2" Residue "K ARG 164": "NH1" <-> "NH2" Residue "K GLU 178": "OE1" <-> "OE2" Residue "L GLU 5": "OE1" <-> "OE2" Residue "L GLU 17": "OE1" <-> "OE2" Residue "L GLU 37": "OE1" <-> "OE2" Residue "L GLU 46": "OE1" <-> "OE2" Residue "L ARG 49": "NH1" <-> "NH2" Residue "L GLU 109": "OE1" <-> "OE2" Residue "L GLU 155": "OE1" <-> "OE2" Residue "L GLU 159": "OE1" <-> "OE2" Residue "M GLU 73": "OE1" <-> "OE2" Residue "M ARG 164": "NH1" <-> "NH2" Residue "M GLU 178": "OE1" <-> "OE2" Residue "N GLU 5": "OE1" <-> "OE2" Residue "N GLU 17": "OE1" <-> "OE2" Residue "N GLU 37": "OE1" <-> "OE2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "N ARG 49": "NH1" <-> "NH2" Residue "N GLU 109": "OE1" <-> "OE2" Residue "N GLU 155": "OE1" <-> "OE2" Residue "N GLU 159": "OE1" <-> "OE2" Residue "O GLU 73": "OE1" <-> "OE2" Residue "O ARG 164": "NH1" <-> "NH2" Residue "O GLU 178": "OE1" <-> "OE2" Residue "P GLU 5": "OE1" <-> "OE2" Residue "P GLU 17": "OE1" <-> "OE2" Residue "P GLU 37": "OE1" <-> "OE2" Residue "P GLU 46": "OE1" <-> "OE2" Residue "P ARG 49": "NH1" <-> "NH2" Residue "P GLU 109": "OE1" <-> "OE2" Residue "P GLU 155": "OE1" <-> "OE2" Residue "P GLU 159": "OE1" <-> "OE2" Residue "Q GLU 73": "OE1" <-> "OE2" Residue "Q ARG 164": "NH1" <-> "NH2" Residue "Q GLU 178": "OE1" <-> "OE2" Residue "R GLU 5": "OE1" <-> "OE2" Residue "R GLU 17": "OE1" <-> "OE2" Residue "R GLU 37": "OE1" <-> "OE2" Residue "R GLU 46": "OE1" <-> "OE2" Residue "R ARG 49": "NH1" <-> "NH2" Residue "R GLU 109": "OE1" <-> "OE2" Residue "R GLU 155": "OE1" <-> "OE2" Residue "R GLU 159": "OE1" <-> "OE2" Residue "S GLU 73": "OE1" <-> "OE2" Residue "S ARG 164": "NH1" <-> "NH2" Residue "S GLU 178": "OE1" <-> "OE2" Residue "T GLU 5": "OE1" <-> "OE2" Residue "T GLU 17": "OE1" <-> "OE2" Residue "T GLU 37": "OE1" <-> "OE2" Residue "T GLU 46": "OE1" <-> "OE2" Residue "T ARG 49": "NH1" <-> "NH2" Residue "T GLU 109": "OE1" <-> "OE2" Residue "T GLU 155": "OE1" <-> "OE2" Residue "T GLU 159": "OE1" <-> "OE2" Residue "V GLU 73": "OE1" <-> "OE2" Residue "V ARG 164": "NH1" <-> "NH2" Residue "V GLU 178": "OE1" <-> "OE2" Residue "W GLU 5": "OE1" <-> "OE2" Residue "W GLU 17": "OE1" <-> "OE2" Residue "W GLU 37": "OE1" <-> "OE2" Residue "W GLU 46": "OE1" <-> "OE2" Residue "W ARG 49": "NH1" <-> "NH2" Residue "W GLU 109": "OE1" <-> "OE2" Residue "W GLU 155": "OE1" <-> "OE2" Residue "W GLU 159": "OE1" <-> "OE2" Residue "X GLU 73": "OE1" <-> "OE2" Residue "X ARG 164": "NH1" <-> "NH2" Residue "X GLU 178": "OE1" <-> "OE2" Residue "Y GLU 5": "OE1" <-> "OE2" Residue "Y GLU 17": "OE1" <-> "OE2" Residue "Y GLU 37": "OE1" <-> "OE2" Residue "Y GLU 46": "OE1" <-> "OE2" Residue "Y ARG 49": "NH1" <-> "NH2" Residue "Y GLU 109": "OE1" <-> "OE2" Residue "Y GLU 155": "OE1" <-> "OE2" Residue "Y GLU 159": "OE1" <-> "OE2" Residue "Z GLU 73": "OE1" <-> "OE2" Residue "Z ARG 164": "NH1" <-> "NH2" Residue "Z GLU 178": "OE1" <-> "OE2" Time to flip residues: 0.23s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 93500 Number of models: 1 Model: "" Number of chains: 68 Chain: "AA" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 173} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "AB" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 173} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "BB" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1406 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "CB" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 173} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "DB" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1406 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "EB" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 173} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "FB" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1406 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "GB" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 173} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "HB" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1406 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "IB" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 173} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "JB" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1406 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "KB" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 173} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "LB" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1406 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "MB" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 173} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "NB" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1406 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "OB" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 173} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "PB" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1406 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "QB" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 173} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "TA" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1406 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "SA" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 173} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "VA" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1406 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "UA" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 173} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "XA" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1406 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "WA" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 173} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "ZA" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1406 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "YA" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 173} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "BA" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1406 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "A" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1406 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "CA" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 173} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "DA" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1406 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "EA" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 173} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "FA" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1406 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "GA" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 173} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "HA" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1406 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "IA" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 173} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "JA" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1406 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "KA" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 173} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "LA" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1406 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "MA" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 173} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "NA" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1406 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "OA" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 173} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "PA" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1406 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "QA" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 173} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "RA" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1406 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 173} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1406 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "D" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 173} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1406 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "F" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 173} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "G" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1406 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "H" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 173} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "I" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1406 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "J" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 173} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "K" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1406 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "L" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 173} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "M" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1406 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "N" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 173} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "O" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1406 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "P" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 173} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "Q" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1406 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "R" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 173} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "S" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1406 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "T" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 173} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "V" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1406 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "W" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 173} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "X" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1406 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "Y" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1344 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 173} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "Z" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1406 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 175} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Time building chain proxies: 35.56, per 1000 atoms: 0.38 Number of scatterers: 93500 At special positions: 0 Unit cell: (258.64, 258.64, 187.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 612 16.00 O 17714 8.00 N 16592 7.00 C 58582 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: 30.63 Conformation dependent library (CDL) restraints added in 10.3 seconds 23800 Ramachandran restraints generated. 11900 Oldfield, 0 Emsley, 11900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 23596 Finding SS restraints... Secondary structure from input PDB file: 510 helices and 0 sheets defined 88.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.93 Creating SS restraints... Processing helix chain 'AA' and resid 3 through 43 removed outlier: 3.557A pdb=" N ALAAA 34 " --> pdb=" O LYSAA 30 " (cutoff:3.500A) Processing helix chain 'AA' and resid 44 through 106 Processing helix chain 'AA' and resid 107 through 140 removed outlier: 3.629A pdb=" N THRAA 140 " --> pdb=" O METAA 136 " (cutoff:3.500A) Processing helix chain 'AA' and resid 145 through 161 Processing helix chain 'AA' and resid 188 through 198 Processing helix chain 'AB' and resid 4 through 43 removed outlier: 3.558A pdb=" N ALAAB 34 " --> pdb=" O LYSAB 30 " (cutoff:3.500A) Processing helix chain 'AB' and resid 44 through 106 Processing helix chain 'AB' and resid 107 through 140 removed outlier: 3.629A pdb=" N THRAB 140 " --> pdb=" O METAB 136 " (cutoff:3.500A) Processing helix chain 'AB' and resid 145 through 161 Processing helix chain 'AB' and resid 188 through 198 Processing helix chain 'BB' and resid 7 through 46 removed outlier: 3.585A pdb=" N ALABB 46 " --> pdb=" O ASPBB 42 " (cutoff:3.500A) Processing helix chain 'BB' and resid 49 through 82 removed outlier: 3.918A pdb=" N ILEBB 54 " --> pdb=" O GLUBB 50 " (cutoff:3.500A) Processing helix chain 'BB' and resid 82 through 89 removed outlier: 3.683A pdb=" N METBB 89 " --> pdb=" O LEUBB 85 " (cutoff:3.500A) Processing helix chain 'BB' and resid 93 through 95 No H-bonds generated for 'chain 'BB' and resid 93 through 95' Processing helix chain 'BB' and resid 96 through 106 Processing helix chain 'BB' and resid 115 through 127 removed outlier: 3.910A pdb=" N ILEBB 119 " --> pdb=" O ALABB 115 " (cutoff:3.500A) Processing helix chain 'BB' and resid 133 through 140 Processing helix chain 'BB' and resid 145 through 152 Processing helix chain 'BB' and resid 158 through 174 Processing helix chain 'BB' and resid 180 through 186 removed outlier: 3.698A pdb=" N GLUBB 186 " --> pdb=" O VALBB 182 " (cutoff:3.500A) Processing helix chain 'CB' and resid 4 through 43 removed outlier: 3.558A pdb=" N ALACB 34 " --> pdb=" O LYSCB 30 " (cutoff:3.500A) Processing helix chain 'CB' and resid 44 through 106 Processing helix chain 'CB' and resid 107 through 140 removed outlier: 3.629A pdb=" N THRCB 140 " --> pdb=" O METCB 136 " (cutoff:3.500A) Processing helix chain 'CB' and resid 145 through 161 Processing helix chain 'CB' and resid 188 through 198 Processing helix chain 'DB' and resid 7 through 46 removed outlier: 3.585A pdb=" N ALADB 46 " --> pdb=" O ASPDB 42 " (cutoff:3.500A) Processing helix chain 'DB' and resid 49 through 82 removed outlier: 3.917A pdb=" N ILEDB 54 " --> pdb=" O GLUDB 50 " (cutoff:3.500A) Processing helix chain 'DB' and resid 82 through 89 removed outlier: 3.684A pdb=" N METDB 89 " --> pdb=" O LEUDB 85 " (cutoff:3.500A) Processing helix chain 'DB' and resid 93 through 95 No H-bonds generated for 'chain 'DB' and resid 93 through 95' Processing helix chain 'DB' and resid 96 through 106 Processing helix chain 'DB' and resid 115 through 127 removed outlier: 3.911A pdb=" N ILEDB 119 " --> pdb=" O ALADB 115 " (cutoff:3.500A) Processing helix chain 'DB' and resid 133 through 140 Processing helix chain 'DB' and resid 145 through 152 Processing helix chain 'DB' and resid 158 through 174 Processing helix chain 'DB' and resid 180 through 186 removed outlier: 3.698A pdb=" N GLUDB 186 " --> pdb=" O VALDB 182 " (cutoff:3.500A) Processing helix chain 'EB' and resid 4 through 43 removed outlier: 3.558A pdb=" N ALAEB 34 " --> pdb=" O LYSEB 30 " (cutoff:3.500A) Processing helix chain 'EB' and resid 44 through 106 Processing helix chain 'EB' and resid 107 through 140 removed outlier: 3.630A pdb=" N THREB 140 " --> pdb=" O METEB 136 " (cutoff:3.500A) Processing helix chain 'EB' and resid 145 through 161 Processing helix chain 'EB' and resid 188 through 198 Processing helix chain 'FB' and resid 7 through 46 removed outlier: 3.584A pdb=" N ALAFB 46 " --> pdb=" O ASPFB 42 " (cutoff:3.500A) Processing helix chain 'FB' and resid 49 through 82 removed outlier: 3.918A pdb=" N ILEFB 54 " --> pdb=" O GLUFB 50 " (cutoff:3.500A) Processing helix chain 'FB' and resid 82 through 89 removed outlier: 3.683A pdb=" N METFB 89 " --> pdb=" O LEUFB 85 " (cutoff:3.500A) Processing helix chain 'FB' and resid 93 through 95 No H-bonds generated for 'chain 'FB' and resid 93 through 95' Processing helix chain 'FB' and resid 96 through 106 Processing helix chain 'FB' and resid 115 through 127 removed outlier: 3.911A pdb=" N ILEFB 119 " --> pdb=" O ALAFB 115 " (cutoff:3.500A) Processing helix chain 'FB' and resid 133 through 140 Processing helix chain 'FB' and resid 145 through 152 Processing helix chain 'FB' and resid 158 through 174 Processing helix chain 'FB' and resid 180 through 186 removed outlier: 3.698A pdb=" N GLUFB 186 " --> pdb=" O VALFB 182 " (cutoff:3.500A) Processing helix chain 'GB' and resid 4 through 43 removed outlier: 3.558A pdb=" N ALAGB 34 " --> pdb=" O LYSGB 30 " (cutoff:3.500A) Processing helix chain 'GB' and resid 44 through 106 Processing helix chain 'GB' and resid 107 through 140 removed outlier: 3.629A pdb=" N THRGB 140 " --> pdb=" O METGB 136 " (cutoff:3.500A) Processing helix chain 'GB' and resid 145 through 161 Processing helix chain 'GB' and resid 188 through 198 Processing helix chain 'HB' and resid 7 through 46 removed outlier: 3.585A pdb=" N ALAHB 46 " --> pdb=" O ASPHB 42 " (cutoff:3.500A) Processing helix chain 'HB' and resid 49 through 82 removed outlier: 3.917A pdb=" N ILEHB 54 " --> pdb=" O GLUHB 50 " (cutoff:3.500A) Processing helix chain 'HB' and resid 82 through 89 removed outlier: 3.685A pdb=" N METHB 89 " --> pdb=" O LEUHB 85 " (cutoff:3.500A) Processing helix chain 'HB' and resid 93 through 95 No H-bonds generated for 'chain 'HB' and resid 93 through 95' Processing helix chain 'HB' and resid 96 through 106 Processing helix chain 'HB' and resid 115 through 127 removed outlier: 3.910A pdb=" N ILEHB 119 " --> pdb=" O ALAHB 115 " (cutoff:3.500A) Processing helix chain 'HB' and resid 133 through 140 Processing helix chain 'HB' and resid 145 through 152 Processing helix chain 'HB' and resid 158 through 174 Processing helix chain 'HB' and resid 180 through 186 removed outlier: 3.698A pdb=" N GLUHB 186 " --> pdb=" O VALHB 182 " (cutoff:3.500A) Processing helix chain 'IB' and resid 4 through 43 removed outlier: 3.557A pdb=" N ALAIB 34 " --> pdb=" O LYSIB 30 " (cutoff:3.500A) Processing helix chain 'IB' and resid 44 through 106 Processing helix chain 'IB' and resid 107 through 140 removed outlier: 3.630A pdb=" N THRIB 140 " --> pdb=" O METIB 136 " (cutoff:3.500A) Processing helix chain 'IB' and resid 145 through 161 Processing helix chain 'IB' and resid 188 through 198 Processing helix chain 'JB' and resid 7 through 46 removed outlier: 3.585A pdb=" N ALAJB 46 " --> pdb=" O ASPJB 42 " (cutoff:3.500A) Processing helix chain 'JB' and resid 49 through 82 removed outlier: 3.919A pdb=" N ILEJB 54 " --> pdb=" O GLUJB 50 " (cutoff:3.500A) Processing helix chain 'JB' and resid 82 through 89 removed outlier: 3.685A pdb=" N METJB 89 " --> pdb=" O LEUJB 85 " (cutoff:3.500A) Processing helix chain 'JB' and resid 93 through 95 No H-bonds generated for 'chain 'JB' and resid 93 through 95' Processing helix chain 'JB' and resid 96 through 106 Processing helix chain 'JB' and resid 115 through 127 removed outlier: 3.911A pdb=" N ILEJB 119 " --> pdb=" O ALAJB 115 " (cutoff:3.500A) Processing helix chain 'JB' and resid 133 through 140 Processing helix chain 'JB' and resid 145 through 152 Processing helix chain 'JB' and resid 158 through 174 Processing helix chain 'JB' and resid 180 through 186 removed outlier: 3.699A pdb=" N GLUJB 186 " --> pdb=" O VALJB 182 " (cutoff:3.500A) Processing helix chain 'KB' and resid 4 through 43 removed outlier: 3.556A pdb=" N ALAKB 34 " --> pdb=" O LYSKB 30 " (cutoff:3.500A) Processing helix chain 'KB' and resid 44 through 106 Processing helix chain 'KB' and resid 107 through 140 removed outlier: 3.629A pdb=" N THRKB 140 " --> pdb=" O METKB 136 " (cutoff:3.500A) Processing helix chain 'KB' and resid 145 through 161 Processing helix chain 'KB' and resid 188 through 198 Processing helix chain 'LB' and resid 7 through 46 removed outlier: 3.585A pdb=" N ALALB 46 " --> pdb=" O ASPLB 42 " (cutoff:3.500A) Processing helix chain 'LB' and resid 49 through 82 removed outlier: 3.917A pdb=" N ILELB 54 " --> pdb=" O GLULB 50 " (cutoff:3.500A) Processing helix chain 'LB' and resid 82 through 89 removed outlier: 3.686A pdb=" N METLB 89 " --> pdb=" O LEULB 85 " (cutoff:3.500A) Processing helix chain 'LB' and resid 93 through 95 No H-bonds generated for 'chain 'LB' and resid 93 through 95' Processing helix chain 'LB' and resid 96 through 106 Processing helix chain 'LB' and resid 115 through 127 removed outlier: 3.912A pdb=" N ILELB 119 " --> pdb=" O ALALB 115 " (cutoff:3.500A) Processing helix chain 'LB' and resid 133 through 140 Processing helix chain 'LB' and resid 145 through 152 Processing helix chain 'LB' and resid 158 through 174 Processing helix chain 'LB' and resid 180 through 186 removed outlier: 3.697A pdb=" N GLULB 186 " --> pdb=" O VALLB 182 " (cutoff:3.500A) Processing helix chain 'MB' and resid 4 through 43 removed outlier: 3.557A pdb=" N ALAMB 34 " --> pdb=" O LYSMB 30 " (cutoff:3.500A) Processing helix chain 'MB' and resid 44 through 106 Processing helix chain 'MB' and resid 107 through 140 removed outlier: 3.630A pdb=" N THRMB 140 " --> pdb=" O METMB 136 " (cutoff:3.500A) Processing helix chain 'MB' and resid 145 through 161 Processing helix chain 'MB' and resid 188 through 198 Processing helix chain 'NB' and resid 7 through 46 removed outlier: 3.585A pdb=" N ALANB 46 " --> pdb=" O ASPNB 42 " (cutoff:3.500A) Processing helix chain 'NB' and resid 49 through 82 removed outlier: 3.916A pdb=" N ILENB 54 " --> pdb=" O GLUNB 50 " (cutoff:3.500A) Processing helix chain 'NB' and resid 82 through 89 removed outlier: 3.685A pdb=" N METNB 89 " --> pdb=" O LEUNB 85 " (cutoff:3.500A) Processing helix chain 'NB' and resid 93 through 95 No H-bonds generated for 'chain 'NB' and resid 93 through 95' Processing helix chain 'NB' and resid 96 through 106 Processing helix chain 'NB' and resid 115 through 127 removed outlier: 3.911A pdb=" N ILENB 119 " --> pdb=" O ALANB 115 " (cutoff:3.500A) Processing helix chain 'NB' and resid 133 through 140 Processing helix chain 'NB' and resid 145 through 152 Processing helix chain 'NB' and resid 158 through 174 Processing helix chain 'NB' and resid 180 through 186 removed outlier: 3.699A pdb=" N GLUNB 186 " --> pdb=" O VALNB 182 " (cutoff:3.500A) Processing helix chain 'OB' and resid 4 through 43 removed outlier: 3.557A pdb=" N ALAOB 34 " --> pdb=" O LYSOB 30 " (cutoff:3.500A) Processing helix chain 'OB' and resid 44 through 106 Processing helix chain 'OB' and resid 107 through 140 removed outlier: 3.629A pdb=" N THROB 140 " --> pdb=" O METOB 136 " (cutoff:3.500A) Processing helix chain 'OB' and resid 145 through 161 Processing helix chain 'OB' and resid 188 through 198 Processing helix chain 'PB' and resid 7 through 46 removed outlier: 3.584A pdb=" N ALAPB 46 " --> pdb=" O ASPPB 42 " (cutoff:3.500A) Processing helix chain 'PB' and resid 49 through 82 removed outlier: 3.918A pdb=" N ILEPB 54 " --> pdb=" O GLUPB 50 " (cutoff:3.500A) Processing helix chain 'PB' and resid 82 through 89 removed outlier: 3.683A pdb=" N METPB 89 " --> pdb=" O LEUPB 85 " (cutoff:3.500A) Processing helix chain 'PB' and resid 93 through 95 No H-bonds generated for 'chain 'PB' and resid 93 through 95' Processing helix chain 'PB' and resid 96 through 106 Processing helix chain 'PB' and resid 115 through 127 removed outlier: 3.912A pdb=" N ILEPB 119 " --> pdb=" O ALAPB 115 " (cutoff:3.500A) Processing helix chain 'PB' and resid 133 through 140 Processing helix chain 'PB' and resid 145 through 152 Processing helix chain 'PB' and resid 158 through 174 Processing helix chain 'PB' and resid 180 through 186 removed outlier: 3.698A pdb=" N GLUPB 186 " --> pdb=" O VALPB 182 " (cutoff:3.500A) Processing helix chain 'QB' and resid 4 through 43 removed outlier: 3.557A pdb=" N ALAQB 34 " --> pdb=" O LYSQB 30 " (cutoff:3.500A) Processing helix chain 'QB' and resid 44 through 106 Processing helix chain 'QB' and resid 107 through 140 removed outlier: 3.629A pdb=" N THRQB 140 " --> pdb=" O METQB 136 " (cutoff:3.500A) Processing helix chain 'QB' and resid 145 through 161 Processing helix chain 'QB' and resid 188 through 198 Processing helix chain 'TA' and resid 7 through 46 removed outlier: 3.584A pdb=" N ALATA 46 " --> pdb=" O ASPTA 42 " (cutoff:3.500A) Processing helix chain 'TA' and resid 49 through 82 removed outlier: 3.917A pdb=" N ILETA 54 " --> pdb=" O GLUTA 50 " (cutoff:3.500A) Processing helix chain 'TA' and resid 82 through 89 removed outlier: 3.685A pdb=" N METTA 89 " --> pdb=" O LEUTA 85 " (cutoff:3.500A) Processing helix chain 'TA' and resid 93 through 95 No H-bonds generated for 'chain 'TA' and resid 93 through 95' Processing helix chain 'TA' and resid 96 through 106 Processing helix chain 'TA' and resid 115 through 127 removed outlier: 3.911A pdb=" N ILETA 119 " --> pdb=" O ALATA 115 " (cutoff:3.500A) Processing helix chain 'TA' and resid 133 through 140 Processing helix chain 'TA' and resid 145 through 152 Processing helix chain 'TA' and resid 158 through 174 Processing helix chain 'TA' and resid 180 through 186 removed outlier: 3.699A pdb=" N GLUTA 186 " --> pdb=" O VALTA 182 " (cutoff:3.500A) Processing helix chain 'SA' and resid 4 through 43 removed outlier: 3.558A pdb=" N ALASA 34 " --> pdb=" O LYSSA 30 " (cutoff:3.500A) Processing helix chain 'SA' and resid 44 through 106 Processing helix chain 'SA' and resid 107 through 140 removed outlier: 3.629A pdb=" N THRSA 140 " --> pdb=" O METSA 136 " (cutoff:3.500A) Processing helix chain 'SA' and resid 145 through 161 Processing helix chain 'SA' and resid 188 through 198 Processing helix chain 'VA' and resid 7 through 46 removed outlier: 3.583A pdb=" N ALAVA 46 " --> pdb=" O ASPVA 42 " (cutoff:3.500A) Processing helix chain 'VA' and resid 49 through 82 removed outlier: 3.918A pdb=" N ILEVA 54 " --> pdb=" O GLUVA 50 " (cutoff:3.500A) Processing helix chain 'VA' and resid 82 through 89 removed outlier: 3.684A pdb=" N METVA 89 " --> pdb=" O LEUVA 85 " (cutoff:3.500A) Processing helix chain 'VA' and resid 93 through 95 No H-bonds generated for 'chain 'VA' and resid 93 through 95' Processing helix chain 'VA' and resid 96 through 106 Processing helix chain 'VA' and resid 115 through 127 removed outlier: 3.911A pdb=" N ILEVA 119 " --> pdb=" O ALAVA 115 " (cutoff:3.500A) Processing helix chain 'VA' and resid 133 through 140 Processing helix chain 'VA' and resid 145 through 152 Processing helix chain 'VA' and resid 158 through 174 Processing helix chain 'VA' and resid 180 through 186 removed outlier: 3.698A pdb=" N GLUVA 186 " --> pdb=" O VALVA 182 " (cutoff:3.500A) Processing helix chain 'UA' and resid 4 through 43 removed outlier: 3.557A pdb=" N ALAUA 34 " --> pdb=" O LYSUA 30 " (cutoff:3.500A) Processing helix chain 'UA' and resid 44 through 106 Processing helix chain 'UA' and resid 107 through 140 removed outlier: 3.629A pdb=" N THRUA 140 " --> pdb=" O METUA 136 " (cutoff:3.500A) Processing helix chain 'UA' and resid 145 through 161 Processing helix chain 'UA' and resid 188 through 198 Processing helix chain 'XA' and resid 7 through 46 removed outlier: 3.584A pdb=" N ALAXA 46 " --> pdb=" O ASPXA 42 " (cutoff:3.500A) Processing helix chain 'XA' and resid 49 through 82 removed outlier: 3.918A pdb=" N ILEXA 54 " --> pdb=" O GLUXA 50 " (cutoff:3.500A) Processing helix chain 'XA' and resid 82 through 89 removed outlier: 3.685A pdb=" N METXA 89 " --> pdb=" O LEUXA 85 " (cutoff:3.500A) Processing helix chain 'XA' and resid 93 through 95 No H-bonds generated for 'chain 'XA' and resid 93 through 95' Processing helix chain 'XA' and resid 96 through 106 Processing helix chain 'XA' and resid 115 through 127 removed outlier: 3.910A pdb=" N ILEXA 119 " --> pdb=" O ALAXA 115 " (cutoff:3.500A) Processing helix chain 'XA' and resid 133 through 140 Processing helix chain 'XA' and resid 145 through 152 Processing helix chain 'XA' and resid 158 through 174 Processing helix chain 'XA' and resid 180 through 186 removed outlier: 3.699A pdb=" N GLUXA 186 " --> pdb=" O VALXA 182 " (cutoff:3.500A) Processing helix chain 'WA' and resid 4 through 43 removed outlier: 3.557A pdb=" N ALAWA 34 " --> pdb=" O LYSWA 30 " (cutoff:3.500A) Processing helix chain 'WA' and resid 44 through 106 Processing helix chain 'WA' and resid 107 through 140 removed outlier: 3.629A pdb=" N THRWA 140 " --> pdb=" O METWA 136 " (cutoff:3.500A) Processing helix chain 'WA' and resid 145 through 161 Processing helix chain 'WA' and resid 188 through 198 Processing helix chain 'ZA' and resid 7 through 46 removed outlier: 3.585A pdb=" N ALAZA 46 " --> pdb=" O ASPZA 42 " (cutoff:3.500A) Processing helix chain 'ZA' and resid 49 through 82 removed outlier: 3.918A pdb=" N ILEZA 54 " --> pdb=" O GLUZA 50 " (cutoff:3.500A) Processing helix chain 'ZA' and resid 82 through 89 removed outlier: 3.685A pdb=" N METZA 89 " --> pdb=" O LEUZA 85 " (cutoff:3.500A) Processing helix chain 'ZA' and resid 93 through 95 No H-bonds generated for 'chain 'ZA' and resid 93 through 95' Processing helix chain 'ZA' and resid 96 through 106 Processing helix chain 'ZA' and resid 115 through 127 removed outlier: 3.911A pdb=" N ILEZA 119 " --> pdb=" O ALAZA 115 " (cutoff:3.500A) Processing helix chain 'ZA' and resid 133 through 140 Processing helix chain 'ZA' and resid 145 through 152 Processing helix chain 'ZA' and resid 158 through 174 Processing helix chain 'ZA' and resid 180 through 186 removed outlier: 3.699A pdb=" N GLUZA 186 " --> pdb=" O VALZA 182 " (cutoff:3.500A) Processing helix chain 'YA' and resid 4 through 43 removed outlier: 3.557A pdb=" N ALAYA 34 " --> pdb=" O LYSYA 30 " (cutoff:3.500A) Processing helix chain 'YA' and resid 44 through 106 Processing helix chain 'YA' and resid 107 through 140 removed outlier: 3.629A pdb=" N THRYA 140 " --> pdb=" O METYA 136 " (cutoff:3.500A) Processing helix chain 'YA' and resid 145 through 161 Processing helix chain 'YA' and resid 188 through 198 Processing helix chain 'BA' and resid 7 through 46 removed outlier: 3.584A pdb=" N ALABA 46 " --> pdb=" O ASPBA 42 " (cutoff:3.500A) Processing helix chain 'BA' and resid 49 through 82 removed outlier: 3.917A pdb=" N ILEBA 54 " --> pdb=" O GLUBA 50 " (cutoff:3.500A) Processing helix chain 'BA' and resid 82 through 89 removed outlier: 3.683A pdb=" N METBA 89 " --> pdb=" O LEUBA 85 " (cutoff:3.500A) Processing helix chain 'BA' and resid 93 through 95 No H-bonds generated for 'chain 'BA' and resid 93 through 95' Processing helix chain 'BA' and resid 96 through 106 Processing helix chain 'BA' and resid 115 through 127 removed outlier: 3.911A pdb=" N ILEBA 119 " --> pdb=" O ALABA 115 " (cutoff:3.500A) Processing helix chain 'BA' and resid 133 through 140 Processing helix chain 'BA' and resid 145 through 152 Processing helix chain 'BA' and resid 158 through 174 Processing helix chain 'BA' and resid 180 through 186 removed outlier: 3.698A pdb=" N GLUBA 186 " --> pdb=" O VALBA 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 46 removed outlier: 3.584A pdb=" N ALA A 46 " --> pdb=" O ASP A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 82 removed outlier: 3.917A pdb=" N ILE A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 89 removed outlier: 3.684A pdb=" N MET A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 96 through 106 Processing helix chain 'A' and resid 115 through 127 removed outlier: 3.910A pdb=" N ILE A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 140 Processing helix chain 'A' and resid 145 through 152 Processing helix chain 'A' and resid 158 through 174 Processing helix chain 'A' and resid 180 through 186 removed outlier: 3.698A pdb=" N GLU A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing helix chain 'CA' and resid 4 through 43 removed outlier: 3.556A pdb=" N ALACA 34 " --> pdb=" O LYSCA 30 " (cutoff:3.500A) Processing helix chain 'CA' and resid 44 through 106 Processing helix chain 'CA' and resid 107 through 140 removed outlier: 3.629A pdb=" N THRCA 140 " --> pdb=" O METCA 136 " (cutoff:3.500A) Processing helix chain 'CA' and resid 145 through 161 Processing helix chain 'CA' and resid 188 through 198 Processing helix chain 'DA' and resid 7 through 46 removed outlier: 3.584A pdb=" N ALADA 46 " --> pdb=" O ASPDA 42 " (cutoff:3.500A) Processing helix chain 'DA' and resid 49 through 82 removed outlier: 3.916A pdb=" N ILEDA 54 " --> pdb=" O GLUDA 50 " (cutoff:3.500A) Processing helix chain 'DA' and resid 82 through 89 removed outlier: 3.685A pdb=" N METDA 89 " --> pdb=" O LEUDA 85 " (cutoff:3.500A) Processing helix chain 'DA' and resid 93 through 95 No H-bonds generated for 'chain 'DA' and resid 93 through 95' Processing helix chain 'DA' and resid 96 through 106 Processing helix chain 'DA' and resid 115 through 127 removed outlier: 3.910A pdb=" N ILEDA 119 " --> pdb=" O ALADA 115 " (cutoff:3.500A) Processing helix chain 'DA' and resid 133 through 140 Processing helix chain 'DA' and resid 145 through 152 Processing helix chain 'DA' and resid 158 through 174 Processing helix chain 'DA' and resid 180 through 186 removed outlier: 3.699A pdb=" N GLUDA 186 " --> pdb=" O VALDA 182 " (cutoff:3.500A) Processing helix chain 'EA' and resid 4 through 43 removed outlier: 3.557A pdb=" N ALAEA 34 " --> pdb=" O LYSEA 30 " (cutoff:3.500A) Processing helix chain 'EA' and resid 44 through 106 Processing helix chain 'EA' and resid 107 through 140 removed outlier: 3.629A pdb=" N THREA 140 " --> pdb=" O METEA 136 " (cutoff:3.500A) Processing helix chain 'EA' and resid 145 through 161 Processing helix chain 'EA' and resid 188 through 198 Processing helix chain 'FA' and resid 7 through 46 removed outlier: 3.585A pdb=" N ALAFA 46 " --> pdb=" O ASPFA 42 " (cutoff:3.500A) Processing helix chain 'FA' and resid 49 through 82 removed outlier: 3.918A pdb=" N ILEFA 54 " --> pdb=" O GLUFA 50 " (cutoff:3.500A) Processing helix chain 'FA' and resid 82 through 89 removed outlier: 3.684A pdb=" N METFA 89 " --> pdb=" O LEUFA 85 " (cutoff:3.500A) Processing helix chain 'FA' and resid 93 through 95 No H-bonds generated for 'chain 'FA' and resid 93 through 95' Processing helix chain 'FA' and resid 96 through 106 Processing helix chain 'FA' and resid 115 through 127 removed outlier: 3.911A pdb=" N ILEFA 119 " --> pdb=" O ALAFA 115 " (cutoff:3.500A) Processing helix chain 'FA' and resid 133 through 140 Processing helix chain 'FA' and resid 145 through 152 Processing helix chain 'FA' and resid 158 through 174 Processing helix chain 'FA' and resid 180 through 186 removed outlier: 3.698A pdb=" N GLUFA 186 " --> pdb=" O VALFA 182 " (cutoff:3.500A) Processing helix chain 'GA' and resid 4 through 43 removed outlier: 3.558A pdb=" N ALAGA 34 " --> pdb=" O LYSGA 30 " (cutoff:3.500A) Processing helix chain 'GA' and resid 44 through 106 Processing helix chain 'GA' and resid 107 through 140 removed outlier: 3.630A pdb=" N THRGA 140 " --> pdb=" O METGA 136 " (cutoff:3.500A) Processing helix chain 'GA' and resid 145 through 161 Processing helix chain 'GA' and resid 188 through 198 Processing helix chain 'HA' and resid 7 through 46 removed outlier: 3.584A pdb=" N ALAHA 46 " --> pdb=" O ASPHA 42 " (cutoff:3.500A) Processing helix chain 'HA' and resid 49 through 82 removed outlier: 3.917A pdb=" N ILEHA 54 " --> pdb=" O GLUHA 50 " (cutoff:3.500A) Processing helix chain 'HA' and resid 82 through 89 removed outlier: 3.684A pdb=" N METHA 89 " --> pdb=" O LEUHA 85 " (cutoff:3.500A) Processing helix chain 'HA' and resid 93 through 95 No H-bonds generated for 'chain 'HA' and resid 93 through 95' Processing helix chain 'HA' and resid 96 through 106 Processing helix chain 'HA' and resid 115 through 127 removed outlier: 3.910A pdb=" N ILEHA 119 " --> pdb=" O ALAHA 115 " (cutoff:3.500A) Processing helix chain 'HA' and resid 133 through 140 Processing helix chain 'HA' and resid 145 through 152 Processing helix chain 'HA' and resid 158 through 174 Processing helix chain 'HA' and resid 180 through 186 removed outlier: 3.698A pdb=" N GLUHA 186 " --> pdb=" O VALHA 182 " (cutoff:3.500A) Processing helix chain 'IA' and resid 4 through 43 removed outlier: 3.557A pdb=" N ALAIA 34 " --> pdb=" O LYSIA 30 " (cutoff:3.500A) Processing helix chain 'IA' and resid 44 through 106 Processing helix chain 'IA' and resid 107 through 140 removed outlier: 3.630A pdb=" N THRIA 140 " --> pdb=" O METIA 136 " (cutoff:3.500A) Processing helix chain 'IA' and resid 145 through 161 Processing helix chain 'IA' and resid 188 through 198 Processing helix chain 'JA' and resid 7 through 46 removed outlier: 3.584A pdb=" N ALAJA 46 " --> pdb=" O ASPJA 42 " (cutoff:3.500A) Processing helix chain 'JA' and resid 49 through 82 removed outlier: 3.918A pdb=" N ILEJA 54 " --> pdb=" O GLUJA 50 " (cutoff:3.500A) Processing helix chain 'JA' and resid 82 through 89 removed outlier: 3.684A pdb=" N METJA 89 " --> pdb=" O LEUJA 85 " (cutoff:3.500A) Processing helix chain 'JA' and resid 93 through 95 No H-bonds generated for 'chain 'JA' and resid 93 through 95' Processing helix chain 'JA' and resid 96 through 106 Processing helix chain 'JA' and resid 115 through 127 removed outlier: 3.910A pdb=" N ILEJA 119 " --> pdb=" O ALAJA 115 " (cutoff:3.500A) Processing helix chain 'JA' and resid 133 through 140 Processing helix chain 'JA' and resid 145 through 152 Processing helix chain 'JA' and resid 158 through 174 Processing helix chain 'JA' and resid 180 through 186 removed outlier: 3.698A pdb=" N GLUJA 186 " --> pdb=" O VALJA 182 " (cutoff:3.500A) Processing helix chain 'KA' and resid 4 through 43 removed outlier: 3.556A pdb=" N ALAKA 34 " --> pdb=" O LYSKA 30 " (cutoff:3.500A) Processing helix chain 'KA' and resid 44 through 106 Processing helix chain 'KA' and resid 107 through 140 removed outlier: 3.629A pdb=" N THRKA 140 " --> pdb=" O METKA 136 " (cutoff:3.500A) Processing helix chain 'KA' and resid 145 through 161 Processing helix chain 'KA' and resid 188 through 198 Processing helix chain 'LA' and resid 7 through 46 removed outlier: 3.586A pdb=" N ALALA 46 " --> pdb=" O ASPLA 42 " (cutoff:3.500A) Processing helix chain 'LA' and resid 49 through 82 removed outlier: 3.917A pdb=" N ILELA 54 " --> pdb=" O GLULA 50 " (cutoff:3.500A) Processing helix chain 'LA' and resid 82 through 89 removed outlier: 3.684A pdb=" N METLA 89 " --> pdb=" O LEULA 85 " (cutoff:3.500A) Processing helix chain 'LA' and resid 93 through 95 No H-bonds generated for 'chain 'LA' and resid 93 through 95' Processing helix chain 'LA' and resid 96 through 106 Processing helix chain 'LA' and resid 115 through 127 removed outlier: 3.911A pdb=" N ILELA 119 " --> pdb=" O ALALA 115 " (cutoff:3.500A) Processing helix chain 'LA' and resid 133 through 140 Processing helix chain 'LA' and resid 145 through 152 Processing helix chain 'LA' and resid 158 through 174 Processing helix chain 'LA' and resid 180 through 186 removed outlier: 3.698A pdb=" N GLULA 186 " --> pdb=" O VALLA 182 " (cutoff:3.500A) Processing helix chain 'MA' and resid 4 through 43 removed outlier: 3.557A pdb=" N ALAMA 34 " --> pdb=" O LYSMA 30 " (cutoff:3.500A) Processing helix chain 'MA' and resid 44 through 106 Processing helix chain 'MA' and resid 107 through 140 removed outlier: 3.629A pdb=" N THRMA 140 " --> pdb=" O METMA 136 " (cutoff:3.500A) Processing helix chain 'MA' and resid 145 through 161 Processing helix chain 'MA' and resid 188 through 198 Processing helix chain 'NA' and resid 7 through 46 removed outlier: 3.585A pdb=" N ALANA 46 " --> pdb=" O ASPNA 42 " (cutoff:3.500A) Processing helix chain 'NA' and resid 49 through 82 removed outlier: 3.917A pdb=" N ILENA 54 " --> pdb=" O GLUNA 50 " (cutoff:3.500A) Processing helix chain 'NA' and resid 82 through 89 removed outlier: 3.684A pdb=" N METNA 89 " --> pdb=" O LEUNA 85 " (cutoff:3.500A) Processing helix chain 'NA' and resid 93 through 95 No H-bonds generated for 'chain 'NA' and resid 93 through 95' Processing helix chain 'NA' and resid 96 through 106 Processing helix chain 'NA' and resid 115 through 127 removed outlier: 3.911A pdb=" N ILENA 119 " --> pdb=" O ALANA 115 " (cutoff:3.500A) Processing helix chain 'NA' and resid 133 through 140 Processing helix chain 'NA' and resid 145 through 152 Processing helix chain 'NA' and resid 158 through 174 Processing helix chain 'NA' and resid 180 through 186 removed outlier: 3.698A pdb=" N GLUNA 186 " --> pdb=" O VALNA 182 " (cutoff:3.500A) Processing helix chain 'OA' and resid 4 through 43 removed outlier: 3.558A pdb=" N ALAOA 34 " --> pdb=" O LYSOA 30 " (cutoff:3.500A) Processing helix chain 'OA' and resid 44 through 106 Processing helix chain 'OA' and resid 107 through 140 removed outlier: 3.630A pdb=" N THROA 140 " --> pdb=" O METOA 136 " (cutoff:3.500A) Processing helix chain 'OA' and resid 145 through 161 Processing helix chain 'OA' and resid 188 through 198 Processing helix chain 'PA' and resid 7 through 46 removed outlier: 3.583A pdb=" N ALAPA 46 " --> pdb=" O ASPPA 42 " (cutoff:3.500A) Processing helix chain 'PA' and resid 49 through 82 removed outlier: 3.917A pdb=" N ILEPA 54 " --> pdb=" O GLUPA 50 " (cutoff:3.500A) Processing helix chain 'PA' and resid 82 through 89 removed outlier: 3.684A pdb=" N METPA 89 " --> pdb=" O LEUPA 85 " (cutoff:3.500A) Processing helix chain 'PA' and resid 93 through 95 No H-bonds generated for 'chain 'PA' and resid 93 through 95' Processing helix chain 'PA' and resid 96 through 106 Processing helix chain 'PA' and resid 115 through 127 removed outlier: 3.910A pdb=" N ILEPA 119 " --> pdb=" O ALAPA 115 " (cutoff:3.500A) Processing helix chain 'PA' and resid 133 through 140 Processing helix chain 'PA' and resid 145 through 152 Processing helix chain 'PA' and resid 158 through 174 Processing helix chain 'PA' and resid 180 through 186 removed outlier: 3.699A pdb=" N GLUPA 186 " --> pdb=" O VALPA 182 " (cutoff:3.500A) Processing helix chain 'QA' and resid 4 through 43 removed outlier: 3.557A pdb=" N ALAQA 34 " --> pdb=" O LYSQA 30 " (cutoff:3.500A) Processing helix chain 'QA' and resid 44 through 106 Processing helix chain 'QA' and resid 107 through 140 removed outlier: 3.629A pdb=" N THRQA 140 " --> pdb=" O METQA 136 " (cutoff:3.500A) Processing helix chain 'QA' and resid 145 through 161 Processing helix chain 'QA' and resid 188 through 198 Processing helix chain 'RA' and resid 7 through 46 removed outlier: 3.584A pdb=" N ALARA 46 " --> pdb=" O ASPRA 42 " (cutoff:3.500A) Processing helix chain 'RA' and resid 49 through 82 removed outlier: 3.918A pdb=" N ILERA 54 " --> pdb=" O GLURA 50 " (cutoff:3.500A) Processing helix chain 'RA' and resid 82 through 89 removed outlier: 3.685A pdb=" N METRA 89 " --> pdb=" O LEURA 85 " (cutoff:3.500A) Processing helix chain 'RA' and resid 93 through 95 No H-bonds generated for 'chain 'RA' and resid 93 through 95' Processing helix chain 'RA' and resid 96 through 106 Processing helix chain 'RA' and resid 115 through 127 removed outlier: 3.910A pdb=" N ILERA 119 " --> pdb=" O ALARA 115 " (cutoff:3.500A) Processing helix chain 'RA' and resid 133 through 140 Processing helix chain 'RA' and resid 145 through 152 Processing helix chain 'RA' and resid 158 through 174 Processing helix chain 'RA' and resid 180 through 186 removed outlier: 3.698A pdb=" N GLURA 186 " --> pdb=" O VALRA 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 43 removed outlier: 3.558A pdb=" N ALA B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 106 Processing helix chain 'B' and resid 107 through 140 removed outlier: 3.629A pdb=" N THR B 140 " --> pdb=" O MET B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 161 Processing helix chain 'B' and resid 188 through 198 Processing helix chain 'C' and resid 7 through 46 removed outlier: 3.585A pdb=" N ALA C 46 " --> pdb=" O ASP C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 82 removed outlier: 3.918A pdb=" N ILE C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 89 removed outlier: 3.684A pdb=" N MET C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 95 No H-bonds generated for 'chain 'C' and resid 93 through 95' Processing helix chain 'C' and resid 96 through 106 Processing helix chain 'C' and resid 115 through 127 removed outlier: 3.911A pdb=" N ILE C 119 " --> pdb=" O ALA C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 140 Processing helix chain 'C' and resid 145 through 152 Processing helix chain 'C' and resid 158 through 174 Processing helix chain 'C' and resid 180 through 186 removed outlier: 3.698A pdb=" N GLU C 186 " --> pdb=" O VAL C 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 43 removed outlier: 3.558A pdb=" N ALA D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 106 Processing helix chain 'D' and resid 107 through 140 removed outlier: 3.630A pdb=" N THR D 140 " --> pdb=" O MET D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 161 Processing helix chain 'D' and resid 188 through 198 Processing helix chain 'E' and resid 7 through 46 removed outlier: 3.585A pdb=" N ALA E 46 " --> pdb=" O ASP E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 82 removed outlier: 3.918A pdb=" N ILE E 54 " --> pdb=" O GLU E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 89 removed outlier: 3.683A pdb=" N MET E 89 " --> pdb=" O LEU E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 95 No H-bonds generated for 'chain 'E' and resid 93 through 95' Processing helix chain 'E' and resid 96 through 106 Processing helix chain 'E' and resid 115 through 127 removed outlier: 3.912A pdb=" N ILE E 119 " --> pdb=" O ALA E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 140 Processing helix chain 'E' and resid 145 through 152 Processing helix chain 'E' and resid 158 through 174 Processing helix chain 'E' and resid 180 through 186 removed outlier: 3.698A pdb=" N GLU E 186 " --> pdb=" O VAL E 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 43 removed outlier: 3.558A pdb=" N ALA F 34 " --> pdb=" O LYS F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 106 Processing helix chain 'F' and resid 107 through 140 removed outlier: 3.629A pdb=" N THR F 140 " --> pdb=" O MET F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 161 Processing helix chain 'F' and resid 188 through 198 Processing helix chain 'G' and resid 7 through 46 removed outlier: 3.584A pdb=" N ALA G 46 " --> pdb=" O ASP G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 82 removed outlier: 3.917A pdb=" N ILE G 54 " --> pdb=" O GLU G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 89 removed outlier: 3.684A pdb=" N MET G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 95 No H-bonds generated for 'chain 'G' and resid 93 through 95' Processing helix chain 'G' and resid 96 through 106 Processing helix chain 'G' and resid 115 through 127 removed outlier: 3.910A pdb=" N ILE G 119 " --> pdb=" O ALA G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 140 Processing helix chain 'G' and resid 145 through 152 Processing helix chain 'G' and resid 158 through 174 Processing helix chain 'G' and resid 180 through 186 removed outlier: 3.699A pdb=" N GLU G 186 " --> pdb=" O VAL G 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 43 removed outlier: 3.557A pdb=" N ALA H 34 " --> pdb=" O LYS H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 106 Processing helix chain 'H' and resid 107 through 140 removed outlier: 3.628A pdb=" N THR H 140 " --> pdb=" O MET H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 161 Processing helix chain 'H' and resid 188 through 198 Processing helix chain 'I' and resid 7 through 46 removed outlier: 3.585A pdb=" N ALA I 46 " --> pdb=" O ASP I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 82 removed outlier: 3.918A pdb=" N ILE I 54 " --> pdb=" O GLU I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 89 removed outlier: 3.684A pdb=" N MET I 89 " --> pdb=" O LEU I 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 95 No H-bonds generated for 'chain 'I' and resid 93 through 95' Processing helix chain 'I' and resid 96 through 106 Processing helix chain 'I' and resid 115 through 127 removed outlier: 3.912A pdb=" N ILE I 119 " --> pdb=" O ALA I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 140 Processing helix chain 'I' and resid 145 through 152 Processing helix chain 'I' and resid 158 through 174 Processing helix chain 'I' and resid 180 through 186 removed outlier: 3.698A pdb=" N GLU I 186 " --> pdb=" O VAL I 182 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 43 removed outlier: 3.556A pdb=" N ALA J 34 " --> pdb=" O LYS J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 106 Processing helix chain 'J' and resid 107 through 140 removed outlier: 3.630A pdb=" N THR J 140 " --> pdb=" O MET J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 145 through 161 Processing helix chain 'J' and resid 188 through 198 Processing helix chain 'K' and resid 7 through 46 removed outlier: 3.586A pdb=" N ALA K 46 " --> pdb=" O ASP K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 82 removed outlier: 3.917A pdb=" N ILE K 54 " --> pdb=" O GLU K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 89 removed outlier: 3.684A pdb=" N MET K 89 " --> pdb=" O LEU K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 95 No H-bonds generated for 'chain 'K' and resid 93 through 95' Processing helix chain 'K' and resid 96 through 106 Processing helix chain 'K' and resid 115 through 127 removed outlier: 3.911A pdb=" N ILE K 119 " --> pdb=" O ALA K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 133 through 140 Processing helix chain 'K' and resid 145 through 152 Processing helix chain 'K' and resid 158 through 174 Processing helix chain 'K' and resid 180 through 186 removed outlier: 3.699A pdb=" N GLU K 186 " --> pdb=" O VAL K 182 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 43 removed outlier: 3.556A pdb=" N ALA L 34 " --> pdb=" O LYS L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 106 Processing helix chain 'L' and resid 107 through 140 removed outlier: 3.630A pdb=" N THR L 140 " --> pdb=" O MET L 136 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 161 Processing helix chain 'L' and resid 188 through 198 Processing helix chain 'M' and resid 7 through 46 removed outlier: 3.584A pdb=" N ALA M 46 " --> pdb=" O ASP M 42 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 82 removed outlier: 3.917A pdb=" N ILE M 54 " --> pdb=" O GLU M 50 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 89 removed outlier: 3.685A pdb=" N MET M 89 " --> pdb=" O LEU M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 93 through 95 No H-bonds generated for 'chain 'M' and resid 93 through 95' Processing helix chain 'M' and resid 96 through 106 Processing helix chain 'M' and resid 115 through 127 removed outlier: 3.911A pdb=" N ILE M 119 " --> pdb=" O ALA M 115 " (cutoff:3.500A) Processing helix chain 'M' and resid 133 through 140 Processing helix chain 'M' and resid 145 through 152 Processing helix chain 'M' and resid 158 through 174 Processing helix chain 'M' and resid 180 through 186 removed outlier: 3.698A pdb=" N GLU M 186 " --> pdb=" O VAL M 182 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 43 removed outlier: 3.557A pdb=" N ALA N 34 " --> pdb=" O LYS N 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 106 Processing helix chain 'N' and resid 107 through 140 removed outlier: 3.630A pdb=" N THR N 140 " --> pdb=" O MET N 136 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 161 Processing helix chain 'N' and resid 188 through 198 Processing helix chain 'O' and resid 7 through 46 removed outlier: 3.584A pdb=" N ALA O 46 " --> pdb=" O ASP O 42 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 82 removed outlier: 3.918A pdb=" N ILE O 54 " --> pdb=" O GLU O 50 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 89 removed outlier: 3.684A pdb=" N MET O 89 " --> pdb=" O LEU O 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 93 through 95 No H-bonds generated for 'chain 'O' and resid 93 through 95' Processing helix chain 'O' and resid 96 through 106 Processing helix chain 'O' and resid 115 through 127 removed outlier: 3.910A pdb=" N ILE O 119 " --> pdb=" O ALA O 115 " (cutoff:3.500A) Processing helix chain 'O' and resid 133 through 140 Processing helix chain 'O' and resid 145 through 152 Processing helix chain 'O' and resid 158 through 174 Processing helix chain 'O' and resid 180 through 186 removed outlier: 3.698A pdb=" N GLU O 186 " --> pdb=" O VAL O 182 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 43 removed outlier: 3.557A pdb=" N ALA P 34 " --> pdb=" O LYS P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 106 Processing helix chain 'P' and resid 107 through 140 removed outlier: 3.629A pdb=" N THR P 140 " --> pdb=" O MET P 136 " (cutoff:3.500A) Processing helix chain 'P' and resid 145 through 161 Processing helix chain 'P' and resid 188 through 198 Processing helix chain 'Q' and resid 7 through 46 removed outlier: 3.584A pdb=" N ALA Q 46 " --> pdb=" O ASP Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 82 removed outlier: 3.917A pdb=" N ILE Q 54 " --> pdb=" O GLU Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 89 removed outlier: 3.684A pdb=" N MET Q 89 " --> pdb=" O LEU Q 85 " (cutoff:3.500A) Processing helix chain 'Q' and resid 93 through 95 No H-bonds generated for 'chain 'Q' and resid 93 through 95' Processing helix chain 'Q' and resid 96 through 106 Processing helix chain 'Q' and resid 115 through 127 removed outlier: 3.911A pdb=" N ILE Q 119 " --> pdb=" O ALA Q 115 " (cutoff:3.500A) Processing helix chain 'Q' and resid 133 through 140 Processing helix chain 'Q' and resid 145 through 152 Processing helix chain 'Q' and resid 158 through 174 Processing helix chain 'Q' and resid 180 through 186 removed outlier: 3.699A pdb=" N GLU Q 186 " --> pdb=" O VAL Q 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 43 removed outlier: 3.558A pdb=" N ALA R 34 " --> pdb=" O LYS R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 106 Processing helix chain 'R' and resid 107 through 140 removed outlier: 3.629A pdb=" N THR R 140 " --> pdb=" O MET R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 161 Processing helix chain 'R' and resid 188 through 198 Processing helix chain 'S' and resid 7 through 46 removed outlier: 3.585A pdb=" N ALA S 46 " --> pdb=" O ASP S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 82 removed outlier: 3.919A pdb=" N ILE S 54 " --> pdb=" O GLU S 50 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 89 removed outlier: 3.684A pdb=" N MET S 89 " --> pdb=" O LEU S 85 " (cutoff:3.500A) Processing helix chain 'S' and resid 93 through 95 No H-bonds generated for 'chain 'S' and resid 93 through 95' Processing helix chain 'S' and resid 96 through 106 Processing helix chain 'S' and resid 115 through 127 removed outlier: 3.912A pdb=" N ILE S 119 " --> pdb=" O ALA S 115 " (cutoff:3.500A) Processing helix chain 'S' and resid 133 through 140 Processing helix chain 'S' and resid 145 through 152 Processing helix chain 'S' and resid 158 through 174 Processing helix chain 'S' and resid 180 through 186 removed outlier: 3.698A pdb=" N GLU S 186 " --> pdb=" O VAL S 182 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 43 removed outlier: 3.556A pdb=" N ALA T 34 " --> pdb=" O LYS T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 106 Processing helix chain 'T' and resid 107 through 140 removed outlier: 3.630A pdb=" N THR T 140 " --> pdb=" O MET T 136 " (cutoff:3.500A) Processing helix chain 'T' and resid 145 through 161 Processing helix chain 'T' and resid 188 through 198 Processing helix chain 'V' and resid 7 through 46 removed outlier: 3.585A pdb=" N ALA V 46 " --> pdb=" O ASP V 42 " (cutoff:3.500A) Processing helix chain 'V' and resid 49 through 82 removed outlier: 3.917A pdb=" N ILE V 54 " --> pdb=" O GLU V 50 " (cutoff:3.500A) Processing helix chain 'V' and resid 82 through 89 removed outlier: 3.683A pdb=" N MET V 89 " --> pdb=" O LEU V 85 " (cutoff:3.500A) Processing helix chain 'V' and resid 93 through 95 No H-bonds generated for 'chain 'V' and resid 93 through 95' Processing helix chain 'V' and resid 96 through 106 Processing helix chain 'V' and resid 115 through 127 removed outlier: 3.911A pdb=" N ILE V 119 " --> pdb=" O ALA V 115 " (cutoff:3.500A) Processing helix chain 'V' and resid 133 through 140 Processing helix chain 'V' and resid 145 through 152 Processing helix chain 'V' and resid 158 through 174 Processing helix chain 'V' and resid 180 through 186 removed outlier: 3.698A pdb=" N GLU V 186 " --> pdb=" O VAL V 182 " (cutoff:3.500A) Processing helix chain 'W' and resid 4 through 43 removed outlier: 3.557A pdb=" N ALA W 34 " --> pdb=" O LYS W 30 " (cutoff:3.500A) Processing helix chain 'W' and resid 44 through 106 Processing helix chain 'W' and resid 107 through 140 removed outlier: 3.630A pdb=" N THR W 140 " --> pdb=" O MET W 136 " (cutoff:3.500A) Processing helix chain 'W' and resid 145 through 161 Processing helix chain 'W' and resid 188 through 198 Processing helix chain 'X' and resid 7 through 46 removed outlier: 3.586A pdb=" N ALA X 46 " --> pdb=" O ASP X 42 " (cutoff:3.500A) Processing helix chain 'X' and resid 49 through 82 removed outlier: 3.918A pdb=" N ILE X 54 " --> pdb=" O GLU X 50 " (cutoff:3.500A) Processing helix chain 'X' and resid 82 through 89 removed outlier: 3.685A pdb=" N MET X 89 " --> pdb=" O LEU X 85 " (cutoff:3.500A) Processing helix chain 'X' and resid 93 through 95 No H-bonds generated for 'chain 'X' and resid 93 through 95' Processing helix chain 'X' and resid 96 through 106 Processing helix chain 'X' and resid 115 through 127 removed outlier: 3.911A pdb=" N ILE X 119 " --> pdb=" O ALA X 115 " (cutoff:3.500A) Processing helix chain 'X' and resid 133 through 140 Processing helix chain 'X' and resid 145 through 152 Processing helix chain 'X' and resid 158 through 174 Processing helix chain 'X' and resid 180 through 186 removed outlier: 3.698A pdb=" N GLU X 186 " --> pdb=" O VAL X 182 " (cutoff:3.500A) Processing helix chain 'Y' and resid 4 through 43 removed outlier: 3.557A pdb=" N ALA Y 34 " --> pdb=" O LYS Y 30 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 106 Processing helix chain 'Y' and resid 107 through 140 removed outlier: 3.628A pdb=" N THR Y 140 " --> pdb=" O MET Y 136 " (cutoff:3.500A) Processing helix chain 'Y' and resid 145 through 161 Processing helix chain 'Y' and resid 188 through 198 Processing helix chain 'Z' and resid 7 through 46 removed outlier: 3.584A pdb=" N ALA Z 46 " --> pdb=" O ASP Z 42 " (cutoff:3.500A) Processing helix chain 'Z' and resid 49 through 82 removed outlier: 3.916A pdb=" N ILE Z 54 " --> pdb=" O GLU Z 50 " (cutoff:3.500A) Processing helix chain 'Z' and resid 82 through 89 removed outlier: 3.684A pdb=" N MET Z 89 " --> pdb=" O LEU Z 85 " (cutoff:3.500A) Processing helix chain 'Z' and resid 93 through 95 No H-bonds generated for 'chain 'Z' and resid 93 through 95' Processing helix chain 'Z' and resid 96 through 106 Processing helix chain 'Z' and resid 115 through 127 removed outlier: 3.910A pdb=" N ILE Z 119 " --> pdb=" O ALA Z 115 " (cutoff:3.500A) Processing helix chain 'Z' and resid 133 through 140 Processing helix chain 'Z' and resid 145 through 152 Processing helix chain 'Z' and resid 158 through 174 Processing helix chain 'Z' and resid 180 through 186 removed outlier: 3.699A pdb=" N GLU Z 186 " --> pdb=" O VAL Z 182 " (cutoff:3.500A) 8433 hydrogen bonds defined for protein. 25299 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: 36.06 Time building geometry restraints manager: 33.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 31786 1.34 - 1.46: 13610 1.46 - 1.58: 47798 1.58 - 1.69: 0 1.69 - 1.81: 1122 Bond restraints: 94316 Sorted by residual: bond pdb=" N VALHA 162 " pdb=" CA VALHA 162 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.29e+00 bond pdb=" N VAL O 162 " pdb=" CA VAL O 162 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 8.00e+00 bond pdb=" N VALDA 162 " pdb=" CA VALDA 162 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 8.00e+00 bond pdb=" N VALZA 162 " pdb=" CA VALZA 162 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 8.00e+00 bond pdb=" N VALDB 162 " pdb=" CA VALDB 162 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 7.98e+00 ... (remaining 94311 not shown) Histogram of bond angle deviations from ideal: 98.46 - 105.56: 1120 105.56 - 112.66: 52292 112.66 - 119.77: 29837 119.77 - 126.87: 42961 126.87 - 133.98: 474 Bond angle restraints: 126684 Sorted by residual: angle pdb=" CA SERBB 181 " pdb=" CB SERBB 181 " pdb=" OG SERBB 181 " ideal model delta sigma weight residual 111.10 117.61 -6.51 2.00e+00 2.50e-01 1.06e+01 angle pdb=" CA SERBA 181 " pdb=" CB SERBA 181 " pdb=" OG SERBA 181 " ideal model delta sigma weight residual 111.10 117.60 -6.50 2.00e+00 2.50e-01 1.06e+01 angle pdb=" CA SER V 181 " pdb=" CB SER V 181 " pdb=" OG SER V 181 " ideal model delta sigma weight residual 111.10 117.60 -6.50 2.00e+00 2.50e-01 1.06e+01 angle pdb=" CA SERJB 181 " pdb=" CB SERJB 181 " pdb=" OG SERJB 181 " ideal model delta sigma weight residual 111.10 117.59 -6.49 2.00e+00 2.50e-01 1.05e+01 angle pdb=" CA SERDB 181 " pdb=" CB SERDB 181 " pdb=" OG SERDB 181 " ideal model delta sigma weight residual 111.10 117.58 -6.48 2.00e+00 2.50e-01 1.05e+01 ... (remaining 126679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 54675 17.90 - 35.80: 4145 35.80 - 53.70: 816 53.70 - 71.60: 68 71.60 - 89.50: 170 Dihedral angle restraints: 59874 sinusoidal: 24038 harmonic: 35836 Sorted by residual: dihedral pdb=" CB GLUNA 178 " pdb=" CG GLUNA 178 " pdb=" CD GLUNA 178 " pdb=" OE1 GLUNA 178 " ideal model delta sinusoidal sigma weight residual 0.00 89.50 -89.50 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU G 178 " pdb=" CG GLU G 178 " pdb=" CD GLU G 178 " pdb=" OE1 GLU G 178 " ideal model delta sinusoidal sigma weight residual 0.00 89.49 -89.49 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLUFA 178 " pdb=" CG GLUFA 178 " pdb=" CD GLUFA 178 " pdb=" OE1 GLUFA 178 " ideal model delta sinusoidal sigma weight residual 0.00 89.48 -89.48 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 59871 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 12420 0.040 - 0.080: 1895 0.080 - 0.120: 577 0.120 - 0.159: 68 0.159 - 0.199: 68 Chirality restraints: 15028 Sorted by residual: chirality pdb=" CA VALZA 162 " pdb=" N VALZA 162 " pdb=" C VALZA 162 " pdb=" CB VALZA 162 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.92e-01 chirality pdb=" CA LEUHA 161 " pdb=" N LEUHA 161 " pdb=" C LEUHA 161 " pdb=" CB LEUHA 161 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.86e-01 chirality pdb=" CA LEUPB 161 " pdb=" N LEUPB 161 " pdb=" C LEUPB 161 " pdb=" CB LEUPB 161 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.74e-01 ... (remaining 15025 not shown) Planarity restraints: 16218 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU H 125 " -0.006 2.00e-02 2.50e+03 1.16e-02 1.35e+00 pdb=" C LEU H 125 " 0.020 2.00e-02 2.50e+03 pdb=" O LEU H 125 " -0.008 2.00e-02 2.50e+03 pdb=" N ASP H 126 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU N 125 " -0.006 2.00e-02 2.50e+03 1.16e-02 1.34e+00 pdb=" C LEU N 125 " 0.020 2.00e-02 2.50e+03 pdb=" O LEU N 125 " -0.008 2.00e-02 2.50e+03 pdb=" N ASP N 126 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU J 125 " -0.006 2.00e-02 2.50e+03 1.16e-02 1.34e+00 pdb=" C LEU J 125 " 0.020 2.00e-02 2.50e+03 pdb=" O LEU J 125 " -0.008 2.00e-02 2.50e+03 pdb=" N ASP J 126 " -0.007 2.00e-02 2.50e+03 ... (remaining 16215 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 20546 2.79 - 3.32: 100159 3.32 - 3.85: 157936 3.85 - 4.37: 178041 4.37 - 4.90: 308765 Nonbonded interactions: 765447 Sorted by model distance: nonbonded pdb=" O THRIA 143 " pdb=" OD1 ASN F 60 " model vdw 2.263 3.040 nonbonded pdb=" OD1 ASPOB 150 " pdb=" NH2 ARGCA 49 " model vdw 2.270 2.520 nonbonded pdb=" OD1 ASPCA 150 " pdb=" NH2 ARG T 49 " model vdw 2.274 2.520 nonbonded pdb=" OD1 ASPEA 150 " pdb=" NH2 ARG P 49 " model vdw 2.276 2.520 nonbonded pdb=" NH2 ARGGB 49 " pdb=" OD1 ASP B 150 " model vdw 2.277 2.520 ... (remaining 765442 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 'BA' selection = chain 'BB' selection = chain 'C' selection = chain 'DA' selection = chain 'DB' selection = chain 'E' selection = chain 'FA' selection = chain 'FB' selection = chain 'G' selection = chain 'HA' selection = chain 'HB' selection = chain 'I' selection = chain 'JA' selection = chain 'JB' selection = chain 'K' selection = chain 'LA' selection = chain 'LB' selection = chain 'M' selection = chain 'NA' selection = chain 'NB' selection = chain 'O' selection = chain 'PA' selection = chain 'PB' selection = chain 'Q' selection = chain 'RA' selection = chain 'S' selection = chain 'TA' selection = chain 'V' selection = chain 'VA' selection = chain 'X' selection = chain 'XA' selection = chain 'Z' selection = chain 'ZA' } ncs_group { reference = chain 'AA' selection = chain 'AB' selection = chain 'B' selection = chain 'CA' selection = chain 'CB' selection = chain 'D' selection = chain 'EA' selection = chain 'EB' selection = chain 'F' selection = chain 'GA' selection = chain 'GB' selection = chain 'H' selection = chain 'IA' selection = chain 'IB' selection = chain 'J' selection = chain 'KA' selection = chain 'KB' selection = chain 'L' selection = chain 'MA' selection = chain 'MB' selection = chain 'N' selection = chain 'OA' selection = chain 'OB' selection = chain 'P' selection = chain 'QA' selection = chain 'QB' selection = chain 'R' selection = chain 'SA' selection = chain 'T' selection = chain 'UA' selection = chain 'W' selection = chain 'WA' selection = chain 'Y' selection = chain 'YA' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.680 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: 0.070 Extract box with map and model: 12.720 Check model and map are aligned: 1.050 Set scattering table: 0.640 Process input model: 188.840 Find NCS groups from input model: 5.610 Set up NCS constraints: 1.480 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 215.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5453 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 : 0.003 0.034 94316 Z= 0.224 Angle : 0.512 6.511 126684 Z= 0.329 Chirality : 0.036 0.199 15028 Planarity : 0.002 0.016 16218 Dihedral : 14.115 89.500 36278 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.07), residues: 11900 helix: 0.68 (0.05), residues: 10030 sheet: None (None), residues: 0 loop : -2.33 (0.12), residues: 1870 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23800 Ramachandran restraints generated. 11900 Oldfield, 0 Emsley, 11900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23800 Ramachandran restraints generated. 11900 Oldfield, 0 Emsley, 11900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3630 residues out of total 10472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3630 time to evaluate : 8.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 3630 average time/residue: 0.8988 time to fit residues: 5448.3280 Evaluate side-chains 2877 residues out of total 10472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2877 time to evaluate : 8.266 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 11.7223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1190 random chunks: chunk 1004 optimal weight: 1.9990 chunk 901 optimal weight: 0.0170 chunk 500 optimal weight: 5.9990 chunk 308 optimal weight: 0.3980 chunk 608 optimal weight: 6.9990 chunk 481 optimal weight: 0.6980 chunk 932 optimal weight: 5.9990 chunk 360 optimal weight: 4.9990 chunk 567 optimal weight: 6.9990 chunk 694 optimal weight: 9.9990 chunk 1080 optimal weight: 30.0000 overall best weight: 1.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 10 ASN AA 41 GLN ** AA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 41 GLN AB 64 ASN ** AB 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 165 ASN AB 190 GLN BB 34 GLN BB 58 HIS BB 172 ASN CB 10 ASN ** CB 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** DB 58 HIS DB 172 ASN EB 10 ASN EB 41 GLN EB 60 ASN EB 120 HIS EB 121 GLN EB 148 GLN EB 165 ASN FB 58 HIS FB 111 GLN FB 145 ASN FB 150 HIS FB 172 ASN GB 10 ASN GB 41 GLN ** GB 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** GB 121 GLN GB 131 GLN HB 58 HIS HB 111 GLN HB 172 ASN IB 41 GLN JB 58 HIS JB 172 ASN KB 41 GLN KB 60 ASN ** KB 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** KB 165 ASN LB 58 HIS LB 87 GLN LB 172 ASN MB 10 ASN MB 41 GLN ** MB 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NB 58 HIS NB 111 GLN NB 172 ASN OB 41 GLN OB 60 ASN ** OB 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** OB 121 GLN PB 111 GLN PB 150 HIS QB 51 HIS ** QB 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TA 58 HIS TA 172 ASN SA 10 ASN SA 41 GLN ** SA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** VA 58 HIS VA 172 ASN UA 7 HIS UA 10 ASN UA 41 GLN UA 60 ASN ** UA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** UA 121 GLN UA 165 ASN XA 172 ASN WA 41 GLN ** WA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** WA 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ZA 58 HIS ZA 172 ASN YA 10 ASN YA 41 GLN YA 60 ASN YA 121 GLN YA 165 ASN BA 58 HIS BA 145 ASN BA 172 ASN A 58 HIS A 87 GLN A 172 ASN CA 10 ASN CA 41 GLN CA 51 HIS CA 60 ASN CA 61 GLN CA 165 ASN DA 111 GLN DA 172 ASN EA 10 ASN EA 60 ASN ** EA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EA 121 GLN EA 165 ASN FA 172 ASN GA 10 ASN GA 41 GLN GA 60 ASN GA 131 GLN GA 165 ASN HA 111 GLN HA 172 ASN IA 41 GLN ** IA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** IA 121 GLN IA 146 GLN JA 87 GLN JA 150 HIS JA 172 ASN ** KA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** KA 121 GLN LA 111 GLN LA 172 ASN MA 10 ASN MA 41 GLN MA 60 ASN MA 61 GLN MA 121 GLN MA 146 GLN MA 165 ASN NA 172 ASN ** OA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** OA 121 GLN OA 131 GLN PA 111 GLN PA 172 ASN QA 10 ASN QA 41 GLN QA 51 HIS QA 61 GLN QA 165 ASN RA 58 HIS RA 150 HIS RA 172 ASN B 41 GLN B 51 HIS ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 ASN B 165 ASN B 190 GLN C 58 HIS C 172 ASN D 41 GLN D 60 ASN D 165 ASN ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 GLN E 145 ASN E 172 ASN F 41 GLN F 60 ASN ** F 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 HIS F 121 GLN F 165 ASN G 111 GLN G 172 ASN H 10 ASN H 41 GLN H 51 HIS H 60 ASN H 165 ASN I 150 HIS I 172 ASN J 10 ASN J 41 GLN ** J 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 60 ASN J 61 GLN ** J 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 121 GLN J 165 ASN K 172 ASN L 41 GLN L 64 ASN L 165 ASN M 87 GLN M 172 ASN N 60 ASN ** N 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 111 GLN O 172 ASN P 10 ASN P 41 GLN P 51 HIS P 60 ASN P 165 ASN Q 58 HIS Q 172 ASN R 10 ASN R 41 GLN R 51 HIS R 60 ASN ** R 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 165 ASN S 87 GLN S 172 ASN T 41 GLN T 61 GLN T 120 HIS T 165 ASN V 58 HIS V 111 GLN V 145 ASN V 172 ASN W 41 GLN W 165 ASN X 58 HIS X 172 ASN Y 41 GLN Y 64 ASN Y 165 ASN Y 190 GLN Z 58 HIS Z 172 ASN Total number of N/Q/H flips: 201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.7046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 94316 Z= 0.274 Angle : 0.717 15.887 126684 Z= 0.370 Chirality : 0.038 0.252 15028 Planarity : 0.005 0.077 16218 Dihedral : 4.238 29.144 12920 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.60 % Allowed : 15.14 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.07), residues: 11900 helix: 1.65 (0.05), residues: 10302 sheet: None (None), residues: 0 loop : -1.85 (0.12), residues: 1598 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23800 Ramachandran restraints generated. 11900 Oldfield, 0 Emsley, 11900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23800 Ramachandran restraints generated. 11900 Oldfield, 0 Emsley, 11900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5250 residues out of total 10472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 349 poor density : 4901 time to evaluate : 8.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 349 outliers final: 127 residues processed: 4992 average time/residue: 0.9196 time to fit residues: 7673.3127 Evaluate side-chains 4400 residues out of total 10472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 4273 time to evaluate : 8.875 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 127 outliers final: 1 residues processed: 127 average time/residue: 0.7425 time to fit residues: 185.3424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1190 random chunks: chunk 600 optimal weight: 4.9990 chunk 335 optimal weight: 10.0000 chunk 899 optimal weight: 6.9990 chunk 735 optimal weight: 8.9990 chunk 298 optimal weight: 8.9990 chunk 1082 optimal weight: 20.0000 chunk 1169 optimal weight: 4.9990 chunk 964 optimal weight: 3.9990 chunk 1073 optimal weight: 6.9990 chunk 369 optimal weight: 9.9990 chunk 868 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 10 ASN AB 54 ASN AB 120 HIS BB 34 GLN BB 145 ASN CB 120 HIS ** CB 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EB 41 GLN EB 61 GLN EB 120 HIS FB 111 GLN FB 145 ASN ** GB 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** GB 146 GLN HB 14 ASN IB 10 ASN IB 58 GLN ** IB 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** IB 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** KB 10 ASN KB 80 GLN KB 120 HIS LB 58 HIS LB 111 GLN LB 123 GLN ** MB 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NB 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** OB 61 GLN PB 150 HIS PB 172 ASN QB 10 ASN QB 147 ASN SA 128 GLN VA 145 ASN UA 10 ASN UA 51 HIS WA 10 ASN WA 61 GLN ** WA 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** YA 41 GLN YA 44 ASN BA 58 HIS BA 145 ASN BA 150 HIS ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 HIS EA 10 ASN EA 51 HIS EA 64 ASN HA 145 ASN IA 51 HIS IA 121 GLN IA 146 GLN KA 7 HIS KA 51 HIS LA 14 ASN MA 10 ASN MA 61 GLN ** MA 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NA 150 HIS OA 10 ASN OA 41 GLN ** OA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** OA 146 GLN PA 111 GLN QA 120 HIS B 10 ASN ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 ASN D 120 HIS D 121 GLN F 41 GLN F 120 HIS ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 GLN H 121 GLN J 41 GLN K 111 GLN L 10 ASN L 61 GLN L 80 GLN L 120 HIS L 121 GLN M 123 GLN M 145 ASN N 7 HIS N 121 GLN P 41 GLN P 80 GLN P 121 GLN Q 34 GLN Q 58 HIS R 51 HIS R 148 GLN T 10 ASN T 120 HIS W 61 GLN W 121 GLN W 190 GLN ** X 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 145 ASN Y 10 ASN Y 61 GLN Y 120 HIS Y 190 GLN Z 145 ASN Total number of N/Q/H flips: 93 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 1.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 94316 Z= 0.365 Angle : 0.742 13.203 126684 Z= 0.385 Chirality : 0.040 0.212 15028 Planarity : 0.005 0.071 16218 Dihedral : 4.038 26.602 12920 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 5.62 % Allowed : 22.61 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.07), residues: 11900 helix: 1.78 (0.05), residues: 10234 sheet: None (None), residues: 0 loop : -1.95 (0.12), residues: 1666 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23800 Ramachandran restraints generated. 11900 Oldfield, 0 Emsley, 11900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23800 Ramachandran restraints generated. 11900 Oldfield, 0 Emsley, 11900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7200 residues out of total 10472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 545 poor density : 6655 time to evaluate : 8.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 545 outliers final: 196 residues processed: 6849 average time/residue: 0.9457 time to fit residues: 10702.6160 Evaluate side-chains 6011 residues out of total 10472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 5815 time to evaluate : 8.653 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 196 outliers final: 1 residues processed: 196 average time/residue: 0.6914 time to fit residues: 268.7507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1190 random chunks: chunk 1069 optimal weight: 0.9980 chunk 813 optimal weight: 8.9990 chunk 561 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 516 optimal weight: 1.9990 chunk 726 optimal weight: 1.9990 chunk 1086 optimal weight: 0.9990 chunk 1150 optimal weight: 30.0000 chunk 567 optimal weight: 5.9990 chunk 1029 optimal weight: 4.9990 chunk 309 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 54 ASN AB 61 GLN AB 121 GLN ** BB 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 61 GLN CB 121 GLN EB 10 ASN EB 41 GLN EB 54 ASN EB 60 ASN EB 61 GLN EB 64 ASN EB 120 HIS ** EB 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** FB 123 GLN GB 54 ASN GB 130 GLN GB 131 GLN GB 146 GLN GB 148 GLN HB 87 GLN HB 150 HIS IB 80 GLN IB 121 GLN IB 130 GLN IB 131 GLN JB 87 GLN JB 150 HIS KB 61 GLN KB 130 GLN KB 131 GLN KB 154 GLN ** LB 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 123 GLN LB 145 ASN LB 150 HIS MB 51 HIS MB 64 ASN MB 121 GLN NB 150 HIS OB 10 ASN OB 54 ASN OB 61 GLN OB 64 ASN ** OB 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** PB 150 HIS QB 121 GLN QB 130 GLN QB 147 ASN QB 148 GLN QB 154 GLN TA 123 GLN TA 150 HIS SA 54 ASN SA 61 GLN ** SA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SA 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SA 148 GLN SA 154 GLN VA 14 ASN ** UA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** XA 123 GLN WA 120 HIS WA 148 GLN ZA 111 GLN YA 41 GLN YA 61 GLN ** BA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 123 GLN ** BA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 GLN A 123 GLN A 150 HIS CA 10 ASN CA 107 ASN CA 120 HIS ** DA 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DA 123 GLN EA 121 GLN FA 123 GLN ** FA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GA 10 ASN GA 41 GLN GA 54 ASN GA 64 ASN GA 121 GLN HA 123 GLN ** IA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** IA 148 GLN JA 150 HIS KA 10 ASN KA 58 GLN KA 120 HIS KA 121 GLN LA 123 GLN LA 150 HIS MA 58 GLN MA 121 GLN OA 107 ASN OA 120 HIS ** OA 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** PA 150 HIS ** QA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** QA 154 GLN RA 123 GLN RA 172 ASN B 54 ASN B 80 GLN B 120 HIS C 150 HIS D 107 ASN E 145 ASN E 150 HIS ** F 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 GLN H 10 ASN H 61 GLN I 14 ASN I 150 HIS J 41 GLN J 107 ASN J 121 GLN K 123 GLN ** K 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 123 GLN M 145 ASN ** M 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 64 ASN N 121 GLN O 150 HIS P 51 HIS ** P 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 120 HIS P 121 GLN ** Q 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 41 GLN T 64 ASN T 130 GLN ** W 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 111 GLN X 150 HIS Y 60 ASN Y 64 ASN Y 120 HIS Y 121 GLN Z 14 ASN Z 111 GLN Z 172 ASN Total number of N/Q/H flips: 128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 1.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 94316 Z= 0.205 Angle : 0.615 11.135 126684 Z= 0.313 Chirality : 0.035 0.189 15028 Planarity : 0.004 0.055 16218 Dihedral : 3.633 24.303 12920 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 4.20 % Allowed : 28.90 % Favored : 66.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.05 (0.07), residues: 11900 helix: 2.51 (0.05), residues: 10336 sheet: None (None), residues: 0 loop : -1.62 (0.13), residues: 1564 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23800 Ramachandran restraints generated. 11900 Oldfield, 0 Emsley, 11900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23800 Ramachandran restraints generated. 11900 Oldfield, 0 Emsley, 11900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 6412 residues out of total 10472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 407 poor density : 6005 time to evaluate : 8.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 407 outliers final: 200 residues processed: 6103 average time/residue: 0.9358 time to fit residues: 9582.3971 Evaluate side-chains 5833 residues out of total 10472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 5633 time to evaluate : 8.595 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 200 outliers final: 1 residues processed: 200 average time/residue: 0.7317 time to fit residues: 279.3238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1190 random chunks: chunk 957 optimal weight: 4.9990 chunk 652 optimal weight: 0.7980 chunk 16 optimal weight: 10.0000 chunk 856 optimal weight: 0.9990 chunk 474 optimal weight: 4.9990 chunk 981 optimal weight: 8.9990 chunk 795 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 587 optimal weight: 9.9990 chunk 1032 optimal weight: 9.9990 chunk 290 optimal weight: 8.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 121 GLN AB 64 ASN AB 154 GLN ** BB 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 51 HIS CB 61 GLN CB 165 ASN DB 150 HIS EB 61 GLN EB 80 GLN EB 120 HIS ** EB 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** FB 20 ASN FB 123 GLN FB 150 HIS GB 54 ASN GB 148 GLN IB 130 GLN IB 131 GLN IB 154 GLN JB 14 ASN JB 123 GLN JB 150 HIS ** KB 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LB 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 145 ASN MB 121 GLN NB 123 GLN NB 150 HIS OB 61 GLN QB 64 ASN TA 150 HIS SA 54 ASN SA 61 GLN ** SA 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** VA 111 GLN UA 64 ASN WA 51 HIS ** WA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** WA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** WA 165 ASN ZA 14 ASN ZA 111 GLN YA 41 GLN YA 148 GLN ** BA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 150 HIS ** DA 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DA 123 GLN EA 121 GLN FA 123 GLN ** FA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GA 64 ASN GA 148 GLN HA 123 GLN IA 61 GLN IA 64 ASN IA 148 GLN KA 51 HIS KA 58 GLN MA 41 GLN MA 58 GLN MA 121 GLN NA 123 GLN PA 150 HIS ** QA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** QA 64 ASN ** RA 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN B 64 ASN B 80 GLN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN D 121 GLN D 131 GLN E 20 ASN ** F 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 ASN ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 ASN G 58 HIS ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 107 ASN K 123 GLN K 150 HIS ** L 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 148 GLN ** M 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 123 GLN M 145 ASN N 10 ASN N 64 ASN N 121 GLN O 123 GLN ** P 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 121 GLN ** Q 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 61 GLN R 121 GLN T 64 ASN T 131 GLN ** W 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 148 GLN W 154 GLN ** X 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 111 GLN Y 64 ASN ** Y 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 154 GLN Z 111 GLN Total number of N/Q/H flips: 87 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 1.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 94316 Z= 0.267 Angle : 0.624 10.314 126684 Z= 0.322 Chirality : 0.036 0.205 15028 Planarity : 0.004 0.060 16218 Dihedral : 3.565 25.498 12920 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.25 % Allowed : 29.85 % Favored : 65.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.27 (0.07), residues: 11900 helix: 2.77 (0.05), residues: 10268 sheet: None (None), residues: 0 loop : -2.21 (0.13), residues: 1632 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23800 Ramachandran restraints generated. 11900 Oldfield, 0 Emsley, 11900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23800 Ramachandran restraints generated. 11900 Oldfield, 0 Emsley, 11900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 6227 residues out of total 10472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 412 poor density : 5815 time to evaluate : 8.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 412 outliers final: 227 residues processed: 5906 average time/residue: 0.8995 time to fit residues: 8845.2049 Evaluate side-chains 5768 residues out of total 10472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 5541 time to evaluate : 8.624 Switching outliers to nearest non-outliers outliers start: 227 outliers final: 0 residues processed: 227 average time/residue: 0.7211 time to fit residues: 312.3531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1190 random chunks: chunk 386 optimal weight: 8.9990 chunk 1035 optimal weight: 6.9990 chunk 227 optimal weight: 9.9990 chunk 675 optimal weight: 5.9990 chunk 283 optimal weight: 4.9990 chunk 1151 optimal weight: 5.9990 chunk 955 optimal weight: 4.9990 chunk 533 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 380 optimal weight: 1.9990 chunk 604 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 64 ASN AB 121 GLN ** AB 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 154 GLN ** BB 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 61 GLN CB 121 GLN CB 165 ASN ** DB 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EB 61 GLN EB 80 GLN EB 120 HIS ** EB 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** FB 123 GLN FB 150 HIS GB 54 ASN GB 61 GLN ** GB 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GB 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** GB 148 GLN HB 145 ASN HB 150 HIS IB 80 GLN ** LB 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MB 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** MB 148 GLN MB 165 ASN NB 123 GLN NB 150 HIS OB 61 GLN QB 64 ASN QB 148 GLN QB 154 GLN TA 150 HIS SA 54 ASN VA 150 HIS ** WA 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** YA 41 GLN YA 148 GLN ** BA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 GLN A 150 HIS ** DA 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EA 10 ASN ** EA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EA 121 GLN ** FA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** GA 64 ASN HA 123 GLN HA 150 HIS IA 61 GLN IA 148 GLN KA 121 GLN MA 54 ASN MA 58 GLN MA 121 GLN ** OA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** RA 123 GLN ** RA 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN B 64 ASN B 148 GLN C 111 GLN ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 GLN D 148 GLN ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 HIS ** F 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 GLN ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 GLN I 87 GLN I 150 HIS J 41 GLN ** K 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 64 ASN ** L 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 130 GLN L 148 GLN ** M 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 123 GLN M 145 ASN N 10 ASN ** P 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 145 ASN R 61 GLN R 64 ASN T 61 GLN T 64 ASN W 121 GLN W 148 GLN ** X 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 123 GLN Y 61 GLN Y 64 ASN Y 121 GLN ** Y 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 73 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 1.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 94316 Z= 0.291 Angle : 0.642 10.576 126684 Z= 0.332 Chirality : 0.036 0.175 15028 Planarity : 0.004 0.061 16218 Dihedral : 3.588 27.428 12920 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.08 % Allowed : 32.05 % Favored : 64.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.25 (0.07), residues: 11900 helix: 2.75 (0.05), residues: 10132 sheet: None (None), residues: 0 loop : -1.76 (0.12), residues: 1768 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23800 Ramachandran restraints generated. 11900 Oldfield, 0 Emsley, 11900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23800 Ramachandran restraints generated. 11900 Oldfield, 0 Emsley, 11900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5988 residues out of total 10472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 298 poor density : 5690 time to evaluate : 8.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 298 outliers final: 156 residues processed: 5754 average time/residue: 0.8977 time to fit residues: 8633.4397 Evaluate side-chains 5653 residues out of total 10472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 5497 time to evaluate : 8.785 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 156 outliers final: 1 residues processed: 156 average time/residue: 0.7384 time to fit residues: 224.4558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1190 random chunks: chunk 1110 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 656 optimal weight: 5.9990 chunk 840 optimal weight: 4.9990 chunk 651 optimal weight: 3.9990 chunk 969 optimal weight: 7.9990 chunk 642 optimal weight: 1.9990 chunk 1146 optimal weight: 0.9980 chunk 717 optimal weight: 4.9990 chunk 699 optimal weight: 7.9990 chunk 529 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AB 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 154 GLN ** BB 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 58 GLN CB 61 GLN CB 165 ASN EB 61 GLN EB 80 GLN ** EB 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EB 148 GLN FB 123 GLN FB 145 ASN FB 150 HIS GB 54 ASN GB 61 GLN GB 64 ASN GB 107 ASN ** GB 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** GB 148 GLN ** IB 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** KB 80 GLN ** KB 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NB 123 GLN QB 64 ASN QB 80 GLN QB 148 GLN TA 111 GLN TA 150 HIS ** SA 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** WA 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** YA 41 GLN YA 121 GLN YA 148 GLN ** BA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 HIS ** DA 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EA 10 ASN EA 41 GLN ** EA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EA 121 GLN GA 64 ASN ** GA 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HA 123 GLN HA 145 ASN ** IA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** IA 148 GLN LA 123 GLN MA 41 GLN MA 54 ASN MA 58 GLN MA 121 GLN ** MA 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** PA 150 HIS ** RA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** RA 123 GLN ** RA 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** RA 150 HIS B 54 ASN B 64 ASN ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 HIS D 148 GLN E 111 GLN E 123 GLN ** F 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 GLN ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 GLN ** K 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 54 ASN L 64 ASN ** M 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 10 ASN N 121 GLN P 60 ASN P 154 GLN ** Q 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 61 GLN R 64 ASN T 64 ASN T 121 GLN W 121 GLN W 148 GLN ** X 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 64 ASN Y 121 GLN ** Y 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 148 GLN Y 154 GLN ** Z 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 65 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 1.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 94316 Z= 0.251 Angle : 0.648 10.194 126684 Z= 0.332 Chirality : 0.035 0.192 15028 Planarity : 0.004 0.050 16218 Dihedral : 3.568 24.457 12920 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.54 % Allowed : 34.27 % Favored : 63.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.38 (0.07), residues: 11900 helix: 2.87 (0.05), residues: 10098 sheet: None (None), residues: 0 loop : -1.83 (0.12), residues: 1802 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23800 Ramachandran restraints generated. 11900 Oldfield, 0 Emsley, 11900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23800 Ramachandran restraints generated. 11900 Oldfield, 0 Emsley, 11900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5827 residues out of total 10472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 5581 time to evaluate : 8.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 246 outliers final: 144 residues processed: 5633 average time/residue: 0.8926 time to fit residues: 8427.1789 Evaluate side-chains 5582 residues out of total 10472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 5438 time to evaluate : 8.512 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 144 outliers final: 2 residues processed: 144 average time/residue: 0.7162 time to fit residues: 200.5873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1190 random chunks: chunk 709 optimal weight: 2.9990 chunk 458 optimal weight: 20.0000 chunk 685 optimal weight: 8.9990 chunk 345 optimal weight: 0.1980 chunk 225 optimal weight: 1.9990 chunk 222 optimal weight: 10.0000 chunk 729 optimal weight: 6.9990 chunk 781 optimal weight: 0.8980 chunk 567 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 901 optimal weight: 6.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AA 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BB 123 GLN ** CB 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 154 GLN CB 165 ASN EB 61 GLN EB 80 GLN ** EB 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EB 131 GLN FB 123 GLN FB 150 HIS GB 54 ASN GB 61 GLN GB 64 ASN ** GB 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** GB 148 GLN HB 150 HIS ** IB 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** IB 165 ASN JB 172 ASN KB 120 HIS ** KB 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NB 123 GLN ** OB 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** QB 64 ASN QB 148 GLN QB 154 GLN TA 111 GLN SA 61 GLN ** SA 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** UA 148 GLN XA 123 GLN ** WA 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ZA 150 HIS YA 41 GLN ** YA 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 145 ASN BA 150 HIS A 150 HIS CA 131 GLN ** DA 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EA 121 GLN GA 64 ASN HA 123 GLN HA 150 HIS ** IA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** IA 148 GLN KA 121 GLN MA 54 ASN MA 58 GLN MA 121 GLN ** OA 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** QA 61 GLN QA 64 ASN ** RA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** RA 123 GLN RA 145 ASN B 54 ASN B 61 GLN B 64 ASN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN E 123 GLN ** F 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 GLN G 123 GLN I 87 GLN I 150 HIS J 41 GLN ** K 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 54 ASN L 64 ASN ** M 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 123 GLN M 150 HIS P 61 GLN P 121 GLN ** Q 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 61 GLN R 64 ASN T 64 ASN T 121 GLN W 148 GLN ** X 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 64 ASN ** Y 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 65 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 1.4513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 94316 Z= 0.234 Angle : 0.668 13.542 126684 Z= 0.339 Chirality : 0.036 0.205 15028 Planarity : 0.004 0.046 16218 Dihedral : 3.556 21.117 12920 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.68 % Allowed : 35.10 % Favored : 63.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.45 (0.07), residues: 11900 helix: 2.92 (0.05), residues: 10098 sheet: None (None), residues: 0 loop : -1.84 (0.12), residues: 1802 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23800 Ramachandran restraints generated. 11900 Oldfield, 0 Emsley, 11900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23800 Ramachandran restraints generated. 11900 Oldfield, 0 Emsley, 11900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5742 residues out of total 10472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 5579 time to evaluate : 9.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 163 outliers final: 79 residues processed: 5606 average time/residue: 0.8897 time to fit residues: 8344.0063 Evaluate side-chains 5544 residues out of total 10472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 5465 time to evaluate : 8.596 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 2 residues processed: 79 average time/residue: 0.7184 time to fit residues: 115.0435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1190 random chunks: chunk 1043 optimal weight: 0.9990 chunk 1098 optimal weight: 2.9990 chunk 1002 optimal weight: 5.9990 chunk 1068 optimal weight: 0.9990 chunk 643 optimal weight: 3.9990 chunk 465 optimal weight: 10.0000 chunk 839 optimal weight: 30.0000 chunk 328 optimal weight: 1.9990 chunk 965 optimal weight: 0.9990 chunk 1010 optimal weight: 20.0000 chunk 1065 optimal weight: 6.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AA 131 GLN ** AB 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 165 ASN ** BB 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BB 172 ASN ** CB 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 121 GLN CB 165 ASN DB 172 ASN ** EB 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EB 120 HIS ** EB 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** FB 123 GLN FB 150 HIS GB 54 ASN GB 61 GLN ** GB 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** GB 148 GLN ** IB 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** JB 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JB 145 ASN KB 80 GLN ** KB 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NB 123 GLN ** OB 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** QB 64 ASN QB 107 ASN SA 61 GLN ** SA 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** UA 121 GLN ** WA 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** YA 41 GLN YA 121 GLN ** YA 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 HIS CA 64 ASN ** DA 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EA 121 GLN GA 64 ASN HA 123 GLN HA 145 ASN ** IA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** IA 148 GLN IA 154 GLN KA 58 GLN MA 54 ASN MA 60 ASN MA 121 GLN ** MA 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** OA 41 GLN ** OA 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OA 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** PA 150 HIS QA 61 GLN QA 64 ASN ** RA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** RA 123 GLN B 54 ASN B 61 GLN B 64 ASN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN E 123 GLN ** F 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 ASN F 121 GLN ** I 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 GLN ** J 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 54 ASN L 64 ASN ** M 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 121 GLN P 61 GLN Q 123 GLN R 61 GLN R 64 ASN R 121 GLN T 121 GLN W 148 GLN ** X 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 64 ASN ** Y 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 1.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 94316 Z= 0.226 Angle : 0.689 13.356 126684 Z= 0.348 Chirality : 0.036 0.306 15028 Planarity : 0.004 0.063 16218 Dihedral : 3.562 26.489 12920 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.28 % Allowed : 35.85 % Favored : 62.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.48 (0.07), residues: 11900 helix: 2.95 (0.05), residues: 10098 sheet: None (None), residues: 0 loop : -1.86 (0.12), residues: 1802 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23800 Ramachandran restraints generated. 11900 Oldfield, 0 Emsley, 11900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23800 Ramachandran restraints generated. 11900 Oldfield, 0 Emsley, 11900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5670 residues out of total 10472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 5546 time to evaluate : 8.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 124 outliers final: 68 residues processed: 5564 average time/residue: 0.8980 time to fit residues: 8386.1113 Evaluate side-chains 5539 residues out of total 10472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 5471 time to evaluate : 8.526 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 2 residues processed: 68 average time/residue: 0.7745 time to fit residues: 105.6624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1190 random chunks: chunk 701 optimal weight: 5.9990 chunk 1130 optimal weight: 1.9990 chunk 689 optimal weight: 4.9990 chunk 536 optimal weight: 0.7980 chunk 785 optimal weight: 0.8980 chunk 1185 optimal weight: 6.9990 chunk 1091 optimal weight: 0.9980 chunk 944 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 729 optimal weight: 6.9990 chunk 578 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AB 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BB 123 GLN ** CB 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CB 121 GLN CB 148 GLN CB 154 GLN ** EB 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EB 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** FB 123 GLN FB 150 HIS GB 54 ASN GB 121 GLN ** GB 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GB 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** GB 148 GLN HB 150 HIS ** JB 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JB 123 GLN JB 172 ASN KB 120 HIS ** KB 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** MB 64 ASN MB 148 GLN NB 123 GLN ** OB 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TA 150 HIS ** SA 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** VA 150 HIS UA 107 ASN UA 148 GLN XA 123 GLN ** WA 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** YA 41 GLN ** YA 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** YA 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 HIS A 174 ASN CA 64 ASN ** DA 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EA 121 GLN GA 64 ASN ** GA 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HA 123 GLN HA 145 ASN HA 150 HIS ** IA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** IA 148 GLN MA 54 ASN MA 60 ASN ** MA 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OA 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** OA 131 GLN ** QA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** QA 64 ASN ** QA 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** RA 123 GLN RA 145 ASN B 54 ASN B 61 GLN B 64 ASN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 GLN ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN E 123 GLN ** F 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 150 HIS J 41 GLN ** J 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 54 ASN L 64 ASN L 148 GLN ** M 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 61 GLN P 121 GLN R 58 GLN R 61 GLN ** R 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 121 GLN R 148 GLN W 121 GLN ** X 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 1.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 94316 Z= 0.225 Angle : 0.715 18.569 126684 Z= 0.359 Chirality : 0.036 0.307 15028 Planarity : 0.004 0.052 16218 Dihedral : 3.591 30.325 12920 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.69 % Allowed : 36.84 % Favored : 62.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 3.52 (0.07), residues: 11900 helix: 2.96 (0.05), residues: 10234 sheet: None (None), residues: 0 loop : -2.16 (0.12), residues: 1666 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23800 Ramachandran restraints generated. 11900 Oldfield, 0 Emsley, 11900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23800 Ramachandran restraints generated. 11900 Oldfield, 0 Emsley, 11900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5589 residues out of total 10472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 5522 time to evaluate : 8.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 32 residues processed: 5527 average time/residue: 0.8973 time to fit residues: 8306.1505 Evaluate side-chains 5457 residues out of total 10472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 5425 time to evaluate : 8.743 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 2 residues processed: 32 average time/residue: 0.7345 time to fit residues: 55.0819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1190 random chunks: chunk 749 optimal weight: 2.9990 chunk 1005 optimal weight: 0.0970 chunk 289 optimal weight: 0.0000 chunk 870 optimal weight: 7.9990 chunk 139 optimal weight: 7.9990 chunk 262 optimal weight: 10.0000 chunk 945 optimal weight: 4.9990 chunk 395 optimal weight: 4.9990 chunk 970 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 174 optimal weight: 0.3980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AB 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 165 ASN BB 172 ASN CB 41 GLN ** CB 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EB 41 GLN ** EB 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** EB 121 GLN EB 148 GLN FB 123 GLN FB 150 HIS GB 41 GLN GB 121 GLN ** GB 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GB 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** GB 148 GLN HB 145 ASN IB 121 GLN ** JB 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JB 87 GLN JB 172 ASN MB 64 ASN MB 121 GLN MB 148 GLN NB 123 GLN ** OB 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** QB 107 ASN QB 121 GLN ** TA 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SA 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** VA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** XA 123 GLN ** WA 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** YA 41 GLN ** YA 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** YA 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 64 ASN ** DA 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DA 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** EA 121 GLN EA 148 GLN GA 64 ASN GA 121 GLN GA 148 GLN HA 123 GLN ** IA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** IA 148 GLN IA 154 GLN MA 54 ASN MA 58 GLN MA 60 ASN MA 107 ASN ** MA 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OA 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** OA 131 GLN ** OA 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** PA 150 HIS ** QA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** QA 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** RA 123 GLN B 54 ASN B 61 GLN B 64 ASN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 GLN D 121 GLN D 148 GLN E 123 GLN ** F 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 HIS H 131 GLN ** J 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 54 ASN L 64 ASN L 148 GLN ** M 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 123 GLN P 61 GLN P 121 GLN R 58 GLN R 61 GLN T 121 GLN W 121 GLN ** X 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 150 HIS Y 41 GLN Y 121 GLN ** Y 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.125326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.106417 restraints weight = 159569.285| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.81 r_work: 0.3180 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 1.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 94316 Z= 0.216 Angle : 0.717 18.141 126684 Z= 0.358 Chirality : 0.036 0.303 15028 Planarity : 0.004 0.054 16218 Dihedral : 3.573 28.038 12920 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.65 % Allowed : 37.12 % Favored : 62.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.58 (0.07), residues: 11900 helix: 2.90 (0.05), residues: 10438 sheet: None (None), residues: 0 loop : -2.07 (0.14), residues: 1462 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 92581.34 seconds wall clock time: 1588 minutes 8.10 seconds (95288.10 seconds total)