Starting phenix.real_space_refine on Wed Feb 21 18:52:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdv_10468/02_2024/6tdv_10468_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdv_10468/02_2024/6tdv_10468.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdv_10468/02_2024/6tdv_10468_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdv_10468/02_2024/6tdv_10468_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdv_10468/02_2024/6tdv_10468_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdv_10468/02_2024/6tdv_10468.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdv_10468/02_2024/6tdv_10468.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdv_10468/02_2024/6tdv_10468_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdv_10468/02_2024/6tdv_10468_trim_updated.pdb" } resolution = 2.8 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: 6 Type Number sf(0) Gaussians P 62 5.49 5 S 180 5.16 5 C 31286 2.51 5 N 7605 2.21 5 O 8613 1.98 5 H 44516 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 87": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 151": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 154": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 157": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 188": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 197": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 320": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 385": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 392": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 412": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 423": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 443": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 465": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 143": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 24": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 74": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 164": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 15": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 53": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 72": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 73": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 42": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 41": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 72": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 185": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 412": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 464": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 61": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 90": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 15": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 56": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 72": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 15": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 51": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 61": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ARG 68": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ARG 47": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 50": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 74": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S ARG 54": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ARG 87": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ARG 151": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 154": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 157": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ARG 188": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 197": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ARG 320": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ARG 385": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 392": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a PHE 412": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ARG 423": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 443": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 465": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ARG 143": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "d ARG 24": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "d ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "d TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d ARG 74": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "d ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "d ARG 164": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "e ARG 15": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "e ARG 53": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "e ARG 72": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "e ARG 73": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g ARG 42": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h ARG 41": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h ARG 72": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h ARG 185": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h ARG 412": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h ARG 464": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "i ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "i PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "i TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "i ARG 61": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "i ARG 90": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "j ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "j PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "k PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "l TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "l TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "l TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "l TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "m ARG 15": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "m ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "m ARG 56": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "m ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "m ARG 72": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "m TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "m TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "n ARG 15": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "n TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "o PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "o ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "o ARG 51": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "o TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "o PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "o PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "o ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "p PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "p TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "q PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "q ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "q ARG 61": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "q ARG 68": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "q PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "r ARG 47": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "r ARG 50": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "r ARG 74": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "s ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "s ARG 54": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "s PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 92262 Number of models: 1 Model: "" Number of chains: 62 Chain: "A" Number of atoms: 7864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 7864 Classifications: {'peptide': 486} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 456} Chain: "B" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 494 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "D" Number of atoms: 3040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 3040 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 5, 'TRANS': 180} Chain: "E" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1574 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 92} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 4639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 4639 Classifications: {'peptide': 274} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 271} Unresolved chain links: 1 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 1803 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 101} Chain: "H" Number of atoms: 6165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 6165 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 34, 'TRANS': 353} Chain breaks: 1 Chain: "I" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1553 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "J" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1734 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 96} Chain: "K" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1637 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "L" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1008 Classifications: {'peptide': 57} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "M" Number of atoms: 2717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2717 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain: "N" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2167 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 10, 'TRANS': 120} Chain: "O" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1652 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "P" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1838 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 104} Chain: "Q" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1476 Classifications: {'peptide': 89} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 82} Chain: "R" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1160 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "S" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1092 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 57} Chain: "T" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1080 Classifications: {'peptide': 66} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain: "a" Number of atoms: 7864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 7864 Classifications: {'peptide': 486} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 456} Chain: "b" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 494 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "d" Number of atoms: 3040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 3040 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 5, 'TRANS': 180} Chain: "e" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1577 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "f" Number of atoms: 4642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 4642 Classifications: {'peptide': 274} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 271} Chain: "g" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 1803 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 101} Chain: "h" Number of atoms: 6165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 6165 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 34, 'TRANS': 353} Chain breaks: 1 Chain: "i" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1553 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "j" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1734 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 96} Chain: "k" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1637 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "l" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1008 Classifications: {'peptide': 57} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "m" Number of atoms: 2717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2717 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain: "n" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2167 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 10, 'TRANS': 120} Chain: "o" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 1652 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "p" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1838 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 104} Chain: "q" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1476 Classifications: {'peptide': 89} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 82} Chain: "r" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1160 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "s" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1092 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 57} Chain: "t" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1080 Classifications: {'peptide': 66} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain: "A" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 307 Unusual residues: {'CDL': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 96 Chain: "D" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 212 Unusual residues: {'CDL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 24 Chain: "E" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 63 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Chain: "F" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'LMT': 1, 'LPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {'TRT': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'LPP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {'CDL': 2, 'TRT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 70 Chain: "N" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 111 Unusual residues: {'LMT': 1, 'LPP': 1, 'TRT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "O" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 120 Unusual residues: {'CDL': 1, 'LPP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 68 Chain: "P" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 99 Unusual residues: {'CDL': 1, 'LPP': 1, 'TRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 70 Chain: "Q" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 132 Unusual residues: {'CDL': 1, 'LPP': 1, 'TRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Chain: "a" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 307 Unusual residues: {'CDL': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 96 Chain: "d" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 212 Unusual residues: {'CDL': 2, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 24 Chain: "e" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 63 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Chain: "f" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'LMT': 1, 'LPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "g" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {'TRT': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "i" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'LPP': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {'CDL': 2, 'TRT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 70 Chain: "n" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 85 Unusual residues: {'LMT': 1, 'TRT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "o" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 120 Unusual residues: {'CDL': 1, 'LPP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 68 Chain: "p" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 171 Unusual residues: {'CDL': 2, 'TRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 54 Chain: "q" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 132 Unusual residues: {'CDL': 1, 'LPP': 1, 'TRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Time building chain proxies: 30.24, per 1000 atoms: 0.33 Number of scatterers: 92262 At special positions: 0 Unit cell: (253.05, 177.45, 168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 180 16.00 P 62 15.00 O 8613 8.00 N 7605 7.00 C 31286 6.00 H 44516 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 30 " - pdb=" SG CYS E 48 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 24 " - pdb=" SG CYS Q 56 " distance=2.03 Simple disulfide: pdb=" SG CYS e 30 " - pdb=" SG CYS e 48 " distance=2.04 Simple disulfide: pdb=" SG CYS q 24 " - pdb=" SG CYS q 56 " distance=2.03 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: 60.37 Conformation dependent library (CDL) restraints added in 6.8 seconds 10764 Ramachandran restraints generated. 5382 Oldfield, 0 Emsley, 5382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10414 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 252 helices and 8 sheets defined 58.2% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.72 Creating SS restraints... Processing helix chain 'A' and resid 3 through 39 removed outlier: 3.897A pdb=" N LYS A 10 " --> pdb=" O LYS A 6 " (cutoff:3.500A) Proline residue: A 12 - end of helix removed outlier: 3.554A pdb=" N THR A 15 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER A 16 " --> pdb=" O PRO A 12 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLN A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS A 38 " --> pdb=" O GLU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 61 No H-bonds generated for 'chain 'A' and resid 58 through 61' Processing helix chain 'A' and resid 72 through 92 removed outlier: 3.910A pdb=" N LEU A 89 " --> pdb=" O MET A 85 " (cutoff:3.500A) Proline residue: A 90 - end of helix Processing helix chain 'A' and resid 94 through 97 No H-bonds generated for 'chain 'A' and resid 94 through 97' Processing helix chain 'A' and resid 103 through 110 Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 125 through 141 removed outlier: 5.772A pdb=" N ASP A 138 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ASP A 139 " --> pdb=" O SER A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 172 through 179 Processing helix chain 'A' and resid 190 through 199 removed outlier: 4.050A pdb=" N LEU A 196 " --> pdb=" O LYS A 192 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ARG A 197 " --> pdb=" O CYS A 193 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LEU A 198 " --> pdb=" O ALA A 194 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N TYR A 199 " --> pdb=" O HIS A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 230 Processing helix chain 'A' and resid 234 through 255 removed outlier: 3.776A pdb=" N LYS A 239 " --> pdb=" O GLU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 262 removed outlier: 3.556A pdb=" N HIS A 262 " --> pdb=" O HIS A 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 259 through 262' Processing helix chain 'A' and resid 276 through 278 No H-bonds generated for 'chain 'A' and resid 276 through 278' Processing helix chain 'A' and resid 289 through 292 Processing helix chain 'A' and resid 295 through 297 No H-bonds generated for 'chain 'A' and resid 295 through 297' Processing helix chain 'A' and resid 320 through 329 removed outlier: 3.887A pdb=" N LYS A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 362 Processing helix chain 'A' and resid 371 through 381 Processing helix chain 'A' and resid 392 through 408 removed outlier: 3.651A pdb=" N LEU A 408 " --> pdb=" O TRP A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 421 removed outlier: 3.770A pdb=" N GLY A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TYR A 421 " --> pdb=" O TRP A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 468 through 470 No H-bonds generated for 'chain 'A' and resid 468 through 470' Processing helix chain 'A' and resid 474 through 477 No H-bonds generated for 'chain 'A' and resid 474 through 477' Processing helix chain 'A' and resid 479 through 486 Processing helix chain 'B' and resid 124 through 150 Processing helix chain 'D' and resid 4 through 17 removed outlier: 4.262A pdb=" N ASP D 10 " --> pdb=" O LEU D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 21 No H-bonds generated for 'chain 'D' and resid 19 through 21' Processing helix chain 'D' and resid 24 through 55 removed outlier: 3.573A pdb=" N TYR D 41 " --> pdb=" O ARG D 37 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR D 55 " --> pdb=" O GLY D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 65 removed outlier: 4.027A pdb=" N LYS D 64 " --> pdb=" O ALA D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 81 No H-bonds generated for 'chain 'D' and resid 78 through 81' Processing helix chain 'D' and resid 88 through 93 Processing helix chain 'D' and resid 99 through 109 removed outlier: 4.555A pdb=" N GLY D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 149 removed outlier: 3.962A pdb=" N GLY D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) Proline residue: D 128 - end of helix Processing helix chain 'D' and resid 154 through 163 Processing helix chain 'D' and resid 168 through 182 removed outlier: 3.714A pdb=" N ARG D 178 " --> pdb=" O SER D 174 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 37 removed outlier: 3.519A pdb=" N CYS E 30 " --> pdb=" O ASP E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 64 removed outlier: 3.542A pdb=" N ASP E 46 " --> pdb=" O ASP E 42 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N TRP E 50 " --> pdb=" O ASP E 46 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N THR E 51 " --> pdb=" O ALA E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 80 Processing helix chain 'E' and resid 91 through 96 removed outlier: 3.646A pdb=" N LYS E 95 " --> pdb=" O TRP E 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 28 removed outlier: 3.777A pdb=" N MET F 20 " --> pdb=" O MET F 16 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE F 21 " --> pdb=" O TYR F 17 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE F 22 " --> pdb=" O SER F 18 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET F 25 " --> pdb=" O ILE F 21 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE F 26 " --> pdb=" O ILE F 22 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU F 27 " --> pdb=" O ILE F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 43 Processing helix chain 'F' and resid 49 through 71 Processing helix chain 'F' and resid 77 through 80 No H-bonds generated for 'chain 'F' and resid 77 through 80' Processing helix chain 'F' and resid 85 through 90 Processing helix chain 'F' and resid 93 through 103 Proline residue: F 100 - end of helix Processing helix chain 'F' and resid 105 through 115 Processing helix chain 'F' and resid 129 through 136 Processing helix chain 'F' and resid 147 through 165 removed outlier: 5.845A pdb=" N ASP F 151 " --> pdb=" O PHE F 148 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASN F 154 " --> pdb=" O ASP F 151 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASN F 163 " --> pdb=" O ARG F 160 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N PHE F 164 " --> pdb=" O SER F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 202 Processing helix chain 'F' and resid 216 through 248 Processing helix chain 'F' and resid 250 through 252 No H-bonds generated for 'chain 'F' and resid 250 through 252' Processing helix chain 'F' and resid 270 through 273 No H-bonds generated for 'chain 'F' and resid 270 through 273' Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 23 through 28 Processing helix chain 'G' and resid 31 through 48 removed outlier: 3.643A pdb=" N VAL G 36 " --> pdb=" O PRO G 32 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLY G 39 " --> pdb=" O LEU G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 111 Processing helix chain 'H' and resid 41 through 57 removed outlier: 3.894A pdb=" N LYS H 56 " --> pdb=" O LYS H 52 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N THR H 57 " --> pdb=" O ALA H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 78 Processing helix chain 'H' and resid 82 through 102 Proline residue: H 100 - end of helix Processing helix chain 'H' and resid 110 through 131 removed outlier: 3.556A pdb=" N ILE H 113 " --> pdb=" O ILE H 110 " (cutoff:3.500A) Proline residue: H 114 - end of helix removed outlier: 4.086A pdb=" N GLU H 129 " --> pdb=" O ALA H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 149 removed outlier: 5.599A pdb=" N MET H 146 " --> pdb=" O GLU H 142 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N TYR H 147 " --> pdb=" O ALA H 143 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE H 148 " --> pdb=" O HIS H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 278 Processing helix chain 'H' and resid 339 through 378 removed outlier: 3.526A pdb=" N GLY H 351 " --> pdb=" O ASN H 347 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR H 366 " --> pdb=" O TYR H 362 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG H 372 " --> pdb=" O GLN H 368 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG H 376 " --> pdb=" O ARG H 372 " (cutoff:3.500A) Processing helix chain 'H' and resid 385 through 390 Processing helix chain 'H' and resid 393 through 405 removed outlier: 3.573A pdb=" N ASP H 398 " --> pdb=" O LEU H 394 " (cutoff:3.500A) Processing helix chain 'H' and resid 412 through 417 Processing helix chain 'H' and resid 419 through 421 No H-bonds generated for 'chain 'H' and resid 419 through 421' Processing helix chain 'H' and resid 427 through 429 No H-bonds generated for 'chain 'H' and resid 427 through 429' Processing helix chain 'H' and resid 444 through 454 removed outlier: 3.503A pdb=" N GLN H 450 " --> pdb=" O ALA H 446 " (cutoff:3.500A) Processing helix chain 'H' and resid 457 through 475 removed outlier: 3.667A pdb=" N ARG H 464 " --> pdb=" O SER H 460 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU H 465 " --> pdb=" O LEU H 461 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 20 removed outlier: 3.762A pdb=" N PHE I 18 " --> pdb=" O TYR I 14 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE I 19 " --> pdb=" O LYS I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 37 removed outlier: 4.118A pdb=" N TYR I 30 " --> pdb=" O HIS I 26 " (cutoff:3.500A) Proline residue: I 34 - end of helix Processing helix chain 'I' and resid 44 through 61 removed outlier: 3.784A pdb=" N GLU I 52 " --> pdb=" O ARG I 48 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA I 53 " --> pdb=" O ASN I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 69 Processing helix chain 'I' and resid 72 through 88 Processing helix chain 'J' and resid 5 through 8 No H-bonds generated for 'chain 'J' and resid 5 through 8' Processing helix chain 'J' and resid 10 through 15 Processing helix chain 'J' and resid 18 through 36 Proline residue: J 23 - end of helix Processing helix chain 'J' and resid 38 through 42 Processing helix chain 'J' and resid 45 through 47 No H-bonds generated for 'chain 'J' and resid 45 through 47' Processing helix chain 'J' and resid 49 through 52 Processing helix chain 'J' and resid 71 through 87 Processing helix chain 'J' and resid 91 through 96 removed outlier: 3.947A pdb=" N VAL J 94 " --> pdb=" O ILE J 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 15 through 36 Processing helix chain 'K' and resid 40 through 42 No H-bonds generated for 'chain 'K' and resid 40 through 42' Processing helix chain 'K' and resid 44 through 51 removed outlier: 3.932A pdb=" N LEU K 51 " --> pdb=" O LYS K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 61 Processing helix chain 'K' and resid 67 through 88 removed outlier: 5.189A pdb=" N GLY K 81 " --> pdb=" O ALA K 77 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N TRP K 82 " --> pdb=" O LEU K 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 12 through 32 Proline residue: L 30 - end of helix Processing helix chain 'L' and resid 39 through 46 Processing helix chain 'M' and resid 3 through 15 removed outlier: 5.235A pdb=" N ILE M 13 " --> pdb=" O TYR M 9 " (cutoff:3.500A) Proline residue: M 14 - end of helix Processing helix chain 'M' and resid 19 through 32 Processing helix chain 'M' and resid 35 through 46 Processing helix chain 'M' and resid 51 through 65 Processing helix chain 'M' and resid 67 through 87 removed outlier: 4.403A pdb=" N VAL M 75 " --> pdb=" O PHE M 71 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL M 76 " --> pdb=" O ARG M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 92 through 117 Processing helix chain 'M' and resid 128 through 131 No H-bonds generated for 'chain 'M' and resid 128 through 131' Processing helix chain 'M' and resid 133 through 166 removed outlier: 3.555A pdb=" N VAL M 150 " --> pdb=" O GLN M 146 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS M 164 " --> pdb=" O GLN M 160 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 9 Processing helix chain 'N' and resid 46 through 81 Processing helix chain 'N' and resid 93 through 103 Processing helix chain 'O' and resid 15 through 18 No H-bonds generated for 'chain 'O' and resid 15 through 18' Processing helix chain 'O' and resid 32 through 49 Processing helix chain 'O' and resid 57 through 75 removed outlier: 4.887A pdb=" N PHE O 65 " --> pdb=" O LEU O 61 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLN O 66 " --> pdb=" O LEU O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 86 No H-bonds generated for 'chain 'O' and resid 83 through 86' Processing helix chain 'O' and resid 100 through 112 Processing helix chain 'P' and resid 15 through 17 No H-bonds generated for 'chain 'P' and resid 15 through 17' Processing helix chain 'P' and resid 22 through 37 removed outlier: 3.851A pdb=" N TYR P 36 " --> pdb=" O PHE P 32 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA P 37 " --> pdb=" O PHE P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 58 through 60 No H-bonds generated for 'chain 'P' and resid 58 through 60' Processing helix chain 'P' and resid 62 through 68 Processing helix chain 'P' and resid 74 through 76 No H-bonds generated for 'chain 'P' and resid 74 through 76' Processing helix chain 'P' and resid 83 through 95 removed outlier: 3.665A pdb=" N ASN P 93 " --> pdb=" O MET P 89 " (cutoff:3.500A) Processing helix chain 'P' and resid 102 through 107 Processing helix chain 'Q' and resid 3 through 7 Processing helix chain 'Q' and resid 9 through 37 Proline residue: Q 15 - end of helix removed outlier: 3.590A pdb=" N HIS Q 20 " --> pdb=" O PHE Q 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 55 Processing helix chain 'Q' and resid 58 through 75 removed outlier: 3.765A pdb=" N TYR Q 63 " --> pdb=" O SER Q 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 36 through 43 Processing helix chain 'R' and resid 51 through 64 Processing helix chain 'R' and resid 69 through 72 No H-bonds generated for 'chain 'R' and resid 69 through 72' Processing helix chain 'S' and resid 20 through 22 No H-bonds generated for 'chain 'S' and resid 20 through 22' Processing helix chain 'S' and resid 26 through 52 removed outlier: 4.021A pdb=" N ARG S 35 " --> pdb=" O GLN S 31 " (cutoff:3.500A) Proline residue: S 36 - end of helix removed outlier: 4.057A pdb=" N TRP S 41 " --> pdb=" O PHE S 37 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE S 42 " --> pdb=" O ILE S 38 " (cutoff:3.500A) Proline residue: S 45 - end of helix Processing helix chain 'T' and resid 38 through 52 Processing helix chain 'T' and resid 59 through 62 Processing helix chain 'a' and resid 3 through 39 removed outlier: 3.898A pdb=" N LYS a 10 " --> pdb=" O LYS a 6 " (cutoff:3.500A) Proline residue: a 12 - end of helix removed outlier: 3.553A pdb=" N THR a 15 " --> pdb=" O LEU a 11 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER a 16 " --> pdb=" O PRO a 12 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLN a 17 " --> pdb=" O ALA a 13 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS a 38 " --> pdb=" O GLU a 34 " (cutoff:3.500A) Processing helix chain 'a' and resid 58 through 61 No H-bonds generated for 'chain 'a' and resid 58 through 61' Processing helix chain 'a' and resid 72 through 92 removed outlier: 3.910A pdb=" N LEU a 89 " --> pdb=" O MET a 85 " (cutoff:3.500A) Proline residue: a 90 - end of helix Processing helix chain 'a' and resid 94 through 97 No H-bonds generated for 'chain 'a' and resid 94 through 97' Processing helix chain 'a' and resid 103 through 110 Processing helix chain 'a' and resid 117 through 119 No H-bonds generated for 'chain 'a' and resid 117 through 119' Processing helix chain 'a' and resid 125 through 141 removed outlier: 5.772A pdb=" N ASP a 138 " --> pdb=" O SER a 134 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ASP a 139 " --> pdb=" O SER a 135 " (cutoff:3.500A) Processing helix chain 'a' and resid 145 through 156 Processing helix chain 'a' and resid 163 through 165 No H-bonds generated for 'chain 'a' and resid 163 through 165' Processing helix chain 'a' and resid 172 through 179 Processing helix chain 'a' and resid 190 through 199 removed outlier: 4.052A pdb=" N LEU a 196 " --> pdb=" O LYS a 192 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ARG a 197 " --> pdb=" O CYS a 193 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU a 198 " --> pdb=" O ALA a 194 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TYR a 199 " --> pdb=" O HIS a 195 " (cutoff:3.500A) Processing helix chain 'a' and resid 218 through 230 Processing helix chain 'a' and resid 234 through 255 removed outlier: 3.777A pdb=" N LYS a 239 " --> pdb=" O GLU a 235 " (cutoff:3.500A) Processing helix chain 'a' and resid 259 through 262 removed outlier: 3.556A pdb=" N HIS a 262 " --> pdb=" O HIS a 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 259 through 262' Processing helix chain 'a' and resid 276 through 278 No H-bonds generated for 'chain 'a' and resid 276 through 278' Processing helix chain 'a' and resid 289 through 292 Processing helix chain 'a' and resid 295 through 297 No H-bonds generated for 'chain 'a' and resid 295 through 297' Processing helix chain 'a' and resid 320 through 329 removed outlier: 3.887A pdb=" N LYS a 324 " --> pdb=" O ARG a 320 " (cutoff:3.500A) Processing helix chain 'a' and resid 339 through 362 Processing helix chain 'a' and resid 371 through 381 Processing helix chain 'a' and resid 392 through 408 removed outlier: 3.651A pdb=" N LEU a 408 " --> pdb=" O TRP a 404 " (cutoff:3.500A) Processing helix chain 'a' and resid 411 through 421 removed outlier: 3.770A pdb=" N GLY a 420 " --> pdb=" O ALA a 416 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR a 421 " --> pdb=" O TRP a 417 " (cutoff:3.500A) Processing helix chain 'a' and resid 445 through 447 No H-bonds generated for 'chain 'a' and resid 445 through 447' Processing helix chain 'a' and resid 468 through 470 No H-bonds generated for 'chain 'a' and resid 468 through 470' Processing helix chain 'a' and resid 474 through 477 No H-bonds generated for 'chain 'a' and resid 474 through 477' Processing helix chain 'a' and resid 479 through 486 Processing helix chain 'b' and resid 124 through 150 Processing helix chain 'd' and resid 4 through 17 removed outlier: 4.262A pdb=" N ASP d 10 " --> pdb=" O LEU d 6 " (cutoff:3.500A) Processing helix chain 'd' and resid 19 through 21 No H-bonds generated for 'chain 'd' and resid 19 through 21' Processing helix chain 'd' and resid 24 through 55 removed outlier: 3.573A pdb=" N TYR d 41 " --> pdb=" O ARG d 37 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL d 42 " --> pdb=" O LEU d 38 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA d 54 " --> pdb=" O VAL d 50 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR d 55 " --> pdb=" O GLY d 51 " (cutoff:3.500A) Processing helix chain 'd' and resid 58 through 65 removed outlier: 4.026A pdb=" N LYS d 64 " --> pdb=" O ALA d 60 " (cutoff:3.500A) Processing helix chain 'd' and resid 78 through 81 No H-bonds generated for 'chain 'd' and resid 78 through 81' Processing helix chain 'd' and resid 88 through 93 Processing helix chain 'd' and resid 99 through 109 removed outlier: 4.555A pdb=" N GLY d 109 " --> pdb=" O LYS d 105 " (cutoff:3.500A) Processing helix chain 'd' and resid 119 through 149 removed outlier: 3.961A pdb=" N GLY d 125 " --> pdb=" O SER d 121 " (cutoff:3.500A) Proline residue: d 128 - end of helix Processing helix chain 'd' and resid 154 through 163 Processing helix chain 'd' and resid 168 through 182 removed outlier: 3.713A pdb=" N ARG d 178 " --> pdb=" O SER d 174 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS d 181 " --> pdb=" O ALA d 177 " (cutoff:3.500A) Processing helix chain 'e' and resid 12 through 37 removed outlier: 3.539A pdb=" N CYS e 30 " --> pdb=" O ASP e 26 " (cutoff:3.500A) Processing helix chain 'e' and resid 41 through 64 removed outlier: 3.523A pdb=" N ASP e 46 " --> pdb=" O ASP e 42 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N TRP e 50 " --> pdb=" O ASP e 46 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N THR e 51 " --> pdb=" O ALA e 47 " (cutoff:3.500A) Processing helix chain 'e' and resid 72 through 80 Processing helix chain 'e' and resid 91 through 96 removed outlier: 3.690A pdb=" N LYS e 95 " --> pdb=" O TRP e 92 " (cutoff:3.500A) Processing helix chain 'f' and resid 15 through 28 removed outlier: 3.782A pdb=" N MET f 20 " --> pdb=" O MET f 16 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE f 21 " --> pdb=" O TYR f 17 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE f 22 " --> pdb=" O SER f 18 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET f 25 " --> pdb=" O ILE f 21 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE f 26 " --> pdb=" O ILE f 22 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU f 27 " --> pdb=" O ILE f 23 " (cutoff:3.500A) Processing helix chain 'f' and resid 33 through 43 Processing helix chain 'f' and resid 49 through 71 Processing helix chain 'f' and resid 77 through 80 No H-bonds generated for 'chain 'f' and resid 77 through 80' Processing helix chain 'f' and resid 85 through 90 Processing helix chain 'f' and resid 93 through 103 Proline residue: f 100 - end of helix Processing helix chain 'f' and resid 105 through 115 Processing helix chain 'f' and resid 129 through 136 Processing helix chain 'f' and resid 147 through 165 removed outlier: 5.855A pdb=" N ASP f 151 " --> pdb=" O PHE f 148 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASN f 154 " --> pdb=" O ASP f 151 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASN f 163 " --> pdb=" O ARG f 160 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N PHE f 164 " --> pdb=" O SER f 161 " (cutoff:3.500A) Processing helix chain 'f' and resid 167 through 202 Processing helix chain 'f' and resid 216 through 248 Processing helix chain 'f' and resid 250 through 252 No H-bonds generated for 'chain 'f' and resid 250 through 252' Processing helix chain 'f' and resid 270 through 273 No H-bonds generated for 'chain 'f' and resid 270 through 273' Processing helix chain 'g' and resid 15 through 17 No H-bonds generated for 'chain 'g' and resid 15 through 17' Processing helix chain 'g' and resid 23 through 28 Processing helix chain 'g' and resid 31 through 48 removed outlier: 3.642A pdb=" N VAL g 36 " --> pdb=" O PRO g 32 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLY g 39 " --> pdb=" O LEU g 35 " (cutoff:3.500A) Processing helix chain 'g' and resid 85 through 111 Processing helix chain 'h' and resid 41 through 57 removed outlier: 3.894A pdb=" N LYS h 56 " --> pdb=" O LYS h 52 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N THR h 57 " --> pdb=" O ALA h 53 " (cutoff:3.500A) Processing helix chain 'h' and resid 60 through 78 Processing helix chain 'h' and resid 82 through 102 Proline residue: h 100 - end of helix Processing helix chain 'h' and resid 110 through 131 removed outlier: 3.556A pdb=" N ILE h 113 " --> pdb=" O ILE h 110 " (cutoff:3.500A) Proline residue: h 114 - end of helix removed outlier: 4.086A pdb=" N GLU h 129 " --> pdb=" O ALA h 126 " (cutoff:3.500A) Processing helix chain 'h' and resid 141 through 149 removed outlier: 5.600A pdb=" N MET h 146 " --> pdb=" O GLU h 142 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N TYR h 147 " --> pdb=" O ALA h 143 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE h 148 " --> pdb=" O HIS h 144 " (cutoff:3.500A) Processing helix chain 'h' and resid 268 through 278 Processing helix chain 'h' and resid 339 through 378 removed outlier: 3.526A pdb=" N GLY h 351 " --> pdb=" O ASN h 347 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR h 366 " --> pdb=" O TYR h 362 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG h 372 " --> pdb=" O GLN h 368 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG h 376 " --> pdb=" O ARG h 372 " (cutoff:3.500A) Processing helix chain 'h' and resid 385 through 390 Processing helix chain 'h' and resid 393 through 405 removed outlier: 3.573A pdb=" N ASP h 398 " --> pdb=" O LEU h 394 " (cutoff:3.500A) Processing helix chain 'h' and resid 412 through 417 Processing helix chain 'h' and resid 419 through 421 No H-bonds generated for 'chain 'h' and resid 419 through 421' Processing helix chain 'h' and resid 427 through 429 No H-bonds generated for 'chain 'h' and resid 427 through 429' Processing helix chain 'h' and resid 444 through 454 removed outlier: 3.502A pdb=" N GLN h 450 " --> pdb=" O ALA h 446 " (cutoff:3.500A) Processing helix chain 'h' and resid 457 through 475 removed outlier: 3.666A pdb=" N ARG h 464 " --> pdb=" O SER h 460 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU h 465 " --> pdb=" O LEU h 461 " (cutoff:3.500A) Processing helix chain 'i' and resid 10 through 20 removed outlier: 3.762A pdb=" N PHE i 18 " --> pdb=" O TYR i 14 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE i 19 " --> pdb=" O LYS i 15 " (cutoff:3.500A) Processing helix chain 'i' and resid 24 through 37 removed outlier: 4.119A pdb=" N TYR i 30 " --> pdb=" O HIS i 26 " (cutoff:3.500A) Proline residue: i 34 - end of helix Processing helix chain 'i' and resid 44 through 61 removed outlier: 3.784A pdb=" N GLU i 52 " --> pdb=" O ARG i 48 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA i 53 " --> pdb=" O ASN i 49 " (cutoff:3.500A) Processing helix chain 'i' and resid 64 through 69 Processing helix chain 'i' and resid 72 through 88 Processing helix chain 'j' and resid 5 through 8 No H-bonds generated for 'chain 'j' and resid 5 through 8' Processing helix chain 'j' and resid 10 through 15 Processing helix chain 'j' and resid 18 through 36 Proline residue: j 23 - end of helix Processing helix chain 'j' and resid 38 through 42 Processing helix chain 'j' and resid 45 through 47 No H-bonds generated for 'chain 'j' and resid 45 through 47' Processing helix chain 'j' and resid 49 through 52 Processing helix chain 'j' and resid 71 through 87 Processing helix chain 'j' and resid 91 through 96 removed outlier: 3.947A pdb=" N VAL j 94 " --> pdb=" O ILE j 91 " (cutoff:3.500A) Processing helix chain 'k' and resid 15 through 36 Processing helix chain 'k' and resid 40 through 42 No H-bonds generated for 'chain 'k' and resid 40 through 42' Processing helix chain 'k' and resid 44 through 51 removed outlier: 3.932A pdb=" N LEU k 51 " --> pdb=" O LYS k 47 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 61 Processing helix chain 'k' and resid 67 through 88 removed outlier: 5.190A pdb=" N GLY k 81 " --> pdb=" O ALA k 77 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N TRP k 82 " --> pdb=" O LEU k 78 " (cutoff:3.500A) Processing helix chain 'l' and resid 12 through 32 Proline residue: l 30 - end of helix Processing helix chain 'l' and resid 39 through 46 Processing helix chain 'm' and resid 3 through 15 removed outlier: 5.236A pdb=" N ILE m 13 " --> pdb=" O TYR m 9 " (cutoff:3.500A) Proline residue: m 14 - end of helix Processing helix chain 'm' and resid 19 through 32 Processing helix chain 'm' and resid 35 through 46 Processing helix chain 'm' and resid 51 through 65 Processing helix chain 'm' and resid 67 through 87 removed outlier: 4.403A pdb=" N VAL m 75 " --> pdb=" O PHE m 71 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL m 76 " --> pdb=" O ARG m 72 " (cutoff:3.500A) Processing helix chain 'm' and resid 92 through 117 Processing helix chain 'm' and resid 128 through 131 No H-bonds generated for 'chain 'm' and resid 128 through 131' Processing helix chain 'm' and resid 133 through 166 removed outlier: 3.555A pdb=" N VAL m 150 " --> pdb=" O GLN m 146 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS m 164 " --> pdb=" O GLN m 160 " (cutoff:3.500A) Processing helix chain 'n' and resid 5 through 9 Processing helix chain 'n' and resid 46 through 81 Processing helix chain 'n' and resid 93 through 103 Processing helix chain 'o' and resid 15 through 18 No H-bonds generated for 'chain 'o' and resid 15 through 18' Processing helix chain 'o' and resid 32 through 49 Processing helix chain 'o' and resid 57 through 75 removed outlier: 4.888A pdb=" N PHE o 65 " --> pdb=" O LEU o 61 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLN o 66 " --> pdb=" O LEU o 62 " (cutoff:3.500A) Processing helix chain 'o' and resid 83 through 86 No H-bonds generated for 'chain 'o' and resid 83 through 86' Processing helix chain 'o' and resid 100 through 112 Processing helix chain 'p' and resid 15 through 17 No H-bonds generated for 'chain 'p' and resid 15 through 17' Processing helix chain 'p' and resid 22 through 37 removed outlier: 3.851A pdb=" N TYR p 36 " --> pdb=" O PHE p 32 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA p 37 " --> pdb=" O PHE p 33 " (cutoff:3.500A) Processing helix chain 'p' and resid 58 through 60 No H-bonds generated for 'chain 'p' and resid 58 through 60' Processing helix chain 'p' and resid 62 through 68 Processing helix chain 'p' and resid 74 through 76 No H-bonds generated for 'chain 'p' and resid 74 through 76' Processing helix chain 'p' and resid 83 through 95 removed outlier: 3.665A pdb=" N ASN p 93 " --> pdb=" O MET p 89 " (cutoff:3.500A) Processing helix chain 'p' and resid 102 through 107 Processing helix chain 'q' and resid 3 through 7 Processing helix chain 'q' and resid 9 through 37 Proline residue: q 15 - end of helix removed outlier: 3.591A pdb=" N HIS q 20 " --> pdb=" O PHE q 16 " (cutoff:3.500A) Processing helix chain 'q' and resid 46 through 55 Processing helix chain 'q' and resid 58 through 75 removed outlier: 3.764A pdb=" N TYR q 63 " --> pdb=" O SER q 59 " (cutoff:3.500A) Processing helix chain 'r' and resid 36 through 43 Processing helix chain 'r' and resid 51 through 64 Processing helix chain 'r' and resid 69 through 72 No H-bonds generated for 'chain 'r' and resid 69 through 72' Processing helix chain 's' and resid 20 through 22 No H-bonds generated for 'chain 's' and resid 20 through 22' Processing helix chain 's' and resid 26 through 52 removed outlier: 4.020A pdb=" N ARG s 35 " --> pdb=" O GLN s 31 " (cutoff:3.500A) Proline residue: s 36 - end of helix removed outlier: 4.057A pdb=" N TRP s 41 " --> pdb=" O PHE s 37 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE s 42 " --> pdb=" O ILE s 38 " (cutoff:3.500A) Proline residue: s 45 - end of helix Processing helix chain 't' and resid 38 through 52 Processing helix chain 't' and resid 59 through 62 Processing sheet with id= A, first strand: chain 'A' and resid 213 through 215 removed outlier: 4.507A pdb=" N ASP A 303 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'G' and resid 54 through 58 Processing sheet with id= C, first strand: chain 'H' and resid 205 through 209 removed outlier: 6.564A pdb=" N SER H 165 " --> pdb=" O ILE H 221 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ILE H 221 " --> pdb=" O SER H 165 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 183 through 188 Processing sheet with id= E, first strand: chain 'a' and resid 213 through 215 removed outlier: 4.508A pdb=" N ASP a 303 " --> pdb=" O LEU a 208 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'g' and resid 54 through 58 Processing sheet with id= G, first strand: chain 'h' and resid 205 through 209 removed outlier: 6.564A pdb=" N SER h 165 " --> pdb=" O ILE h 221 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ILE h 221 " --> pdb=" O SER h 165 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'h' and resid 183 through 188 2032 hydrogen bonds defined for protein. 5862 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: 31.00 Time building geometry restraints manager: 63.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 44466 1.03 - 1.23: 312 1.23 - 1.43: 20484 1.43 - 1.62: 27835 1.62 - 1.82: 414 Bond restraints: 93511 Sorted by residual: bond pdb=" CA7 CDL A 504 " pdb=" OA8 CDL A 504 " ideal model delta sigma weight residual 1.334 1.402 -0.068 1.10e-02 8.26e+03 3.77e+01 bond pdb=" CA7 CDL a 504 " pdb=" OA8 CDL a 504 " ideal model delta sigma weight residual 1.334 1.401 -0.067 1.10e-02 8.26e+03 3.76e+01 bond pdb=" CB7 CDL A 502 " pdb=" OB8 CDL A 502 " ideal model delta sigma weight residual 1.334 1.401 -0.067 1.10e-02 8.26e+03 3.71e+01 bond pdb=" CB7 CDL a 502 " pdb=" OB8 CDL a 502 " ideal model delta sigma weight residual 1.334 1.401 -0.067 1.10e-02 8.26e+03 3.70e+01 bond pdb=" CB7 CDL r 101 " pdb=" OB8 CDL r 101 " ideal model delta sigma weight residual 1.334 1.400 -0.066 1.10e-02 8.26e+03 3.59e+01 ... (remaining 93506 not shown) Histogram of bond angle deviations from ideal: 81.81 - 95.88: 8 95.88 - 109.95: 73837 109.95 - 124.02: 86325 124.02 - 138.09: 7153 138.09 - 152.16: 4 Bond angle restraints: 167327 Sorted by residual: angle pdb=" C7 TRT P 203 " pdb=" C6 TRT P 203 " pdb=" C8 TRT P 203 " ideal model delta sigma weight residual 109.35 152.16 -42.81 3.00e+00 1.11e-01 2.04e+02 angle pdb=" C7 TRT p 203 " pdb=" C6 TRT p 203 " pdb=" C8 TRT p 203 " ideal model delta sigma weight residual 109.35 152.14 -42.79 3.00e+00 1.11e-01 2.03e+02 angle pdb=" C5 TRT P 203 " pdb=" C6 TRT P 203 " pdb=" C9 TRT P 203 " ideal model delta sigma weight residual 109.47 139.47 -30.00 3.00e+00 1.11e-01 1.00e+02 angle pdb=" C5 TRT p 203 " pdb=" C6 TRT p 203 " pdb=" C9 TRT p 203 " ideal model delta sigma weight residual 109.47 139.46 -29.99 3.00e+00 1.11e-01 9.99e+01 angle pdb=" C8 TRT p 203 " pdb=" C6 TRT p 203 " pdb=" C9 TRT p 203 " ideal model delta sigma weight residual 108.45 81.81 26.64 3.00e+00 1.11e-01 7.88e+01 ... (remaining 167322 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.58: 43081 30.58 - 61.16: 2283 61.16 - 91.73: 83 91.73 - 122.31: 7 122.31 - 152.89: 10 Dihedral angle restraints: 45464 sinusoidal: 25477 harmonic: 19987 Sorted by residual: dihedral pdb=" CA PHE T 13 " pdb=" C PHE T 13 " pdb=" N ARG T 14 " pdb=" CA ARG T 14 " ideal model delta harmonic sigma weight residual 180.00 156.67 23.33 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA PHE t 13 " pdb=" C PHE t 13 " pdb=" N ARG t 14 " pdb=" CA ARG t 14 " ideal model delta harmonic sigma weight residual 180.00 156.71 23.29 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA5 CDL p 202 " pdb=" CA4 CDL p 202 " pdb=" OA6 CDL p 202 " pdb=" CA6 CDL p 202 " ideal model delta sinusoidal sigma weight residual 168.24 -38.87 -152.89 1 3.00e+01 1.11e-03 2.02e+01 ... (remaining 45461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 5321 0.048 - 0.097: 1237 0.097 - 0.145: 206 0.145 - 0.193: 26 0.193 - 0.242: 21 Chirality restraints: 6811 Sorted by residual: chirality pdb=" CA4 CDL O 201 " pdb=" CA3 CDL O 201 " pdb=" CA6 CDL O 201 " pdb=" OA6 CDL O 201 " both_signs ideal model delta sigma weight residual False -2.57 -2.33 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA4 CDL o 201 " pdb=" CA3 CDL o 201 " pdb=" CA6 CDL o 201 " pdb=" OA6 CDL o 201 " both_signs ideal model delta sigma weight residual False -2.57 -2.34 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C5' LMT F 302 " pdb=" C4' LMT F 302 " pdb=" C6' LMT F 302 " pdb=" O5' LMT F 302 " both_signs ideal model delta sigma weight residual False -2.51 -2.29 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 6808 not shown) Planarity restraints: 13208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS F 59 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.31e+00 pdb=" C CYS F 59 " -0.050 2.00e-02 2.50e+03 pdb=" O CYS F 59 " 0.019 2.00e-02 2.50e+03 pdb=" N THR F 60 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS f 59 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.28e+00 pdb=" C CYS f 59 " 0.050 2.00e-02 2.50e+03 pdb=" O CYS f 59 " -0.019 2.00e-02 2.50e+03 pdb=" N THR f 60 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS f 57 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.75e+00 pdb=" C CYS f 57 " 0.041 2.00e-02 2.50e+03 pdb=" O CYS f 57 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN f 58 " -0.014 2.00e-02 2.50e+03 ... (remaining 13205 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.27: 12753 2.27 - 2.85: 205058 2.85 - 3.43: 239392 3.43 - 4.02: 336992 4.02 - 4.60: 526815 Nonbonded interactions: 1321010 Sorted by model distance: nonbonded pdb=" H HIS M 34 " pdb=" OE1 GLN m 61 " model vdw 1.683 1.850 nonbonded pdb=" HG1 THR a 54 " pdb=" OA3 CDL a 502 " model vdw 1.685 1.850 nonbonded pdb=" O GLY i 32 " pdb=" H VAL i 36 " model vdw 1.685 1.850 nonbonded pdb=" O GLY I 32 " pdb=" H VAL I 36 " model vdw 1.685 1.850 nonbonded pdb="HH11 ARG G 47 " pdb=" O TYR H 147 " model vdw 1.688 1.850 ... (remaining 1321005 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 'a' } ncs_group { reference = chain 'B' selection = chain 'b' } ncs_group { reference = chain 'D' selection = chain 'd' } ncs_group { reference = chain 'E' selection = (chain 'e' and (resid 2 through 88 or (resid 89 and (name N or name CA or name C \ or name O or name CB or name CG or name CD2 or name NE1 or name CE2 or name CE3 \ or name CZ2 or name CZ3 or name CH2 or name H or name HA or name HB2 or name HB \ 3 or name HE3 or name HZ2 or name HZ3 or name HH2)) or resid 90 through 97 or re \ sid 101)) } ncs_group { reference = chain 'F' selection = (chain 'f' and (resid 1 through 9 or (resid 10 and (name CA or name C or name O \ or name CB or name CG1 or name CG2 or name CD1 or name HB or name HG12 or name H \ G13 or name HG21 or name HG22 or name HG23 or name HD11 or name HD12 or name HD1 \ 3)) or resid 11 through 274 or resid 301 through 302)) } ncs_group { reference = chain 'G' selection = chain 'g' } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'I' selection = chain 'i' } ncs_group { reference = chain 'J' selection = chain 'j' } ncs_group { reference = chain 'K' selection = chain 'k' } ncs_group { reference = chain 'L' selection = chain 'l' } ncs_group { reference = (chain 'M' and resid 2 through 167) selection = (chain 'm' and resid 2 through 167) } ncs_group { reference = (chain 'N' and (resid 2 through 132 or resid 202)) selection = (chain 'n' and (resid 2 through 132 or resid 202)) } ncs_group { reference = chain 'O' selection = chain 'o' } ncs_group { reference = (chain 'P' and (resid 7 through 120 or resid 201 or resid 203)) selection = (chain 'p' and (resid 7 through 120 or (resid 201 and (name CB2 or name OB2 or n \ ame CB3 or name OB3 or name C1 or name C11 or name C12 or name C13 or name C14 o \ r name C31 or name C32 or name C33 or name C34 or name C35 or name C51 or name C \ 71 or name C72 or name C73 or name C74 or name C75 or name C76 or name CA2 or na \ me CA3 or name CA4 or name CA5 or name CA6 or name CA7 or name CB4 or name CB5 o \ r name CB6 or name CB7 or name O1 or name OA2 or name OA3 or name OA4 or name OA \ 5 or name OA6 or name OA7 or name OA8 or name OA9 or name OB4 or name OB5 or nam \ e OB6 or name OB7 or name OB8 or name OB9 or name PA1 or name PB2)) or resid 203 \ )) } ncs_group { reference = chain 'Q' selection = chain 'q' } ncs_group { reference = chain 'R' selection = chain 'r' } ncs_group { reference = chain 'S' selection = chain 's' } ncs_group { reference = chain 'T' selection = chain 't' } 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: 4.100 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: 1.000 Extract box with map and model: 20.410 Check model and map are aligned: 1.040 Set scattering table: 0.670 Process input model: 230.820 Find NCS groups from input model: 3.280 Set up NCS constraints: 1.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 273.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 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 : 0.009 0.071 48995 Z= 0.567 Angle : 1.083 42.813 66058 Z= 0.533 Chirality : 0.043 0.242 6811 Planarity : 0.005 0.053 8081 Dihedral : 18.030 152.889 19677 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: -1.24 (0.11), residues: 5382 helix: -0.37 (0.08), residues: 3158 sheet: -1.24 (0.54), residues: 66 loop : -1.38 (0.13), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP h 223 HIS 0.013 0.001 HIS a 45 PHE 0.016 0.002 PHE p 61 TYR 0.019 0.001 TYR f 53 ARG 0.005 0.000 ARG q 17 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10764 Ramachandran restraints generated. 5382 Oldfield, 0 Emsley, 5382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10764 Ramachandran restraints generated. 5382 Oldfield, 0 Emsley, 5382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1057 residues out of total 4804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1057 time to evaluate : 5.717 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: A 217 THR cc_start: 0.8284 (p) cc_final: 0.8022 (m) REVERT: A 441 LEU cc_start: 0.8838 (tp) cc_final: 0.8634 (tt) REVERT: F 114 ASP cc_start: 0.7527 (t70) cc_final: 0.7193 (t0) REVERT: G 28 MET cc_start: 0.8513 (mtt) cc_final: 0.8219 (mtt) REVERT: G 54 ARG cc_start: 0.8264 (mtm-85) cc_final: 0.7928 (mtm180) REVERT: I 69 LYS cc_start: 0.8406 (mttt) cc_final: 0.8203 (mtpt) REVERT: K 63 MET cc_start: 0.8913 (mtp) cc_final: 0.8680 (mtt) REVERT: M 165 THR cc_start: 0.6126 (p) cc_final: 0.5695 (p) REVERT: P 70 ILE cc_start: 0.8262 (mt) cc_final: 0.8024 (mp) REVERT: R 44 LYS cc_start: 0.8098 (ttpt) cc_final: 0.7479 (tptm) REVERT: S 50 ASP cc_start: 0.7941 (t0) cc_final: 0.7683 (t70) REVERT: T 7 GLU cc_start: 0.8386 (mt-10) cc_final: 0.7997 (mt-10) REVERT: a 217 THR cc_start: 0.8271 (p) cc_final: 0.7988 (m) REVERT: e 25 LYS cc_start: 0.7874 (mttt) cc_final: 0.7652 (mttp) REVERT: f 114 ASP cc_start: 0.7579 (t70) cc_final: 0.7267 (t0) REVERT: g 28 MET cc_start: 0.8450 (mtt) cc_final: 0.8182 (mtt) REVERT: g 104 LYS cc_start: 0.8271 (mtmt) cc_final: 0.8067 (mtmm) REVERT: i 69 LYS cc_start: 0.8425 (mttt) cc_final: 0.8223 (mtpt) REVERT: j 98 LYS cc_start: 0.7829 (tptp) cc_final: 0.7511 (tmtt) REVERT: k 63 MET cc_start: 0.8908 (mtp) cc_final: 0.8631 (mtt) REVERT: m 165 THR cc_start: 0.6116 (p) cc_final: 0.5835 (p) REVERT: r 44 LYS cc_start: 0.8093 (ttpt) cc_final: 0.7477 (tptm) REVERT: s 22 ASP cc_start: 0.8655 (m-30) cc_final: 0.8428 (m-30) REVERT: s 50 ASP cc_start: 0.7995 (t0) cc_final: 0.7739 (t70) REVERT: t 7 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8021 (mt-10) outliers start: 0 outliers final: 1 residues processed: 1057 average time/residue: 2.9441 time to fit residues: 3860.0438 Evaluate side-chains 602 residues out of total 4804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 601 time to evaluate : 5.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 76 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 445 optimal weight: 1.9990 chunk 400 optimal weight: 3.9990 chunk 222 optimal weight: 0.6980 chunk 136 optimal weight: 3.9990 chunk 269 optimal weight: 0.7980 chunk 213 optimal weight: 4.9990 chunk 413 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 251 optimal weight: 2.9990 chunk 308 optimal weight: 2.9990 chunk 479 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN D 146 ASN F 24 GLN ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 ASN F 116 ASN F 140 ASN F 167 ASN F 260 ASN F 266 ASN I 21 ASN I 47 ASN I 91 ASN K 34 GLN K 103 ASN L 37 ASN L 56 ASN N 110 HIS O 69 ASN O 105 HIS Q 82 ASN Q 87 GLN T 53 ASN a 142 GLN a 278 ASN d 146 ASN f 24 GLN ** f 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 69 ASN f 140 ASN f 167 ASN f 260 ASN f 266 ASN i 21 ASN i 47 ASN i 91 ASN j 79 GLN k 103 ASN l 37 ASN l 56 ASN n 110 HIS o 69 ASN o 105 HIS q 67 GLN q 82 ASN q 87 GLN t 53 ASN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 48995 Z= 0.283 Angle : 0.657 32.477 66058 Z= 0.299 Chirality : 0.038 0.153 6811 Planarity : 0.005 0.058 8081 Dihedral : 17.595 145.895 8713 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.12 % Allowed : 10.10 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: 0.09 (0.11), residues: 5382 helix: 0.75 (0.09), residues: 3162 sheet: -0.95 (0.52), residues: 76 loop : -0.86 (0.14), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 404 HIS 0.008 0.001 HIS F 70 PHE 0.016 0.001 PHE g 37 TYR 0.020 0.001 TYR L 22 ARG 0.008 0.001 ARG G 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10764 Ramachandran restraints generated. 5382 Oldfield, 0 Emsley, 5382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10764 Ramachandran restraints generated. 5382 Oldfield, 0 Emsley, 5382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 4804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 691 time to evaluate : 5.733 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: A 26 GLN cc_start: 0.7258 (tm-30) cc_final: 0.7011 (tp-100) REVERT: E 25 LYS cc_start: 0.7879 (mttt) cc_final: 0.7637 (mttp) REVERT: F 14 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7605 (mp) REVERT: G 28 MET cc_start: 0.8480 (mtt) cc_final: 0.8160 (mtt) REVERT: H 237 THR cc_start: 0.8672 (OUTLIER) cc_final: 0.8465 (m) REVERT: H 463 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8145 (mtpm) REVERT: L 22 TYR cc_start: 0.8470 (m-80) cc_final: 0.8179 (m-80) REVERT: M 106 TYR cc_start: 0.8365 (t80) cc_final: 0.8143 (t80) REVERT: O 58 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8144 (mp10) REVERT: Q 43 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6525 (mp0) REVERT: Q 74 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8607 (mp) REVERT: S 35 ARG cc_start: 0.7646 (mtt180) cc_final: 0.7432 (mtt180) REVERT: S 50 ASP cc_start: 0.8093 (t0) cc_final: 0.7831 (t70) REVERT: T 7 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8087 (mt-10) REVERT: a 441 LEU cc_start: 0.9023 (tp) cc_final: 0.8734 (tt) REVERT: f 14 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7722 (mp) REVERT: g 28 MET cc_start: 0.8514 (mtt) cc_final: 0.8207 (mtt) REVERT: h 463 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8121 (mtpm) REVERT: l 22 TYR cc_start: 0.8491 (m-80) cc_final: 0.8191 (m-80) REVERT: m 106 TYR cc_start: 0.8377 (t80) cc_final: 0.8174 (t80) REVERT: o 58 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8201 (mp10) REVERT: q 43 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.6489 (mp0) REVERT: r 44 LYS cc_start: 0.8217 (ttpt) cc_final: 0.7596 (tptm) REVERT: s 50 ASP cc_start: 0.8175 (t0) cc_final: 0.7880 (t70) REVERT: t 7 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8073 (mt-10) outliers start: 102 outliers final: 47 residues processed: 741 average time/residue: 2.6573 time to fit residues: 2505.6322 Evaluate side-chains 659 residues out of total 4804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 602 time to evaluate : 5.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain F residue 266 ASN Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain H residue 237 THR Chi-restraints excluded: chain H residue 271 MET Chi-restraints excluded: chain H residue 463 LYS Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain M residue 138 ILE Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain O residue 23 ASP Chi-restraints excluded: chain O residue 58 GLN Chi-restraints excluded: chain O residue 86 ASP Chi-restraints excluded: chain P residue 28 GLU Chi-restraints excluded: chain Q residue 24 CYS Chi-restraints excluded: chain Q residue 43 GLU Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 74 LEU Chi-restraints excluded: chain R residue 14 GLU Chi-restraints excluded: chain T residue 56 SER Chi-restraints excluded: chain a residue 112 ASP Chi-restraints excluded: chain a residue 313 THR Chi-restraints excluded: chain a residue 338 SER Chi-restraints excluded: chain a residue 425 THR Chi-restraints excluded: chain d residue 83 SER Chi-restraints excluded: chain d residue 174 SER Chi-restraints excluded: chain e residue 86 SER Chi-restraints excluded: chain f residue 14 ILE Chi-restraints excluded: chain f residue 226 ILE Chi-restraints excluded: chain f residue 263 SER Chi-restraints excluded: chain f residue 266 ASN Chi-restraints excluded: chain h residue 165 SER Chi-restraints excluded: chain h residue 170 ASP Chi-restraints excluded: chain h residue 212 ASP Chi-restraints excluded: chain h residue 463 LYS Chi-restraints excluded: chain i residue 23 LYS Chi-restraints excluded: chain j residue 41 SER Chi-restraints excluded: chain j residue 68 SER Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain m residue 138 ILE Chi-restraints excluded: chain o residue 58 GLN Chi-restraints excluded: chain o residue 86 ASP Chi-restraints excluded: chain p residue 28 GLU Chi-restraints excluded: chain q residue 24 CYS Chi-restraints excluded: chain q residue 43 GLU Chi-restraints excluded: chain q residue 58 ASP Chi-restraints excluded: chain r residue 14 GLU Chi-restraints excluded: chain t residue 56 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 266 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 399 optimal weight: 0.0070 chunk 326 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 480 optimal weight: 5.9990 chunk 518 optimal weight: 2.9990 chunk 427 optimal weight: 1.9990 chunk 476 optimal weight: 0.3980 chunk 163 optimal weight: 3.9990 chunk 385 optimal weight: 3.9990 overall best weight: 1.0804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN A 278 ASN ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 ASN I 21 ASN L 37 ASN L 56 ASN Q 33 GLN Q 82 ASN a 222 GLN ** f 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 142 ASN i 21 ASN l 37 ASN l 56 ASN q 82 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 48995 Z= 0.196 Angle : 0.602 32.766 66058 Z= 0.272 Chirality : 0.036 0.149 6811 Planarity : 0.004 0.068 8081 Dihedral : 16.461 143.622 8711 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.67 % Allowed : 12.08 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: 0.79 (0.12), residues: 5382 helix: 1.30 (0.09), residues: 3158 sheet: -0.73 (0.50), residues: 76 loop : -0.54 (0.14), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 404 HIS 0.004 0.001 HIS a 475 PHE 0.010 0.001 PHE g 37 TYR 0.018 0.001 TYR L 22 ARG 0.014 0.000 ARG Q 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10764 Ramachandran restraints generated. 5382 Oldfield, 0 Emsley, 5382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10764 Ramachandran restraints generated. 5382 Oldfield, 0 Emsley, 5382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 4804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 623 time to evaluate : 6.382 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: A 26 GLN cc_start: 0.7297 (tm-30) cc_final: 0.7047 (tp-100) REVERT: F 14 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7674 (mp) REVERT: G 28 MET cc_start: 0.8451 (mtt) cc_final: 0.8102 (mtt) REVERT: G 70 ARG cc_start: 0.8333 (ttm170) cc_final: 0.8016 (ttt180) REVERT: I 78 ILE cc_start: 0.8747 (mt) cc_final: 0.8471 (mt) REVERT: L 22 TYR cc_start: 0.8473 (m-80) cc_final: 0.8200 (m-80) REVERT: M 106 TYR cc_start: 0.8403 (t80) cc_final: 0.8174 (t80) REVERT: N 93 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.8072 (tt0) REVERT: N 110 HIS cc_start: 0.8294 (m90) cc_final: 0.8038 (m90) REVERT: O 58 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8078 (mp10) REVERT: Q 22 ARG cc_start: 0.7543 (mtm110) cc_final: 0.7178 (mtm-85) REVERT: Q 43 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6643 (mp0) REVERT: Q 74 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8499 (mp) REVERT: T 7 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8120 (mt-10) REVERT: a 131 GLU cc_start: 0.7585 (tp30) cc_final: 0.7372 (tp30) REVERT: a 284 TYR cc_start: 0.7834 (m-80) cc_final: 0.7530 (m-80) REVERT: a 441 LEU cc_start: 0.9013 (tp) cc_final: 0.8743 (tt) REVERT: f 14 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7796 (mp) REVERT: g 28 MET cc_start: 0.8469 (mtt) cc_final: 0.8169 (mtt) REVERT: h 146 MET cc_start: 0.8603 (mtm) cc_final: 0.8392 (mtt) REVERT: i 78 ILE cc_start: 0.8764 (mt) cc_final: 0.8489 (mt) REVERT: l 22 TYR cc_start: 0.8480 (m-80) cc_final: 0.8195 (m-80) REVERT: m 106 TYR cc_start: 0.8422 (t80) cc_final: 0.8222 (t80) REVERT: n 93 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8091 (tt0) REVERT: o 58 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8107 (mp10) REVERT: q 43 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6499 (mp0) REVERT: r 44 LYS cc_start: 0.8246 (ttpt) cc_final: 0.7616 (tptm) REVERT: s 50 ASP cc_start: 0.8144 (t0) cc_final: 0.7916 (t70) REVERT: t 7 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8128 (mt-10) outliers start: 80 outliers final: 35 residues processed: 661 average time/residue: 2.6682 time to fit residues: 2238.6841 Evaluate side-chains 638 residues out of total 4804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 594 time to evaluate : 6.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain H residue 170 ASP Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 93 GLU Chi-restraints excluded: chain O residue 58 GLN Chi-restraints excluded: chain O residue 86 ASP Chi-restraints excluded: chain P residue 28 GLU Chi-restraints excluded: chain Q residue 43 GLU Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 74 LEU Chi-restraints excluded: chain R residue 14 GLU Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 56 SER Chi-restraints excluded: chain d residue 169 ASP Chi-restraints excluded: chain e residue 86 SER Chi-restraints excluded: chain f residue 14 ILE Chi-restraints excluded: chain f residue 226 ILE Chi-restraints excluded: chain h residue 233 LEU Chi-restraints excluded: chain h residue 271 MET Chi-restraints excluded: chain h residue 343 GLN Chi-restraints excluded: chain i residue 23 LYS Chi-restraints excluded: chain j residue 41 SER Chi-restraints excluded: chain j residue 68 SER Chi-restraints excluded: chain m residue 138 ILE Chi-restraints excluded: chain m residue 165 THR Chi-restraints excluded: chain n residue 31 ASN Chi-restraints excluded: chain n residue 93 GLU Chi-restraints excluded: chain o residue 58 GLN Chi-restraints excluded: chain o residue 86 ASP Chi-restraints excluded: chain p residue 28 GLU Chi-restraints excluded: chain q residue 43 GLU Chi-restraints excluded: chain q residue 58 ASP Chi-restraints excluded: chain r residue 14 GLU Chi-restraints excluded: chain t residue 27 VAL Chi-restraints excluded: chain t residue 56 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 474 optimal weight: 3.9990 chunk 361 optimal weight: 3.9990 chunk 249 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 229 optimal weight: 1.9990 chunk 322 optimal weight: 2.9990 chunk 482 optimal weight: 4.9990 chunk 510 optimal weight: 0.9990 chunk 251 optimal weight: 4.9990 chunk 456 optimal weight: 0.9990 chunk 137 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 266 ASN I 21 ASN L 37 ASN L 56 ASN Q 82 ASN ** f 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 116 ASN f 266 ASN g 19 HIS i 21 ASN l 37 ASN l 56 ASN q 65 ASN q 82 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 48995 Z= 0.262 Angle : 0.613 32.780 66058 Z= 0.279 Chirality : 0.038 0.144 6811 Planarity : 0.004 0.061 8081 Dihedral : 15.690 143.440 8711 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.21 % Allowed : 12.39 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: 1.18 (0.12), residues: 5382 helix: 1.58 (0.09), residues: 3152 sheet: 0.00 (0.44), residues: 100 loop : -0.33 (0.14), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 404 HIS 0.005 0.001 HIS F 70 PHE 0.013 0.001 PHE g 37 TYR 0.027 0.001 TYR a 284 ARG 0.005 0.000 ARG a 398 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10764 Ramachandran restraints generated. 5382 Oldfield, 0 Emsley, 5382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10764 Ramachandran restraints generated. 5382 Oldfield, 0 Emsley, 5382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 4804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 646 time to evaluate : 5.643 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: A 26 GLN cc_start: 0.7407 (tm-30) cc_final: 0.7155 (tp-100) REVERT: A 284 TYR cc_start: 0.7578 (m-80) cc_final: 0.7356 (m-80) REVERT: F 14 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7725 (mp) REVERT: G 28 MET cc_start: 0.8453 (mtt) cc_final: 0.8112 (mtt) REVERT: H 237 THR cc_start: 0.8649 (OUTLIER) cc_final: 0.8443 (m) REVERT: H 463 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8121 (mtpm) REVERT: I 92 LYS cc_start: 0.8816 (mtpp) cc_final: 0.8417 (mtmt) REVERT: L 22 TYR cc_start: 0.8551 (m-80) cc_final: 0.8199 (m-80) REVERT: M 106 TYR cc_start: 0.8518 (t80) cc_final: 0.8272 (t80) REVERT: N 110 HIS cc_start: 0.8307 (m90) cc_final: 0.8049 (m90) REVERT: O 58 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8201 (mp10) REVERT: Q 43 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6674 (mp0) REVERT: T 7 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8140 (mt-10) REVERT: a 131 GLU cc_start: 0.7687 (tp30) cc_final: 0.7475 (tp30) REVERT: a 441 LEU cc_start: 0.9048 (tp) cc_final: 0.8798 (tt) REVERT: d 3 HIS cc_start: 0.7713 (OUTLIER) cc_final: 0.7404 (t70) REVERT: f 14 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.7851 (mp) REVERT: g 28 MET cc_start: 0.8467 (mtt) cc_final: 0.8136 (mtt) REVERT: h 146 MET cc_start: 0.8624 (mtm) cc_final: 0.8394 (mtt) REVERT: h 463 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8179 (mtpm) REVERT: i 92 LYS cc_start: 0.8796 (mtpp) cc_final: 0.8397 (mtmt) REVERT: l 22 TYR cc_start: 0.8556 (m-80) cc_final: 0.8196 (m-80) REVERT: m 106 TYR cc_start: 0.8528 (t80) cc_final: 0.8319 (t80) REVERT: o 58 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8214 (mp10) REVERT: q 43 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6554 (mp0) REVERT: q 74 LEU cc_start: 0.8931 (mt) cc_final: 0.8655 (mm) REVERT: s 50 ASP cc_start: 0.8335 (t0) cc_final: 0.7987 (t0) REVERT: t 7 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8121 (mt-10) outliers start: 106 outliers final: 45 residues processed: 707 average time/residue: 2.7517 time to fit residues: 2471.5737 Evaluate side-chains 651 residues out of total 4804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 596 time to evaluate : 5.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 148 PHE Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 237 THR Chi-restraints excluded: chain H residue 463 LYS Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain M residue 138 ILE Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain O residue 58 GLN Chi-restraints excluded: chain O residue 70 SER Chi-restraints excluded: chain O residue 86 ASP Chi-restraints excluded: chain P residue 28 GLU Chi-restraints excluded: chain Q residue 24 CYS Chi-restraints excluded: chain Q residue 43 GLU Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 59 SER Chi-restraints excluded: chain a residue 112 ASP Chi-restraints excluded: chain a residue 313 THR Chi-restraints excluded: chain a residue 338 SER Chi-restraints excluded: chain d residue 3 HIS Chi-restraints excluded: chain d residue 83 SER Chi-restraints excluded: chain d residue 169 ASP Chi-restraints excluded: chain d residue 174 SER Chi-restraints excluded: chain e residue 86 SER Chi-restraints excluded: chain f residue 14 ILE Chi-restraints excluded: chain f residue 226 ILE Chi-restraints excluded: chain f residue 263 SER Chi-restraints excluded: chain f residue 264 ILE Chi-restraints excluded: chain h residue 233 LEU Chi-restraints excluded: chain h residue 343 GLN Chi-restraints excluded: chain h residue 450 GLN Chi-restraints excluded: chain h residue 463 LYS Chi-restraints excluded: chain i residue 23 LYS Chi-restraints excluded: chain j residue 68 SER Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain m residue 138 ILE Chi-restraints excluded: chain m residue 165 THR Chi-restraints excluded: chain n residue 31 ASN Chi-restraints excluded: chain o residue 58 GLN Chi-restraints excluded: chain o residue 70 SER Chi-restraints excluded: chain q residue 24 CYS Chi-restraints excluded: chain q residue 43 GLU Chi-restraints excluded: chain q residue 58 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 425 optimal weight: 2.9990 chunk 289 optimal weight: 0.1980 chunk 7 optimal weight: 3.9990 chunk 380 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 435 optimal weight: 3.9990 chunk 352 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 260 optimal weight: 2.9990 chunk 458 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 HIS I 21 ASN L 37 ASN L 56 ASN ** f 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 21 ASN l 37 ASN l 56 ASN q 82 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 48995 Z= 0.204 Angle : 0.596 32.518 66058 Z= 0.268 Chirality : 0.037 0.158 6811 Planarity : 0.004 0.072 8081 Dihedral : 15.168 141.636 8711 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.90 % Allowed : 13.20 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: 1.39 (0.12), residues: 5382 helix: 1.73 (0.09), residues: 3154 sheet: 0.28 (0.45), residues: 96 loop : -0.21 (0.14), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 404 HIS 0.004 0.001 HIS f 70 PHE 0.011 0.001 PHE g 37 TYR 0.020 0.001 TYR l 22 ARG 0.010 0.000 ARG q 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10764 Ramachandran restraints generated. 5382 Oldfield, 0 Emsley, 5382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10764 Ramachandran restraints generated. 5382 Oldfield, 0 Emsley, 5382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 4804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 621 time to evaluate : 5.779 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: A 26 GLN cc_start: 0.7420 (tm-30) cc_final: 0.7171 (tp-100) REVERT: F 14 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7726 (mp) REVERT: G 28 MET cc_start: 0.8405 (mtt) cc_final: 0.8052 (mtt) REVERT: G 54 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7915 (mtm180) REVERT: H 463 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8171 (mtpm) REVERT: L 22 TYR cc_start: 0.8530 (m-80) cc_final: 0.8194 (m-80) REVERT: M 106 TYR cc_start: 0.8525 (t80) cc_final: 0.8266 (t80) REVERT: O 58 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8161 (mp10) REVERT: Q 43 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.6677 (mp0) REVERT: Q 74 LEU cc_start: 0.8878 (mt) cc_final: 0.8622 (mm) REVERT: S 50 ASP cc_start: 0.8208 (t70) cc_final: 0.7714 (t0) REVERT: T 7 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8138 (mt-10) REVERT: a 131 GLU cc_start: 0.7692 (tp30) cc_final: 0.7482 (tp30) REVERT: a 441 LEU cc_start: 0.9057 (tp) cc_final: 0.8818 (tt) REVERT: d 3 HIS cc_start: 0.7808 (OUTLIER) cc_final: 0.7540 (t-90) REVERT: g 28 MET cc_start: 0.8447 (mtt) cc_final: 0.8114 (mtt) REVERT: h 146 MET cc_start: 0.8615 (mtm) cc_final: 0.8378 (mtt) REVERT: h 463 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8140 (mtpm) REVERT: l 22 TYR cc_start: 0.8523 (m-80) cc_final: 0.8226 (m-80) REVERT: m 106 TYR cc_start: 0.8536 (t80) cc_final: 0.8272 (t80) REVERT: o 58 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8182 (mp10) REVERT: o 73 LYS cc_start: 0.8517 (mmmm) cc_final: 0.8125 (mmtm) REVERT: q 43 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6640 (mp0) REVERT: q 74 LEU cc_start: 0.8771 (mt) cc_final: 0.8501 (mm) REVERT: s 50 ASP cc_start: 0.8351 (t0) cc_final: 0.8001 (t0) REVERT: t 7 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8113 (mt-10) outliers start: 91 outliers final: 46 residues processed: 666 average time/residue: 2.7747 time to fit residues: 2348.0265 Evaluate side-chains 656 residues out of total 4804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 601 time to evaluate : 5.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 54 ARG Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 463 LYS Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain M residue 138 ILE Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain O residue 58 GLN Chi-restraints excluded: chain P residue 28 GLU Chi-restraints excluded: chain Q residue 43 GLU Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain R residue 14 GLU Chi-restraints excluded: chain S residue 40 MET Chi-restraints excluded: chain T residue 56 SER Chi-restraints excluded: chain a residue 313 THR Chi-restraints excluded: chain a residue 338 SER Chi-restraints excluded: chain a residue 384 ILE Chi-restraints excluded: chain d residue 3 HIS Chi-restraints excluded: chain d residue 83 SER Chi-restraints excluded: chain d residue 169 ASP Chi-restraints excluded: chain e residue 22 GLU Chi-restraints excluded: chain e residue 26 ASP Chi-restraints excluded: chain e residue 86 SER Chi-restraints excluded: chain f residue 68 LEU Chi-restraints excluded: chain f residue 226 ILE Chi-restraints excluded: chain f residue 264 ILE Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain h residue 233 LEU Chi-restraints excluded: chain h residue 343 GLN Chi-restraints excluded: chain h residue 463 LYS Chi-restraints excluded: chain i residue 23 LYS Chi-restraints excluded: chain j residue 68 SER Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain m residue 138 ILE Chi-restraints excluded: chain m residue 165 THR Chi-restraints excluded: chain n residue 31 ASN Chi-restraints excluded: chain o residue 58 GLN Chi-restraints excluded: chain q residue 43 GLU Chi-restraints excluded: chain q residue 58 ASP Chi-restraints excluded: chain r residue 14 GLU Chi-restraints excluded: chain s residue 40 MET Chi-restraints excluded: chain t residue 56 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 171 optimal weight: 5.9990 chunk 459 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 299 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 510 optimal weight: 2.9990 chunk 424 optimal weight: 2.9990 chunk 236 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 268 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 21 ASN L 37 ASN L 56 ASN P 63 ASN Q 65 ASN T 17 HIS i 21 ASN l 37 ASN l 56 ASN m 130 HIS p 63 ASN t 17 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 48995 Z= 0.314 Angle : 0.630 32.631 66058 Z= 0.288 Chirality : 0.039 0.182 6811 Planarity : 0.004 0.048 8081 Dihedral : 15.072 142.094 8711 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.02 % Allowed : 13.49 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.34 % 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: 1.36 (0.12), residues: 5382 helix: 1.64 (0.09), residues: 3187 sheet: 0.16 (0.44), residues: 100 loop : -0.13 (0.14), residues: 2095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 404 HIS 0.005 0.001 HIS Q 20 PHE 0.015 0.001 PHE F 148 TYR 0.023 0.002 TYR L 22 ARG 0.004 0.000 ARG A 398 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10764 Ramachandran restraints generated. 5382 Oldfield, 0 Emsley, 5382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10764 Ramachandran restraints generated. 5382 Oldfield, 0 Emsley, 5382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 4804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 615 time to evaluate : 5.753 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: A 26 GLN cc_start: 0.7508 (tm-30) cc_final: 0.7258 (tp-100) REVERT: F 14 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.7800 (mp) REVERT: G 28 MET cc_start: 0.8432 (mtt) cc_final: 0.8070 (mtt) REVERT: G 54 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7937 (mtm180) REVERT: H 237 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8388 (m) REVERT: H 463 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8166 (mtpm) REVERT: K 85 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7336 (mm-30) REVERT: L 22 TYR cc_start: 0.8595 (m-80) cc_final: 0.8240 (m-80) REVERT: M 106 TYR cc_start: 0.8536 (t80) cc_final: 0.8243 (t80) REVERT: O 58 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8257 (mp10) REVERT: Q 43 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6667 (mp0) REVERT: Q 74 LEU cc_start: 0.8763 (mt) cc_final: 0.8483 (mm) REVERT: S 50 ASP cc_start: 0.8251 (t70) cc_final: 0.7733 (t0) REVERT: T 7 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8154 (mt-10) REVERT: a 131 GLU cc_start: 0.7746 (tp30) cc_final: 0.7526 (tp30) REVERT: f 14 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.7889 (mp) REVERT: g 28 MET cc_start: 0.8455 (mtt) cc_final: 0.8116 (mtt) REVERT: h 237 THR cc_start: 0.8676 (OUTLIER) cc_final: 0.8424 (m) REVERT: h 463 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8160 (mtpm) REVERT: k 85 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7338 (mm-30) REVERT: l 22 TYR cc_start: 0.8628 (m-80) cc_final: 0.8321 (m-80) REVERT: m 106 TYR cc_start: 0.8551 (t80) cc_final: 0.8238 (t80) REVERT: o 58 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8239 (mp10) REVERT: q 43 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6636 (mp0) REVERT: q 74 LEU cc_start: 0.8766 (mt) cc_final: 0.8501 (mm) REVERT: s 50 ASP cc_start: 0.8443 (t0) cc_final: 0.8105 (t0) REVERT: t 7 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8163 (mt-10) outliers start: 97 outliers final: 57 residues processed: 672 average time/residue: 2.7092 time to fit residues: 2307.1727 Evaluate side-chains 658 residues out of total 4804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 590 time to evaluate : 5.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 148 PHE Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 54 ARG Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 237 THR Chi-restraints excluded: chain H residue 450 GLN Chi-restraints excluded: chain H residue 463 LYS Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain M residue 138 ILE Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain O residue 58 GLN Chi-restraints excluded: chain O residue 70 SER Chi-restraints excluded: chain P residue 28 GLU Chi-restraints excluded: chain Q residue 43 GLU Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 59 SER Chi-restraints excluded: chain S residue 40 MET Chi-restraints excluded: chain T residue 56 SER Chi-restraints excluded: chain a residue 112 ASP Chi-restraints excluded: chain a residue 313 THR Chi-restraints excluded: chain a residue 338 SER Chi-restraints excluded: chain d residue 83 SER Chi-restraints excluded: chain d residue 167 THR Chi-restraints excluded: chain d residue 169 ASP Chi-restraints excluded: chain d residue 174 SER Chi-restraints excluded: chain e residue 22 GLU Chi-restraints excluded: chain e residue 86 SER Chi-restraints excluded: chain f residue 14 ILE Chi-restraints excluded: chain f residue 144 THR Chi-restraints excluded: chain f residue 226 ILE Chi-restraints excluded: chain f residue 263 SER Chi-restraints excluded: chain f residue 264 ILE Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain h residue 233 LEU Chi-restraints excluded: chain h residue 237 THR Chi-restraints excluded: chain h residue 343 GLN Chi-restraints excluded: chain h residue 450 GLN Chi-restraints excluded: chain h residue 463 LYS Chi-restraints excluded: chain i residue 23 LYS Chi-restraints excluded: chain j residue 68 SER Chi-restraints excluded: chain l residue 21 LEU Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain m residue 138 ILE Chi-restraints excluded: chain m residue 165 THR Chi-restraints excluded: chain n residue 31 ASN Chi-restraints excluded: chain o residue 58 GLN Chi-restraints excluded: chain o residue 70 SER Chi-restraints excluded: chain q residue 43 GLU Chi-restraints excluded: chain q residue 58 ASP Chi-restraints excluded: chain s residue 40 MET Chi-restraints excluded: chain t residue 56 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 492 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 291 optimal weight: 4.9990 chunk 373 optimal weight: 2.9990 chunk 289 optimal weight: 0.3980 chunk 430 optimal weight: 2.9990 chunk 285 optimal weight: 1.9990 chunk 508 optimal weight: 4.9990 chunk 318 optimal weight: 2.9990 chunk 310 optimal weight: 0.5980 chunk 234 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 125 ASN L 37 ASN L 56 ASN M 130 HIS P 63 ASN ** f 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 88 HIS l 37 ASN l 56 ASN p 63 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 48995 Z= 0.177 Angle : 0.595 32.640 66058 Z= 0.268 Chirality : 0.036 0.173 6811 Planarity : 0.004 0.081 8081 Dihedral : 14.591 140.120 8711 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.52 % Allowed : 14.58 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.34 % 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: 1.56 (0.12), residues: 5382 helix: 1.82 (0.09), residues: 3167 sheet: 0.21 (0.44), residues: 100 loop : -0.06 (0.14), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 404 HIS 0.004 0.001 HIS F 70 PHE 0.011 0.001 PHE F 148 TYR 0.020 0.001 TYR L 22 ARG 0.009 0.000 ARG Q 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10764 Ramachandran restraints generated. 5382 Oldfield, 0 Emsley, 5382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10764 Ramachandran restraints generated. 5382 Oldfield, 0 Emsley, 5382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 4804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 618 time to evaluate : 5.769 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: A 26 GLN cc_start: 0.7487 (tm-30) cc_final: 0.7252 (tp-100) REVERT: A 363 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7184 (mp0) REVERT: G 28 MET cc_start: 0.8391 (mtt) cc_final: 0.8037 (mtt) REVERT: G 54 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7888 (mtm180) REVERT: H 463 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8166 (mtpm) REVERT: L 22 TYR cc_start: 0.8545 (m-80) cc_final: 0.8208 (m-80) REVERT: M 106 TYR cc_start: 0.8525 (t80) cc_final: 0.8259 (t80) REVERT: O 58 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8171 (mp10) REVERT: P 103 ASP cc_start: 0.8088 (m-30) cc_final: 0.7664 (m-30) REVERT: Q 22 ARG cc_start: 0.7682 (mtm110) cc_final: 0.7207 (mtm-85) REVERT: Q 43 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6664 (mp0) REVERT: Q 74 LEU cc_start: 0.8715 (mt) cc_final: 0.8461 (mm) REVERT: R 14 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8239 (mt-10) REVERT: S 50 ASP cc_start: 0.8233 (t70) cc_final: 0.7742 (t0) REVERT: T 7 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8129 (mt-10) REVERT: a 131 GLU cc_start: 0.7731 (tp30) cc_final: 0.7520 (tp30) REVERT: a 363 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7203 (mp0) REVERT: f 262 LYS cc_start: 0.8657 (mmtp) cc_final: 0.8438 (mmtt) REVERT: g 28 MET cc_start: 0.8421 (mtt) cc_final: 0.8088 (mtt) REVERT: h 146 MET cc_start: 0.8635 (mtm) cc_final: 0.8333 (mtt) REVERT: h 463 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8158 (mtpm) REVERT: l 22 TYR cc_start: 0.8555 (m-80) cc_final: 0.8257 (m-80) REVERT: m 106 TYR cc_start: 0.8559 (t80) cc_final: 0.8289 (t80) REVERT: o 58 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8209 (mp10) REVERT: q 43 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6667 (mp0) REVERT: s 50 ASP cc_start: 0.8439 (t0) cc_final: 0.8121 (t0) REVERT: t 7 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8123 (mt-10) outliers start: 73 outliers final: 47 residues processed: 653 average time/residue: 2.7261 time to fit residues: 2261.6755 Evaluate side-chains 654 residues out of total 4804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 597 time to evaluate : 5.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 54 ARG Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 450 GLN Chi-restraints excluded: chain H residue 463 LYS Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain M residue 138 ILE Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain O residue 58 GLN Chi-restraints excluded: chain O residue 70 SER Chi-restraints excluded: chain P residue 28 GLU Chi-restraints excluded: chain Q residue 43 GLU Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain R residue 14 GLU Chi-restraints excluded: chain S residue 40 MET Chi-restraints excluded: chain T residue 56 SER Chi-restraints excluded: chain a residue 313 THR Chi-restraints excluded: chain a residue 363 GLU Chi-restraints excluded: chain d residue 83 SER Chi-restraints excluded: chain d residue 169 ASP Chi-restraints excluded: chain e residue 22 GLU Chi-restraints excluded: chain e residue 26 ASP Chi-restraints excluded: chain e residue 86 SER Chi-restraints excluded: chain f residue 144 THR Chi-restraints excluded: chain f residue 226 ILE Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain h residue 194 MET Chi-restraints excluded: chain h residue 233 LEU Chi-restraints excluded: chain h residue 450 GLN Chi-restraints excluded: chain h residue 463 LYS Chi-restraints excluded: chain i residue 23 LYS Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain j residue 68 SER Chi-restraints excluded: chain l residue 21 LEU Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain m residue 138 ILE Chi-restraints excluded: chain m residue 165 THR Chi-restraints excluded: chain n residue 31 ASN Chi-restraints excluded: chain o residue 58 GLN Chi-restraints excluded: chain q residue 43 GLU Chi-restraints excluded: chain q residue 58 ASP Chi-restraints excluded: chain s residue 40 MET Chi-restraints excluded: chain t residue 56 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 314 optimal weight: 8.9990 chunk 203 optimal weight: 0.9980 chunk 303 optimal weight: 2.9990 chunk 153 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 323 optimal weight: 2.9990 chunk 346 optimal weight: 0.9980 chunk 251 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 400 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 125 ASN L 37 ASN L 56 ASN l 37 ASN l 56 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 48995 Z= 0.265 Angle : 0.613 32.545 66058 Z= 0.277 Chirality : 0.038 0.169 6811 Planarity : 0.004 0.049 8081 Dihedral : 14.482 140.545 8711 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.62 % Allowed : 14.60 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: 1.57 (0.12), residues: 5382 helix: 1.80 (0.09), residues: 3179 sheet: 0.26 (0.44), residues: 100 loop : -0.02 (0.14), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 404 HIS 0.004 0.001 HIS F 70 PHE 0.012 0.001 PHE g 37 TYR 0.022 0.001 TYR L 22 ARG 0.010 0.000 ARG Q 22 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10764 Ramachandran restraints generated. 5382 Oldfield, 0 Emsley, 5382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10764 Ramachandran restraints generated. 5382 Oldfield, 0 Emsley, 5382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 4804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 605 time to evaluate : 6.694 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: A 26 GLN cc_start: 0.7523 (tm-30) cc_final: 0.7289 (tp-100) REVERT: A 363 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7216 (mp0) REVERT: G 28 MET cc_start: 0.8403 (mtt) cc_final: 0.8043 (mtt) REVERT: G 54 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7899 (mtm180) REVERT: H 463 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8186 (mtpm) REVERT: K 85 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7332 (mm-30) REVERT: L 22 TYR cc_start: 0.8574 (m-80) cc_final: 0.8265 (m-80) REVERT: M 106 TYR cc_start: 0.8542 (t80) cc_final: 0.8255 (t80) REVERT: O 58 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8193 (mp10) REVERT: Q 22 ARG cc_start: 0.7605 (mtm110) cc_final: 0.7243 (mtm-85) REVERT: Q 43 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6684 (mp0) REVERT: Q 74 LEU cc_start: 0.8713 (mt) cc_final: 0.8457 (mm) REVERT: S 50 ASP cc_start: 0.8255 (t70) cc_final: 0.7754 (t0) REVERT: T 7 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8121 (mt-10) REVERT: a 131 GLU cc_start: 0.7751 (tp30) cc_final: 0.7544 (tp30) REVERT: a 363 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7214 (mp0) REVERT: g 28 MET cc_start: 0.8443 (mtt) cc_final: 0.8106 (mtt) REVERT: h 85 LYS cc_start: 0.8473 (mmmm) cc_final: 0.8263 (mmmm) REVERT: h 463 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8197 (mtpm) REVERT: k 85 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7340 (mm-30) REVERT: l 22 TYR cc_start: 0.8567 (m-80) cc_final: 0.8206 (m-80) REVERT: m 106 TYR cc_start: 0.8557 (t80) cc_final: 0.8266 (t80) REVERT: o 58 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8233 (mp10) REVERT: q 43 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6643 (mp0) REVERT: s 50 ASP cc_start: 0.8460 (t0) cc_final: 0.8142 (t0) REVERT: t 7 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8095 (mt-10) outliers start: 78 outliers final: 55 residues processed: 646 average time/residue: 2.7075 time to fit residues: 2229.5000 Evaluate side-chains 656 residues out of total 4804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 592 time to evaluate : 5.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 54 ARG Chi-restraints excluded: chain H residue 194 MET Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 450 GLN Chi-restraints excluded: chain H residue 463 LYS Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain M residue 138 ILE Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain O residue 58 GLN Chi-restraints excluded: chain O residue 70 SER Chi-restraints excluded: chain P residue 28 GLU Chi-restraints excluded: chain Q residue 43 GLU Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain S residue 40 MET Chi-restraints excluded: chain T residue 56 SER Chi-restraints excluded: chain a residue 112 ASP Chi-restraints excluded: chain a residue 313 THR Chi-restraints excluded: chain a residue 338 SER Chi-restraints excluded: chain a residue 363 GLU Chi-restraints excluded: chain d residue 83 SER Chi-restraints excluded: chain d residue 169 ASP Chi-restraints excluded: chain e residue 22 GLU Chi-restraints excluded: chain e residue 86 SER Chi-restraints excluded: chain f residue 144 THR Chi-restraints excluded: chain f residue 226 ILE Chi-restraints excluded: chain f residue 263 SER Chi-restraints excluded: chain f residue 264 ILE Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain h residue 194 MET Chi-restraints excluded: chain h residue 233 LEU Chi-restraints excluded: chain h residue 450 GLN Chi-restraints excluded: chain h residue 463 LYS Chi-restraints excluded: chain i residue 23 LYS Chi-restraints excluded: chain i residue 70 LEU Chi-restraints excluded: chain j residue 68 SER Chi-restraints excluded: chain l residue 21 LEU Chi-restraints excluded: chain l residue 29 ILE Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain m residue 138 ILE Chi-restraints excluded: chain m residue 165 THR Chi-restraints excluded: chain n residue 31 ASN Chi-restraints excluded: chain o residue 58 GLN Chi-restraints excluded: chain q residue 43 GLU Chi-restraints excluded: chain q residue 58 ASP Chi-restraints excluded: chain s residue 40 MET Chi-restraints excluded: chain t residue 56 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 462 optimal weight: 2.9990 chunk 487 optimal weight: 3.9990 chunk 444 optimal weight: 4.9990 chunk 474 optimal weight: 0.9980 chunk 285 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 chunk 372 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 428 optimal weight: 0.9980 chunk 448 optimal weight: 1.9990 chunk 472 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 125 ASN L 37 ASN L 56 ASN f 125 ASN l 37 ASN l 56 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 48995 Z= 0.219 Angle : 0.605 32.572 66058 Z= 0.273 Chirality : 0.037 0.186 6811 Planarity : 0.004 0.104 8081 Dihedral : 14.255 140.603 8711 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.50 % Allowed : 14.74 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: 1.65 (0.12), residues: 5382 helix: 1.86 (0.09), residues: 3180 sheet: 0.14 (0.43), residues: 104 loop : 0.03 (0.14), residues: 2098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 404 HIS 0.004 0.001 HIS f 70 PHE 0.011 0.001 PHE i 55 TYR 0.021 0.001 TYR L 22 ARG 0.014 0.000 ARG Q 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10764 Ramachandran restraints generated. 5382 Oldfield, 0 Emsley, 5382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10764 Ramachandran restraints generated. 5382 Oldfield, 0 Emsley, 5382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 4804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 614 time to evaluate : 5.901 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: A 26 GLN cc_start: 0.7534 (tm-30) cc_final: 0.7302 (tp-100) REVERT: A 363 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7242 (mp0) REVERT: G 28 MET cc_start: 0.8399 (mtt) cc_final: 0.8031 (mtt) REVERT: G 54 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7888 (mtm180) REVERT: H 463 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8166 (mtpm) REVERT: K 85 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7332 (mm-30) REVERT: L 22 TYR cc_start: 0.8552 (m-80) cc_final: 0.8235 (m-80) REVERT: M 106 TYR cc_start: 0.8531 (t80) cc_final: 0.8249 (t80) REVERT: O 58 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8170 (mp10) REVERT: Q 19 ARG cc_start: 0.7910 (mtm110) cc_final: 0.7699 (mtm-85) REVERT: Q 22 ARG cc_start: 0.7644 (mtm110) cc_final: 0.7182 (mtm-85) REVERT: Q 43 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6658 (mp0) REVERT: Q 74 LEU cc_start: 0.8726 (mt) cc_final: 0.8473 (mm) REVERT: S 50 ASP cc_start: 0.8256 (t70) cc_final: 0.7762 (t0) REVERT: T 7 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8111 (mt-10) REVERT: a 131 GLU cc_start: 0.7713 (tp30) cc_final: 0.7511 (tp30) REVERT: a 363 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7264 (mp0) REVERT: g 28 MET cc_start: 0.8437 (mtt) cc_final: 0.8093 (mtt) REVERT: h 85 LYS cc_start: 0.8472 (mmmm) cc_final: 0.8265 (mmmm) REVERT: h 463 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8183 (mtpm) REVERT: k 85 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7399 (mm-30) REVERT: l 22 TYR cc_start: 0.8555 (m-80) cc_final: 0.8194 (m-80) REVERT: m 106 TYR cc_start: 0.8548 (t80) cc_final: 0.8279 (t80) REVERT: o 34 LYS cc_start: 0.8713 (tptt) cc_final: 0.8356 (tppp) REVERT: o 58 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.8203 (mp10) REVERT: q 43 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6650 (mp0) REVERT: s 50 ASP cc_start: 0.8439 (t0) cc_final: 0.8132 (t0) REVERT: t 7 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8087 (mt-10) outliers start: 72 outliers final: 48 residues processed: 652 average time/residue: 2.7324 time to fit residues: 2268.4447 Evaluate side-chains 655 residues out of total 4804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 598 time to evaluate : 5.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 54 ARG Chi-restraints excluded: chain H residue 194 MET Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 450 GLN Chi-restraints excluded: chain H residue 463 LYS Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain O residue 58 GLN Chi-restraints excluded: chain O residue 70 SER Chi-restraints excluded: chain P residue 28 GLU Chi-restraints excluded: chain Q residue 43 GLU Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 59 SER Chi-restraints excluded: chain S residue 40 MET Chi-restraints excluded: chain T residue 56 SER Chi-restraints excluded: chain a residue 112 ASP Chi-restraints excluded: chain a residue 313 THR Chi-restraints excluded: chain a residue 338 SER Chi-restraints excluded: chain a residue 363 GLU Chi-restraints excluded: chain d residue 83 SER Chi-restraints excluded: chain d residue 167 THR Chi-restraints excluded: chain e residue 22 GLU Chi-restraints excluded: chain e residue 86 SER Chi-restraints excluded: chain f residue 144 THR Chi-restraints excluded: chain f residue 226 ILE Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain h residue 194 MET Chi-restraints excluded: chain h residue 233 LEU Chi-restraints excluded: chain h residue 450 GLN Chi-restraints excluded: chain h residue 463 LYS Chi-restraints excluded: chain i residue 23 LYS Chi-restraints excluded: chain j residue 68 SER Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain m residue 138 ILE Chi-restraints excluded: chain m residue 165 THR Chi-restraints excluded: chain n residue 31 ASN Chi-restraints excluded: chain o residue 58 GLN Chi-restraints excluded: chain o residue 70 SER Chi-restraints excluded: chain q residue 43 GLU Chi-restraints excluded: chain q residue 58 ASP Chi-restraints excluded: chain s residue 40 MET Chi-restraints excluded: chain t residue 56 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 311 optimal weight: 0.7980 chunk 501 optimal weight: 2.9990 chunk 306 optimal weight: 0.9980 chunk 237 optimal weight: 4.9990 chunk 348 optimal weight: 2.9990 chunk 526 optimal weight: 2.9990 chunk 484 optimal weight: 3.9990 chunk 418 optimal weight: 0.5980 chunk 43 optimal weight: 0.4980 chunk 323 optimal weight: 3.9990 chunk 256 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 125 ASN L 37 ASN L 56 ASN f 125 ASN l 37 ASN l 56 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 48995 Z= 0.207 Angle : 0.603 32.484 66058 Z= 0.271 Chirality : 0.037 0.174 6811 Planarity : 0.004 0.071 8081 Dihedral : 14.016 140.033 8711 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.42 % Allowed : 14.99 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: 1.74 (0.12), residues: 5382 helix: 1.93 (0.09), residues: 3174 sheet: 0.34 (0.44), residues: 100 loop : 0.07 (0.14), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 404 HIS 0.004 0.001 HIS F 70 PHE 0.011 0.001 PHE g 37 TYR 0.021 0.001 TYR L 22 ARG 0.013 0.000 ARG Q 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10764 Ramachandran restraints generated. 5382 Oldfield, 0 Emsley, 5382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10764 Ramachandran restraints generated. 5382 Oldfield, 0 Emsley, 5382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 4804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 610 time to evaluate : 5.934 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: A 26 GLN cc_start: 0.7539 (tm-30) cc_final: 0.7313 (tp-100) REVERT: A 363 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7267 (mp0) REVERT: G 28 MET cc_start: 0.8396 (mtt) cc_final: 0.8025 (mtt) REVERT: G 54 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7889 (mtm180) REVERT: H 463 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8193 (mtpm) REVERT: K 85 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7328 (mm-30) REVERT: L 22 TYR cc_start: 0.8545 (m-80) cc_final: 0.8185 (m-80) REVERT: M 106 TYR cc_start: 0.8533 (t80) cc_final: 0.8251 (t80) REVERT: O 58 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8177 (mp10) REVERT: Q 19 ARG cc_start: 0.7834 (mtm110) cc_final: 0.7566 (mtm-85) REVERT: Q 22 ARG cc_start: 0.7658 (mtm110) cc_final: 0.7209 (mtm-85) REVERT: Q 43 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6657 (mp0) REVERT: Q 74 LEU cc_start: 0.8721 (mt) cc_final: 0.8484 (mm) REVERT: S 50 ASP cc_start: 0.8249 (t70) cc_final: 0.7776 (t0) REVERT: T 7 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8104 (mt-10) REVERT: a 363 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: g 28 MET cc_start: 0.8446 (mtt) cc_final: 0.8080 (mtt) REVERT: k 85 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7406 (mm-30) REVERT: l 22 TYR cc_start: 0.8544 (m-80) cc_final: 0.8181 (m-80) REVERT: m 106 TYR cc_start: 0.8551 (t80) cc_final: 0.8279 (t80) REVERT: o 34 LYS cc_start: 0.8715 (tptt) cc_final: 0.8357 (tppp) REVERT: q 43 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6646 (mp0) REVERT: s 50 ASP cc_start: 0.8437 (t0) cc_final: 0.8140 (t0) REVERT: t 7 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8077 (mt-10) outliers start: 68 outliers final: 46 residues processed: 644 average time/residue: 2.6892 time to fit residues: 2213.3846 Evaluate side-chains 644 residues out of total 4804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 591 time to evaluate : 5.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain D residue 83 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 144 THR Chi-restraints excluded: chain F residue 263 SER Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 54 ARG Chi-restraints excluded: chain H residue 194 MET Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 450 GLN Chi-restraints excluded: chain H residue 463 LYS Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain O residue 58 GLN Chi-restraints excluded: chain O residue 70 SER Chi-restraints excluded: chain P residue 28 GLU Chi-restraints excluded: chain Q residue 43 GLU Chi-restraints excluded: chain Q residue 58 ASP Chi-restraints excluded: chain Q residue 59 SER Chi-restraints excluded: chain S residue 40 MET Chi-restraints excluded: chain T residue 56 SER Chi-restraints excluded: chain a residue 112 ASP Chi-restraints excluded: chain a residue 313 THR Chi-restraints excluded: chain a residue 338 SER Chi-restraints excluded: chain a residue 363 GLU Chi-restraints excluded: chain d residue 83 SER Chi-restraints excluded: chain d residue 167 THR Chi-restraints excluded: chain e residue 22 GLU Chi-restraints excluded: chain e residue 86 SER Chi-restraints excluded: chain f residue 144 THR Chi-restraints excluded: chain f residue 226 ILE Chi-restraints excluded: chain g residue 22 SER Chi-restraints excluded: chain h residue 194 MET Chi-restraints excluded: chain h residue 233 LEU Chi-restraints excluded: chain h residue 450 GLN Chi-restraints excluded: chain i residue 23 LYS Chi-restraints excluded: chain j residue 68 SER Chi-restraints excluded: chain l residue 29 ILE Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain m residue 138 ILE Chi-restraints excluded: chain m residue 165 THR Chi-restraints excluded: chain n residue 31 ASN Chi-restraints excluded: chain o residue 70 SER Chi-restraints excluded: chain q residue 43 GLU Chi-restraints excluded: chain q residue 58 ASP Chi-restraints excluded: chain s residue 40 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 332 optimal weight: 5.9990 chunk 446 optimal weight: 3.9990 chunk 128 optimal weight: 0.5980 chunk 386 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 116 optimal weight: 8.9990 chunk 419 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 430 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 125 ASN L 37 ASN L 56 ASN l 37 ASN l 56 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.111461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.085141 restraints weight = 194436.520| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.53 r_work: 0.2866 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 48995 Z= 0.236 Angle : 0.610 32.450 66058 Z= 0.276 Chirality : 0.037 0.196 6811 Planarity : 0.004 0.072 8081 Dihedral : 13.952 140.325 8711 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.31 % Allowed : 15.24 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % 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: 1.73 (0.12), residues: 5382 helix: 1.91 (0.09), residues: 3174 sheet: 0.35 (0.44), residues: 100 loop : 0.08 (0.14), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 404 HIS 0.005 0.001 HIS H 451 PHE 0.012 0.001 PHE g 37 TYR 0.022 0.001 TYR L 22 ARG 0.013 0.000 ARG Q 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33321.43 seconds wall clock time: 573 minutes 22.91 seconds (34402.91 seconds total)