Starting phenix.real_space_refine on Sat Feb 24 19:16:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pep_20317/02_2024/6pep_20317_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pep_20317/02_2024/6pep_20317.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pep_20317/02_2024/6pep_20317.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pep_20317/02_2024/6pep_20317.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pep_20317/02_2024/6pep_20317_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pep_20317/02_2024/6pep_20317_neut.pdb" } resolution = 3.8 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= -0.012 sd= 0.211 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 212 5.16 5 C 29517 2.51 5 N 7462 2.21 5 O 8263 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ASP 93": "OD1" <-> "OD2" Residue "0 GLU 94": "OE1" <-> "OE2" Residue "0 ASP 97": "OD1" <-> "OD2" Residue "0 TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 109": "NH1" <-> "NH2" Residue "0 GLU 110": "OE1" <-> "OE2" Residue "0 GLU 116": "OE1" <-> "OE2" Residue "0 PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 4": "OD1" <-> "OD2" Residue "1 PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 70": "OD1" <-> "OD2" Residue "1 PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 77": "OD1" <-> "OD2" Residue "1 ASP 84": "OD1" <-> "OD2" Residue "1 ASP 97": "OD1" <-> "OD2" Residue "1 ASP 108": "OD1" <-> "OD2" Residue "1 ARG 109": "NH1" <-> "NH2" Residue "1 GLU 154": "OE1" <-> "OE2" Residue "1 TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 206": "OD1" <-> "OD2" Residue "1 TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ASP 221": "OD1" <-> "OD2" Residue "2 PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 76": "OE1" <-> "OE2" Residue "2 GLU 94": "OE1" <-> "OE2" Residue "2 PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 84": "OD1" <-> "OD2" Residue "3 ASP 93": "OD1" <-> "OD2" Residue "3 TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 109": "NH1" <-> "NH2" Residue "3 PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 206": "OD1" <-> "OD2" Residue "4 PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 84": "OD1" <-> "OD2" Residue "4 GLU 94": "OE1" <-> "OE2" Residue "4 TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 137": "OE1" <-> "OE2" Residue "4 GLU 154": "OE1" <-> "OE2" Residue "4 ASP 173": "OD1" <-> "OD2" Residue "5 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 148": "OD1" <-> "OD2" Residue "5 ASP 158": "OD1" <-> "OD2" Residue "5 GLU 196": "OE1" <-> "OE2" Residue "5 ARG 204": "NH1" <-> "NH2" Residue "5 PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 3": "OD1" <-> "OD2" Residue "7 GLU 44": "OE1" <-> "OE2" Residue "7 PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 69": "OE1" <-> "OE2" Residue "7 ARG 76": "NH1" <-> "NH2" Residue "7 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 69": "OE1" <-> "OE2" Residue "8 ARG 76": "NH1" <-> "NH2" Residue "9 GLU 69": "OE1" <-> "OE2" Residue "9 ARG 76": "NH1" <-> "NH2" Residue "9 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 39": "OD1" <-> "OD2" Residue "A ASP 40": "OD1" <-> "OD2" Residue "A TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A ASP 141": "OD1" <-> "OD2" Residue "A PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AM TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AM ARG 89": "NH1" <-> "NH2" Residue "AN ASP 63": "OD1" <-> "OD2" Residue "AN GLU 72": "OE1" <-> "OE2" Residue "AN TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AN GLU 96": "OE1" <-> "OE2" Residue "AO ASP 25": "OD1" <-> "OD2" Residue "AO PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AO ARG 54": "NH1" <-> "NH2" Residue "AO ASP 57": "OD1" <-> "OD2" Residue "AO GLU 66": "OE1" <-> "OE2" Residue "AO ASP 76": "OD1" <-> "OD2" Residue "AO TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AO GLU 96": "OE1" <-> "OE2" Residue "AP ASP 30": "OD1" <-> "OD2" Residue "AP ARG 54": "NH1" <-> "NH2" Residue "AP ASP 57": "OD1" <-> "OD2" Residue "AP ASP 63": "OD1" <-> "OD2" Residue "AP GLU 72": "OE1" <-> "OE2" Residue "AP TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AQ ASP 25": "OD1" <-> "OD2" Residue "AQ ASP 30": "OD1" <-> "OD2" Residue "AQ ASP 31": "OD1" <-> "OD2" Residue "AQ ARG 32": "NH1" <-> "NH2" Residue "AQ ASP 47": "OD1" <-> "OD2" Residue "AQ ARG 54": "NH1" <-> "NH2" Residue "AQ ASP 57": "OD1" <-> "OD2" Residue "AQ GLU 66": "OE1" <-> "OE2" Residue "AQ GLU 72": "OE1" <-> "OE2" Residue "AQ ASP 76": "OD1" <-> "OD2" Residue "AQ TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AR ASP 25": "OD1" <-> "OD2" Residue "AR ASP 31": "OD1" <-> "OD2" Residue "AR ARG 54": "NH1" <-> "NH2" Residue "AR ASP 57": "OD1" <-> "OD2" Residue "AR GLU 72": "OE1" <-> "OE2" Residue "AR TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AS GLU 29": "OE1" <-> "OE2" Residue "AT GLU 29": "OE1" <-> "OE2" Residue "AU GLU 29": "OE1" <-> "OE2" Residue "AU ASP 32": "OD1" <-> "OD2" Residue "AV GLU 53": "OE1" <-> "OE2" Residue "AV ASP 70": "OD1" <-> "OD2" Residue "AW ASP 72": "OD1" <-> "OD2" Residue "AX ASP 17": "OD1" <-> "OD2" Residue "AX GLU 29": "OE1" <-> "OE2" Residue "AX TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AX GLU 53": "OE1" <-> "OE2" Residue "AX ASP 70": "OD1" <-> "OD2" Residue "AX ASP 72": "OD1" <-> "OD2" Residue "AX PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AY ASP 17": "OD1" <-> "OD2" Residue "AY ASP 21": "OD1" <-> "OD2" Residue "AY ASP 40": "OD1" <-> "OD2" Residue "AY GLU 53": "OE1" <-> "OE2" Residue "AY ASP 72": "OD1" <-> "OD2" Residue "AZ ASP 17": "OD1" <-> "OD2" Residue "B TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 115": "NH1" <-> "NH2" Residue "B ARG 139": "NH1" <-> "NH2" Residue "B PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 167": "OD1" <-> "OD2" Residue "BA ASP 11": "OD1" <-> "OD2" Residue "BA PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BA PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BB ASP 10": "OD1" <-> "OD2" Residue "BB PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BB ASP 17": "OD1" <-> "OD2" Residue "BC TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC ASP 10": "OD1" <-> "OD2" Residue "BC ASP 17": "OD1" <-> "OD2" Residue "BC GLU 53": "OE1" <-> "OE2" Residue "BC ASP 72": "OD1" <-> "OD2" Residue "BD ASP 10": "OD1" <-> "OD2" Residue "BD ASP 11": "OD1" <-> "OD2" Residue "BD GLU 53": "OE1" <-> "OE2" Residue "BE ASP 10": "OD1" <-> "OD2" Residue "BE PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BE ASP 17": "OD1" <-> "OD2" Residue "C ASP 39": "OD1" <-> "OD2" Residue "C ASP 40": "OD1" <-> "OD2" Residue "C ASP 47": "OD1" <-> "OD2" Residue "C GLU 55": "OE1" <-> "OE2" Residue "C GLU 73": "OE1" <-> "OE2" Residue "C TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 103": "OD1" <-> "OD2" Residue "C ARG 115": "NH1" <-> "NH2" Residue "C GLU 121": "OE1" <-> "OE2" Residue "C ARG 139": "NH1" <-> "NH2" Residue "D ASP 76": "OD1" <-> "OD2" Residue "D TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D ARG 139": "NH1" <-> "NH2" Residue "D ASP 141": "OD1" <-> "OD2" Residue "D PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 157": "OD1" <-> "OD2" Residue "E ARG 369": "NH1" <-> "NH2" Residue "E TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 39": "OD1" <-> "OD2" Residue "F ARG 43": "NH1" <-> "NH2" Residue "F TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "F GLU 121": "OE1" <-> "OE2" Residue "F ARG 139": "NH1" <-> "NH2" Residue "F PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 39": "OD1" <-> "OD2" Residue "G ARG 43": "NH1" <-> "NH2" Residue "G ASP 47": "OD1" <-> "OD2" Residue "G GLU 55": "OE1" <-> "OE2" Residue "G GLU 82": "OE1" <-> "OE2" Residue "G TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 103": "OD1" <-> "OD2" Residue "G ARG 115": "NH1" <-> "NH2" Residue "G GLU 121": "OE1" <-> "OE2" Residue "G ARG 139": "NH1" <-> "NH2" Residue "G ASP 141": "OD1" <-> "OD2" Residue "G ASP 157": "OD1" <-> "OD2" Residue "H ASP 39": "OD1" <-> "OD2" Residue "H ASP 76": "OD1" <-> "OD2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 115": "NH1" <-> "NH2" Residue "H ARG 139": "NH1" <-> "NH2" Residue "H ASP 167": "OD1" <-> "OD2" Residue "I ASP 39": "OD1" <-> "OD2" Residue "I ASP 47": "OD1" <-> "OD2" Residue "I ASP 76": "OD1" <-> "OD2" Residue "I TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 115": "NH1" <-> "NH2" Residue "I GLU 121": "OE1" <-> "OE2" Residue "I ARG 139": "NH1" <-> "NH2" Residue "J ASP 47": "OD1" <-> "OD2" Residue "J GLU 55": "OE1" <-> "OE2" Residue "J ASP 76": "OD1" <-> "OD2" Residue "J GLU 82": "OE1" <-> "OE2" Residue "J TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 115": "NH1" <-> "NH2" Residue "J ARG 139": "NH1" <-> "NH2" Residue "J ASP 157": "OD1" <-> "OD2" Residue "J ASP 167": "OD1" <-> "OD2" Residue "K ASP 47": "OD1" <-> "OD2" Residue "K GLU 73": "OE1" <-> "OE2" Residue "K ASP 76": "OD1" <-> "OD2" Residue "K TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 115": "NH1" <-> "NH2" Residue "K ARG 139": "NH1" <-> "NH2" Residue "L ASP 40": "OD1" <-> "OD2" Residue "L ASP 76": "OD1" <-> "OD2" Residue "L GLU 82": "OE1" <-> "OE2" Residue "L TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 115": "NH1" <-> "NH2" Residue "L ARG 139": "NH1" <-> "NH2" Residue "L ASP 141": "OD1" <-> "OD2" Residue "M GLU 55": "OE1" <-> "OE2" Residue "M ASP 76": "OD1" <-> "OD2" Residue "M GLU 82": "OE1" <-> "OE2" Residue "M TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 115": "NH1" <-> "NH2" Residue "M ARG 139": "NH1" <-> "NH2" Residue "M ASP 157": "OD1" <-> "OD2" Residue "N ASP 39": "OD1" <-> "OD2" Residue "N ASP 40": "OD1" <-> "OD2" Residue "N ARG 43": "NH1" <-> "NH2" Residue "N GLU 55": "OE1" <-> "OE2" Residue "N TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 115": "NH1" <-> "NH2" Residue "N ARG 139": "NH1" <-> "NH2" Residue "N PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 167": "OD1" <-> "OD2" Residue "O GLU 82": "OE1" <-> "OE2" Residue "O TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 115": "NH1" <-> "NH2" Residue "O ARG 139": "NH1" <-> "NH2" Residue "O ASP 141": "OD1" <-> "OD2" Residue "P ASP 39": "OD1" <-> "OD2" Residue "P ASP 40": "OD1" <-> "OD2" Residue "P GLU 73": "OE1" <-> "OE2" Residue "P TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 115": "NH1" <-> "NH2" Residue "P ARG 139": "NH1" <-> "NH2" Residue "P ASP 167": "OD1" <-> "OD2" Residue "Q ASP 40": "OD1" <-> "OD2" Residue "Q ASP 47": "OD1" <-> "OD2" Residue "Q GLU 55": "OE1" <-> "OE2" Residue "Q ASP 76": "OD1" <-> "OD2" Residue "Q TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 106": "OE1" <-> "OE2" Residue "Q ARG 115": "NH1" <-> "NH2" Residue "Q ARG 139": "NH1" <-> "NH2" Residue "R TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 369": "NH1" <-> "NH2" Residue "T TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 369": "NH1" <-> "NH2" Residue "W GLU 376": "OE1" <-> "OE2" Residue "W TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 369": "NH1" <-> "NH2" Residue "Z GLU 376": "OE1" <-> "OE2" Residue "Z TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 369": "NH1" <-> "NH2" Residue "c GLU 376": "OE1" <-> "OE2" Residue "c TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 369": "NH1" <-> "NH2" Residue "f TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 369": "NH1" <-> "NH2" Residue "i GLU 376": "OE1" <-> "OE2" Residue "i TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 369": "NH1" <-> "NH2" Residue "l GLU 376": "OE1" <-> "OE2" Residue "l TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 45454 Number of models: 1 Model: "" Number of chains: 69 Chain: "0" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1562 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 190} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "1" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1569 Classifications: {'peptide': 199} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 190} Chain breaks: 1 Chain: "2" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1553 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain breaks: 1 Chain: "3" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1606 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 195} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "4" Number of atoms: 1758 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 221, 1752 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 212} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 221, 1752 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 212} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 1783 Chain: "5" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1885 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 230} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "6" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 405 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "7" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 644 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 81} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "8" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 644 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 81} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "9" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 647 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "A" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1108 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "AM" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 298 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "AN" Number of atoms: 644 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 78, 592 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 75} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 78, 592 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 75} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 544 Chain: "AO" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 667 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "AP" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 675 Classifications: {'peptide': 89} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 86} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "AQ" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 675 Classifications: {'peptide': 89} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 86} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "AR" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 667 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "AS" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 466 Classifications: {'peptide': 59} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "AT" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 466 Classifications: {'peptide': 59} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "AU" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 466 Classifications: {'peptide': 59} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "AV" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 466 Classifications: {'peptide': 59} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "AW" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 466 Classifications: {'peptide': 59} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "AX" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 574 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "AY" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "AZ" Number of atoms: 460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 460 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain breaks: 1 Chain: "B" Number of atoms: 1154 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 144, 1146 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Conformer: "B" Number of residues, atoms: 144, 1146 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} bond proxies already assigned to first conformer: 1161 Chain: "BA" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 437 Classifications: {'peptide': 54} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain breaks: 1 Chain: "BB" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 388 Classifications: {'peptide': 48} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain breaks: 1 Chain: "BC" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 388 Classifications: {'peptide': 48} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain breaks: 1 Chain: "BD" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 388 Classifications: {'peptide': 48} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain breaks: 1 Chain: "BE" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 346 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain breaks: 1 Chain: "C" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1108 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "D" Number of atoms: 1146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1146 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "E" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 236 Classifications: {'peptide': 28} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 24} Chain: "F" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1108 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "G" Number of atoms: 1154 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 144, 1146 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Conformer: "B" Number of residues, atoms: 144, 1146 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} bond proxies already assigned to first conformer: 1161 Chain: "H" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1108 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "I" Number of atoms: 1154 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 144, 1146 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Conformer: "B" Number of residues, atoms: 144, 1146 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} bond proxies already assigned to first conformer: 1161 Chain: "J" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1108 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "K" Number of atoms: 1154 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 144, 1146 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Conformer: "B" Number of residues, atoms: 144, 1146 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} bond proxies already assigned to first conformer: 1161 Chain: "L" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1108 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "M" Number of atoms: 1146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1146 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "N" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1108 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "O" Number of atoms: 1154 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 144, 1146 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Conformer: "B" Number of residues, atoms: 144, 1146 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} bond proxies already assigned to first conformer: 1161 Chain: "P" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1108 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "Q" Number of atoms: 1154 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 144, 1146 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Conformer: "B" Number of residues, atoms: 144, 1146 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} bond proxies already assigned to first conformer: 1161 Chain: "R" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 227 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 3, 'TRANS': 23} Chain: "S" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 231 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 24} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 236 Classifications: {'peptide': 28} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 24} Chain: "U" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 227 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 3, 'TRANS': 23} Chain: "V" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 231 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 24} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 236 Classifications: {'peptide': 28} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 24} Chain: "X" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 227 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 3, 'TRANS': 23} Chain: "Y" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 231 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 24} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "Z" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 236 Classifications: {'peptide': 28} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 24} Chain: "a" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 227 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 3, 'TRANS': 23} Chain: "b" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 231 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 24} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 236 Classifications: {'peptide': 28} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 24} Chain: "d" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 227 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 3, 'TRANS': 23} Chain: "e" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 231 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 24} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "f" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 236 Classifications: {'peptide': 28} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 24} Chain: "g" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 227 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 3, 'TRANS': 23} Chain: "h" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 231 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 24} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "i" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 236 Classifications: {'peptide': 28} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 24} Chain: "j" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 227 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 3, 'TRANS': 23} Chain: "k" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 231 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 24} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "l" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 236 Classifications: {'peptide': 28} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 24} Chain: "m" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 227 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 3, 'TRANS': 23} Chain: "n" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 231 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 24} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N AGLYAN 14 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLYAN 14 " occ=0.50 residue: pdb=" N AGLNAN 15 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLNAN 15 " occ=0.50 residue: pdb=" N AALAAN 16 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALAAN 16 " occ=0.50 residue: pdb=" N AVALAN 17 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVALAN 17 " occ=0.50 residue: pdb=" N AASNAN 18 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASNAN 18 " occ=0.50 residue: pdb=" N AILEAN 19 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILEAN 19 " occ=0.50 residue: pdb=" N AARGAN 20 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARGAN 20 " occ=0.50 Time building chain proxies: 26.32, per 1000 atoms: 0.58 Number of scatterers: 45454 At special positions: 0 Unit cell: (182.97, 167.58, 174.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 212 16.00 O 8263 8.00 N 7462 7.00 C 29517 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 5 157 " - pdb=" SG CYS 5 163 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.24 Conformation dependent library (CDL) restraints added in 9.3 seconds 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10718 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 48 sheets defined 55.7% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.08 Creating SS restraints... Processing helix chain '0' and resid 4 through 24 removed outlier: 3.808A pdb=" N ILE 0 8 " --> pdb=" O ASP 0 4 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA 0 9 " --> pdb=" O ILE 0 5 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N SER 0 14 " --> pdb=" O LEU 0 10 " (cutoff:3.500A) Proline residue: 0 18 - end of helix removed outlier: 3.525A pdb=" N ALA 0 22 " --> pdb=" O PRO 0 18 " (cutoff:3.500A) Processing helix chain '0' and resid 26 through 42 removed outlier: 3.527A pdb=" N ILE 0 32 " --> pdb=" O VAL 0 28 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL 0 33 " --> pdb=" O LYS 0 29 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE 0 34 " --> pdb=" O PHE 0 30 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL 0 35 " --> pdb=" O SER 0 31 " (cutoff:3.500A) Processing helix chain '0' and resid 49 through 76 removed outlier: 3.548A pdb=" N LEU 0 57 " --> pdb=" O ASN 0 53 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU 0 58 " --> pdb=" O GLY 0 54 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL 0 63 " --> pdb=" O LEU 0 59 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET 0 64 " --> pdb=" O SER 0 60 " (cutoff:3.500A) Proline residue: 0 66 - end of helix removed outlier: 3.684A pdb=" N TYR 0 72 " --> pdb=" O MET 0 68 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR 0 74 " --> pdb=" O ASP 0 70 " (cutoff:3.500A) Processing helix chain '0' and resid 84 through 107 removed outlier: 3.544A pdb=" N LEU 0 88 " --> pdb=" O ASP 0 84 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N HIS 0 91 " --> pdb=" O SER 0 87 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL 0 92 " --> pdb=" O LEU 0 88 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLY 0 98 " --> pdb=" O GLU 0 94 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N TYR 0 99 " --> pdb=" O GLY 0 95 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR 0 102 " --> pdb=" O GLY 0 98 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS 0 105 " --> pdb=" O ASP 0 101 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR 0 106 " --> pdb=" O TYR 0 102 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER 0 107 " --> pdb=" O LEU 0 103 " (cutoff:3.500A) Processing helix chain '0' and resid 113 through 118 removed outlier: 3.953A pdb=" N ALA 0 118 " --> pdb=" O PHE 0 114 " (cutoff:3.500A) Processing helix chain '0' and resid 146 through 167 removed outlier: 3.880A pdb=" N LYS 0 160 " --> pdb=" O LYS 0 156 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE 0 161 " --> pdb=" O SER 0 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR 0 164 " --> pdb=" O LYS 0 160 " (cutoff:3.500A) Processing helix chain '0' and resid 168 through 170 No H-bonds generated for 'chain '0' and resid 168 through 170' Processing helix chain '0' and resid 171 through 183 removed outlier: 3.539A pdb=" N LEU 0 180 " --> pdb=" O VAL 0 176 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU 0 181 " --> pdb=" O SER 0 177 " (cutoff:3.500A) Processing helix chain '0' and resid 190 through 205 Proline residue: 0 196 - end of helix removed outlier: 3.592A pdb=" N PHE 0 202 " --> pdb=" O LYS 0 198 " (cutoff:3.500A) Processing helix chain '0' and resid 206 through 220 removed outlier: 3.510A pdb=" N LEU 0 210 " --> pdb=" O ASP 0 206 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER 0 212 " --> pdb=" O TRP 0 208 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS 0 213 " --> pdb=" O THR 0 209 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLN 0 218 " --> pdb=" O GLY 0 214 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR 0 219 " --> pdb=" O LEU 0 215 " (cutoff:3.500A) Processing helix chain '1' and resid 4 through 24 removed outlier: 3.524A pdb=" N ILE 1 8 " --> pdb=" O ASP 1 4 " (cutoff:3.500A) Proline residue: 1 18 - end of helix Processing helix chain '1' and resid 26 through 42 removed outlier: 3.645A pdb=" N PHE 1 30 " --> pdb=" O CYS 1 26 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE 1 32 " --> pdb=" O VAL 1 28 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL 1 33 " --> pdb=" O LYS 1 29 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL 1 35 " --> pdb=" O SER 1 31 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG 1 38 " --> pdb=" O PHE 1 34 " (cutoff:3.500A) Processing helix chain '1' and resid 49 through 76 removed outlier: 3.530A pdb=" N GLY 1 54 " --> pdb=" O MET 1 50 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU 1 59 " --> pdb=" O VAL 1 55 " (cutoff:3.500A) Proline residue: 1 66 - end of helix removed outlier: 3.558A pdb=" N ALA 1 71 " --> pdb=" O ILE 1 67 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR 1 72 " --> pdb=" O MET 1 68 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL 1 73 " --> pdb=" O HIS 1 69 " (cutoff:3.500A) Processing helix chain '1' and resid 84 through 96 removed outlier: 3.618A pdb=" N LEU 1 88 " --> pdb=" O ASP 1 84 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU 1 96 " --> pdb=" O VAL 1 92 " (cutoff:3.500A) Processing helix chain '1' and resid 96 through 107 Processing helix chain '1' and resid 108 through 118 removed outlier: 3.863A pdb=" N VAL 1 112 " --> pdb=" O ASP 1 108 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA 1 118 " --> pdb=" O PHE 1 114 " (cutoff:3.500A) Processing helix chain '1' and resid 142 through 183 removed outlier: 3.558A pdb=" N LEU 1 146 " --> pdb=" O SER 1 142 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU 1 147 " --> pdb=" O ILE 1 143 " (cutoff:3.500A) Proline residue: 1 148 - end of helix removed outlier: 3.669A pdb=" N ALA 1 151 " --> pdb=" O LEU 1 147 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER 1 153 " --> pdb=" O ALA 1 149 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS 1 156 " --> pdb=" O LEU 1 152 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE 1 161 " --> pdb=" O SER 1 157 " (cutoff:3.500A) Proline residue: 1 168 - end of helix removed outlier: 4.033A pdb=" N VAL 1 171 " --> pdb=" O LEU 1 167 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER 1 177 " --> pdb=" O ASP 1 173 " (cutoff:3.500A) Processing helix chain '1' and resid 190 through 204 Proline residue: 1 196 - end of helix removed outlier: 3.734A pdb=" N LEU 1 199 " --> pdb=" O THR 1 195 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU 1 201 " --> pdb=" O ILE 1 197 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N PHE 1 202 " --> pdb=" O LYS 1 198 " (cutoff:3.500A) Processing helix chain '1' and resid 206 through 218 removed outlier: 3.719A pdb=" N SER 1 212 " --> pdb=" O TRP 1 208 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN 1 218 " --> pdb=" O GLY 1 214 " (cutoff:3.500A) Processing helix chain '2' and resid 5 through 21 Proline residue: 2 18 - end of helix Processing helix chain '2' and resid 26 through 41 removed outlier: 4.806A pdb=" N ILE 2 32 " --> pdb=" O VAL 2 28 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL 2 33 " --> pdb=" O LYS 2 29 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE 2 34 " --> pdb=" O PHE 2 30 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL 2 35 " --> pdb=" O SER 2 31 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG 2 38 " --> pdb=" O PHE 2 34 " (cutoff:3.500A) Processing helix chain '2' and resid 50 through 77 removed outlier: 3.798A pdb=" N PHE 2 62 " --> pdb=" O LEU 2 58 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL 2 63 " --> pdb=" O LEU 2 59 " (cutoff:3.500A) Proline residue: 2 66 - end of helix removed outlier: 3.690A pdb=" N ASP 2 70 " --> pdb=" O PRO 2 66 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA 2 71 " --> pdb=" O ILE 2 67 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR 2 74 " --> pdb=" O ASP 2 70 " (cutoff:3.500A) Processing helix chain '2' and resid 84 through 106 removed outlier: 3.925A pdb=" N HIS 2 91 " --> pdb=" O SER 2 87 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL 2 92 " --> pdb=" O LEU 2 88 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP 2 93 " --> pdb=" O SER 2 89 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU 2 94 " --> pdb=" O LYS 2 90 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLY 2 98 " --> pdb=" O GLU 2 94 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N TYR 2 99 " --> pdb=" O GLY 2 95 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG 2 100 " --> pdb=" O LEU 2 96 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TYR 2 102 " --> pdb=" O GLY 2 98 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR 2 106 " --> pdb=" O TYR 2 102 " (cutoff:3.500A) Processing helix chain '2' and resid 108 through 116 removed outlier: 3.567A pdb=" N VAL 2 112 " --> pdb=" O ASP 2 108 " (cutoff:3.500A) Processing helix chain '2' and resid 146 through 165 removed outlier: 3.603A pdb=" N ALA 2 151 " --> pdb=" O LEU 2 147 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU 2 152 " --> pdb=" O PRO 2 148 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS 2 156 " --> pdb=" O LEU 2 152 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS 2 160 " --> pdb=" O LYS 2 156 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE 2 161 " --> pdb=" O SER 2 157 " (cutoff:3.500A) Processing helix chain '2' and resid 166 through 182 removed outlier: 3.693A pdb=" N VAL 2 171 " --> pdb=" O LEU 2 167 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL 2 172 " --> pdb=" O PRO 2 168 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASP 2 173 " --> pdb=" O PHE 2 169 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU 2 174 " --> pdb=" O VAL 2 170 " (cutoff:3.500A) Processing helix chain '2' and resid 190 through 206 Proline residue: 2 196 - end of helix removed outlier: 3.630A pdb=" N LEU 2 199 " --> pdb=" O THR 2 195 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU 2 201 " --> pdb=" O ILE 2 197 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N PHE 2 202 " --> pdb=" O LYS 2 198 " (cutoff:3.500A) Processing helix chain '2' and resid 206 through 215 removed outlier: 4.050A pdb=" N SER 2 212 " --> pdb=" O TRP 2 208 " (cutoff:3.500A) Processing helix chain '3' and resid 4 through 16 removed outlier: 3.604A pdb=" N ILE 3 8 " --> pdb=" O ASP 3 4 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER 3 14 " --> pdb=" O LEU 3 10 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU 3 16 " --> pdb=" O ALA 3 12 " (cutoff:3.500A) Processing helix chain '3' and resid 16 through 24 removed outlier: 3.834A pdb=" N ALA 3 22 " --> pdb=" O PRO 3 18 " (cutoff:3.500A) Processing helix chain '3' and resid 26 through 42 removed outlier: 4.167A pdb=" N VAL 3 35 " --> pdb=" O SER 3 31 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG 3 38 " --> pdb=" O PHE 3 34 " (cutoff:3.500A) Processing helix chain '3' and resid 50 through 76 removed outlier: 3.729A pdb=" N VAL 3 55 " --> pdb=" O THR 3 51 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL 3 63 " --> pdb=" O LEU 3 59 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET 3 64 " --> pdb=" O SER 3 60 " (cutoff:3.500A) Proline residue: 3 66 - end of helix removed outlier: 3.722A pdb=" N ALA 3 71 " --> pdb=" O ILE 3 67 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TYR 3 72 " --> pdb=" O MET 3 68 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL 3 73 " --> pdb=" O HIS 3 69 " (cutoff:3.500A) Processing helix chain '3' and resid 84 through 96 removed outlier: 3.637A pdb=" N LEU 3 88 " --> pdb=" O ASP 3 84 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU 3 96 " --> pdb=" O VAL 3 92 " (cutoff:3.500A) Processing helix chain '3' and resid 96 through 107 removed outlier: 3.521A pdb=" N TYR 3 102 " --> pdb=" O GLY 3 98 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS 3 105 " --> pdb=" O ASP 3 101 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TYR 3 106 " --> pdb=" O TYR 3 102 " (cutoff:3.500A) Processing helix chain '3' and resid 108 through 118 removed outlier: 3.595A pdb=" N ALA 3 118 " --> pdb=" O PHE 3 114 " (cutoff:3.500A) Processing helix chain '3' and resid 142 through 145 Processing helix chain '3' and resid 146 through 183 removed outlier: 3.710A pdb=" N LYS 3 156 " --> pdb=" O LEU 3 152 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR 3 164 " --> pdb=" O LYS 3 160 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU 3 165 " --> pdb=" O ILE 3 161 " (cutoff:3.500A) Proline residue: 3 168 - end of helix removed outlier: 4.038A pdb=" N VAL 3 171 " --> pdb=" O LEU 3 167 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL 3 172 " --> pdb=" O PRO 3 168 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL 3 176 " --> pdb=" O VAL 3 172 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER 3 177 " --> pdb=" O ASP 3 173 " (cutoff:3.500A) Processing helix chain '3' and resid 190 through 205 removed outlier: 3.575A pdb=" N THR 3 195 " --> pdb=" O VAL 3 191 " (cutoff:3.500A) Proline residue: 3 196 - end of helix removed outlier: 3.609A pdb=" N LEU 3 199 " --> pdb=" O THR 3 195 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL 3 200 " --> pdb=" O PRO 3 196 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU 3 201 " --> pdb=" O ILE 3 197 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE 3 202 " --> pdb=" O LYS 3 198 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU 3 205 " --> pdb=" O LEU 3 201 " (cutoff:3.500A) Processing helix chain '3' and resid 206 through 218 removed outlier: 3.751A pdb=" N LEU 3 210 " --> pdb=" O ASP 3 206 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER 3 212 " --> pdb=" O TRP 3 208 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS 3 213 " --> pdb=" O THR 3 209 " (cutoff:3.500A) Processing helix chain '4' and resid 4 through 16 removed outlier: 3.555A pdb=" N ILE 4 8 " --> pdb=" O ASP 4 4 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU 4 16 " --> pdb=" O ALA 4 12 " (cutoff:3.500A) Processing helix chain '4' and resid 16 through 24 removed outlier: 3.614A pdb=" N ILE 4 20 " --> pdb=" O LEU 4 16 " (cutoff:3.500A) Processing helix chain '4' and resid 26 through 41 removed outlier: 3.720A pdb=" N PHE 4 30 " --> pdb=" O CYS 4 26 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE 4 32 " --> pdb=" O VAL 4 28 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL 4 33 " --> pdb=" O LYS 4 29 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU 4 41 " --> pdb=" O VAL 4 37 " (cutoff:3.500A) Processing helix chain '4' and resid 49 through 76 removed outlier: 3.768A pdb=" N GLY 4 54 " --> pdb=" O MET 4 50 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU 4 59 " --> pdb=" O VAL 4 55 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER 4 60 " --> pdb=" O ALA 4 56 " (cutoff:3.500A) Proline residue: 4 66 - end of helix removed outlier: 3.882A pdb=" N ASP 4 70 " --> pdb=" O PRO 4 66 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA 4 71 " --> pdb=" O ILE 4 67 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR 4 72 " --> pdb=" O MET 4 68 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL 4 73 " --> pdb=" O HIS 4 69 " (cutoff:3.500A) Processing helix chain '4' and resid 84 through 107 removed outlier: 3.707A pdb=" N VAL 4 92 " --> pdb=" O LEU 4 88 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP 4 93 " --> pdb=" O SER 4 89 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLY 4 98 " --> pdb=" O GLU 4 94 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N TYR 4 99 " --> pdb=" O GLY 4 95 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR 4 102 " --> pdb=" O GLY 4 98 " (cutoff:3.500A) Processing helix chain '4' and resid 108 through 124 removed outlier: 3.532A pdb=" N VAL 4 112 " --> pdb=" O ASP 4 108 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE 4 115 " --> pdb=" O LEU 4 111 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU 4 116 " --> pdb=" O VAL 4 112 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASN 4 117 " --> pdb=" O GLN 4 113 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS 4 121 " --> pdb=" O ASN 4 117 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG 4 122 " --> pdb=" O ALA 4 118 " (cutoff:3.500A) Processing helix chain '4' and resid 132 through 138 removed outlier: 3.770A pdb=" N LYS 4 135 " --> pdb=" O LYS 4 132 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLU 4 137 " --> pdb=" O ASP 4 134 " (cutoff:3.500A) Processing helix chain '4' and resid 146 through 165 removed outlier: 3.977A pdb=" N TYR 4 164 " --> pdb=" O LYS 4 160 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU 4 165 " --> pdb=" O ILE 4 161 " (cutoff:3.500A) Processing helix chain '4' and resid 166 through 183 removed outlier: 3.649A pdb=" N VAL 4 170 " --> pdb=" O TYR 4 166 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL 4 172 " --> pdb=" O PRO 4 168 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL 4 175 " --> pdb=" O VAL 4 171 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER 4 177 " --> pdb=" O ASP 4 173 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU 4 181 " --> pdb=" O SER 4 177 " (cutoff:3.500A) Processing helix chain '4' and resid 190 through 204 Proline residue: 4 196 - end of helix removed outlier: 3.655A pdb=" N PHE 4 202 " --> pdb=" O LYS 4 198 " (cutoff:3.500A) Processing helix chain '4' and resid 207 through 218 removed outlier: 4.602A pdb=" N LYS 4 213 " --> pdb=" O THR 4 209 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE 4 216 " --> pdb=" O SER 4 212 " (cutoff:3.500A) Processing helix chain '5' and resid 3 through 24 removed outlier: 3.744A pdb=" N ILE 5 9 " --> pdb=" O LEU 5 5 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA 5 14 " --> pdb=" O HIS 5 10 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA 5 17 " --> pdb=" O VAL 5 13 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU 5 18 " --> pdb=" O ALA 5 14 " (cutoff:3.500A) Processing helix chain '5' and resid 25 through 27 No H-bonds generated for 'chain '5' and resid 25 through 27' Processing helix chain '5' and resid 42 through 55 removed outlier: 3.626A pdb=" N ILE 5 46 " --> pdb=" O PRO 5 42 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE 5 48 " --> pdb=" O ASN 5 44 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU 5 49 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA 5 51 " --> pdb=" O ILE 5 47 " (cutoff:3.500A) Processing helix chain '5' and resid 69 through 89 removed outlier: 3.547A pdb=" N LEU 5 75 " --> pdb=" O ILE 5 71 " (cutoff:3.500A) Processing helix chain '5' and resid 89 through 106 removed outlier: 3.868A pdb=" N ARG 5 106 " --> pdb=" O ILE 5 102 " (cutoff:3.500A) Processing helix chain '5' and resid 124 through 140 removed outlier: 3.551A pdb=" N ASN 5 130 " --> pdb=" O ALA 5 126 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ASN 5 140 " --> pdb=" O VAL 5 136 " (cutoff:3.500A) Processing helix chain '5' and resid 142 through 157 removed outlier: 3.608A pdb=" N VAL 5 149 " --> pdb=" O THR 5 145 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU 5 150 " --> pdb=" O MET 5 146 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR 5 154 " --> pdb=" O LEU 5 150 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN 5 155 " --> pdb=" O ASN 5 151 " (cutoff:3.500A) Processing helix chain '5' and resid 172 through 183 removed outlier: 3.693A pdb=" N ASN 5 180 " --> pdb=" O GLN 5 176 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL 5 183 " --> pdb=" O GLN 5 179 " (cutoff:3.500A) Processing helix chain '5' and resid 185 through 206 removed outlier: 4.130A pdb=" N VAL 5 189 " --> pdb=" O ALA 5 185 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU 5 190 " --> pdb=" O SER 5 186 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL 5 191 " --> pdb=" O PRO 5 187 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU 5 202 " --> pdb=" O PHE 5 198 " (cutoff:3.500A) Processing helix chain '5' and resid 207 through 209 No H-bonds generated for 'chain '5' and resid 207 through 209' Processing helix chain '5' and resid 210 through 230 removed outlier: 3.999A pdb=" N ILE 5 214 " --> pdb=" O ASN 5 210 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU 5 216 " --> pdb=" O PHE 5 212 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR 5 217 " --> pdb=" O ALA 5 213 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER 5 220 " --> pdb=" O LEU 5 216 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLY 5 221 " --> pdb=" O THR 5 217 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL 5 224 " --> pdb=" O SER 5 220 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N MET 5 227 " --> pdb=" O ALA 5 223 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU 5 229 " --> pdb=" O LEU 5 225 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N TYR 5 230 " --> pdb=" O ILE 5 226 " (cutoff:3.500A) Processing helix chain '5' and resid 230 through 242 removed outlier: 3.725A pdb=" N VAL 5 234 " --> pdb=" O TYR 5 230 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU 5 235 " --> pdb=" O PHE 5 231 " (cutoff:3.500A) Proline residue: 5 236 - end of helix removed outlier: 3.706A pdb=" N VAL 5 239 " --> pdb=" O LEU 5 235 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU 5 240 " --> pdb=" O PRO 5 236 " (cutoff:3.500A) Processing helix chain '5' and resid 245 through 253 removed outlier: 4.182A pdb=" N SER 5 250 " --> pdb=" O THR 5 247 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TRP 5 252 " --> pdb=" O LEU 5 249 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE 5 253 " --> pdb=" O SER 5 250 " (cutoff:3.500A) Processing helix chain '6' and resid 3 through 19 removed outlier: 3.804A pdb=" N ALA 6 11 " --> pdb=" O ALA 6 7 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LEU 6 12 " --> pdb=" O GLY 6 8 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL 6 15 " --> pdb=" O ALA 6 11 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU 6 16 " --> pdb=" O LEU 6 12 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE 6 17 " --> pdb=" O TYR 6 13 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER 6 19 " --> pdb=" O VAL 6 15 " (cutoff:3.500A) Processing helix chain '6' and resid 20 through 27 Processing helix chain '6' and resid 66 through 83 removed outlier: 4.046A pdb=" N VAL 6 70 " --> pdb=" O TRP 6 66 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU 6 71 " --> pdb=" O TYR 6 67 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU 6 72 " --> pdb=" O GLY 6 68 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N SER 6 73 " --> pdb=" O GLU 6 69 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU 6 81 " --> pdb=" O GLN 6 77 " (cutoff:3.500A) Processing helix chain '7' and resid 2 through 25 removed outlier: 3.646A pdb=" N GLY 7 8 " --> pdb=" O LEU 7 4 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA 7 11 " --> pdb=" O ALA 7 7 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU 7 16 " --> pdb=" O LEU 7 12 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE 7 17 " --> pdb=" O TYR 7 13 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TRP 7 21 " --> pdb=" O ILE 7 17 " (cutoff:3.500A) Proline residue: 7 22 - end of helix removed outlier: 3.649A pdb=" N VAL 7 25 " --> pdb=" O TRP 7 21 " (cutoff:3.500A) Processing helix chain '7' and resid 27 through 37 removed outlier: 3.599A pdb=" N GLY 7 34 " --> pdb=" O GLY 7 30 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN 7 37 " --> pdb=" O VAL 7 33 " (cutoff:3.500A) Processing helix chain '7' and resid 47 through 63 removed outlier: 4.519A pdb=" N ILE 7 51 " --> pdb=" O LEU 7 47 " (cutoff:3.500A) Processing helix chain '7' and resid 63 through 84 removed outlier: 3.631A pdb=" N ILE 7 79 " --> pdb=" O GLY 7 75 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 41 removed outlier: 3.503A pdb=" N GLY 8 8 " --> pdb=" O LEU 8 4 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU 8 16 " --> pdb=" O LEU 8 12 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TRP 8 21 " --> pdb=" O ILE 8 17 " (cutoff:3.500A) Proline residue: 8 22 - end of helix removed outlier: 3.679A pdb=" N VAL 8 25 " --> pdb=" O TRP 8 21 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL 8 39 " --> pdb=" O LEU 8 35 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR 8 40 " --> pdb=" O PHE 8 36 " (cutoff:3.500A) Processing helix chain '8' and resid 46 through 84 removed outlier: 3.545A pdb=" N ILE 8 51 " --> pdb=" O LEU 8 47 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS 8 52 " --> pdb=" O PRO 8 48 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU 8 54 " --> pdb=" O GLY 8 50 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLY 8 65 " --> pdb=" O PHE 8 61 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N TRP 8 66 " --> pdb=" O LEU 8 62 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY 8 68 " --> pdb=" O SER 8 64 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU 8 69 " --> pdb=" O GLY 8 65 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR 8 74 " --> pdb=" O VAL 8 70 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG 8 76 " --> pdb=" O LEU 8 72 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA 8 84 " --> pdb=" O PHE 8 80 " (cutoff:3.500A) Processing helix chain '9' and resid 2 through 19 removed outlier: 3.772A pdb=" N VAL 9 15 " --> pdb=" O ALA 9 11 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU 9 16 " --> pdb=" O LEU 9 12 " (cutoff:3.500A) Processing helix chain '9' and resid 19 through 40 removed outlier: 3.604A pdb=" N ILE 9 29 " --> pdb=" O VAL 9 25 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY 9 30 " --> pdb=" O ALA 9 26 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL 9 33 " --> pdb=" O ILE 9 29 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY 9 34 " --> pdb=" O GLY 9 30 " (cutoff:3.500A) Processing helix chain '9' and resid 48 through 84 removed outlier: 4.049A pdb=" N LEU 9 54 " --> pdb=" O GLY 9 50 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLY 9 65 " --> pdb=" O PHE 9 61 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N TRP 9 66 " --> pdb=" O LEU 9 62 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLY 9 68 " --> pdb=" O SER 9 64 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N GLU 9 69 " --> pdb=" O GLY 9 65 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL 9 70 " --> pdb=" O TRP 9 66 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU 9 71 " --> pdb=" O TYR 9 67 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE 9 79 " --> pdb=" O GLY 9 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 65 removed outlier: 3.733A pdb=" N ARG A 65 " --> pdb=" O MET A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 88 removed outlier: 3.860A pdb=" N GLU A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 86 " --> pdb=" O GLU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 107 No H-bonds generated for 'chain 'A' and resid 105 through 107' Processing helix chain 'A' and resid 118 through 130 removed outlier: 3.649A pdb=" N PHE A 122 " --> pdb=" O SER A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 165 removed outlier: 3.711A pdb=" N ASP A 157 " --> pdb=" O PRO A 153 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET A 158 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 170 Processing helix chain 'AM' and resid 64 through 101 removed outlier: 3.602A pdb=" N ALAAM 68 " --> pdb=" O PROAM 64 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SERAM 75 " --> pdb=" O GLNAM 71 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYRAM 77 " --> pdb=" O METAM 73 " (cutoff:3.500A) Processing helix chain 'AN' and resid 32 through 57 removed outlier: 3.860A pdb=" N SERAN 38 " --> pdb=" O LEUAN 34 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILEAN 42 " --> pdb=" O SERAN 38 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALAAN 43 " --> pdb=" O GLYAN 39 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THRAN 44 " --> pdb=" O SERAN 40 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALAAN 45 " --> pdb=" O ALAAN 41 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASPAN 47 " --> pdb=" O ALAAN 43 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILEAN 51 " --> pdb=" O ASPAN 47 " (cutoff:3.500A) Processing helix chain 'AN' and resid 63 through 101 removed outlier: 3.707A pdb=" N ILEAN 69 " --> pdb=" O LYSAN 65 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VALAN 95 " --> pdb=" O GLYAN 91 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLUAN 96 " --> pdb=" O VALAN 92 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N THRAN 97 " --> pdb=" O GLYAN 93 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEUAN 98 " --> pdb=" O ALAAN 94 " (cutoff:3.500A) Processing helix chain 'AO' and resid 29 through 57 removed outlier: 3.546A pdb=" N LEUAO 33 " --> pdb=" O LEUAO 29 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALAAO 36 " --> pdb=" O ARGAO 32 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLNAO 49 " --> pdb=" O ALAAO 45 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILEAO 51 " --> pdb=" O ASPAO 47 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THRAO 52 " --> pdb=" O LYSAO 48 " (cutoff:3.500A) Processing helix chain 'AO' and resid 63 through 101 removed outlier: 3.511A pdb=" N SERAO 70 " --> pdb=" O GLUAO 66 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILEAO 74 " --> pdb=" O SERAO 70 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SERAO 75 " --> pdb=" O GLNAO 71 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYRAO 80 " --> pdb=" O ASPAO 76 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THRAO 88 " --> pdb=" O VALAO 84 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VALAO 95 " --> pdb=" O GLYAO 91 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEUAO 98 " --> pdb=" O ALAAO 94 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEUAO 99 " --> pdb=" O VALAO 95 " (cutoff:3.500A) Processing helix chain 'AP' and resid 28 through 57 removed outlier: 3.897A pdb=" N GLNAP 35 " --> pdb=" O ASPAP 31 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILEAP 42 " --> pdb=" O SERAP 38 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALAAP 43 " --> pdb=" O GLYAP 39 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYSAP 48 " --> pdb=" O THRAP 44 " (cutoff:3.500A) Processing helix chain 'AP' and resid 63 through 101 removed outlier: 3.876A pdb=" N LEUAP 67 " --> pdb=" O ASPAP 63 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ALAAP 68 " --> pdb=" O PROAP 64 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILEAP 69 " --> pdb=" O LYSAP 65 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VALAP 81 " --> pdb=" O TYRAP 77 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEUAP 87 " --> pdb=" O METAP 83 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEUAP 98 " --> pdb=" O ALAAP 94 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 29 through 57 removed outlier: 3.700A pdb=" N LEUAQ 33 " --> pdb=" O LEUAQ 29 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALAAQ 43 " --> pdb=" O GLYAQ 39 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASPAQ 47 " --> pdb=" O ALAAQ 43 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYSAQ 48 " --> pdb=" O THRAQ 44 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLNAQ 49 " --> pdb=" O ALAAQ 45 " (cutoff:3.500A) Processing helix chain 'AQ' and resid 63 through 100 removed outlier: 3.514A pdb=" N ALAAQ 68 " --> pdb=" O PROAQ 64 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILEAQ 69 " --> pdb=" O LYSAQ 65 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLUAQ 72 " --> pdb=" O ALAAQ 68 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILEAQ 74 " --> pdb=" O SERAQ 70 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SERAQ 75 " --> pdb=" O GLNAQ 71 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VALAQ 81 " --> pdb=" O TYRAQ 77 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SERAQ 82 " --> pdb=" O ASNAQ 78 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEUAQ 98 " --> pdb=" O ALAAQ 94 " (cutoff:3.500A) Processing helix chain 'AR' and resid 29 through 57 removed outlier: 3.850A pdb=" N ILEAR 42 " --> pdb=" O SERAR 38 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALAAR 43 " --> pdb=" O GLYAR 39 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VALAR 46 " --> pdb=" O ILEAR 42 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THRAR 52 " --> pdb=" O LYSAR 48 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARGAR 54 " --> pdb=" O THRAR 50 " (cutoff:3.500A) Processing helix chain 'AR' and resid 57 through 63 removed outlier: 3.776A pdb=" N VALAR 61 " --> pdb=" O ASPAR 57 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASPAR 63 " --> pdb=" O ASNAR 59 " (cutoff:3.500A) Processing helix chain 'AR' and resid 63 through 101 removed outlier: 3.624A pdb=" N ILEAR 69 " --> pdb=" O LYSAR 65 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VALAR 81 " --> pdb=" O TYRAR 77 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SERAR 82 " --> pdb=" O ASNAR 78 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEUAR 87 " --> pdb=" O METAR 83 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THRAR 97 " --> pdb=" O GLYAR 93 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEUAR 98 " --> pdb=" O ALAAR 94 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N SERAR 101 " --> pdb=" O THRAR 97 " (cutoff:3.500A) Processing helix chain 'AS' and resid 23 through 28 Processing helix chain 'AS' and resid 30 through 37 removed outlier: 3.953A pdb=" N LEUAS 34 " --> pdb=" O ALAAS 30 " (cutoff:3.500A) Processing helix chain 'AS' and resid 40 through 80 removed outlier: 3.518A pdb=" N LEUAS 44 " --> pdb=" O ASPAS 40 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLUAS 53 " --> pdb=" O SERAS 49 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASNAS 59 " --> pdb=" O ASNAS 55 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALAAS 60 " --> pdb=" O LEUAS 56 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VALAS 67 " --> pdb=" O ASNAS 63 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHEAS 68 " --> pdb=" O THRAS 64 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASPAS 72 " --> pdb=" O PHEAS 68 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILEAS 75 " --> pdb=" O ILEAS 71 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILEAS 76 " --> pdb=" O ASPAS 72 " (cutoff:3.500A) Processing helix chain 'AT' and resid 23 through 29 Processing helix chain 'AT' and resid 30 through 37 removed outlier: 3.697A pdb=" N LEUAT 34 " --> pdb=" O ALAAT 30 " (cutoff:3.500A) Processing helix chain 'AT' and resid 40 through 80 removed outlier: 3.568A pdb=" N ALAAT 45 " --> pdb=" O PROAT 41 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLUAT 53 " --> pdb=" O SERAT 49 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASNAT 59 " --> pdb=" O ASNAT 55 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALAAT 60 " --> pdb=" O LEUAT 56 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VALAT 67 " --> pdb=" O ASNAT 63 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHEAT 68 " --> pdb=" O THRAT 64 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASPAT 72 " --> pdb=" O PHEAT 68 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILEAT 75 " --> pdb=" O ILEAT 71 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILEAT 76 " --> pdb=" O ASPAT 72 " (cutoff:3.500A) Processing helix chain 'AU' and resid 23 through 29 Processing helix chain 'AU' and resid 30 through 37 removed outlier: 3.872A pdb=" N LEUAU 34 " --> pdb=" O ALAAU 30 " (cutoff:3.500A) Processing helix chain 'AU' and resid 40 through 80 removed outlier: 3.589A pdb=" N LEUAU 44 " --> pdb=" O ASPAU 40 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALAAU 45 " --> pdb=" O PROAU 41 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLUAU 53 " --> pdb=" O SERAU 49 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASNAU 59 " --> pdb=" O ASNAU 55 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALAAU 60 " --> pdb=" O LEUAU 56 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYSAU 66 " --> pdb=" O SERAU 62 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VALAU 67 " --> pdb=" O ASNAU 63 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHEAU 68 " --> pdb=" O THRAU 64 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASPAU 72 " --> pdb=" O PHEAU 68 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILEAU 75 " --> pdb=" O ILEAU 71 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILEAU 76 " --> pdb=" O ASPAU 72 " (cutoff:3.500A) Processing helix chain 'AV' and resid 23 through 29 Processing helix chain 'AV' and resid 30 through 37 removed outlier: 3.838A pdb=" N LEUAV 34 " --> pdb=" O ALAAV 30 " (cutoff:3.500A) Processing helix chain 'AV' and resid 40 through 80 removed outlier: 3.538A pdb=" N LEUAV 44 " --> pdb=" O ASPAV 40 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALAAV 45 " --> pdb=" O PROAV 41 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLUAV 53 " --> pdb=" O SERAV 49 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASNAV 59 " --> pdb=" O ASNAV 55 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALAAV 60 " --> pdb=" O LEUAV 56 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYSAV 66 " --> pdb=" O SERAV 62 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VALAV 67 " --> pdb=" O ASNAV 63 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHEAV 68 " --> pdb=" O THRAV 64 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASPAV 72 " --> pdb=" O PHEAV 68 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILEAV 75 " --> pdb=" O ILEAV 71 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILEAV 76 " --> pdb=" O ASPAV 72 " (cutoff:3.500A) Processing helix chain 'AW' and resid 23 through 28 Processing helix chain 'AW' and resid 30 through 37 removed outlier: 3.745A pdb=" N LEUAW 34 " --> pdb=" O ALAAW 30 " (cutoff:3.500A) Processing helix chain 'AW' and resid 40 through 80 removed outlier: 3.711A pdb=" N LEUAW 44 " --> pdb=" O ASPAW 40 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALAAW 45 " --> pdb=" O PROAW 41 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLUAW 53 " --> pdb=" O SERAW 49 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASNAW 59 " --> pdb=" O ASNAW 55 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALAAW 60 " --> pdb=" O LEUAW 56 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYSAW 66 " --> pdb=" O SERAW 62 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VALAW 67 " --> pdb=" O ASNAW 63 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHEAW 68 " --> pdb=" O THRAW 64 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASPAW 72 " --> pdb=" O PHEAW 68 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILEAW 75 " --> pdb=" O ILEAW 71 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILEAW 76 " --> pdb=" O ASPAW 72 " (cutoff:3.500A) Processing helix chain 'AX' and resid 10 through 20 removed outlier: 4.778A pdb=" N PHEAX 16 " --> pdb=" O VALAX 12 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASPAX 17 " --> pdb=" O SERAX 13 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VALAX 20 " --> pdb=" O PHEAX 16 " (cutoff:3.500A) Processing helix chain 'AX' and resid 22 through 37 removed outlier: 3.892A pdb=" N THRAX 28 " --> pdb=" O GLNAX 24 " (cutoff:3.500A) Processing helix chain 'AX' and resid 40 through 78 removed outlier: 4.193A pdb=" N GLUAX 53 " --> pdb=" O SERAX 49 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYRAX 54 " --> pdb=" O LYSAX 50 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASNAX 55 " --> pdb=" O LEUAX 51 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEUAX 56 " --> pdb=" O SERAX 52 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THRAX 64 " --> pdb=" O ALAAX 60 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VALAX 65 " --> pdb=" O GLNAX 61 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASNAX 78 " --> pdb=" O ALAAX 74 " (cutoff:3.500A) Processing helix chain 'AY' and resid 7 through 20 Processing helix chain 'AY' and resid 22 through 35 removed outlier: 3.646A pdb=" N VALAY 27 " --> pdb=" O LEUAY 23 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N THRAY 28 " --> pdb=" O GLNAY 24 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALAAY 35 " --> pdb=" O LEUAY 31 " (cutoff:3.500A) Processing helix chain 'AY' and resid 40 through 78 removed outlier: 3.637A pdb=" N ALAAY 45 " --> pdb=" O PROAY 41 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALAAY 46 " --> pdb=" O ALAAY 42 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SERAY 52 " --> pdb=" O GLNAY 48 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLUAY 53 " --> pdb=" O SERAY 49 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SERAY 62 " --> pdb=" O ARGAY 58 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THRAY 64 " --> pdb=" O ALAAY 60 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VALAY 65 " --> pdb=" O GLNAY 61 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYSAY 66 " --> pdb=" O SERAY 62 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILEAY 71 " --> pdb=" O VALAY 67 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASPAY 72 " --> pdb=" O PHEAY 68 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 7 through 19 removed outlier: 3.633A pdb=" N PHEAZ 16 " --> pdb=" O VALAZ 12 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASPAZ 17 " --> pdb=" O SERAZ 13 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 22 through 27 removed outlier: 3.834A pdb=" N VALAZ 27 " --> pdb=" O LEUAZ 23 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 52 through 72 removed outlier: 3.586A pdb=" N ARGAZ 58 " --> pdb=" O TYRAZ 54 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLNAZ 61 " --> pdb=" O TYRAZ 57 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASPAZ 72 " --> pdb=" O PHEAZ 68 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 72 through 78 removed outlier: 3.549A pdb=" N GLNAZ 77 " --> pdb=" O ALAAZ 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 65 removed outlier: 3.619A pdb=" N ARG B 65 " --> pdb=" O MET B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 89 removed outlier: 3.770A pdb=" N LEU B 80 " --> pdb=" O ASP B 76 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 86 " --> pdb=" O GLU B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 107 No H-bonds generated for 'chain 'B' and resid 105 through 107' Processing helix chain 'B' and resid 118 through 130 removed outlier: 4.001A pdb=" N ASN B 124 " --> pdb=" O ASN B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 167 removed outlier: 3.514A pdb=" N ASP B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET B 158 " --> pdb=" O VAL B 154 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASN B 161 " --> pdb=" O ASP B 157 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET B 165 " --> pdb=" O ASN B 161 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP B 167 " --> pdb=" O ALA B 163 " (cutoff:3.500A) Processing helix chain 'BA' and resid 7 through 20 removed outlier: 3.744A pdb=" N PHEBA 16 " --> pdb=" O VALBA 12 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASPBA 17 " --> pdb=" O SERBA 13 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VALBA 20 " --> pdb=" O PHEBA 16 " (cutoff:3.500A) Processing helix chain 'BA' and resid 52 through 78 removed outlier: 3.625A pdb=" N VALBA 65 " --> pdb=" O GLNBA 61 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYSBA 66 " --> pdb=" O SERBA 62 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASPBA 70 " --> pdb=" O LYSBA 66 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASPBA 72 " --> pdb=" O PHEBA 68 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALABA 73 " --> pdb=" O LYSBA 69 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ILEBA 75 " --> pdb=" O ILEBA 71 " (cutoff:3.500A) Processing helix chain 'BB' and resid 7 through 18 removed outlier: 3.616A pdb=" N PHEBB 16 " --> pdb=" O VALBB 12 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THRBB 18 " --> pdb=" O ALABB 14 " (cutoff:3.500A) Processing helix chain 'BB' and resid 52 through 56 Processing helix chain 'BB' and resid 56 through 70 removed outlier: 3.925A pdb=" N ALABB 60 " --> pdb=" O LEUBB 56 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLNBB 61 " --> pdb=" O TYRBB 57 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SERBB 62 " --> pdb=" O ARGBB 58 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASNBB 63 " --> pdb=" O ASNBB 59 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VALBB 65 " --> pdb=" O GLNBB 61 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASPBB 70 " --> pdb=" O LYSBB 66 " (cutoff:3.500A) Processing helix chain 'BB' and resid 72 through 78 Processing helix chain 'BC' and resid 7 through 18 Processing helix chain 'BC' and resid 52 through 77 removed outlier: 3.689A pdb=" N LEUBC 56 " --> pdb=" O SERBC 52 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLNBC 61 " --> pdb=" O TYRBC 57 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASNBC 63 " --> pdb=" O ASNBC 59 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THRBC 64 " --> pdb=" O ALABC 60 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VALBC 65 " --> pdb=" O GLNBC 61 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYSBC 66 " --> pdb=" O SERBC 62 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASPBC 72 " --> pdb=" O PHEBC 68 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILEBC 75 " --> pdb=" O ILEBC 71 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILEBC 76 " --> pdb=" O ASPBC 72 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLNBC 77 " --> pdb=" O ALABC 73 " (cutoff:3.500A) Processing helix chain 'BD' and resid 7 through 19 removed outlier: 3.571A pdb=" N SERBD 13 " --> pdb=" O LEUBD 9 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHEBD 16 " --> pdb=" O VALBD 12 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASPBD 17 " --> pdb=" O SERBD 13 " (cutoff:3.500A) Processing helix chain 'BD' and resid 52 through 74 removed outlier: 3.825A pdb=" N TYRBD 57 " --> pdb=" O GLUBD 53 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALABD 60 " --> pdb=" O LEUBD 56 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASNBD 63 " --> pdb=" O ASNBD 59 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THRBD 64 " --> pdb=" O ALABD 60 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASPBD 72 " --> pdb=" O PHEBD 68 " (cutoff:3.500A) Processing helix chain 'BE' and resid 7 through 19 removed outlier: 3.721A pdb=" N SERBE 13 " --> pdb=" O LEUBE 9 " (cutoff:3.500A) Processing helix chain 'BE' and resid 56 through 78 removed outlier: 3.777A pdb=" N SERBE 62 " --> pdb=" O ARGBE 58 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASNBE 63 " --> pdb=" O ASNBE 59 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYSBE 66 " --> pdb=" O SERBE 62 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHEBE 68 " --> pdb=" O THRBE 64 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASPBE 70 " --> pdb=" O LYSBE 66 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALABE 73 " --> pdb=" O LYSBE 69 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILEBE 76 " --> pdb=" O ASPBE 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 49 removed outlier: 3.565A pdb=" N ASP C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA C 48 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET C 49 " --> pdb=" O PHE C 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 43 through 49' Processing helix chain 'C' and resid 76 through 89 removed outlier: 3.810A pdb=" N GLU C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 107 removed outlier: 3.723A pdb=" N MET C 107 " --> pdb=" O ALA C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 129 removed outlier: 3.895A pdb=" N PHE C 122 " --> pdb=" O SER C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 168 removed outlier: 3.677A pdb=" N ASP C 157 " --> pdb=" O PRO C 153 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET C 158 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN C 161 " --> pdb=" O ASP C 157 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET C 166 " --> pdb=" O ALA C 162 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP C 167 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS C 168 " --> pdb=" O THR C 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 65 removed outlier: 3.665A pdb=" N ALA D 64 " --> pdb=" O LYS D 61 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG D 65 " --> pdb=" O MET D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 65' Processing helix chain 'D' and resid 76 through 88 removed outlier: 3.895A pdb=" N GLU D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU D 86 " --> pdb=" O GLU D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 107 No H-bonds generated for 'chain 'D' and resid 105 through 107' Processing helix chain 'D' and resid 118 through 130 Processing helix chain 'D' and resid 152 through 164 removed outlier: 3.901A pdb=" N ASP D 157 " --> pdb=" O PRO D 153 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET D 158 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 89 removed outlier: 3.571A pdb=" N GLU F 82 " --> pdb=" O ASN F 78 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU F 86 " --> pdb=" O GLU F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 107 No H-bonds generated for 'chain 'F' and resid 105 through 107' Processing helix chain 'F' and resid 118 through 130 Processing helix chain 'F' and resid 152 through 168 removed outlier: 3.537A pdb=" N MET F 158 " --> pdb=" O VAL F 154 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN F 161 " --> pdb=" O ASP F 157 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET F 166 " --> pdb=" O ALA F 162 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS F 168 " --> pdb=" O THR F 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 65 removed outlier: 3.936A pdb=" N ARG G 65 " --> pdb=" O MET G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 88 removed outlier: 3.659A pdb=" N LEU G 80 " --> pdb=" O ASP G 76 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU G 82 " --> pdb=" O ASN G 78 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU G 86 " --> pdb=" O GLU G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 107 removed outlier: 3.754A pdb=" N MET G 107 " --> pdb=" O ALA G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 129 removed outlier: 4.133A pdb=" N PHE G 125 " --> pdb=" O GLU G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 168 removed outlier: 3.504A pdb=" N MET G 158 " --> pdb=" O VAL G 154 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN G 161 " --> pdb=" O ASP G 157 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N MET G 166 " --> pdb=" O ALA G 162 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP G 167 " --> pdb=" O ALA G 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 51 removed outlier: 4.062A pdb=" N LEU H 51 " --> pdb=" O ALA H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 65 removed outlier: 3.518A pdb=" N ALA H 64 " --> pdb=" O LYS H 61 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG H 65 " --> pdb=" O MET H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 65' Processing helix chain 'H' and resid 76 through 88 removed outlier: 3.856A pdb=" N GLU H 82 " --> pdb=" O ASN H 78 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS H 83 " --> pdb=" O ALA H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 107 No H-bonds generated for 'chain 'H' and resid 105 through 107' Processing helix chain 'H' and resid 118 through 130 removed outlier: 3.662A pdb=" N PHE H 122 " --> pdb=" O SER H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 168 removed outlier: 3.708A pdb=" N ASP H 157 " --> pdb=" O PRO H 153 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N MET H 158 " --> pdb=" O VAL H 154 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN H 161 " --> pdb=" O ASP H 157 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET H 166 " --> pdb=" O ALA H 162 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP H 167 " --> pdb=" O ALA H 163 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS H 168 " --> pdb=" O THR H 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 49 removed outlier: 3.612A pdb=" N ALA I 48 " --> pdb=" O THR I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 65 removed outlier: 3.901A pdb=" N ARG I 65 " --> pdb=" O MET I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 88 removed outlier: 3.932A pdb=" N GLU I 82 " --> pdb=" O ASN I 78 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS I 83 " --> pdb=" O ALA I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 107 No H-bonds generated for 'chain 'I' and resid 105 through 107' Processing helix chain 'I' and resid 118 through 130 removed outlier: 3.714A pdb=" N ASN I 124 " --> pdb=" O ASN I 120 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE I 125 " --> pdb=" O GLU I 121 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU I 126 " --> pdb=" O PHE I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 165 removed outlier: 3.613A pdb=" N MET I 158 " --> pdb=" O VAL I 154 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASN I 161 " --> pdb=" O ASP I 157 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 49 removed outlier: 3.625A pdb=" N ALA J 48 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET J 49 " --> pdb=" O PHE J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 88 removed outlier: 3.537A pdb=" N LEU J 80 " --> pdb=" O ASP J 76 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU J 82 " --> pdb=" O ASN J 78 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU J 86 " --> pdb=" O GLU J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 105 through 107 No H-bonds generated for 'chain 'J' and resid 105 through 107' Processing helix chain 'J' and resid 118 through 130 removed outlier: 3.524A pdb=" N LYS J 127 " --> pdb=" O ASN J 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 168 removed outlier: 4.014A pdb=" N ASN J 161 " --> pdb=" O ASP J 157 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP J 167 " --> pdb=" O ALA J 163 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS J 168 " --> pdb=" O THR J 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 66 removed outlier: 3.937A pdb=" N ARG K 65 " --> pdb=" O MET K 62 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS K 66 " --> pdb=" O ALA K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 88 removed outlier: 3.645A pdb=" N GLU K 82 " --> pdb=" O ASN K 78 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS K 83 " --> pdb=" O ALA K 79 " (cutoff:3.500A) Processing helix chain 'K' and resid 103 through 107 removed outlier: 3.778A pdb=" N MET K 107 " --> pdb=" O ALA K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 130 removed outlier: 3.616A pdb=" N PHE K 122 " --> pdb=" O SER K 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 168 removed outlier: 3.848A pdb=" N ASN K 161 " --> pdb=" O ASP K 157 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET K 166 " --> pdb=" O ALA K 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 51 removed outlier: 4.100A pdb=" N LEU L 51 " --> pdb=" O ALA L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 65 removed outlier: 3.761A pdb=" N ARG L 65 " --> pdb=" O MET L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 89 removed outlier: 3.929A pdb=" N LEU L 86 " --> pdb=" O GLU L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 107 No H-bonds generated for 'chain 'L' and resid 105 through 107' Processing helix chain 'L' and resid 118 through 130 removed outlier: 3.528A pdb=" N ASN L 124 " --> pdb=" O ASN L 120 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE L 125 " --> pdb=" O GLU L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 169 removed outlier: 3.601A pdb=" N MET L 158 " --> pdb=" O VAL L 154 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASN L 161 " --> pdb=" O ASP L 157 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP L 167 " --> pdb=" O ALA L 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 65 removed outlier: 3.828A pdb=" N ARG M 65 " --> pdb=" O MET M 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 76 through 89 removed outlier: 3.515A pdb=" N GLU M 82 " --> pdb=" O ASN M 78 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU M 86 " --> pdb=" O GLU M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 105 through 107 No H-bonds generated for 'chain 'M' and resid 105 through 107' Processing helix chain 'M' and resid 118 through 129 removed outlier: 3.544A pdb=" N ASN M 124 " --> pdb=" O ASN M 120 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE M 125 " --> pdb=" O GLU M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 152 through 164 removed outlier: 3.825A pdb=" N ASP M 157 " --> pdb=" O PRO M 153 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET M 158 " --> pdb=" O VAL M 154 " (cutoff:3.500A) Processing helix chain 'N' and resid 47 through 51 removed outlier: 4.156A pdb=" N LEU N 51 " --> pdb=" O ALA N 48 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 65 removed outlier: 3.995A pdb=" N ARG N 65 " --> pdb=" O MET N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 76 through 89 Processing helix chain 'N' and resid 105 through 107 No H-bonds generated for 'chain 'N' and resid 105 through 107' Processing helix chain 'N' and resid 118 through 130 Processing helix chain 'N' and resid 152 through 167 removed outlier: 3.682A pdb=" N ASP N 157 " --> pdb=" O PRO N 153 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET N 158 " --> pdb=" O VAL N 154 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET N 165 " --> pdb=" O ASN N 161 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 49 Processing helix chain 'O' and resid 76 through 89 removed outlier: 3.838A pdb=" N GLU O 82 " --> pdb=" O ASN O 78 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU O 86 " --> pdb=" O GLU O 82 " (cutoff:3.500A) Processing helix chain 'O' and resid 105 through 107 No H-bonds generated for 'chain 'O' and resid 105 through 107' Processing helix chain 'O' and resid 118 through 130 removed outlier: 3.622A pdb=" N ASN O 124 " --> pdb=" O ASN O 120 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE O 125 " --> pdb=" O GLU O 121 " (cutoff:3.500A) Processing helix chain 'O' and resid 152 through 162 removed outlier: 3.635A pdb=" N MET O 158 " --> pdb=" O VAL O 154 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN O 161 " --> pdb=" O ASP O 157 " (cutoff:3.500A) Processing helix chain 'P' and resid 43 through 49 removed outlier: 3.557A pdb=" N MET P 49 " --> pdb=" O PHE P 45 " (cutoff:3.500A) Processing helix chain 'P' and resid 61 through 65 removed outlier: 3.813A pdb=" N ARG P 65 " --> pdb=" O MET P 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 76 through 88 removed outlier: 3.832A pdb=" N LEU P 86 " --> pdb=" O GLU P 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 105 through 107 No H-bonds generated for 'chain 'P' and resid 105 through 107' Processing helix chain 'P' and resid 118 through 129 removed outlier: 3.505A pdb=" N PHE P 125 " --> pdb=" O GLU P 121 " (cutoff:3.500A) Processing helix chain 'P' and resid 152 through 168 removed outlier: 3.644A pdb=" N ASP P 157 " --> pdb=" O PRO P 153 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET P 158 " --> pdb=" O VAL P 154 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET P 165 " --> pdb=" O ASN P 161 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N MET P 166 " --> pdb=" O ALA P 162 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP P 167 " --> pdb=" O ALA P 163 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS P 168 " --> pdb=" O THR P 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 49 removed outlier: 3.620A pdb=" N ALA Q 48 " --> pdb=" O THR Q 44 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET Q 49 " --> pdb=" O PHE Q 45 " (cutoff:3.500A) Processing helix chain 'Q' and resid 61 through 65 removed outlier: 3.661A pdb=" N ALA Q 64 " --> pdb=" O LYS Q 61 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG Q 65 " --> pdb=" O MET Q 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 61 through 65' Processing helix chain 'Q' and resid 76 through 89 removed outlier: 3.832A pdb=" N GLU Q 82 " --> pdb=" O ASN Q 78 " (cutoff:3.500A) Processing helix chain 'Q' and resid 105 through 107 No H-bonds generated for 'chain 'Q' and resid 105 through 107' Processing helix chain 'Q' and resid 118 through 130 Processing helix chain 'Q' and resid 152 through 168 removed outlier: 3.626A pdb=" N ASP Q 157 " --> pdb=" O PRO Q 153 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN Q 161 " --> pdb=" O ASP Q 157 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '5' and resid 163 through 164 removed outlier: 3.669A pdb=" N TYR 5 254 " --> pdb=" O THR 5 164 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 40 removed outlier: 5.738A pdb=" N ILE A 68 " --> pdb=" O ASP A 39 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYS A 67 " --> pdb=" O TRP X 386 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N PHE X 388 " --> pdb=" O LYS A 67 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR A 69 " --> pdb=" O PHE X 388 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N HIS X 385 " --> pdb=" O MET X 381 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER X 370 " --> pdb=" O LYS X 380 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY Q 34 " --> pdb=" O TYR X 373 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ILE Q 68 " --> pdb=" O ASP Q 39 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LYS Q 67 " --> pdb=" O TRP V 386 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N PHE V 388 " --> pdb=" O LYS Q 67 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N THR Q 69 " --> pdb=" O PHE V 388 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N HIS V 385 " --> pdb=" O MET V 381 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET V 381 " --> pdb=" O HIS V 385 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER V 370 " --> pdb=" O LYS V 380 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 57 through 59 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 113 removed outlier: 3.683A pdb=" N ARG A 108 " --> pdb=" O GLY A 151 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY A 151 " --> pdb=" O ARG A 108 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'AN' and resid 16 through 19 removed outlier: 17.370A pdb=" N BVALAN 17 " --> pdb=" O VAL Q 111 " (cutoff:3.500A) removed outlier: 19.250A pdb=" N VAL Q 111 " --> pdb=" O BVALAN 17 " (cutoff:3.500A) removed outlier: 20.067A pdb=" N BILEAN 19 " --> pdb=" O ASN Q 109 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN Q 109 " --> pdb=" O AILEAN 19 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL Q 112 " --> pdb=" O PHE Q 147 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'AO' and resid 16 through 18 removed outlier: 3.900A pdb=" N VALAO 17 " --> pdb=" O VAL N 111 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL N 111 " --> pdb=" O VALAO 17 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'AP' and resid 16 through 18 Processing sheet with id=AA8, first strand: chain 'AQ' and resid 15 through 18 removed outlier: 4.507A pdb=" N GLNAQ 15 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER H 113 " --> pdb=" O GLNAQ 15 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG H 108 " --> pdb=" O GLY H 151 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'AR' and resid 16 through 18 removed outlier: 3.599A pdb=" N VALAR 17 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL D 112 " --> pdb=" O PHE D 147 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Y' and resid 379 through 382 removed outlier: 6.329A pdb=" N HIS Y 385 " --> pdb=" O MET Y 381 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LYS B 67 " --> pdb=" O TRP Y 386 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N PHE Y 388 " --> pdb=" O LYS B 67 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N THR B 69 " --> pdb=" O PHE Y 388 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE B 68 " --> pdb=" O ASP B 39 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP B 39 " --> pdb=" O ILE B 68 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY B 34 " --> pdb=" O TYR a 373 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER a 370 " --> pdb=" O LYS a 380 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N HIS a 385 " --> pdb=" O MET a 381 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LYS C 67 " --> pdb=" O TRP a 386 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N PHE a 388 " --> pdb=" O LYS C 67 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR C 69 " --> pdb=" O PHE a 388 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ILE C 68 " --> pdb=" O ASP C 39 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE b 371 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 57 through 59 Processing sheet with id=AB3, first strand: chain 'B' and resid 108 through 113 Processing sheet with id=AB4, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.473A pdb=" N ILE C 58 " --> pdb=" O ILE C 101 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 108 through 113 Processing sheet with id=AB6, first strand: chain 'F' and resid 35 through 40 removed outlier: 5.905A pdb=" N ILE F 68 " --> pdb=" O ASP F 39 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LYS F 67 " --> pdb=" O TRP d 386 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N PHE d 388 " --> pdb=" O LYS F 67 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N THR F 69 " --> pdb=" O PHE d 388 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N HIS d 385 " --> pdb=" O MET d 381 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER d 370 " --> pdb=" O LYS d 380 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY D 34 " --> pdb=" O TYR d 373 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP D 39 " --> pdb=" O ILE D 68 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE D 68 " --> pdb=" O ASP D 39 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LYS D 67 " --> pdb=" O TRP b 386 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N PHE b 388 " --> pdb=" O LYS D 67 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N THR D 69 " --> pdb=" O PHE b 388 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N HIS b 385 " --> pdb=" O MET b 381 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 57 through 59 Processing sheet with id=AB8, first strand: chain 'E' and resid 371 through 373 Processing sheet with id=AB9, first strand: chain 'F' and resid 57 through 59 Processing sheet with id=AC1, first strand: chain 'F' and resid 108 through 113 removed outlier: 3.638A pdb=" N VAL F 112 " --> pdb=" O PHE F 147 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE F 147 " --> pdb=" O VAL F 112 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 35 through 37 removed outlier: 6.927A pdb=" N LYS J 67 " --> pdb=" O TRP j 386 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N HIS j 385 " --> pdb=" O MET j 381 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER j 370 " --> pdb=" O LYS j 380 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP I 39 " --> pdb=" O ILE I 68 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ILE I 68 " --> pdb=" O ASP I 39 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LYS I 67 " --> pdb=" O TRP h 386 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N PHE h 388 " --> pdb=" O LYS I 67 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N THR I 69 " --> pdb=" O PHE h 388 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N HIS h 385 " --> pdb=" O MET h 381 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR h 378 " --> pdb=" O GLN h 372 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER h 370 " --> pdb=" O LYS h 380 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE h 371 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP H 39 " --> pdb=" O ILE H 68 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ILE H 68 " --> pdb=" O ASP H 39 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LYS H 67 " --> pdb=" O TRP g 386 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N PHE g 388 " --> pdb=" O LYS H 67 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR H 69 " --> pdb=" O PHE g 388 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N HIS g 385 " --> pdb=" O MET g 381 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER g 370 " --> pdb=" O LYS g 380 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY G 34 " --> pdb=" O TYR g 373 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP G 39 " --> pdb=" O ILE G 68 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE G 68 " --> pdb=" O ASP G 39 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS G 67 " --> pdb=" O TRP e 386 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N PHE e 388 " --> pdb=" O LYS G 67 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N THR G 69 " --> pdb=" O PHE e 388 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N HIS e 385 " --> pdb=" O MET e 381 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER e 370 " --> pdb=" O LYS e 380 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.590A pdb=" N ILE G 58 " --> pdb=" O ILE G 101 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 108 through 113 removed outlier: 3.772A pdb=" N VAL G 112 " --> pdb=" O PHE G 147 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.461A pdb=" N ILE H 58 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N ASP H 103 " --> pdb=" O ILE H 58 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 57 through 59 removed outlier: 6.515A pdb=" N ILE I 58 " --> pdb=" O ILE I 101 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N ASP I 103 " --> pdb=" O ILE I 58 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 108 through 113 removed outlier: 3.523A pdb=" N VAL I 112 " --> pdb=" O PHE I 147 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.361A pdb=" N ILE J 58 " --> pdb=" O ILE J 101 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N ASP J 103 " --> pdb=" O ILE J 58 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 108 through 113 Processing sheet with id=AD1, first strand: chain 'L' and resid 35 through 37 removed outlier: 6.851A pdb=" N LYS L 67 " --> pdb=" O TRP m 386 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N HIS m 385 " --> pdb=" O MET m 381 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER m 370 " --> pdb=" O LYS m 380 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY K 34 " --> pdb=" O TYR m 373 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ILE K 68 " --> pdb=" O ASP K 39 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LYS K 67 " --> pdb=" O TRP k 386 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N PHE k 388 " --> pdb=" O LYS K 67 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N THR K 69 " --> pdb=" O PHE k 388 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N HIS k 385 " --> pdb=" O MET k 381 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR k 378 " --> pdb=" O GLN k 372 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N SER k 370 " --> pdb=" O LYS k 380 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 57 through 59 Processing sheet with id=AD3, first strand: chain 'L' and resid 57 through 59 removed outlier: 6.378A pdb=" N ILE L 58 " --> pdb=" O ILE L 101 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N ASP L 103 " --> pdb=" O ILE L 58 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 108 through 113 removed outlier: 3.687A pdb=" N ARG L 108 " --> pdb=" O GLY L 151 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY L 151 " --> pdb=" O ARG L 108 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 35 through 40 removed outlier: 3.540A pdb=" N ASP N 39 " --> pdb=" O ILE N 68 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE N 68 " --> pdb=" O ASP N 39 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LYS N 67 " --> pdb=" O TRP R 386 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N PHE R 388 " --> pdb=" O LYS N 67 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR N 69 " --> pdb=" O PHE R 388 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N HIS R 385 " --> pdb=" O MET R 381 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER R 370 " --> pdb=" O LYS R 380 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE R 371 " --> pdb=" O VAL M 36 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR R 373 " --> pdb=" O GLY M 34 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY M 34 " --> pdb=" O TYR R 373 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP M 39 " --> pdb=" O ILE M 68 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ILE M 68 " --> pdb=" O ASP M 39 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS M 67 " --> pdb=" O TRP n 386 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N PHE n 388 " --> pdb=" O LYS M 67 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N THR M 69 " --> pdb=" O PHE n 388 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N HIS n 385 " --> pdb=" O MET n 381 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 57 through 59 Processing sheet with id=AD7, first strand: chain 'M' and resid 108 through 113 removed outlier: 3.590A pdb=" N VAL M 112 " --> pdb=" O PHE M 147 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE M 147 " --> pdb=" O VAL M 112 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 57 through 59 removed outlier: 6.403A pdb=" N ILE N 58 " --> pdb=" O ILE N 101 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ASP N 103 " --> pdb=" O ILE N 58 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'P' and resid 35 through 40 removed outlier: 3.962A pdb=" N ASP P 39 " --> pdb=" O ILE P 68 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE P 68 " --> pdb=" O ASP P 39 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LYS P 67 " --> pdb=" O TRP U 386 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N PHE U 388 " --> pdb=" O LYS P 67 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N THR P 69 " --> pdb=" O PHE U 388 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N HIS U 385 " --> pdb=" O MET U 381 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER U 370 " --> pdb=" O LYS U 380 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY O 34 " --> pdb=" O TYR U 373 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP O 39 " --> pdb=" O ILE O 68 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ILE O 68 " --> pdb=" O ASP O 39 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LYS O 67 " --> pdb=" O TRP S 386 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N PHE S 388 " --> pdb=" O LYS O 67 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N THR O 69 " --> pdb=" O PHE S 388 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N HIS S 385 " --> pdb=" O MET S 381 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER S 370 " --> pdb=" O LYS S 380 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 57 through 59 Processing sheet with id=AE2, first strand: chain 'O' and resid 108 through 113 removed outlier: 3.525A pdb=" N VAL O 112 " --> pdb=" O PHE O 147 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 57 through 59 Processing sheet with id=AE4, first strand: chain 'P' and resid 108 through 113 Processing sheet with id=AE5, first strand: chain 'Q' and resid 57 through 59 Processing sheet with id=AE6, first strand: chain 'T' and resid 371 through 373 Processing sheet with id=AE7, first strand: chain 'W' and resid 371 through 373 removed outlier: 3.600A pdb=" N GLN W 372 " --> pdb=" O ILE W 379 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Z' and resid 371 through 373 Processing sheet with id=AE9, first strand: chain 'c' and resid 371 through 373 Processing sheet with id=AF1, first strand: chain 'f' and resid 371 through 373 Processing sheet with id=AF2, first strand: chain 'i' and resid 371 through 373 Processing sheet with id=AF3, first strand: chain 'l' and resid 371 through 373 2125 hydrogen bonds defined for protein. 6147 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 18.01 Time building geometry restraints manager: 17.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 12559 1.33 - 1.46: 10448 1.46 - 1.58: 23090 1.58 - 1.70: 10 1.70 - 1.82: 408 Bond restraints: 46515 Sorted by residual: bond pdb=" C THR 1 195 " pdb=" N PRO 1 196 " ideal model delta sigma weight residual 1.334 1.397 -0.063 2.34e-02 1.83e+03 7.36e+00 bond pdb=" CG ARG 0 109 " pdb=" CD ARG 0 109 " ideal model delta sigma weight residual 1.520 1.439 0.081 3.00e-02 1.11e+03 7.21e+00 bond pdb=" CB VALAY 67 " pdb=" CG2 VALAY 67 " ideal model delta sigma weight residual 1.521 1.438 0.083 3.30e-02 9.18e+02 6.27e+00 bond pdb=" C ILE 2 46 " pdb=" N PRO 2 47 " ideal model delta sigma weight residual 1.334 1.391 -0.057 2.34e-02 1.83e+03 5.96e+00 bond pdb=" CA ARG N 143 " pdb=" CB ARG N 143 " ideal model delta sigma weight residual 1.531 1.606 -0.075 3.12e-02 1.03e+03 5.81e+00 ... (remaining 46510 not shown) Histogram of bond angle deviations from ideal: 97.02 - 104.64: 881 104.64 - 112.26: 21829 112.26 - 119.88: 19980 119.88 - 127.50: 19868 127.50 - 135.12: 437 Bond angle restraints: 62995 Sorted by residual: angle pdb=" CA LEU A 90 " pdb=" CB LEU A 90 " pdb=" CG LEU A 90 " ideal model delta sigma weight residual 116.30 134.93 -18.63 3.50e+00 8.16e-02 2.83e+01 angle pdb=" N LEU 1 167 " pdb=" CA LEU 1 167 " pdb=" C LEU 1 167 " ideal model delta sigma weight residual 109.81 121.31 -11.50 2.21e+00 2.05e-01 2.71e+01 angle pdb=" CA ARG H 143 " pdb=" CB ARG H 143 " pdb=" CG ARG H 143 " ideal model delta sigma weight residual 114.10 124.47 -10.37 2.00e+00 2.50e-01 2.69e+01 angle pdb=" C PRO G 29 " pdb=" N VAL G 30 " pdb=" CA VAL G 30 " ideal model delta sigma weight residual 121.97 131.18 -9.21 1.80e+00 3.09e-01 2.62e+01 angle pdb=" N LYSBE 15 " pdb=" CA LYSBE 15 " pdb=" CB LYSBE 15 " ideal model delta sigma weight residual 110.28 117.56 -7.28 1.55e+00 4.16e-01 2.21e+01 ... (remaining 62990 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 24590 18.01 - 36.01: 2468 36.01 - 54.02: 429 54.02 - 72.02: 72 72.02 - 90.03: 31 Dihedral angle restraints: 27590 sinusoidal: 10919 harmonic: 16671 Sorted by residual: dihedral pdb=" CA GLN 8 41 " pdb=" C GLN 8 41 " pdb=" N LEU 8 42 " pdb=" CA LEU 8 42 " ideal model delta harmonic sigma weight residual 180.00 135.81 44.19 0 5.00e+00 4.00e-02 7.81e+01 dihedral pdb=" CA LEU b 366 " pdb=" C LEU b 366 " pdb=" N LYS b 367 " pdb=" CA LYS b 367 " ideal model delta harmonic sigma weight residual -180.00 -145.99 -34.01 0 5.00e+00 4.00e-02 4.63e+01 dihedral pdb=" CA LEU k 366 " pdb=" C LEU k 366 " pdb=" N LYS k 367 " pdb=" CA LYS k 367 " ideal model delta harmonic sigma weight residual -180.00 -151.08 -28.92 0 5.00e+00 4.00e-02 3.34e+01 ... (remaining 27587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 6136 0.095 - 0.189: 766 0.189 - 0.284: 40 0.284 - 0.378: 5 0.378 - 0.473: 1 Chirality restraints: 6948 Sorted by residual: chirality pdb=" CB ILE Q 28 " pdb=" CA ILE Q 28 " pdb=" CG1 ILE Q 28 " pdb=" CG2 ILE Q 28 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.59e+00 chirality pdb=" CA THR 1 195 " pdb=" N THR 1 195 " pdb=" C THR 1 195 " pdb=" CB THR 1 195 " both_signs ideal model delta sigma weight residual False 2.53 2.16 0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" CB ILE P 58 " pdb=" CA ILE P 58 " pdb=" CG1 ILE P 58 " pdb=" CG2 ILE P 58 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.91e+00 ... (remaining 6945 not shown) Planarity restraints: 7985 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VALAN 84 " 0.024 2.00e-02 2.50e+03 4.86e-02 2.36e+01 pdb=" C VALAN 84 " -0.084 2.00e-02 2.50e+03 pdb=" O VALAN 84 " 0.031 2.00e-02 2.50e+03 pdb=" N SERAN 85 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU 8 16 " -0.024 2.00e-02 2.50e+03 4.71e-02 2.21e+01 pdb=" C LEU 8 16 " 0.081 2.00e-02 2.50e+03 pdb=" O LEU 8 16 " -0.030 2.00e-02 2.50e+03 pdb=" N ILE 8 17 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASNAQ 53 " -0.023 2.00e-02 2.50e+03 4.57e-02 2.09e+01 pdb=" C ASNAQ 53 " 0.079 2.00e-02 2.50e+03 pdb=" O ASNAQ 53 " -0.029 2.00e-02 2.50e+03 pdb=" N ARGAQ 54 " -0.027 2.00e-02 2.50e+03 ... (remaining 7982 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 7532 2.75 - 3.29: 41153 3.29 - 3.83: 72520 3.83 - 4.36: 83167 4.36 - 4.90: 145108 Nonbonded interactions: 349480 Sorted by model distance: nonbonded pdb=" O GLNAS 24 " pdb=" OG1 THRAS 28 " model vdw 2.214 2.440 nonbonded pdb=" O VAL 2 191 " pdb=" OG1 THR 2 195 " model vdw 2.226 2.440 nonbonded pdb=" OD2 ASP J 40 " pdb=" OG1 THR J 44 " model vdw 2.240 2.440 nonbonded pdb=" O LYSAN 48 " pdb=" OG1 THRAN 52 " model vdw 2.257 2.440 nonbonded pdb=" O LEU 7 60 " pdb=" OG SER 7 64 " model vdw 2.257 2.440 ... (remaining 349475 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 '0' and resid 3 through 220) selection = (chain '1' and (resid 3 through 118 or resid 141 through 220)) selection = (chain '2' and (resid 3 through 118 or resid 141 through 220)) selection = (chain '3' and (resid 3 through 118 or resid 141 through 220)) selection = (chain '4' and (resid 3 through 118 or resid 141 through 220)) } ncs_group { reference = chain '7' selection = chain '8' selection = (chain '9' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 84)) } ncs_group { reference = (chain 'A' and (resid 32 through 42 or resid 44 through 170)) selection = (chain 'B' and (resid 32 through 42 or resid 44 through 170)) selection = (chain 'C' and (resid 32 through 42 or resid 44 through 170)) selection = (chain 'D' and (resid 32 through 42 or resid 44 through 170)) selection = (chain 'F' and (resid 32 through 42 or resid 44 through 170)) selection = (chain 'G' and (resid 32 through 42 or resid 44 through 170)) selection = (chain 'H' and (resid 32 through 42 or resid 44 through 170)) selection = (chain 'I' and (resid 32 through 42 or resid 44 through 170)) selection = (chain 'J' and (resid 32 through 42 or resid 44 through 170)) selection = (chain 'K' and (resid 32 through 42 or resid 44 through 170)) selection = (chain 'L' and (resid 32 through 42 or resid 44 through 170)) selection = (chain 'M' and (resid 32 through 42 or resid 44 through 170)) selection = (chain 'N' and (resid 32 through 42 or resid 44 through 170)) selection = (chain 'O' and (resid 32 through 42 or resid 44 through 170)) selection = (chain 'P' and (resid 32 through 42 or resid 44 through 170)) selection = (chain 'Q' and (resid 32 through 42 or resid 44 through 170)) } ncs_group { reference = (chain 'AN' and resid 31 through 101) selection = (chain 'AO' and resid 31 through 101) selection = (chain 'AP' and resid 31 through 101) selection = (chain 'AQ' and resid 31 through 101) selection = (chain 'AR' and resid 31 through 101) } ncs_group { reference = chain 'AS' selection = chain 'AT' selection = chain 'AU' selection = chain 'AV' selection = chain 'AW' } ncs_group { reference = chain 'AX' selection = (chain 'AY' and resid 8 through 80) } ncs_group { reference = (chain 'AZ' and (resid 3 through 26 or resid 51 through 80)) selection = chain 'BA' } ncs_group { reference = (chain 'BB' and (resid 3 through 19 or resid 55 through 80)) selection = (chain 'BC' and (resid 3 through 19 or resid 55 through 80)) selection = (chain 'BD' and (resid 3 through 19 or resid 55 through 80)) selection = chain 'BE' } ncs_group { reference = (chain 'E' and (resid 365 through 389 or (resid 390 and (name N or name CA or na \ me C or name O or name CB )) or resid 391)) selection = (chain 'R' and (resid 365 through 389 or (resid 390 and (name N or name CA or na \ me C or name O or name CB )) or resid 391)) selection = (chain 'S' and resid 365 through 391) selection = (chain 'T' and (resid 365 through 389 or (resid 390 and (name N or name CA or na \ me C or name O or name CB )) or resid 391)) selection = (chain 'U' and (resid 365 through 389 or (resid 390 and (name N or name CA or na \ me C or name O or name CB )) or resid 391)) selection = (chain 'V' and resid 365 through 391) selection = (chain 'W' and (resid 365 through 389 or (resid 390 and (name N or name CA or na \ me C or name O or name CB )) or resid 391)) selection = (chain 'X' and (resid 365 through 389 or (resid 390 and (name N or name CA or na \ me C or name O or name CB )) or resid 391)) selection = (chain 'Y' and resid 365 through 391) selection = (chain 'Z' and (resid 365 through 389 or (resid 390 and (name N or name CA or na \ me C or name O or name CB )) or resid 391)) selection = (chain 'a' and (resid 365 through 389 or (resid 390 and (name N or name CA or na \ me C or name O or name CB )) or resid 391)) selection = (chain 'b' and resid 365 through 391) selection = (chain 'c' and (resid 365 through 389 or (resid 390 and (name N or name CA or na \ me C or name O or name CB )) or resid 391)) selection = (chain 'd' and (resid 365 through 389 or (resid 390 and (name N or name CA or na \ me C or name O or name CB )) or resid 391)) selection = (chain 'e' and resid 365 through 391) selection = (chain 'f' and (resid 365 through 389 or (resid 390 and (name N or name CA or na \ me C or name O or name CB )) or resid 391)) selection = (chain 'g' and (resid 365 through 389 or (resid 390 and (name N or name CA or na \ me C or name O or name CB )) or resid 391)) selection = (chain 'h' and resid 365 through 391) selection = (chain 'i' and (resid 365 through 389 or (resid 390 and (name N or name CA or na \ me C or name O or name CB )) or resid 391)) selection = (chain 'j' and (resid 365 through 389 or (resid 390 and (name N or name CA or na \ me C or name O or name CB )) or resid 391)) selection = (chain 'k' and resid 365 through 391) selection = (chain 'l' and (resid 365 through 389 or (resid 390 and (name N or name CA or na \ me C or name O or name CB )) or resid 391)) selection = (chain 'm' and (resid 365 through 389 or (resid 390 and (name N or name CA or na \ me C or name O or name CB )) or resid 391)) selection = (chain 'n' and resid 365 through 391) } 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.950 Check model and map are aligned: 0.650 Set scattering table: 0.370 Process input model: 116.450 Find NCS groups from input model: 3.210 Set up NCS constraints: 0.310 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: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 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 : 0.007 0.088 46515 Z= 0.453 Angle : 1.100 18.630 62995 Z= 0.599 Chirality : 0.061 0.473 6948 Planarity : 0.010 0.099 7985 Dihedral : 14.751 90.027 16869 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.14 % Favored : 95.78 % Rotamer: Outliers : 1.08 % Allowed : 8.12 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -5.56 (0.07), residues: 5563 helix: -4.28 (0.04), residues: 3010 sheet: -1.65 (0.17), residues: 696 loop : -2.99 (0.11), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.003 TRP V 365 HIS 0.011 0.002 HIS F 75 PHE 0.045 0.003 PHE J 147 TYR 0.030 0.003 TYR 0 166 ARG 0.029 0.001 ARG O 115 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2003 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 1950 time to evaluate : 4.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 29 LYS cc_start: 0.9005 (tttt) cc_final: 0.8734 (ttmm) REVERT: 0 36 MET cc_start: 0.8993 (ttm) cc_final: 0.8744 (ttp) REVERT: 0 68 MET cc_start: 0.8828 (tpt) cc_final: 0.8590 (tpp) REVERT: 0 156 LYS cc_start: 0.9224 (ttmt) cc_final: 0.8890 (tppt) REVERT: 0 160 LYS cc_start: 0.9007 (ptpp) cc_final: 0.8664 (pttm) REVERT: 1 50 MET cc_start: 0.8663 (ttt) cc_final: 0.8444 (tmm) REVERT: 1 94 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8168 (tp30) REVERT: 1 165 LEU cc_start: 0.8667 (mm) cc_final: 0.8310 (mm) REVERT: 1 173 ASP cc_start: 0.8203 (t70) cc_final: 0.7882 (t0) REVERT: 2 17 LEU cc_start: 0.9344 (tp) cc_final: 0.9132 (tp) REVERT: 2 29 LYS cc_start: 0.9166 (ttmm) cc_final: 0.8896 (tptp) REVERT: 2 72 TYR cc_start: 0.8691 (t80) cc_final: 0.8168 (t80) REVERT: 2 74 TYR cc_start: 0.7965 (m-80) cc_final: 0.7148 (m-80) REVERT: 2 76 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8099 (mm-30) REVERT: 2 193 ILE cc_start: 0.9597 (mt) cc_final: 0.9389 (mp) REVERT: 3 57 LEU cc_start: 0.9055 (tp) cc_final: 0.8835 (tt) REVERT: 3 77 ASP cc_start: 0.8798 (m-30) cc_final: 0.8430 (m-30) REVERT: 3 90 LYS cc_start: 0.9320 (mttt) cc_final: 0.8906 (tppp) REVERT: 3 156 LYS cc_start: 0.9537 (tmtt) cc_final: 0.9222 (ptmm) REVERT: 3 187 MET cc_start: 0.6143 (mtp) cc_final: 0.5835 (mtm) REVERT: 3 188 MET cc_start: 0.8814 (tpt) cc_final: 0.8563 (tpp) REVERT: 3 206 ASP cc_start: 0.8390 (t0) cc_final: 0.8057 (t0) REVERT: 3 211 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8931 (pt) REVERT: 3 215 LEU cc_start: 0.9327 (mt) cc_final: 0.8910 (mt) REVERT: 4 10 LEU cc_start: 0.9204 (tt) cc_final: 0.8874 (pp) REVERT: 4 17 LEU cc_start: 0.9090 (tt) cc_final: 0.8533 (mt) REVERT: 4 26 CYS cc_start: 0.8750 (p) cc_final: 0.8382 (p) REVERT: 4 50 MET cc_start: 0.8784 (tmm) cc_final: 0.8560 (tmm) REVERT: 4 90 LYS cc_start: 0.9279 (tppt) cc_final: 0.9035 (tppp) REVERT: 4 110 GLU cc_start: 0.8290 (pm20) cc_final: 0.7794 (tp30) REVERT: 4 166 TYR cc_start: 0.8612 (t80) cc_final: 0.8208 (t80) REVERT: 4 209 THR cc_start: 0.9377 (p) cc_final: 0.8637 (p) REVERT: 4 210 LEU cc_start: 0.8641 (pp) cc_final: 0.8426 (pp) REVERT: 5 86 CYS cc_start: 0.8619 (p) cc_final: 0.8390 (p) REVERT: 5 98 LEU cc_start: 0.9620 (tp) cc_final: 0.9144 (tt) REVERT: 5 146 MET cc_start: 0.8680 (tmm) cc_final: 0.8456 (ppp) REVERT: 5 182 LEU cc_start: 0.9300 (mm) cc_final: 0.9045 (pp) REVERT: 6 14 LEU cc_start: 0.9564 (mt) cc_final: 0.8992 (mt) REVERT: 6 67 TYR cc_start: 0.7535 (m-10) cc_final: 0.6771 (m-10) REVERT: 6 74 TYR cc_start: 0.8485 (t80) cc_final: 0.8067 (t80) REVERT: 6 80 PHE cc_start: 0.8815 (t80) cc_final: 0.8337 (m-80) REVERT: 7 10 LYS cc_start: 0.8433 (tptt) cc_final: 0.8174 (tppt) REVERT: 7 49 PHE cc_start: 0.7749 (m-80) cc_final: 0.7355 (m-80) REVERT: 8 19 SER cc_start: 0.8257 (m) cc_final: 0.7916 (p) REVERT: 8 54 LEU cc_start: 0.9308 (tp) cc_final: 0.8940 (mt) REVERT: 9 52 LYS cc_start: 0.9192 (ttmm) cc_final: 0.8946 (ttpt) REVERT: 9 53 LEU cc_start: 0.9033 (tp) cc_final: 0.8586 (tp) REVERT: 9 74 TYR cc_start: 0.8340 (t80) cc_final: 0.7815 (t80) REVERT: 9 76 ARG cc_start: 0.8493 (ttm110) cc_final: 0.8222 (ptm160) REVERT: A 100 TYR cc_start: 0.7534 (m-80) cc_final: 0.7106 (m-10) REVERT: A 107 MET cc_start: 0.8706 (ttm) cc_final: 0.8455 (ttt) REVERT: AN 47 ASP cc_start: 0.8983 (m-30) cc_final: 0.8725 (m-30) REVERT: AN 87 LEU cc_start: 0.9474 (mt) cc_final: 0.8800 (mm) REVERT: AN 90 LYS cc_start: 0.9346 (mmmt) cc_final: 0.9011 (tptp) REVERT: AO 67 LEU cc_start: 0.9487 (mt) cc_final: 0.9282 (mp) REVERT: AO 69 ILE cc_start: 0.9589 (tp) cc_final: 0.8521 (tp) REVERT: AP 18 ASN cc_start: 0.9072 (p0) cc_final: 0.8691 (p0) REVERT: AP 31 ASP cc_start: 0.8747 (t0) cc_final: 0.7532 (t0) REVERT: AP 51 ILE cc_start: 0.8812 (tp) cc_final: 0.8511 (tp) REVERT: AP 55 ILE cc_start: 0.9138 (mm) cc_final: 0.8706 (pt) REVERT: AP 77 TYR cc_start: 0.8866 (t80) cc_final: 0.8314 (t80) REVERT: AP 99 LEU cc_start: 0.9282 (mm) cc_final: 0.8684 (mm) REVERT: AQ 40 SER cc_start: 0.9021 (m) cc_final: 0.8799 (p) REVERT: AQ 57 ASP cc_start: 0.8551 (t70) cc_final: 0.8080 (p0) REVERT: AQ 67 LEU cc_start: 0.9427 (mm) cc_final: 0.8872 (mm) REVERT: AQ 69 ILE cc_start: 0.9293 (mt) cc_final: 0.8313 (tp) REVERT: AQ 73 MET cc_start: 0.8770 (mtm) cc_final: 0.7292 (mtm) REVERT: AQ 86 THR cc_start: 0.9449 (p) cc_final: 0.9188 (t) REVERT: AQ 100 ARG cc_start: 0.8565 (tpp80) cc_final: 0.8197 (mtt-85) REVERT: AR 22 MET cc_start: 0.5402 (tpp) cc_final: 0.5082 (tpt) REVERT: AR 63 ASP cc_start: 0.7816 (t0) cc_final: 0.7590 (t70) REVERT: AR 69 ILE cc_start: 0.9212 (mm) cc_final: 0.8727 (mm) REVERT: AR 72 GLU cc_start: 0.8950 (tp30) cc_final: 0.8460 (tp30) REVERT: AR 73 MET cc_start: 0.9354 (mpp) cc_final: 0.9111 (mpp) REVERT: AR 76 ASP cc_start: 0.8931 (m-30) cc_final: 0.8450 (m-30) REVERT: AR 86 THR cc_start: 0.9336 (t) cc_final: 0.9081 (m) REVERT: AS 50 LYS cc_start: 0.8706 (tptt) cc_final: 0.8452 (tttt) REVERT: AS 56 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9238 (mm) REVERT: AT 23 LEU cc_start: 0.8330 (tp) cc_final: 0.7559 (mm) REVERT: AT 26 GLN cc_start: 0.8725 (pt0) cc_final: 0.8521 (pm20) REVERT: AT 28 THR cc_start: 0.7586 (OUTLIER) cc_final: 0.7308 (p) REVERT: AT 58 ARG cc_start: 0.8045 (mmt180) cc_final: 0.7712 (mmm-85) REVERT: AT 66 LYS cc_start: 0.8738 (tptp) cc_final: 0.8145 (tppp) REVERT: AU 43 LEU cc_start: 0.8820 (mt) cc_final: 0.8502 (tt) REVERT: AU 44 LEU cc_start: 0.8110 (pp) cc_final: 0.7765 (pt) REVERT: AU 66 LYS cc_start: 0.9060 (tptp) cc_final: 0.8789 (tppp) REVERT: AV 40 ASP cc_start: 0.8475 (m-30) cc_final: 0.7900 (t0) REVERT: AV 47 TYR cc_start: 0.8689 (t80) cc_final: 0.8310 (t80) REVERT: AV 59 ASN cc_start: 0.8667 (p0) cc_final: 0.8348 (p0) REVERT: AV 64 THR cc_start: 0.9218 (t) cc_final: 0.8968 (p) REVERT: AV 69 LYS cc_start: 0.9385 (tttt) cc_final: 0.8942 (tttt) REVERT: AW 44 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8275 (mt) REVERT: AW 47 TYR cc_start: 0.8523 (t80) cc_final: 0.8102 (t80) REVERT: AW 58 ARG cc_start: 0.8722 (mmt180) cc_final: 0.8506 (mmt180) REVERT: AW 66 LYS cc_start: 0.8879 (tptp) cc_final: 0.8274 (tppt) REVERT: AY 63 ASN cc_start: 0.8415 (t0) cc_final: 0.7741 (t0) REVERT: AY 69 LYS cc_start: 0.9463 (tmtt) cc_final: 0.9149 (tttt) REVERT: AZ 16 PHE cc_start: 0.7949 (m-80) cc_final: 0.7627 (m-80) REVERT: AZ 79 PHE cc_start: 0.8174 (m-10) cc_final: 0.7829 (m-80) REVERT: B 102 TYR cc_start: 0.8063 (m-80) cc_final: 0.7741 (m-10) REVERT: BA 58 ARG cc_start: 0.7073 (ttt180) cc_final: 0.6473 (ttt180) REVERT: BB 57 TYR cc_start: 0.3422 (t80) cc_final: 0.3147 (t80) REVERT: BB 75 ILE cc_start: 0.9469 (pt) cc_final: 0.9194 (pt) REVERT: BE 63 ASN cc_start: 0.8269 (m-40) cc_final: 0.7947 (p0) REVERT: D 102 TYR cc_start: 0.7790 (m-80) cc_final: 0.7561 (m-80) REVERT: D 105 SER cc_start: 0.9003 (m) cc_final: 0.8708 (t) REVERT: F 136 TYR cc_start: 0.8397 (m-80) cc_final: 0.8121 (m-10) REVERT: F 155 TYR cc_start: 0.7813 (t80) cc_final: 0.7467 (t80) REVERT: F 159 VAL cc_start: 0.9266 (p) cc_final: 0.8902 (m) REVERT: G 159 VAL cc_start: 0.9065 (p) cc_final: 0.8850 (t) REVERT: H 113 SER cc_start: 0.8270 (t) cc_final: 0.7901 (p) REVERT: I 68 ILE cc_start: 0.8893 (tp) cc_final: 0.8613 (tt) REVERT: I 136 TYR cc_start: 0.8196 (m-80) cc_final: 0.7753 (m-10) REVERT: J 39 ASP cc_start: 0.7346 (t0) cc_final: 0.7119 (t0) REVERT: J 103 ASP cc_start: 0.7653 (p0) cc_final: 0.7259 (p0) REVERT: J 167 ASP cc_start: 0.7439 (p0) cc_final: 0.7164 (p0) REVERT: K 100 TYR cc_start: 0.8148 (m-80) cc_final: 0.7765 (m-10) REVERT: M 146 THR cc_start: 0.8658 (m) cc_final: 0.8410 (p) REVERT: N 58 ILE cc_start: 0.8525 (mp) cc_final: 0.8290 (mp) REVERT: N 158 MET cc_start: 0.7937 (tmm) cc_final: 0.7726 (ppp) REVERT: O 103 ASP cc_start: 0.6911 (p0) cc_final: 0.6396 (p0) REVERT: O 136 TYR cc_start: 0.8452 (m-80) cc_final: 0.8074 (m-10) REVERT: P 44 THR cc_start: 0.8833 (m) cc_final: 0.8402 (p) REVERT: S 378 TYR cc_start: 0.8521 (p90) cc_final: 0.7981 (p90) REVERT: V 372 GLN cc_start: 0.8520 (tm-30) cc_final: 0.8024 (tm-30) REVERT: b 381 MET cc_start: 0.7907 (mmt) cc_final: 0.7457 (mmm) REVERT: e 378 TYR cc_start: 0.8424 (p90) cc_final: 0.8169 (p90) REVERT: g 366 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7792 (pp) REVERT: g 379 ILE cc_start: 0.8998 (mt) cc_final: 0.8658 (mm) REVERT: m 366 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8425 (pp) REVERT: m 380 LYS cc_start: 0.7993 (mmmt) cc_final: 0.7548 (tptp) outliers start: 53 outliers final: 15 residues processed: 1970 average time/residue: 0.6060 time to fit residues: 1896.4454 Evaluate side-chains 1318 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 1297 time to evaluate : 4.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 81 THR Chi-restraints excluded: chain 3 residue 211 LEU Chi-restraints excluded: chain 5 residue 68 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain AS residue 56 LEU Chi-restraints excluded: chain AT residue 28 THR Chi-restraints excluded: chain AU residue 64 THR Chi-restraints excluded: chain AW residue 28 THR Chi-restraints excluded: chain AW residue 44 LEU Chi-restraints excluded: chain AW residue 64 THR Chi-restraints excluded: chain BA residue 20 VAL Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain R residue 366 LEU Chi-restraints excluded: chain U residue 366 LEU Chi-restraints excluded: chain V residue 366 LEU Chi-restraints excluded: chain d residue 366 LEU Chi-restraints excluded: chain g residue 366 LEU Chi-restraints excluded: chain m residue 366 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 441 optimal weight: 3.9990 chunk 396 optimal weight: 7.9990 chunk 219 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 267 optimal weight: 9.9990 chunk 211 optimal weight: 0.8980 chunk 409 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 chunk 249 optimal weight: 9.9990 chunk 305 optimal weight: 1.9990 chunk 474 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 69 HIS ** 3 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 117 ASN 3 218 GLN ** 4 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 44 ASN 5 104 ASN 5 130 ASN ** 5 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 176 GLN 5 179 GLN 7 37 GLN 8 9 ASN 8 37 GLN 9 37 GLN A 71 ASN A 87 GLN ** AO 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AR 15 GLN AS 22 ASN AS 26 GLN ** AS 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 26 GLN AU 22 ASN AU 55 ASN AU 77 GLN AV 77 GLN AW 22 ASN AW 24 GLN AW 63 ASN AX 59 ASN ** AX 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AY 55 ASN AZ 26 GLN AZ 78 ASN B 170 ASN BA 26 GLN ** BA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 61 GLN C 123 ASN C 161 ASN D 87 GLN ** D 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 GLN G 97 GLN G 124 ASN ** G 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 GLN I 169 GLN K 97 GLN K 169 GLN L 97 GLN L 170 ASN M 161 ASN N 97 GLN N 170 ASN O 169 GLN P 169 GLN Q 97 GLN ** Z 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 372 GLN ** n 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 46515 Z= 0.254 Angle : 0.779 11.413 62995 Z= 0.399 Chirality : 0.046 0.231 6948 Planarity : 0.005 0.067 7985 Dihedral : 6.174 76.469 6233 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.36 % Favored : 95.59 % Rotamer: Outliers : 3.40 % Allowed : 19.75 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.09), residues: 5563 helix: -2.00 (0.08), residues: 3045 sheet: -1.30 (0.17), residues: 672 loop : -2.51 (0.12), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP i 365 HIS 0.011 0.001 HIS Q 75 PHE 0.035 0.002 PHE I 45 TYR 0.028 0.002 TYR e 387 ARG 0.010 0.001 ARG O 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1610 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1444 time to evaluate : 5.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 116 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7675 (mm-30) REVERT: 0 156 LYS cc_start: 0.9140 (ttmt) cc_final: 0.8783 (tppt) REVERT: 0 160 LYS cc_start: 0.9129 (ptpp) cc_final: 0.8676 (pttm) REVERT: 0 186 MET cc_start: 0.8654 (tpp) cc_final: 0.8368 (tpp) REVERT: 0 218 GLN cc_start: 0.9040 (tm-30) cc_final: 0.8656 (tm-30) REVERT: 0 219 TYR cc_start: 0.8730 (m-80) cc_final: 0.8153 (m-10) REVERT: 1 50 MET cc_start: 0.8866 (ttt) cc_final: 0.8656 (tmm) REVERT: 1 110 GLU cc_start: 0.8495 (pm20) cc_final: 0.8217 (pm20) REVERT: 1 160 LYS cc_start: 0.9466 (mtmm) cc_final: 0.8988 (mtmm) REVERT: 1 165 LEU cc_start: 0.8916 (mm) cc_final: 0.8430 (mm) REVERT: 1 169 PHE cc_start: 0.8293 (m-80) cc_final: 0.7585 (m-80) REVERT: 1 173 ASP cc_start: 0.7842 (t70) cc_final: 0.7335 (t0) REVERT: 2 29 LYS cc_start: 0.9181 (ttmm) cc_final: 0.8770 (tttp) REVERT: 2 72 TYR cc_start: 0.8762 (t80) cc_final: 0.8443 (t80) REVERT: 2 76 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8095 (mm-30) REVERT: 2 105 LYS cc_start: 0.8918 (ttmm) cc_final: 0.8598 (ttpp) REVERT: 2 206 ASP cc_start: 0.8137 (t0) cc_final: 0.7804 (t0) REVERT: 3 180 LEU cc_start: 0.9577 (OUTLIER) cc_final: 0.9273 (mp) REVERT: 3 181 LEU cc_start: 0.8469 (mt) cc_final: 0.7771 (tp) REVERT: 3 188 MET cc_start: 0.8871 (tpt) cc_final: 0.8643 (tpp) REVERT: 3 206 ASP cc_start: 0.8009 (t0) cc_final: 0.7569 (t0) REVERT: 3 215 LEU cc_start: 0.9388 (mt) cc_final: 0.9053 (mt) REVERT: 3 220 MET cc_start: 0.8147 (tpp) cc_final: 0.7780 (tpp) REVERT: 4 10 LEU cc_start: 0.9158 (tt) cc_final: 0.8917 (pp) REVERT: 4 17 LEU cc_start: 0.9146 (tt) cc_final: 0.8712 (mt) REVERT: 4 26 CYS cc_start: 0.8433 (p) cc_final: 0.8230 (p) REVERT: 4 50 MET cc_start: 0.9000 (tmm) cc_final: 0.8694 (tmm) REVERT: 4 74 TYR cc_start: 0.8379 (t80) cc_final: 0.7940 (t80) REVERT: 4 96 LEU cc_start: 0.9131 (mm) cc_final: 0.8915 (mm) REVERT: 4 160 LYS cc_start: 0.9298 (tppt) cc_final: 0.9071 (tppt) REVERT: 4 166 TYR cc_start: 0.8324 (t80) cc_final: 0.8071 (t80) REVERT: 4 188 MET cc_start: 0.8489 (tpp) cc_final: 0.8143 (tpp) REVERT: 5 65 PHE cc_start: 0.7430 (m-10) cc_final: 0.7209 (m-10) REVERT: 5 95 MET cc_start: 0.8364 (tpp) cc_final: 0.8111 (tpp) REVERT: 5 160 MET cc_start: 0.9406 (mpp) cc_final: 0.8759 (mpp) REVERT: 6 14 LEU cc_start: 0.9553 (mt) cc_final: 0.9121 (mt) REVERT: 6 67 TYR cc_start: 0.7588 (m-10) cc_final: 0.7137 (m-10) REVERT: 7 49 PHE cc_start: 0.7943 (m-80) cc_final: 0.7417 (m-80) REVERT: 8 76 ARG cc_start: 0.9182 (mtm180) cc_final: 0.8966 (mtt90) REVERT: 8 77 GLN cc_start: 0.9170 (tp40) cc_final: 0.8690 (tm-30) REVERT: 8 81 LEU cc_start: 0.9327 (tp) cc_final: 0.9117 (tp) REVERT: 9 52 LYS cc_start: 0.9117 (ttmm) cc_final: 0.8893 (ttpt) REVERT: A 165 MET cc_start: 0.8277 (mmm) cc_final: 0.8053 (ttm) REVERT: AN 47 ASP cc_start: 0.9212 (m-30) cc_final: 0.8752 (m-30) REVERT: AN 75 SER cc_start: 0.8934 (m) cc_final: 0.8658 (p) REVERT: AN 87 LEU cc_start: 0.9492 (mt) cc_final: 0.9149 (mm) REVERT: AO 49 GLN cc_start: 0.8647 (tp-100) cc_final: 0.8121 (tp-100) REVERT: AO 69 ILE cc_start: 0.9293 (tp) cc_final: 0.8782 (tp) REVERT: AO 72 GLU cc_start: 0.8899 (pp20) cc_final: 0.8692 (pp20) REVERT: AO 73 MET cc_start: 0.8532 (mmt) cc_final: 0.7864 (mmt) REVERT: AO 83 MET cc_start: 0.8930 (tpp) cc_final: 0.8610 (tmm) REVERT: AP 31 ASP cc_start: 0.8008 (t0) cc_final: 0.6856 (t0) REVERT: AP 42 ILE cc_start: 0.9075 (mm) cc_final: 0.8808 (mt) REVERT: AP 48 LYS cc_start: 0.8892 (ttmm) cc_final: 0.8625 (tppp) REVERT: AP 55 ILE cc_start: 0.9242 (mm) cc_final: 0.8597 (pt) REVERT: AP 77 TYR cc_start: 0.8873 (t80) cc_final: 0.8458 (t80) REVERT: AQ 40 SER cc_start: 0.9107 (m) cc_final: 0.8903 (p) REVERT: AQ 57 ASP cc_start: 0.8415 (t70) cc_final: 0.8113 (p0) REVERT: AQ 59 ASN cc_start: 0.9252 (t0) cc_final: 0.9003 (t0) REVERT: AQ 67 LEU cc_start: 0.9416 (mm) cc_final: 0.9146 (mm) REVERT: AQ 72 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8076 (mp0) REVERT: AR 54 ARG cc_start: 0.7982 (mmm-85) cc_final: 0.7577 (mmm-85) REVERT: AR 63 ASP cc_start: 0.7788 (t0) cc_final: 0.7476 (t70) REVERT: AR 69 ILE cc_start: 0.9237 (mm) cc_final: 0.8679 (mm) REVERT: AR 72 GLU cc_start: 0.8829 (tp30) cc_final: 0.8567 (tp30) REVERT: AR 73 MET cc_start: 0.9372 (mpp) cc_final: 0.9127 (mpp) REVERT: AR 76 ASP cc_start: 0.8783 (m-30) cc_final: 0.8365 (m-30) REVERT: AR 99 LEU cc_start: 0.9047 (tt) cc_final: 0.8786 (tt) REVERT: AS 50 LYS cc_start: 0.8787 (tptt) cc_final: 0.8387 (tptt) REVERT: AS 51 LEU cc_start: 0.9568 (tt) cc_final: 0.9160 (mm) REVERT: AT 23 LEU cc_start: 0.8189 (tp) cc_final: 0.7817 (mm) REVERT: AT 47 TYR cc_start: 0.9208 (t80) cc_final: 0.8861 (t80) REVERT: AT 61 GLN cc_start: 0.8860 (pp30) cc_final: 0.8380 (pp30) REVERT: AT 66 LYS cc_start: 0.8768 (tptp) cc_final: 0.8503 (tptm) REVERT: AU 51 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8436 (pp) REVERT: AU 66 LYS cc_start: 0.9282 (tptp) cc_final: 0.8974 (tppp) REVERT: AV 40 ASP cc_start: 0.8642 (m-30) cc_final: 0.8335 (t70) REVERT: AV 47 TYR cc_start: 0.9034 (t80) cc_final: 0.8831 (t80) REVERT: AV 51 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.9048 (mm) REVERT: AV 53 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7448 (mp0) REVERT: AV 69 LYS cc_start: 0.9375 (tttt) cc_final: 0.8996 (tttt) REVERT: AW 24 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7796 (pp30) REVERT: AW 47 TYR cc_start: 0.8633 (t80) cc_final: 0.8347 (t80) REVERT: AW 58 ARG cc_start: 0.8736 (mmt180) cc_final: 0.8046 (mmt-90) REVERT: AY 43 LEU cc_start: 0.6711 (tp) cc_final: 0.6418 (tt) REVERT: AY 63 ASN cc_start: 0.7880 (t0) cc_final: 0.7606 (t0) REVERT: AY 79 PHE cc_start: 0.8815 (m-80) cc_final: 0.8450 (m-80) REVERT: AZ 72 ASP cc_start: 0.9074 (p0) cc_final: 0.8870 (p0) REVERT: AZ 76 ILE cc_start: 0.9249 (mp) cc_final: 0.8749 (mp) REVERT: AZ 79 PHE cc_start: 0.8190 (m-10) cc_final: 0.7805 (m-80) REVERT: B 38 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7559 (mtpt) REVERT: B 49 MET cc_start: 0.6331 (OUTLIER) cc_final: 0.6058 (mtm) REVERT: B 82 GLU cc_start: 0.7034 (tp30) cc_final: 0.6763 (tp30) REVERT: B 102 TYR cc_start: 0.8248 (m-80) cc_final: 0.7919 (m-10) REVERT: B 103 ASP cc_start: 0.8149 (p0) cc_final: 0.7748 (p0) REVERT: BA 54 TYR cc_start: 0.5993 (t80) cc_final: 0.5765 (m-80) REVERT: BA 79 PHE cc_start: 0.9169 (m-80) cc_final: 0.8763 (m-80) REVERT: BC 75 ILE cc_start: 0.7915 (mp) cc_final: 0.7665 (mp) REVERT: BE 63 ASN cc_start: 0.8269 (m-40) cc_final: 0.7931 (p0) REVERT: D 41 SER cc_start: 0.7969 (p) cc_final: 0.7626 (p) REVERT: D 101 ILE cc_start: 0.9196 (mm) cc_final: 0.8927 (mt) REVERT: D 165 MET cc_start: 0.7533 (mmm) cc_final: 0.7281 (mtt) REVERT: F 106 GLU cc_start: 0.7535 (mp0) cc_final: 0.7173 (mp0) REVERT: F 107 MET cc_start: 0.7836 (tmm) cc_final: 0.7369 (tmm) REVERT: G 82 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7316 (mm-30) REVERT: G 167 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.7260 (t0) REVERT: I 39 ASP cc_start: 0.7767 (t0) cc_final: 0.7488 (t0) REVERT: I 54 LYS cc_start: 0.8321 (mmtm) cc_final: 0.8069 (mmmt) REVERT: M 146 THR cc_start: 0.9086 (m) cc_final: 0.8830 (p) REVERT: M 155 TYR cc_start: 0.8042 (t80) cc_final: 0.7777 (t80) REVERT: M 157 ASP cc_start: 0.7148 (p0) cc_final: 0.6768 (p0) REVERT: a 380 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8823 (ttmm) REVERT: b 379 ILE cc_start: 0.9342 (mm) cc_final: 0.9056 (mm) REVERT: g 366 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.7920 (pp) REVERT: g 381 MET cc_start: 0.7098 (mmm) cc_final: 0.6596 (mmm) REVERT: i 376 GLU cc_start: 0.6553 (tm-30) cc_final: 0.6172 (tm-30) REVERT: j 366 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8695 (pp) REVERT: j 381 MET cc_start: 0.7718 (ttm) cc_final: 0.7292 (tpp) REVERT: k 381 MET cc_start: 0.6580 (mmm) cc_final: 0.6055 (mmm) REVERT: m 366 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8501 (pp) REVERT: m 380 LYS cc_start: 0.8245 (mmmt) cc_final: 0.7953 (tptp) outliers start: 166 outliers final: 77 residues processed: 1526 average time/residue: 0.5828 time to fit residues: 1445.8702 Evaluate side-chains 1362 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1272 time to evaluate : 5.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 191 VAL Chi-restraints excluded: chain 1 residue 72 TYR Chi-restraints excluded: chain 1 residue 221 ASP Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 2 residue 83 ASN Chi-restraints excluded: chain 2 residue 165 LEU Chi-restraints excluded: chain 2 residue 194 SER Chi-restraints excluded: chain 2 residue 201 LEU Chi-restraints excluded: chain 3 residue 50 MET Chi-restraints excluded: chain 3 residue 83 ASN Chi-restraints excluded: chain 3 residue 85 ILE Chi-restraints excluded: chain 3 residue 94 GLU Chi-restraints excluded: chain 3 residue 161 ILE Chi-restraints excluded: chain 3 residue 180 LEU Chi-restraints excluded: chain 4 residue 23 SER Chi-restraints excluded: chain 4 residue 51 THR Chi-restraints excluded: chain 5 residue 68 VAL Chi-restraints excluded: chain 5 residue 179 GLN Chi-restraints excluded: chain 8 residue 15 VAL Chi-restraints excluded: chain 8 residue 63 LEU Chi-restraints excluded: chain 8 residue 69 GLU Chi-restraints excluded: chain 8 residue 78 VAL Chi-restraints excluded: chain 9 residue 15 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain AN residue 33 LEU Chi-restraints excluded: chain AN residue 74 ILE Chi-restraints excluded: chain AO residue 86 THR Chi-restraints excluded: chain AO residue 88 THR Chi-restraints excluded: chain AP residue 59 ASN Chi-restraints excluded: chain AP residue 75 SER Chi-restraints excluded: chain AP residue 86 THR Chi-restraints excluded: chain AQ residue 19 ILE Chi-restraints excluded: chain AQ residue 72 GLU Chi-restraints excluded: chain AR residue 34 LEU Chi-restraints excluded: chain AR residue 92 VAL Chi-restraints excluded: chain AT residue 52 SER Chi-restraints excluded: chain AT residue 65 VAL Chi-restraints excluded: chain AU residue 22 ASN Chi-restraints excluded: chain AU residue 23 LEU Chi-restraints excluded: chain AU residue 51 LEU Chi-restraints excluded: chain AV residue 28 THR Chi-restraints excluded: chain AV residue 48 GLN Chi-restraints excluded: chain AV residue 51 LEU Chi-restraints excluded: chain AV residue 53 GLU Chi-restraints excluded: chain AV residue 62 SER Chi-restraints excluded: chain AW residue 24 GLN Chi-restraints excluded: chain AX residue 44 LEU Chi-restraints excluded: chain AX residue 71 ILE Chi-restraints excluded: chain AY residue 10 ASP Chi-restraints excluded: chain AY residue 55 ASN Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain BA residue 20 VAL Chi-restraints excluded: chain BB residue 54 TYR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 108 ARG Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain J residue 71 ASN Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 132 TYR Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain M residue 107 MET Chi-restraints excluded: chain N residue 78 ASN Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 61 LYS Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain R residue 366 LEU Chi-restraints excluded: chain U residue 366 LEU Chi-restraints excluded: chain U residue 381 MET Chi-restraints excluded: chain V residue 370 SER Chi-restraints excluded: chain a residue 380 LYS Chi-restraints excluded: chain c residue 379 ILE Chi-restraints excluded: chain e residue 366 LEU Chi-restraints excluded: chain g residue 366 LEU Chi-restraints excluded: chain g residue 370 SER Chi-restraints excluded: chain j residue 366 LEU Chi-restraints excluded: chain j residue 390 SER Chi-restraints excluded: chain l residue 370 SER Chi-restraints excluded: chain m residue 366 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 263 optimal weight: 0.6980 chunk 147 optimal weight: 8.9990 chunk 395 optimal weight: 1.9990 chunk 323 optimal weight: 10.0000 chunk 131 optimal weight: 9.9990 chunk 475 optimal weight: 0.6980 chunk 513 optimal weight: 8.9990 chunk 423 optimal weight: 10.0000 chunk 471 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 381 optimal weight: 0.4980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 45 GLN ** 3 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 218 GLN ** 4 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 176 GLN 5 238 ASN A 97 GLN ** AO 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 71 GLN ** AR 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AS 22 ASN ** AS 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 22 ASN AU 61 GLN AU 77 GLN AX 78 ASN AZ 24 GLN ** BA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 61 GLN C 87 GLN G 169 GLN H 87 GLN I 87 GLN K 169 GLN L 97 GLN Q 169 GLN U 372 GLN ** Z 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 372 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 46515 Z= 0.232 Angle : 0.729 13.686 62995 Z= 0.367 Chirality : 0.046 0.313 6948 Planarity : 0.005 0.072 7985 Dihedral : 5.794 76.288 6218 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.11 % Favored : 95.82 % Rotamer: Outliers : 3.68 % Allowed : 21.85 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.10), residues: 5563 helix: -0.88 (0.09), residues: 3029 sheet: -0.60 (0.20), residues: 496 loop : -2.15 (0.12), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRPBA 5 HIS 0.016 0.001 HIS Q 75 PHE 0.025 0.001 PHE 7 6 TYR 0.032 0.002 TYRAY 47 ARG 0.010 0.001 ARG B 65 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1542 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 1363 time to evaluate : 5.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 38 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.7228 (ttm-80) REVERT: 0 116 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7916 (mm-30) REVERT: 0 160 LYS cc_start: 0.9152 (ptpp) cc_final: 0.8791 (pttm) REVERT: 0 213 LYS cc_start: 0.9354 (ptmt) cc_final: 0.9106 (ptmm) REVERT: 0 218 GLN cc_start: 0.9085 (tm-30) cc_final: 0.8849 (tm-30) REVERT: 0 219 TYR cc_start: 0.8720 (m-80) cc_final: 0.8513 (m-10) REVERT: 1 4 ASP cc_start: 0.8376 (m-30) cc_final: 0.7481 (p0) REVERT: 1 50 MET cc_start: 0.8834 (ttt) cc_final: 0.8612 (tmm) REVERT: 1 94 GLU cc_start: 0.8646 (pt0) cc_final: 0.8249 (tm-30) REVERT: 1 97 ASP cc_start: 0.8979 (m-30) cc_final: 0.8733 (m-30) REVERT: 1 110 GLU cc_start: 0.8513 (pm20) cc_final: 0.8279 (pm20) REVERT: 1 160 LYS cc_start: 0.9424 (mtmm) cc_final: 0.9187 (mtmm) REVERT: 1 165 LEU cc_start: 0.9159 (mm) cc_final: 0.8767 (mm) REVERT: 1 166 TYR cc_start: 0.8450 (t80) cc_final: 0.7639 (m-80) REVERT: 1 169 PHE cc_start: 0.8288 (m-80) cc_final: 0.7655 (m-80) REVERT: 1 173 ASP cc_start: 0.7935 (t70) cc_final: 0.7694 (t70) REVERT: 1 188 MET cc_start: 0.8535 (tpp) cc_final: 0.8319 (tmm) REVERT: 2 29 LYS cc_start: 0.9243 (ttmm) cc_final: 0.8839 (tttp) REVERT: 2 76 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8123 (mm-30) REVERT: 2 166 TYR cc_start: 0.8997 (OUTLIER) cc_final: 0.8667 (t80) REVERT: 2 206 ASP cc_start: 0.8045 (t0) cc_final: 0.7607 (t0) REVERT: 3 111 LEU cc_start: 0.9617 (tp) cc_final: 0.9398 (tp) REVERT: 3 180 LEU cc_start: 0.9588 (OUTLIER) cc_final: 0.9378 (mp) REVERT: 3 206 ASP cc_start: 0.8178 (t0) cc_final: 0.7752 (t0) REVERT: 3 215 LEU cc_start: 0.9472 (mt) cc_final: 0.9233 (mt) REVERT: 3 220 MET cc_start: 0.8081 (tpp) cc_final: 0.7703 (tpp) REVERT: 4 26 CYS cc_start: 0.8605 (p) cc_final: 0.8178 (p) REVERT: 4 50 MET cc_start: 0.8989 (tmm) cc_final: 0.8773 (tmm) REVERT: 4 72 TYR cc_start: 0.7993 (t80) cc_final: 0.7224 (t80) REVERT: 4 188 MET cc_start: 0.8558 (tpp) cc_final: 0.8271 (tpp) REVERT: 4 201 LEU cc_start: 0.9464 (tp) cc_final: 0.9195 (tp) REVERT: 5 95 MET cc_start: 0.8434 (tpp) cc_final: 0.8133 (tpp) REVERT: 5 131 MET cc_start: 0.8117 (ttm) cc_final: 0.7846 (ttm) REVERT: 5 160 MET cc_start: 0.9427 (mpp) cc_final: 0.9028 (mpp) REVERT: 6 14 LEU cc_start: 0.9523 (mt) cc_final: 0.9126 (mt) REVERT: 6 67 TYR cc_start: 0.7395 (m-10) cc_final: 0.6724 (m-10) REVERT: 7 18 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9101 (mt) REVERT: 7 49 PHE cc_start: 0.8016 (m-80) cc_final: 0.7458 (m-80) REVERT: 7 52 LYS cc_start: 0.7433 (ttmt) cc_final: 0.7096 (tttt) REVERT: 8 61 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.7931 (t80) REVERT: 8 76 ARG cc_start: 0.9253 (mtm180) cc_final: 0.8597 (mtt90) REVERT: 8 77 GLN cc_start: 0.9131 (tp40) cc_final: 0.8569 (tm-30) REVERT: 8 81 LEU cc_start: 0.9306 (tp) cc_final: 0.9058 (tp) REVERT: 9 12 LEU cc_start: 0.9476 (mt) cc_final: 0.8675 (tt) REVERT: 9 52 LYS cc_start: 0.9284 (ttmm) cc_final: 0.8765 (ttpt) REVERT: 9 61 PHE cc_start: 0.9039 (t80) cc_final: 0.8697 (t80) REVERT: 9 77 GLN cc_start: 0.8905 (pt0) cc_final: 0.8624 (tt0) REVERT: A 103 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7515 (p0) REVERT: A 158 MET cc_start: 0.7830 (tmm) cc_final: 0.7576 (tmm) REVERT: AN 47 ASP cc_start: 0.9099 (m-30) cc_final: 0.8842 (m-30) REVERT: AN 75 SER cc_start: 0.9009 (m) cc_final: 0.8543 (p) REVERT: AN 87 LEU cc_start: 0.9372 (mt) cc_final: 0.8769 (mt) REVERT: AO 49 GLN cc_start: 0.8666 (tp-100) cc_final: 0.8069 (tp-100) REVERT: AO 69 ILE cc_start: 0.9304 (tp) cc_final: 0.8755 (tp) REVERT: AO 73 MET cc_start: 0.8434 (mmt) cc_final: 0.7757 (mmt) REVERT: AO 83 MET cc_start: 0.8906 (tpp) cc_final: 0.8612 (tpt) REVERT: AO 99 LEU cc_start: 0.9091 (mm) cc_final: 0.8479 (mm) REVERT: AP 42 ILE cc_start: 0.9166 (mm) cc_final: 0.8871 (mt) REVERT: AP 48 LYS cc_start: 0.8976 (ttmm) cc_final: 0.8685 (tppp) REVERT: AP 55 ILE cc_start: 0.8993 (mm) cc_final: 0.8441 (pt) REVERT: AP 66 GLU cc_start: 0.8670 (mt-10) cc_final: 0.7895 (mp0) REVERT: AP 77 TYR cc_start: 0.8919 (t80) cc_final: 0.8482 (t80) REVERT: AQ 53 ASN cc_start: 0.8635 (m-40) cc_final: 0.8270 (m110) REVERT: AQ 57 ASP cc_start: 0.8639 (t70) cc_final: 0.8345 (p0) REVERT: AQ 59 ASN cc_start: 0.9366 (t0) cc_final: 0.9124 (t0) REVERT: AQ 67 LEU cc_start: 0.9410 (mm) cc_final: 0.9145 (mm) REVERT: AQ 69 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.7657 (tp) REVERT: AQ 72 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8411 (mp0) REVERT: AQ 99 LEU cc_start: 0.9235 (mt) cc_final: 0.9017 (mp) REVERT: AR 59 ASN cc_start: 0.8805 (t0) cc_final: 0.8586 (t0) REVERT: AR 63 ASP cc_start: 0.7848 (t0) cc_final: 0.7440 (t70) REVERT: AR 72 GLU cc_start: 0.8734 (tp30) cc_final: 0.8327 (tm-30) REVERT: AR 76 ASP cc_start: 0.8820 (m-30) cc_final: 0.7506 (m-30) REVERT: AS 27 VAL cc_start: 0.9151 (t) cc_final: 0.8695 (m) REVERT: AS 50 LYS cc_start: 0.8820 (tptt) cc_final: 0.8369 (tttt) REVERT: AS 51 LEU cc_start: 0.9550 (tt) cc_final: 0.9151 (mm) REVERT: AT 23 LEU cc_start: 0.8038 (tp) cc_final: 0.7810 (mm) REVERT: AT 28 THR cc_start: 0.7675 (p) cc_final: 0.7374 (p) REVERT: AT 47 TYR cc_start: 0.9263 (t80) cc_final: 0.8708 (t80) REVERT: AT 53 GLU cc_start: 0.7469 (mt-10) cc_final: 0.7186 (mt-10) REVERT: AT 61 GLN cc_start: 0.8886 (pp30) cc_final: 0.8482 (pp30) REVERT: AT 66 LYS cc_start: 0.8700 (tptp) cc_final: 0.8470 (tptm) REVERT: AT 72 ASP cc_start: 0.8899 (m-30) cc_final: 0.8077 (p0) REVERT: AT 76 ILE cc_start: 0.8972 (tp) cc_final: 0.8710 (tp) REVERT: AU 51 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8421 (pp) REVERT: AV 40 ASP cc_start: 0.8617 (m-30) cc_final: 0.8398 (t70) REVERT: AV 47 TYR cc_start: 0.9048 (t80) cc_final: 0.8574 (t80) REVERT: AV 53 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7575 (mp0) REVERT: AV 66 LYS cc_start: 0.8788 (tptt) cc_final: 0.8532 (tptt) REVERT: AV 69 LYS cc_start: 0.9441 (tttt) cc_final: 0.8968 (tttt) REVERT: AW 47 TYR cc_start: 0.8635 (t80) cc_final: 0.8367 (t80) REVERT: AW 58 ARG cc_start: 0.8706 (mmt180) cc_final: 0.8129 (mmt180) REVERT: AW 61 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8336 (pp30) REVERT: AW 68 PHE cc_start: 0.9180 (m-80) cc_final: 0.8899 (m-80) REVERT: AY 43 LEU cc_start: 0.6328 (tp) cc_final: 0.5899 (tt) REVERT: AY 63 ASN cc_start: 0.7881 (t0) cc_final: 0.7659 (t0) REVERT: AY 79 PHE cc_start: 0.8853 (m-80) cc_final: 0.8466 (m-80) REVERT: AZ 8 TYR cc_start: 0.8237 (t80) cc_final: 0.7524 (t80) REVERT: AZ 61 GLN cc_start: 0.9646 (pp30) cc_final: 0.9434 (pp30) REVERT: AZ 72 ASP cc_start: 0.9088 (p0) cc_final: 0.8257 (p0) REVERT: AZ 76 ILE cc_start: 0.9278 (mp) cc_final: 0.9068 (mp) REVERT: AZ 79 PHE cc_start: 0.8271 (m-10) cc_final: 0.8017 (m-80) REVERT: B 38 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7613 (mtpt) REVERT: B 49 MET cc_start: 0.6631 (OUTLIER) cc_final: 0.6358 (mtm) REVERT: B 62 MET cc_start: 0.8203 (tpp) cc_final: 0.7886 (tpp) REVERT: B 103 ASP cc_start: 0.7961 (p0) cc_final: 0.6917 (p0) REVERT: B 106 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6797 (mp0) REVERT: BA 79 PHE cc_start: 0.9238 (m-80) cc_final: 0.8979 (m-80) REVERT: D 41 SER cc_start: 0.7887 (p) cc_final: 0.7548 (p) REVERT: D 101 ILE cc_start: 0.9220 (mm) cc_final: 0.9020 (mt) REVERT: D 114 LEU cc_start: 0.8701 (mm) cc_final: 0.8439 (tp) REVERT: F 80 LEU cc_start: 0.8702 (tp) cc_final: 0.8454 (tt) REVERT: F 106 GLU cc_start: 0.7421 (mp0) cc_final: 0.7130 (mp0) REVERT: F 107 MET cc_start: 0.8310 (tmm) cc_final: 0.7738 (tmm) REVERT: G 55 GLU cc_start: 0.7802 (mp0) cc_final: 0.7498 (mp0) REVERT: G 82 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7344 (mm-30) REVERT: G 115 ARG cc_start: 0.8163 (ptm-80) cc_final: 0.7917 (ptm-80) REVERT: G 167 ASP cc_start: 0.7602 (OUTLIER) cc_final: 0.6988 (t0) REVERT: H 167 ASP cc_start: 0.7341 (p0) cc_final: 0.6221 (p0) REVERT: H 168 LYS cc_start: 0.9097 (mmmt) cc_final: 0.8650 (mmtt) REVERT: I 39 ASP cc_start: 0.7669 (t0) cc_final: 0.7438 (t0) REVERT: J 165 MET cc_start: 0.8045 (mtp) cc_final: 0.7750 (ttm) REVERT: L 62 MET cc_start: 0.7425 (tmm) cc_final: 0.7203 (tmm) REVERT: M 157 ASP cc_start: 0.7392 (p0) cc_final: 0.7050 (p0) REVERT: O 136 TYR cc_start: 0.7982 (m-80) cc_final: 0.7761 (m-10) REVERT: O 138 LEU cc_start: 0.8452 (mp) cc_final: 0.8248 (mp) REVERT: P 76 ASP cc_start: 0.7744 (t0) cc_final: 0.7473 (t0) REVERT: P 93 TYR cc_start: 0.7657 (t80) cc_final: 0.7265 (t80) REVERT: P 155 TYR cc_start: 0.8445 (t80) cc_final: 0.7144 (t80) REVERT: Q 165 MET cc_start: 0.7673 (mpp) cc_final: 0.7395 (mpp) REVERT: a 380 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8794 (ttmm) REVERT: b 379 ILE cc_start: 0.9357 (mm) cc_final: 0.8983 (mm) REVERT: f 371 PHE cc_start: 0.8077 (m-10) cc_final: 0.7846 (m-80) REVERT: g 366 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7909 (pp) REVERT: i 371 PHE cc_start: 0.8098 (m-80) cc_final: 0.7846 (m-10) REVERT: i 376 GLU cc_start: 0.6816 (tm-30) cc_final: 0.6254 (tm-30) REVERT: j 366 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8831 (pp) REVERT: j 381 MET cc_start: 0.7741 (ttm) cc_final: 0.7332 (tpp) REVERT: k 381 MET cc_start: 0.6541 (mmm) cc_final: 0.6076 (mmm) REVERT: m 366 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8442 (pp) outliers start: 179 outliers final: 109 residues processed: 1448 average time/residue: 0.5860 time to fit residues: 1370.3033 Evaluate side-chains 1380 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 1253 time to evaluate : 5.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 38 ARG Chi-restraints excluded: chain 0 residue 81 THR Chi-restraints excluded: chain 0 residue 107 SER Chi-restraints excluded: chain 0 residue 166 TYR Chi-restraints excluded: chain 0 residue 170 VAL Chi-restraints excluded: chain 0 residue 188 MET Chi-restraints excluded: chain 0 residue 191 VAL Chi-restraints excluded: chain 1 residue 72 TYR Chi-restraints excluded: chain 1 residue 85 ILE Chi-restraints excluded: chain 1 residue 221 ASP Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 2 residue 45 GLN Chi-restraints excluded: chain 2 residue 83 ASN Chi-restraints excluded: chain 2 residue 166 TYR Chi-restraints excluded: chain 2 residue 201 LEU Chi-restraints excluded: chain 3 residue 50 MET Chi-restraints excluded: chain 3 residue 83 ASN Chi-restraints excluded: chain 3 residue 85 ILE Chi-restraints excluded: chain 3 residue 94 GLU Chi-restraints excluded: chain 3 residue 161 ILE Chi-restraints excluded: chain 3 residue 180 LEU Chi-restraints excluded: chain 4 residue 23 SER Chi-restraints excluded: chain 4 residue 51 THR Chi-restraints excluded: chain 4 residue 138 ILE Chi-restraints excluded: chain 5 residue 68 VAL Chi-restraints excluded: chain 5 residue 226 ILE Chi-restraints excluded: chain 6 residue 18 LEU Chi-restraints excluded: chain 7 residue 2 ASP Chi-restraints excluded: chain 7 residue 18 LEU Chi-restraints excluded: chain 8 residue 3 ASP Chi-restraints excluded: chain 8 residue 15 VAL Chi-restraints excluded: chain 8 residue 61 PHE Chi-restraints excluded: chain 8 residue 63 LEU Chi-restraints excluded: chain 8 residue 69 GLU Chi-restraints excluded: chain 9 residue 15 VAL Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain AN residue 74 ILE Chi-restraints excluded: chain AO residue 29 LEU Chi-restraints excluded: chain AO residue 86 THR Chi-restraints excluded: chain AP residue 59 ASN Chi-restraints excluded: chain AP residue 75 SER Chi-restraints excluded: chain AP residue 86 THR Chi-restraints excluded: chain AQ residue 69 ILE Chi-restraints excluded: chain AQ residue 72 GLU Chi-restraints excluded: chain AQ residue 88 THR Chi-restraints excluded: chain AR residue 29 LEU Chi-restraints excluded: chain AR residue 34 LEU Chi-restraints excluded: chain AR residue 92 VAL Chi-restraints excluded: chain AS residue 22 ASN Chi-restraints excluded: chain AS residue 47 TYR Chi-restraints excluded: chain AS residue 67 VAL Chi-restraints excluded: chain AT residue 52 SER Chi-restraints excluded: chain AU residue 31 LEU Chi-restraints excluded: chain AU residue 51 LEU Chi-restraints excluded: chain AU residue 52 SER Chi-restraints excluded: chain AU residue 64 THR Chi-restraints excluded: chain AU residue 67 VAL Chi-restraints excluded: chain AV residue 28 THR Chi-restraints excluded: chain AV residue 31 LEU Chi-restraints excluded: chain AV residue 48 GLN Chi-restraints excluded: chain AV residue 53 GLU Chi-restraints excluded: chain AV residue 72 ASP Chi-restraints excluded: chain AW residue 61 GLN Chi-restraints excluded: chain AX residue 44 LEU Chi-restraints excluded: chain AX residue 71 ILE Chi-restraints excluded: chain AY residue 75 ILE Chi-restraints excluded: chain AY residue 76 ILE Chi-restraints excluded: chain AZ residue 9 LEU Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain BA residue 20 VAL Chi-restraints excluded: chain BA residue 77 GLN Chi-restraints excluded: chain BB residue 54 TYR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 108 ARG Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 116 ASN Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 166 MET Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain L residue 38 LYS Chi-restraints excluded: chain L residue 103 ASP Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 116 ASN Chi-restraints excluded: chain L residue 132 TYR Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain N residue 78 ASN Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 61 LYS Chi-restraints excluded: chain P residue 38 LYS Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain R residue 366 LEU Chi-restraints excluded: chain U residue 366 LEU Chi-restraints excluded: chain V residue 370 SER Chi-restraints excluded: chain Z residue 367 LYS Chi-restraints excluded: chain Z residue 392 LEU Chi-restraints excluded: chain a residue 380 LYS Chi-restraints excluded: chain b residue 366 LEU Chi-restraints excluded: chain e residue 366 LEU Chi-restraints excluded: chain g residue 366 LEU Chi-restraints excluded: chain j residue 366 LEU Chi-restraints excluded: chain j residue 390 SER Chi-restraints excluded: chain m residue 366 LEU Chi-restraints excluded: chain m residue 390 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 470 optimal weight: 2.9990 chunk 357 optimal weight: 0.8980 chunk 246 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 227 optimal weight: 0.0670 chunk 319 optimal weight: 4.9990 chunk 477 optimal weight: 6.9990 chunk 505 optimal weight: 7.9990 chunk 249 optimal weight: 5.9990 chunk 452 optimal weight: 9.9990 chunk 136 optimal weight: 7.9990 overall best weight: 1.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 45 GLN ** 3 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 218 GLN ** 4 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 127 ASN ** 5 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AS 22 ASN AU 61 GLN AU 77 GLN AU 78 ASN ** AZ 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 GLN K 87 GLN ** P 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 372 GLN ** Z 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 46515 Z= 0.238 Angle : 0.723 11.237 62995 Z= 0.362 Chirality : 0.045 0.245 6948 Planarity : 0.004 0.063 7985 Dihedral : 5.604 75.350 6218 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.29 % Favored : 95.68 % Rotamer: Outliers : 3.95 % Allowed : 23.06 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 (0.11), residues: 5563 helix: -0.24 (0.09), residues: 2973 sheet: -0.29 (0.21), residues: 496 loop : -2.01 (0.12), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRPBA 5 HIS 0.004 0.001 HIS G 75 PHE 0.024 0.002 PHE 8 49 TYR 0.023 0.002 TYR 7 74 ARG 0.013 0.001 ARG Q 143 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1502 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1310 time to evaluate : 5.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 38 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7113 (ttm-80) REVERT: 0 108 ASP cc_start: 0.7550 (p0) cc_final: 0.6552 (p0) REVERT: 0 116 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7662 (mm-30) REVERT: 0 156 LYS cc_start: 0.8888 (ttmm) cc_final: 0.8486 (mttm) REVERT: 0 186 MET cc_start: 0.8296 (tpp) cc_final: 0.7956 (tpp) REVERT: 0 213 LYS cc_start: 0.9457 (ptmt) cc_final: 0.9193 (ptmm) REVERT: 0 218 GLN cc_start: 0.8998 (tm-30) cc_final: 0.8761 (tm-30) REVERT: 1 70 ASP cc_start: 0.8571 (m-30) cc_final: 0.8126 (p0) REVERT: 1 110 GLU cc_start: 0.8499 (pm20) cc_final: 0.8284 (pm20) REVERT: 1 160 LYS cc_start: 0.9411 (mtmm) cc_final: 0.9158 (mtmm) REVERT: 1 166 TYR cc_start: 0.8526 (OUTLIER) cc_final: 0.7967 (m-80) REVERT: 1 167 LEU cc_start: 0.9328 (mt) cc_final: 0.9077 (mt) REVERT: 1 173 ASP cc_start: 0.7969 (t70) cc_final: 0.7693 (t70) REVERT: 1 188 MET cc_start: 0.8615 (tpp) cc_final: 0.8408 (tmm) REVERT: 2 29 LYS cc_start: 0.9220 (ttmm) cc_final: 0.8764 (tttp) REVERT: 2 45 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7559 (tp-100) REVERT: 2 76 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8237 (mm-30) REVERT: 2 166 TYR cc_start: 0.9216 (OUTLIER) cc_final: 0.8681 (t80) REVERT: 2 187 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.8063 (mmm) REVERT: 3 154 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8440 (mm-30) REVERT: 3 180 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9315 (mp) REVERT: 3 206 ASP cc_start: 0.8271 (t0) cc_final: 0.7713 (t0) REVERT: 3 211 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9025 (pt) REVERT: 3 213 LYS cc_start: 0.9212 (mmmm) cc_final: 0.9003 (mmmm) REVERT: 3 215 LEU cc_start: 0.9519 (mt) cc_final: 0.9234 (mt) REVERT: 3 220 MET cc_start: 0.8089 (tpp) cc_final: 0.7630 (tpp) REVERT: 4 26 CYS cc_start: 0.8783 (p) cc_final: 0.8092 (p) REVERT: 4 50 MET cc_start: 0.9038 (tmm) cc_final: 0.8779 (tmm) REVERT: 4 76 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7099 (mm-30) REVERT: 4 201 LEU cc_start: 0.9491 (tp) cc_final: 0.9227 (tp) REVERT: 5 95 MET cc_start: 0.8585 (tpp) cc_final: 0.8346 (tpp) REVERT: 5 131 MET cc_start: 0.8334 (ttm) cc_final: 0.8073 (ttm) REVERT: 5 160 MET cc_start: 0.9376 (mpp) cc_final: 0.8919 (mpp) REVERT: 6 14 LEU cc_start: 0.9521 (mt) cc_final: 0.9130 (mt) REVERT: 6 67 TYR cc_start: 0.7419 (m-10) cc_final: 0.6709 (m-10) REVERT: 7 18 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9203 (mt) REVERT: 7 49 PHE cc_start: 0.8095 (m-80) cc_final: 0.7577 (m-80) REVERT: 7 52 LYS cc_start: 0.7492 (ttmt) cc_final: 0.7278 (ttpt) REVERT: 8 61 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.8004 (t80) REVERT: 8 76 ARG cc_start: 0.9252 (mtm180) cc_final: 0.8609 (mtt90) REVERT: 8 77 GLN cc_start: 0.9223 (tp40) cc_final: 0.8595 (tm-30) REVERT: 9 12 LEU cc_start: 0.9490 (mt) cc_final: 0.8630 (tt) REVERT: 9 52 LYS cc_start: 0.9352 (ttmm) cc_final: 0.8574 (ttpt) REVERT: 9 61 PHE cc_start: 0.9120 (t80) cc_final: 0.8821 (t80) REVERT: 9 76 ARG cc_start: 0.8827 (ttm110) cc_final: 0.8490 (mtm110) REVERT: 9 77 GLN cc_start: 0.8868 (pt0) cc_final: 0.8667 (tt0) REVERT: A 103 ASP cc_start: 0.8643 (OUTLIER) cc_final: 0.8304 (p0) REVERT: A 147 PHE cc_start: 0.7555 (p90) cc_final: 0.7338 (p90) REVERT: AN 49 GLN cc_start: 0.9628 (mm110) cc_final: 0.9115 (mm-40) REVERT: AN 87 LEU cc_start: 0.9381 (mt) cc_final: 0.8793 (mt) REVERT: AO 69 ILE cc_start: 0.9275 (tp) cc_final: 0.8865 (tp) REVERT: AO 73 MET cc_start: 0.8531 (mmt) cc_final: 0.8264 (mmt) REVERT: AO 83 MET cc_start: 0.8947 (tpp) cc_final: 0.8665 (tpt) REVERT: AO 99 LEU cc_start: 0.8952 (mm) cc_final: 0.8702 (mm) REVERT: AP 48 LYS cc_start: 0.8997 (ttmm) cc_final: 0.8717 (tppp) REVERT: AP 55 ILE cc_start: 0.8955 (mm) cc_final: 0.8431 (pt) REVERT: AP 66 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8014 (mp0) REVERT: AP 77 TYR cc_start: 0.8777 (t80) cc_final: 0.8435 (t80) REVERT: AQ 59 ASN cc_start: 0.9397 (t0) cc_final: 0.9194 (t0) REVERT: AQ 67 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9156 (mm) REVERT: AQ 69 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.7674 (tp) REVERT: AQ 72 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8083 (mp0) REVERT: AQ 99 LEU cc_start: 0.9205 (mt) cc_final: 0.8973 (mp) REVERT: AR 48 LYS cc_start: 0.7782 (tttt) cc_final: 0.7393 (tmtt) REVERT: AR 63 ASP cc_start: 0.7842 (t0) cc_final: 0.7455 (t70) REVERT: AR 72 GLU cc_start: 0.8596 (tp30) cc_final: 0.7952 (tm-30) REVERT: AR 73 MET cc_start: 0.9306 (mpp) cc_final: 0.8868 (mmm) REVERT: AR 76 ASP cc_start: 0.8719 (m-30) cc_final: 0.7278 (m-30) REVERT: AS 27 VAL cc_start: 0.9061 (t) cc_final: 0.8647 (m) REVERT: AS 50 LYS cc_start: 0.8872 (tptt) cc_final: 0.8504 (tttt) REVERT: AS 51 LEU cc_start: 0.9563 (tt) cc_final: 0.9135 (mm) REVERT: AT 23 LEU cc_start: 0.8019 (tp) cc_final: 0.7753 (mm) REVERT: AT 28 THR cc_start: 0.7754 (p) cc_final: 0.7442 (p) REVERT: AT 47 TYR cc_start: 0.9250 (t80) cc_final: 0.8664 (t80) REVERT: AT 61 GLN cc_start: 0.8991 (pp30) cc_final: 0.8597 (pp30) REVERT: AT 72 ASP cc_start: 0.8966 (m-30) cc_final: 0.8254 (p0) REVERT: AU 38 PRO cc_start: 0.6371 (Cg_endo) cc_final: 0.6138 (Cg_exo) REVERT: AU 47 TYR cc_start: 0.9127 (t80) cc_final: 0.8766 (t80) REVERT: AU 58 ARG cc_start: 0.8359 (mmt180) cc_final: 0.8095 (mmt-90) REVERT: AV 47 TYR cc_start: 0.9055 (t80) cc_final: 0.8601 (t80) REVERT: AV 53 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: AV 69 LYS cc_start: 0.9483 (tttt) cc_final: 0.9142 (tttt) REVERT: AW 23 LEU cc_start: 0.8987 (tp) cc_final: 0.8677 (tt) REVERT: AW 47 TYR cc_start: 0.8506 (t80) cc_final: 0.8261 (t80) REVERT: AW 58 ARG cc_start: 0.8773 (mmt180) cc_final: 0.8401 (mmt-90) REVERT: AW 61 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8569 (pp30) REVERT: AW 68 PHE cc_start: 0.9170 (m-80) cc_final: 0.8968 (m-80) REVERT: AY 79 PHE cc_start: 0.8859 (m-80) cc_final: 0.8494 (m-80) REVERT: AZ 8 TYR cc_start: 0.8359 (t80) cc_final: 0.7423 (t80) REVERT: AZ 61 GLN cc_start: 0.9633 (pp30) cc_final: 0.9425 (pp30) REVERT: AZ 72 ASP cc_start: 0.9060 (p0) cc_final: 0.8720 (p0) REVERT: AZ 76 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.8948 (mt) REVERT: AZ 79 PHE cc_start: 0.8411 (m-10) cc_final: 0.7843 (m-10) REVERT: B 49 MET cc_start: 0.6707 (OUTLIER) cc_final: 0.6481 (mtm) REVERT: B 103 ASP cc_start: 0.7971 (p0) cc_final: 0.6939 (p0) REVERT: B 106 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6655 (mp0) REVERT: BA 54 TYR cc_start: 0.4439 (OUTLIER) cc_final: 0.4168 (m-80) REVERT: BA 79 PHE cc_start: 0.9090 (m-80) cc_final: 0.8229 (m-80) REVERT: BB 75 ILE cc_start: 0.9381 (pt) cc_final: 0.9102 (pt) REVERT: C 93 TYR cc_start: 0.8183 (t80) cc_final: 0.7855 (t80) REVERT: C 165 MET cc_start: 0.7784 (mmm) cc_final: 0.7384 (tpt) REVERT: D 41 SER cc_start: 0.7759 (p) cc_final: 0.7510 (p) REVERT: D 165 MET cc_start: 0.7725 (mmm) cc_final: 0.7502 (mtt) REVERT: F 80 LEU cc_start: 0.8822 (tp) cc_final: 0.8504 (tt) REVERT: F 107 MET cc_start: 0.8420 (tmm) cc_final: 0.7724 (tmm) REVERT: G 82 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7299 (mm-30) REVERT: G 115 ARG cc_start: 0.8093 (ptm-80) cc_final: 0.7849 (ptm-80) REVERT: G 167 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7244 (t0) REVERT: H 167 ASP cc_start: 0.7455 (p0) cc_final: 0.7202 (m-30) REVERT: I 39 ASP cc_start: 0.7828 (t0) cc_final: 0.7626 (t0) REVERT: L 62 MET cc_start: 0.7517 (tmm) cc_final: 0.7302 (tmm) REVERT: L 67 LYS cc_start: 0.7894 (mptt) cc_final: 0.7653 (mmtt) REVERT: L 107 MET cc_start: 0.8297 (tmm) cc_final: 0.7667 (tmm) REVERT: M 157 ASP cc_start: 0.7373 (p0) cc_final: 0.7129 (p0) REVERT: P 76 ASP cc_start: 0.7536 (t0) cc_final: 0.7197 (t0) REVERT: P 93 TYR cc_start: 0.7684 (t80) cc_final: 0.7451 (t80) REVERT: P 155 TYR cc_start: 0.8505 (t80) cc_final: 0.7686 (t80) REVERT: U 376 GLU cc_start: 0.7014 (mm-30) cc_final: 0.6751 (mm-30) REVERT: V 376 GLU cc_start: 0.8394 (mp0) cc_final: 0.8190 (mp0) REVERT: b 379 ILE cc_start: 0.9395 (mm) cc_final: 0.9009 (mm) REVERT: e 367 LYS cc_start: 0.6383 (mmmt) cc_final: 0.6124 (mmmt) REVERT: f 371 PHE cc_start: 0.8074 (m-10) cc_final: 0.7761 (m-80) REVERT: g 366 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8234 (pp) REVERT: i 371 PHE cc_start: 0.8378 (m-80) cc_final: 0.7888 (m-10) REVERT: i 376 GLU cc_start: 0.7437 (tm-30) cc_final: 0.6943 (tm-30) REVERT: j 366 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8903 (pp) REVERT: j 381 MET cc_start: 0.7720 (ttm) cc_final: 0.7176 (tpp) REVERT: k 381 MET cc_start: 0.6828 (mmm) cc_final: 0.6533 (mmm) REVERT: m 366 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8440 (pp) outliers start: 192 outliers final: 116 residues processed: 1405 average time/residue: 0.5946 time to fit residues: 1363.3674 Evaluate side-chains 1365 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1227 time to evaluate : 5.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 38 ARG Chi-restraints excluded: chain 0 residue 105 LYS Chi-restraints excluded: chain 0 residue 107 SER Chi-restraints excluded: chain 0 residue 112 VAL Chi-restraints excluded: chain 0 residue 166 TYR Chi-restraints excluded: chain 0 residue 188 MET Chi-restraints excluded: chain 0 residue 191 VAL Chi-restraints excluded: chain 0 residue 211 LEU Chi-restraints excluded: chain 1 residue 72 TYR Chi-restraints excluded: chain 1 residue 84 ASP Chi-restraints excluded: chain 1 residue 85 ILE Chi-restraints excluded: chain 1 residue 103 LEU Chi-restraints excluded: chain 1 residue 166 TYR Chi-restraints excluded: chain 1 residue 186 MET Chi-restraints excluded: chain 1 residue 221 ASP Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 2 residue 45 GLN Chi-restraints excluded: chain 2 residue 83 ASN Chi-restraints excluded: chain 2 residue 166 TYR Chi-restraints excluded: chain 2 residue 187 MET Chi-restraints excluded: chain 2 residue 201 LEU Chi-restraints excluded: chain 3 residue 36 MET Chi-restraints excluded: chain 3 residue 50 MET Chi-restraints excluded: chain 3 residue 83 ASN Chi-restraints excluded: chain 3 residue 85 ILE Chi-restraints excluded: chain 3 residue 180 LEU Chi-restraints excluded: chain 3 residue 211 LEU Chi-restraints excluded: chain 4 residue 23 SER Chi-restraints excluded: chain 4 residue 51 THR Chi-restraints excluded: chain 5 residue 68 VAL Chi-restraints excluded: chain 5 residue 129 LEU Chi-restraints excluded: chain 5 residue 177 VAL Chi-restraints excluded: chain 5 residue 182 LEU Chi-restraints excluded: chain 6 residue 18 LEU Chi-restraints excluded: chain 7 residue 2 ASP Chi-restraints excluded: chain 7 residue 18 LEU Chi-restraints excluded: chain 8 residue 3 ASP Chi-restraints excluded: chain 8 residue 15 VAL Chi-restraints excluded: chain 8 residue 57 CYS Chi-restraints excluded: chain 8 residue 61 PHE Chi-restraints excluded: chain 9 residue 15 VAL Chi-restraints excluded: chain 9 residue 19 SER Chi-restraints excluded: chain 9 residue 63 LEU Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain AN residue 74 ILE Chi-restraints excluded: chain AO residue 29 LEU Chi-restraints excluded: chain AO residue 86 THR Chi-restraints excluded: chain AO residue 87 LEU Chi-restraints excluded: chain AO residue 88 THR Chi-restraints excluded: chain AP residue 30 ASP Chi-restraints excluded: chain AP residue 59 ASN Chi-restraints excluded: chain AP residue 75 SER Chi-restraints excluded: chain AP residue 86 THR Chi-restraints excluded: chain AP residue 98 LEU Chi-restraints excluded: chain AQ residue 67 LEU Chi-restraints excluded: chain AQ residue 69 ILE Chi-restraints excluded: chain AQ residue 72 GLU Chi-restraints excluded: chain AQ residue 97 THR Chi-restraints excluded: chain AR residue 29 LEU Chi-restraints excluded: chain AR residue 34 LEU Chi-restraints excluded: chain AR residue 92 VAL Chi-restraints excluded: chain AS residue 47 TYR Chi-restraints excluded: chain AT residue 52 SER Chi-restraints excluded: chain AU residue 31 LEU Chi-restraints excluded: chain AU residue 33 LYS Chi-restraints excluded: chain AU residue 64 THR Chi-restraints excluded: chain AU residue 67 VAL Chi-restraints excluded: chain AV residue 31 LEU Chi-restraints excluded: chain AV residue 48 GLN Chi-restraints excluded: chain AV residue 53 GLU Chi-restraints excluded: chain AV residue 72 ASP Chi-restraints excluded: chain AW residue 61 GLN Chi-restraints excluded: chain AX residue 21 ASP Chi-restraints excluded: chain AX residue 44 LEU Chi-restraints excluded: chain AY residue 75 ILE Chi-restraints excluded: chain AY residue 76 ILE Chi-restraints excluded: chain AZ residue 76 ILE Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain BA residue 20 VAL Chi-restraints excluded: chain BA residue 54 TYR Chi-restraints excluded: chain BA residue 55 ASN Chi-restraints excluded: chain BA residue 77 GLN Chi-restraints excluded: chain BB residue 54 TYR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 108 ARG Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 116 ASN Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 166 MET Chi-restraints excluded: chain J residue 71 ASN Chi-restraints excluded: chain L residue 38 LYS Chi-restraints excluded: chain L residue 68 ILE Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 116 ASN Chi-restraints excluded: chain L residue 132 TYR Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain M residue 105 SER Chi-restraints excluded: chain N residue 38 LYS Chi-restraints excluded: chain N residue 78 ASN Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 61 LYS Chi-restraints excluded: chain P residue 38 LYS Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain R residue 366 LEU Chi-restraints excluded: chain U residue 366 LEU Chi-restraints excluded: chain V residue 370 SER Chi-restraints excluded: chain Z residue 367 LYS Chi-restraints excluded: chain a residue 366 LEU Chi-restraints excluded: chain b residue 366 LEU Chi-restraints excluded: chain e residue 366 LEU Chi-restraints excluded: chain g residue 366 LEU Chi-restraints excluded: chain h residue 379 ILE Chi-restraints excluded: chain j residue 366 LEU Chi-restraints excluded: chain j residue 390 SER Chi-restraints excluded: chain m residue 366 LEU Chi-restraints excluded: chain m residue 390 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 421 optimal weight: 1.9990 chunk 286 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 376 optimal weight: 7.9990 chunk 208 optimal weight: 7.9990 chunk 431 optimal weight: 0.9980 chunk 349 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 258 optimal weight: 1.9990 chunk 453 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 218 GLN ** 4 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 127 ASN ** 5 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AR 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AS 22 ASN AT 48 GLN AU 26 GLN AU 61 GLN ** AW 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AY 55 ASN AY 63 ASN BA 61 GLN ** BC 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 GLN K 87 GLN ** P 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 97 GLN U 372 GLN Z 372 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 46515 Z= 0.201 Angle : 0.712 11.615 62995 Z= 0.354 Chirality : 0.045 0.320 6948 Planarity : 0.004 0.062 7985 Dihedral : 5.423 76.389 6218 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.80 % Favored : 96.14 % Rotamer: Outliers : 4.19 % Allowed : 23.27 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.05 (0.11), residues: 5563 helix: 0.04 (0.10), residues: 2977 sheet: 0.07 (0.21), residues: 496 loop : -1.92 (0.12), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRPBA 5 HIS 0.004 0.001 HIS G 75 PHE 0.029 0.001 PHE 7 6 TYR 0.027 0.001 TYR 4 166 ARG 0.012 0.001 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1526 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1322 time to evaluate : 5.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 38 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7570 (ttm-80) REVERT: 0 116 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7734 (mm-30) REVERT: 0 186 MET cc_start: 0.8275 (tpp) cc_final: 0.7908 (tpp) REVERT: 0 213 LYS cc_start: 0.9367 (ptmt) cc_final: 0.9100 (ptmm) REVERT: 0 218 GLN cc_start: 0.9017 (tm-30) cc_final: 0.8636 (pp30) REVERT: 0 219 TYR cc_start: 0.8725 (m-10) cc_final: 0.8489 (m-10) REVERT: 1 70 ASP cc_start: 0.8866 (m-30) cc_final: 0.8242 (p0) REVERT: 1 93 ASP cc_start: 0.8087 (t0) cc_final: 0.7871 (t0) REVERT: 1 166 TYR cc_start: 0.8530 (OUTLIER) cc_final: 0.7977 (m-80) REVERT: 1 167 LEU cc_start: 0.9359 (mt) cc_final: 0.8966 (tp) REVERT: 1 173 ASP cc_start: 0.7959 (t70) cc_final: 0.7686 (t70) REVERT: 2 29 LYS cc_start: 0.9205 (ttmm) cc_final: 0.8754 (tttp) REVERT: 2 45 GLN cc_start: 0.8195 (pt0) cc_final: 0.7521 (tp-100) REVERT: 2 76 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8259 (mm-30) REVERT: 2 166 TYR cc_start: 0.9250 (OUTLIER) cc_final: 0.8638 (t80) REVERT: 2 205 LEU cc_start: 0.9674 (tt) cc_final: 0.9299 (pp) REVERT: 3 154 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8398 (mm-30) REVERT: 3 173 ASP cc_start: 0.8475 (t0) cc_final: 0.8130 (t0) REVERT: 3 180 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9275 (mp) REVERT: 3 206 ASP cc_start: 0.8234 (t0) cc_final: 0.7772 (t0) REVERT: 3 211 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8923 (pt) REVERT: 3 215 LEU cc_start: 0.9518 (mt) cc_final: 0.9241 (mt) REVERT: 3 220 MET cc_start: 0.8089 (tpp) cc_final: 0.7601 (tpp) REVERT: 4 26 CYS cc_start: 0.8765 (p) cc_final: 0.8061 (p) REVERT: 4 50 MET cc_start: 0.9032 (tmm) cc_final: 0.8809 (tmm) REVERT: 4 72 TYR cc_start: 0.8216 (t80) cc_final: 0.7640 (t80) REVERT: 4 76 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7255 (mm-30) REVERT: 4 101 ASP cc_start: 0.8404 (p0) cc_final: 0.8127 (p0) REVERT: 4 185 MET cc_start: 0.9059 (mmm) cc_final: 0.8715 (mmp) REVERT: 4 188 MET cc_start: 0.8230 (tpp) cc_final: 0.7857 (tpp) REVERT: 4 201 LEU cc_start: 0.9498 (tp) cc_final: 0.9250 (tp) REVERT: 5 95 MET cc_start: 0.8554 (tpp) cc_final: 0.8288 (tpp) REVERT: 5 131 MET cc_start: 0.8414 (ttm) cc_final: 0.8050 (ttm) REVERT: 5 160 MET cc_start: 0.9370 (mpp) cc_final: 0.8893 (mpp) REVERT: 6 14 LEU cc_start: 0.9510 (mt) cc_final: 0.9117 (mt) REVERT: 7 18 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9100 (mt) REVERT: 7 49 PHE cc_start: 0.8205 (m-80) cc_final: 0.7460 (m-80) REVERT: 7 52 LYS cc_start: 0.7501 (ttmt) cc_final: 0.7287 (ttpt) REVERT: 7 74 TYR cc_start: 0.8779 (t80) cc_final: 0.8569 (t80) REVERT: 8 61 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.8054 (t80) REVERT: 8 76 ARG cc_start: 0.9218 (mtm180) cc_final: 0.8518 (mtt90) REVERT: 8 77 GLN cc_start: 0.8993 (tp40) cc_final: 0.8433 (tm-30) REVERT: 8 81 LEU cc_start: 0.9364 (tp) cc_final: 0.9093 (tp) REVERT: 9 12 LEU cc_start: 0.9502 (mt) cc_final: 0.8680 (tt) REVERT: 9 52 LYS cc_start: 0.9333 (ttmm) cc_final: 0.8713 (ttpt) REVERT: 9 61 PHE cc_start: 0.9057 (t80) cc_final: 0.8724 (t80) REVERT: 9 74 TYR cc_start: 0.8782 (t80) cc_final: 0.7998 (t80) REVERT: AM 83 MET cc_start: 0.8288 (tmm) cc_final: 0.8048 (tmm) REVERT: AN 87 LEU cc_start: 0.9364 (mt) cc_final: 0.8858 (mt) REVERT: AO 35 GLN cc_start: 0.8368 (pp30) cc_final: 0.8148 (pp30) REVERT: AO 67 LEU cc_start: 0.9416 (mm) cc_final: 0.9109 (mm) REVERT: AO 69 ILE cc_start: 0.9279 (tp) cc_final: 0.8861 (tp) REVERT: AO 73 MET cc_start: 0.8544 (mmt) cc_final: 0.8306 (mmt) REVERT: AO 83 MET cc_start: 0.8939 (tpp) cc_final: 0.8654 (tpt) REVERT: AO 99 LEU cc_start: 0.8960 (mm) cc_final: 0.8635 (mm) REVERT: AP 25 ASP cc_start: 0.7571 (p0) cc_final: 0.6931 (t70) REVERT: AP 48 LYS cc_start: 0.9003 (ttmm) cc_final: 0.8708 (tppp) REVERT: AP 55 ILE cc_start: 0.8847 (mm) cc_final: 0.8381 (pt) REVERT: AP 66 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8029 (mp0) REVERT: AP 77 TYR cc_start: 0.8703 (t80) cc_final: 0.8449 (t80) REVERT: AQ 47 ASP cc_start: 0.7723 (p0) cc_final: 0.7445 (m-30) REVERT: AQ 53 ASN cc_start: 0.8552 (m-40) cc_final: 0.8191 (m110) REVERT: AQ 67 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9156 (mm) REVERT: AQ 69 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.7969 (tp) REVERT: AQ 72 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8114 (mp0) REVERT: AQ 96 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8887 (mm-30) REVERT: AQ 99 LEU cc_start: 0.9173 (mt) cc_final: 0.8771 (mp) REVERT: AR 63 ASP cc_start: 0.7777 (t0) cc_final: 0.7378 (t70) REVERT: AR 72 GLU cc_start: 0.8509 (tp30) cc_final: 0.7783 (tm-30) REVERT: AR 73 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8941 (mmm) REVERT: AR 76 ASP cc_start: 0.8679 (m-30) cc_final: 0.7202 (m-30) REVERT: AS 27 VAL cc_start: 0.9064 (t) cc_final: 0.8594 (m) REVERT: AS 50 LYS cc_start: 0.8871 (tptt) cc_final: 0.8499 (tttt) REVERT: AS 51 LEU cc_start: 0.9513 (tt) cc_final: 0.9096 (pp) REVERT: AT 23 LEU cc_start: 0.7765 (tp) cc_final: 0.7545 (mm) REVERT: AT 28 THR cc_start: 0.7725 (p) cc_final: 0.7443 (p) REVERT: AT 47 TYR cc_start: 0.9247 (t80) cc_final: 0.8542 (t80) REVERT: AT 50 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8544 (ttmt) REVERT: AT 61 GLN cc_start: 0.9107 (pp30) cc_final: 0.8728 (pp30) REVERT: AT 72 ASP cc_start: 0.8894 (m-30) cc_final: 0.8109 (p0) REVERT: AU 38 PRO cc_start: 0.6394 (Cg_endo) cc_final: 0.6158 (Cg_exo) REVERT: AV 47 TYR cc_start: 0.9065 (t80) cc_final: 0.8599 (t80) REVERT: AV 53 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7817 (mp0) REVERT: AV 69 LYS cc_start: 0.9506 (tttt) cc_final: 0.9133 (tttt) REVERT: AW 23 LEU cc_start: 0.8977 (tp) cc_final: 0.8699 (tt) REVERT: AW 47 TYR cc_start: 0.8499 (t80) cc_final: 0.8261 (t80) REVERT: AW 54 TYR cc_start: 0.7668 (t80) cc_final: 0.7354 (t80) REVERT: AW 58 ARG cc_start: 0.8730 (mmt180) cc_final: 0.8406 (mmt-90) REVERT: AW 61 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.8569 (pp30) REVERT: AW 79 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.7943 (t80) REVERT: AY 50 LYS cc_start: 0.7570 (mmmt) cc_final: 0.7143 (ptpp) REVERT: AY 79 PHE cc_start: 0.8801 (m-80) cc_final: 0.8484 (m-80) REVERT: AZ 8 TYR cc_start: 0.8399 (t80) cc_final: 0.7468 (t80) REVERT: AZ 61 GLN cc_start: 0.9589 (pp30) cc_final: 0.9359 (pp30) REVERT: AZ 72 ASP cc_start: 0.8912 (p0) cc_final: 0.8312 (p0) REVERT: B 49 MET cc_start: 0.6688 (OUTLIER) cc_final: 0.6423 (mtm) REVERT: B 103 ASP cc_start: 0.7951 (p0) cc_final: 0.7311 (p0) REVERT: BA 54 TYR cc_start: 0.4441 (OUTLIER) cc_final: 0.3800 (m-80) REVERT: BA 61 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8390 (pp30) REVERT: BA 79 PHE cc_start: 0.8834 (m-80) cc_final: 0.8021 (m-80) REVERT: BB 75 ILE cc_start: 0.9344 (pt) cc_final: 0.9036 (pt) REVERT: BD 59 ASN cc_start: 0.6804 (OUTLIER) cc_final: 0.6019 (m110) REVERT: BD 61 GLN cc_start: 0.6568 (tt0) cc_final: 0.6329 (mt0) REVERT: C 93 TYR cc_start: 0.8305 (t80) cc_final: 0.8025 (t80) REVERT: C 166 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7581 (mtm) REVERT: D 164 THR cc_start: 0.9162 (OUTLIER) cc_final: 0.8927 (p) REVERT: F 80 LEU cc_start: 0.8791 (tp) cc_final: 0.8585 (tt) REVERT: F 106 GLU cc_start: 0.7433 (mp0) cc_final: 0.7200 (mp0) REVERT: F 107 MET cc_start: 0.8522 (tmm) cc_final: 0.7636 (tmm) REVERT: G 115 ARG cc_start: 0.8018 (ptm-80) cc_final: 0.7785 (ptm-80) REVERT: G 167 ASP cc_start: 0.7839 (OUTLIER) cc_final: 0.7351 (t0) REVERT: H 167 ASP cc_start: 0.7188 (p0) cc_final: 0.6624 (p0) REVERT: I 39 ASP cc_start: 0.7755 (t0) cc_final: 0.7550 (t0) REVERT: K 107 MET cc_start: 0.7903 (tmm) cc_final: 0.7617 (tmm) REVERT: L 62 MET cc_start: 0.7626 (tmm) cc_final: 0.7285 (tmm) REVERT: L 67 LYS cc_start: 0.7965 (mptt) cc_final: 0.7691 (mmtt) REVERT: P 76 ASP cc_start: 0.7485 (t0) cc_final: 0.7130 (t0) REVERT: P 93 TYR cc_start: 0.7861 (t80) cc_final: 0.7618 (t80) REVERT: P 134 LYS cc_start: 0.9052 (pptt) cc_final: 0.8818 (pptt) REVERT: P 155 TYR cc_start: 0.8518 (t80) cc_final: 0.7712 (t80) REVERT: U 376 GLU cc_start: 0.7007 (mm-30) cc_final: 0.6769 (mm-30) REVERT: V 376 GLU cc_start: 0.8344 (mp0) cc_final: 0.8143 (mp0) REVERT: b 379 ILE cc_start: 0.9404 (mm) cc_final: 0.9005 (mm) REVERT: f 371 PHE cc_start: 0.7996 (m-10) cc_final: 0.7624 (m-80) REVERT: g 366 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8297 (pp) REVERT: i 371 PHE cc_start: 0.8325 (m-80) cc_final: 0.7816 (m-10) REVERT: i 376 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7270 (tm-30) REVERT: j 366 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8819 (pp) REVERT: j 371 PHE cc_start: 0.8568 (p90) cc_final: 0.8286 (p90) REVERT: k 381 MET cc_start: 0.6911 (mmm) cc_final: 0.6642 (mmm) REVERT: m 366 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8431 (pp) outliers start: 204 outliers final: 123 residues processed: 1428 average time/residue: 0.5760 time to fit residues: 1331.8841 Evaluate side-chains 1371 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1223 time to evaluate : 4.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 38 ARG Chi-restraints excluded: chain 0 residue 81 THR Chi-restraints excluded: chain 0 residue 105 LYS Chi-restraints excluded: chain 0 residue 166 TYR Chi-restraints excluded: chain 0 residue 188 MET Chi-restraints excluded: chain 0 residue 211 LEU Chi-restraints excluded: chain 1 residue 72 TYR Chi-restraints excluded: chain 1 residue 84 ASP Chi-restraints excluded: chain 1 residue 85 ILE Chi-restraints excluded: chain 1 residue 103 LEU Chi-restraints excluded: chain 1 residue 166 TYR Chi-restraints excluded: chain 1 residue 186 MET Chi-restraints excluded: chain 1 residue 221 ASP Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 2 residue 57 LEU Chi-restraints excluded: chain 2 residue 83 ASN Chi-restraints excluded: chain 2 residue 166 TYR Chi-restraints excluded: chain 2 residue 201 LEU Chi-restraints excluded: chain 3 residue 50 MET Chi-restraints excluded: chain 3 residue 83 ASN Chi-restraints excluded: chain 3 residue 85 ILE Chi-restraints excluded: chain 3 residue 180 LEU Chi-restraints excluded: chain 3 residue 211 LEU Chi-restraints excluded: chain 4 residue 23 SER Chi-restraints excluded: chain 4 residue 51 THR Chi-restraints excluded: chain 4 residue 215 LEU Chi-restraints excluded: chain 5 residue 10 HIS Chi-restraints excluded: chain 5 residue 12 LEU Chi-restraints excluded: chain 5 residue 68 VAL Chi-restraints excluded: chain 5 residue 182 LEU Chi-restraints excluded: chain 6 residue 18 LEU Chi-restraints excluded: chain 7 residue 2 ASP Chi-restraints excluded: chain 7 residue 18 LEU Chi-restraints excluded: chain 7 residue 42 LEU Chi-restraints excluded: chain 8 residue 3 ASP Chi-restraints excluded: chain 8 residue 57 CYS Chi-restraints excluded: chain 8 residue 61 PHE Chi-restraints excluded: chain 8 residue 69 GLU Chi-restraints excluded: chain 9 residue 15 VAL Chi-restraints excluded: chain 9 residue 19 SER Chi-restraints excluded: chain 9 residue 51 ILE Chi-restraints excluded: chain 9 residue 63 LEU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain AN residue 42 ILE Chi-restraints excluded: chain AN residue 74 ILE Chi-restraints excluded: chain AO residue 50 THR Chi-restraints excluded: chain AO residue 86 THR Chi-restraints excluded: chain AO residue 87 LEU Chi-restraints excluded: chain AO residue 88 THR Chi-restraints excluded: chain AP residue 75 SER Chi-restraints excluded: chain AP residue 86 THR Chi-restraints excluded: chain AP residue 98 LEU Chi-restraints excluded: chain AQ residue 21 SER Chi-restraints excluded: chain AQ residue 67 LEU Chi-restraints excluded: chain AQ residue 69 ILE Chi-restraints excluded: chain AQ residue 72 GLU Chi-restraints excluded: chain AQ residue 83 MET Chi-restraints excluded: chain AQ residue 88 THR Chi-restraints excluded: chain AQ residue 97 THR Chi-restraints excluded: chain AR residue 34 LEU Chi-restraints excluded: chain AR residue 73 MET Chi-restraints excluded: chain AR residue 92 VAL Chi-restraints excluded: chain AS residue 22 ASN Chi-restraints excluded: chain AS residue 47 TYR Chi-restraints excluded: chain AS residue 67 VAL Chi-restraints excluded: chain AT residue 50 LYS Chi-restraints excluded: chain AT residue 52 SER Chi-restraints excluded: chain AU residue 31 LEU Chi-restraints excluded: chain AU residue 64 THR Chi-restraints excluded: chain AU residue 67 VAL Chi-restraints excluded: chain AV residue 28 THR Chi-restraints excluded: chain AV residue 31 LEU Chi-restraints excluded: chain AV residue 48 GLN Chi-restraints excluded: chain AV residue 53 GLU Chi-restraints excluded: chain AV residue 62 SER Chi-restraints excluded: chain AV residue 72 ASP Chi-restraints excluded: chain AW residue 61 GLN Chi-restraints excluded: chain AW residue 79 PHE Chi-restraints excluded: chain AX residue 21 ASP Chi-restraints excluded: chain AX residue 44 LEU Chi-restraints excluded: chain AX residue 71 ILE Chi-restraints excluded: chain AY residue 76 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain BA residue 20 VAL Chi-restraints excluded: chain BA residue 54 TYR Chi-restraints excluded: chain BA residue 55 ASN Chi-restraints excluded: chain BA residue 61 GLN Chi-restraints excluded: chain BA residue 77 GLN Chi-restraints excluded: chain BB residue 54 TYR Chi-restraints excluded: chain BD residue 59 ASN Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 108 ARG Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 116 ASN Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain L residue 38 LYS Chi-restraints excluded: chain L residue 68 ILE Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 116 ASN Chi-restraints excluded: chain L residue 132 TYR Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain M residue 118 SER Chi-restraints excluded: chain N residue 78 ASN Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 61 LYS Chi-restraints excluded: chain P residue 38 LYS Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 165 MET Chi-restraints excluded: chain R residue 366 LEU Chi-restraints excluded: chain U residue 366 LEU Chi-restraints excluded: chain V residue 370 SER Chi-restraints excluded: chain Z residue 367 LYS Chi-restraints excluded: chain a residue 366 LEU Chi-restraints excluded: chain b residue 366 LEU Chi-restraints excluded: chain c residue 376 GLU Chi-restraints excluded: chain e residue 366 LEU Chi-restraints excluded: chain g residue 366 LEU Chi-restraints excluded: chain h residue 379 ILE Chi-restraints excluded: chain j residue 366 LEU Chi-restraints excluded: chain j residue 390 SER Chi-restraints excluded: chain m residue 366 LEU Chi-restraints excluded: chain m residue 390 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 170 optimal weight: 5.9990 chunk 455 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 296 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 506 optimal weight: 7.9990 chunk 420 optimal weight: 4.9990 chunk 234 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 167 optimal weight: 9.9990 chunk 265 optimal weight: 0.0570 overall best weight: 2.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 218 GLN ** 4 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 37 GLN 9 77 GLN ** AO 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AR 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AR 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 48 GLN ** BC 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN H 87 GLN I 87 GLN L 97 GLN ** N 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 372 GLN Z 372 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 46515 Z= 0.269 Angle : 0.750 11.564 62995 Z= 0.375 Chirality : 0.045 0.248 6948 Planarity : 0.005 0.062 7985 Dihedral : 5.400 75.448 6218 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.70 % Favored : 95.26 % Rotamer: Outliers : 4.22 % Allowed : 24.70 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.74 (0.11), residues: 5563 helix: 0.31 (0.10), residues: 2941 sheet: 0.37 (0.22), residues: 456 loop : -1.78 (0.12), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP i 365 HIS 0.007 0.001 HIS a 385 PHE 0.027 0.002 PHE 8 49 TYR 0.030 0.002 TYRAY 47 ARG 0.013 0.001 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1455 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 1250 time to evaluate : 5.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 38 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.6993 (ttm-80) REVERT: 0 116 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7757 (mm-30) REVERT: 0 156 LYS cc_start: 0.8930 (ttmm) cc_final: 0.8445 (mttt) REVERT: 0 186 MET cc_start: 0.8254 (tpp) cc_final: 0.7925 (tpp) REVERT: 0 213 LYS cc_start: 0.9421 (ptmt) cc_final: 0.9128 (ptmm) REVERT: 0 218 GLN cc_start: 0.9103 (tm-30) cc_final: 0.8692 (pp30) REVERT: 0 219 TYR cc_start: 0.8870 (m-10) cc_final: 0.8636 (m-10) REVERT: 1 70 ASP cc_start: 0.8880 (m-30) cc_final: 0.8220 (p0) REVERT: 1 110 GLU cc_start: 0.8503 (pm20) cc_final: 0.8258 (pm20) REVERT: 1 160 LYS cc_start: 0.9534 (OUTLIER) cc_final: 0.9280 (mtmm) REVERT: 1 166 TYR cc_start: 0.8548 (OUTLIER) cc_final: 0.7983 (m-80) REVERT: 1 167 LEU cc_start: 0.9401 (mt) cc_final: 0.8731 (tp) REVERT: 1 173 ASP cc_start: 0.8023 (t70) cc_final: 0.7767 (t70) REVERT: 1 220 MET cc_start: 0.6175 (tpt) cc_final: 0.5857 (mmt) REVERT: 2 29 LYS cc_start: 0.9103 (ttmm) cc_final: 0.8577 (tttp) REVERT: 2 45 GLN cc_start: 0.8114 (pt0) cc_final: 0.7542 (tp-100) REVERT: 2 64 MET cc_start: 0.8880 (mmm) cc_final: 0.8571 (mmm) REVERT: 2 76 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8279 (mm-30) REVERT: 2 166 TYR cc_start: 0.9312 (OUTLIER) cc_final: 0.8576 (t80) REVERT: 2 187 MET cc_start: 0.8703 (mmm) cc_final: 0.8346 (mmm) REVERT: 2 206 ASP cc_start: 0.8463 (t0) cc_final: 0.8231 (t0) REVERT: 3 105 LYS cc_start: 0.9237 (tptp) cc_final: 0.9024 (tptm) REVERT: 3 154 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8489 (mm-30) REVERT: 3 173 ASP cc_start: 0.8646 (t0) cc_final: 0.8384 (t0) REVERT: 3 180 LEU cc_start: 0.9543 (OUTLIER) cc_final: 0.9293 (mp) REVERT: 3 206 ASP cc_start: 0.8358 (t0) cc_final: 0.7856 (t0) REVERT: 3 215 LEU cc_start: 0.9514 (mt) cc_final: 0.9240 (mt) REVERT: 4 26 CYS cc_start: 0.8766 (p) cc_final: 0.8087 (p) REVERT: 4 50 MET cc_start: 0.9110 (tmm) cc_final: 0.8806 (tmm) REVERT: 4 185 MET cc_start: 0.9053 (mmm) cc_final: 0.8767 (mmm) REVERT: 4 188 MET cc_start: 0.8269 (tpp) cc_final: 0.7959 (tpp) REVERT: 4 201 LEU cc_start: 0.9519 (tp) cc_final: 0.9315 (tp) REVERT: 5 95 MET cc_start: 0.8608 (tpp) cc_final: 0.8322 (tpp) REVERT: 5 131 MET cc_start: 0.8534 (ttm) cc_final: 0.8151 (ttm) REVERT: 5 160 MET cc_start: 0.9379 (mpp) cc_final: 0.8934 (mpp) REVERT: 6 14 LEU cc_start: 0.9503 (mt) cc_final: 0.9179 (mt) REVERT: 6 74 TYR cc_start: 0.8798 (t80) cc_final: 0.7854 (t80) REVERT: 7 18 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9154 (mt) REVERT: 7 49 PHE cc_start: 0.8281 (m-80) cc_final: 0.7500 (m-80) REVERT: 7 52 LYS cc_start: 0.7558 (ttmt) cc_final: 0.7159 (tttt) REVERT: 7 74 TYR cc_start: 0.8838 (t80) cc_final: 0.8634 (t80) REVERT: 8 52 LYS cc_start: 0.9105 (ttmt) cc_final: 0.8813 (mtmt) REVERT: 8 76 ARG cc_start: 0.9241 (mtm180) cc_final: 0.8521 (mtt90) REVERT: 8 77 GLN cc_start: 0.8986 (tp40) cc_final: 0.8383 (tm-30) REVERT: 8 81 LEU cc_start: 0.9264 (tp) cc_final: 0.8989 (tp) REVERT: 9 52 LYS cc_start: 0.9372 (ttmm) cc_final: 0.8596 (ttpt) REVERT: 9 61 PHE cc_start: 0.9088 (t80) cc_final: 0.8725 (t80) REVERT: 9 76 ARG cc_start: 0.8918 (ttm110) cc_final: 0.8574 (mtm110) REVERT: AM 83 MET cc_start: 0.8324 (tmm) cc_final: 0.8120 (tmm) REVERT: AM 98 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8745 (mm) REVERT: AN 87 LEU cc_start: 0.9370 (mt) cc_final: 0.8898 (mt) REVERT: AO 67 LEU cc_start: 0.9420 (mm) cc_final: 0.9091 (mm) REVERT: AO 69 ILE cc_start: 0.9257 (tp) cc_final: 0.8901 (tp) REVERT: AO 83 MET cc_start: 0.8945 (tpp) cc_final: 0.8655 (tpt) REVERT: AO 99 LEU cc_start: 0.8944 (mm) cc_final: 0.8712 (mm) REVERT: AP 25 ASP cc_start: 0.7579 (p0) cc_final: 0.6860 (t70) REVERT: AP 48 LYS cc_start: 0.8999 (ttmm) cc_final: 0.8707 (tppp) REVERT: AP 66 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8044 (mp0) REVERT: AP 77 TYR cc_start: 0.8787 (t80) cc_final: 0.8533 (t80) REVERT: AQ 67 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9163 (mm) REVERT: AQ 72 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8163 (mp0) REVERT: AQ 99 LEU cc_start: 0.8966 (mt) cc_final: 0.8675 (mp) REVERT: AR 48 LYS cc_start: 0.8714 (tmtt) cc_final: 0.8263 (tmtt) REVERT: AR 63 ASP cc_start: 0.8227 (t0) cc_final: 0.7840 (t70) REVERT: AR 72 GLU cc_start: 0.8573 (tp30) cc_final: 0.7874 (tm-30) REVERT: AR 73 MET cc_start: 0.9200 (mpp) cc_final: 0.8968 (mmm) REVERT: AR 76 ASP cc_start: 0.8698 (m-30) cc_final: 0.7284 (m-30) REVERT: AS 27 VAL cc_start: 0.9231 (t) cc_final: 0.8963 (m) REVERT: AS 50 LYS cc_start: 0.8946 (tptt) cc_final: 0.8467 (tttt) REVERT: AS 51 LEU cc_start: 0.9529 (tt) cc_final: 0.9108 (pp) REVERT: AT 28 THR cc_start: 0.8045 (p) cc_final: 0.7765 (p) REVERT: AT 47 TYR cc_start: 0.9221 (t80) cc_final: 0.8625 (t80) REVERT: AT 61 GLN cc_start: 0.9057 (pp30) cc_final: 0.8768 (pp30) REVERT: AT 72 ASP cc_start: 0.8958 (m-30) cc_final: 0.8019 (p0) REVERT: AU 38 PRO cc_start: 0.6367 (Cg_endo) cc_final: 0.6112 (Cg_exo) REVERT: AU 80 ARG cc_start: 0.7887 (ptm-80) cc_final: 0.7663 (ttm170) REVERT: AV 47 TYR cc_start: 0.9049 (t80) cc_final: 0.8594 (t80) REVERT: AV 53 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7858 (mp0) REVERT: AV 69 LYS cc_start: 0.9470 (tttt) cc_final: 0.9150 (tttt) REVERT: AW 23 LEU cc_start: 0.8895 (tp) cc_final: 0.8641 (tt) REVERT: AW 47 TYR cc_start: 0.8518 (t80) cc_final: 0.8275 (t80) REVERT: AW 54 TYR cc_start: 0.7821 (t80) cc_final: 0.7576 (t80) REVERT: AW 58 ARG cc_start: 0.8680 (mmt180) cc_final: 0.8447 (mmt-90) REVERT: AW 61 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8314 (pp30) REVERT: AW 79 PHE cc_start: 0.8624 (OUTLIER) cc_final: 0.8038 (t80) REVERT: AY 50 LYS cc_start: 0.7523 (mmmt) cc_final: 0.7253 (ptpp) REVERT: AY 61 GLN cc_start: 0.8382 (pt0) cc_final: 0.7788 (pt0) REVERT: AY 79 PHE cc_start: 0.8881 (m-80) cc_final: 0.8536 (m-80) REVERT: AZ 72 ASP cc_start: 0.9124 (p0) cc_final: 0.8746 (p0) REVERT: B 103 ASP cc_start: 0.7996 (p0) cc_final: 0.7743 (p0) REVERT: B 107 MET cc_start: 0.8747 (tpp) cc_final: 0.8411 (tpt) REVERT: BA 54 TYR cc_start: 0.4428 (OUTLIER) cc_final: 0.4183 (m-80) REVERT: BA 79 PHE cc_start: 0.8873 (m-80) cc_final: 0.8004 (m-80) REVERT: BB 75 ILE cc_start: 0.9323 (pt) cc_final: 0.9095 (pt) REVERT: BD 59 ASN cc_start: 0.6983 (OUTLIER) cc_final: 0.6227 (m110) REVERT: BD 61 GLN cc_start: 0.6664 (tt0) cc_final: 0.6388 (mt0) REVERT: C 93 TYR cc_start: 0.8311 (t80) cc_final: 0.8000 (t80) REVERT: C 165 MET cc_start: 0.7791 (mmm) cc_final: 0.7532 (tpt) REVERT: C 166 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7656 (mtm) REVERT: F 107 MET cc_start: 0.8745 (tmm) cc_final: 0.7849 (tmm) REVERT: G 115 ARG cc_start: 0.8110 (ptm-80) cc_final: 0.7904 (ptm-80) REVERT: G 167 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7394 (t0) REVERT: I 39 ASP cc_start: 0.7797 (t0) cc_final: 0.7388 (t0) REVERT: I 87 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7768 (mt0) REVERT: J 44 THR cc_start: 0.8493 (p) cc_final: 0.8187 (t) REVERT: K 107 MET cc_start: 0.7912 (tmm) cc_final: 0.7615 (tmm) REVERT: L 67 LYS cc_start: 0.8171 (mptt) cc_final: 0.7897 (mmtt) REVERT: N 38 LYS cc_start: 0.8320 (pttt) cc_final: 0.8034 (pttt) REVERT: O 105 SER cc_start: 0.8736 (m) cc_final: 0.8256 (t) REVERT: P 76 ASP cc_start: 0.7656 (t0) cc_final: 0.7269 (t0) REVERT: Q 61 LYS cc_start: 0.8973 (tmtt) cc_final: 0.8772 (tptp) REVERT: U 376 GLU cc_start: 0.7222 (mm-30) cc_final: 0.6719 (mm-30) REVERT: V 376 GLU cc_start: 0.8409 (mp0) cc_final: 0.8193 (mp0) REVERT: g 366 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8293 (pp) REVERT: i 371 PHE cc_start: 0.8356 (m-80) cc_final: 0.7818 (m-10) REVERT: j 366 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8884 (pp) REVERT: m 366 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8275 (pp) outliers start: 205 outliers final: 148 residues processed: 1347 average time/residue: 0.5843 time to fit residues: 1277.3801 Evaluate side-chains 1358 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1190 time to evaluate : 5.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 38 ARG Chi-restraints excluded: chain 0 residue 81 THR Chi-restraints excluded: chain 0 residue 105 LYS Chi-restraints excluded: chain 0 residue 166 TYR Chi-restraints excluded: chain 0 residue 170 VAL Chi-restraints excluded: chain 0 residue 188 MET Chi-restraints excluded: chain 0 residue 211 LEU Chi-restraints excluded: chain 1 residue 72 TYR Chi-restraints excluded: chain 1 residue 84 ASP Chi-restraints excluded: chain 1 residue 85 ILE Chi-restraints excluded: chain 1 residue 103 LEU Chi-restraints excluded: chain 1 residue 160 LYS Chi-restraints excluded: chain 1 residue 166 TYR Chi-restraints excluded: chain 1 residue 170 VAL Chi-restraints excluded: chain 1 residue 186 MET Chi-restraints excluded: chain 1 residue 211 LEU Chi-restraints excluded: chain 1 residue 221 ASP Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 2 residue 57 LEU Chi-restraints excluded: chain 2 residue 83 ASN Chi-restraints excluded: chain 2 residue 84 ASP Chi-restraints excluded: chain 2 residue 160 LYS Chi-restraints excluded: chain 2 residue 166 TYR Chi-restraints excluded: chain 2 residue 172 VAL Chi-restraints excluded: chain 2 residue 201 LEU Chi-restraints excluded: chain 3 residue 50 MET Chi-restraints excluded: chain 3 residue 83 ASN Chi-restraints excluded: chain 3 residue 85 ILE Chi-restraints excluded: chain 3 residue 180 LEU Chi-restraints excluded: chain 4 residue 23 SER Chi-restraints excluded: chain 4 residue 51 THR Chi-restraints excluded: chain 4 residue 215 LEU Chi-restraints excluded: chain 5 residue 10 HIS Chi-restraints excluded: chain 5 residue 12 LEU Chi-restraints excluded: chain 5 residue 68 VAL Chi-restraints excluded: chain 5 residue 129 LEU Chi-restraints excluded: chain 5 residue 177 VAL Chi-restraints excluded: chain 5 residue 182 LEU Chi-restraints excluded: chain 6 residue 18 LEU Chi-restraints excluded: chain 7 residue 2 ASP Chi-restraints excluded: chain 7 residue 18 LEU Chi-restraints excluded: chain 7 residue 42 LEU Chi-restraints excluded: chain 8 residue 3 ASP Chi-restraints excluded: chain 8 residue 14 LEU Chi-restraints excluded: chain 8 residue 16 LEU Chi-restraints excluded: chain 8 residue 57 CYS Chi-restraints excluded: chain 8 residue 69 GLU Chi-restraints excluded: chain 9 residue 15 VAL Chi-restraints excluded: chain 9 residue 19 SER Chi-restraints excluded: chain 9 residue 51 ILE Chi-restraints excluded: chain 9 residue 63 LEU Chi-restraints excluded: chain 9 residue 69 GLU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain AM residue 98 LEU Chi-restraints excluded: chain AN residue 74 ILE Chi-restraints excluded: chain AO residue 50 THR Chi-restraints excluded: chain AO residue 86 THR Chi-restraints excluded: chain AO residue 87 LEU Chi-restraints excluded: chain AO residue 88 THR Chi-restraints excluded: chain AO residue 98 LEU Chi-restraints excluded: chain AP residue 19 ILE Chi-restraints excluded: chain AP residue 34 LEU Chi-restraints excluded: chain AP residue 75 SER Chi-restraints excluded: chain AP residue 86 THR Chi-restraints excluded: chain AP residue 98 LEU Chi-restraints excluded: chain AQ residue 21 SER Chi-restraints excluded: chain AQ residue 57 ASP Chi-restraints excluded: chain AQ residue 67 LEU Chi-restraints excluded: chain AQ residue 69 ILE Chi-restraints excluded: chain AQ residue 72 GLU Chi-restraints excluded: chain AQ residue 83 MET Chi-restraints excluded: chain AQ residue 88 THR Chi-restraints excluded: chain AQ residue 97 THR Chi-restraints excluded: chain AR residue 34 LEU Chi-restraints excluded: chain AR residue 42 ILE Chi-restraints excluded: chain AR residue 92 VAL Chi-restraints excluded: chain AS residue 47 TYR Chi-restraints excluded: chain AS residue 67 VAL Chi-restraints excluded: chain AS residue 79 PHE Chi-restraints excluded: chain AT residue 52 SER Chi-restraints excluded: chain AU residue 31 LEU Chi-restraints excluded: chain AU residue 64 THR Chi-restraints excluded: chain AU residue 67 VAL Chi-restraints excluded: chain AV residue 28 THR Chi-restraints excluded: chain AV residue 31 LEU Chi-restraints excluded: chain AV residue 53 GLU Chi-restraints excluded: chain AV residue 62 SER Chi-restraints excluded: chain AV residue 72 ASP Chi-restraints excluded: chain AW residue 48 GLN Chi-restraints excluded: chain AW residue 61 GLN Chi-restraints excluded: chain AW residue 75 ILE Chi-restraints excluded: chain AW residue 79 PHE Chi-restraints excluded: chain AX residue 21 ASP Chi-restraints excluded: chain AX residue 44 LEU Chi-restraints excluded: chain AX residue 71 ILE Chi-restraints excluded: chain AY residue 65 VAL Chi-restraints excluded: chain AY residue 76 ILE Chi-restraints excluded: chain AZ residue 75 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain BA residue 20 VAL Chi-restraints excluded: chain BA residue 54 TYR Chi-restraints excluded: chain BA residue 77 GLN Chi-restraints excluded: chain BB residue 54 TYR Chi-restraints excluded: chain BD residue 59 ASN Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 108 ARG Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 116 ASN Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain J residue 71 ASN Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain L residue 38 LYS Chi-restraints excluded: chain L residue 68 ILE Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 116 ASN Chi-restraints excluded: chain L residue 132 TYR Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 49 MET Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain M residue 105 SER Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 78 ASN Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 61 LYS Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain Q residue 42 LEU Chi-restraints excluded: chain R residue 366 LEU Chi-restraints excluded: chain U residue 366 LEU Chi-restraints excluded: chain V residue 370 SER Chi-restraints excluded: chain Y residue 367 LYS Chi-restraints excluded: chain Z residue 367 LYS Chi-restraints excluded: chain a residue 366 LEU Chi-restraints excluded: chain b residue 366 LEU Chi-restraints excluded: chain c residue 376 GLU Chi-restraints excluded: chain e residue 366 LEU Chi-restraints excluded: chain g residue 366 LEU Chi-restraints excluded: chain h residue 379 ILE Chi-restraints excluded: chain j residue 366 LEU Chi-restraints excluded: chain j residue 390 SER Chi-restraints excluded: chain m residue 366 LEU Chi-restraints excluded: chain m residue 390 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 487 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 288 optimal weight: 5.9990 chunk 369 optimal weight: 10.0000 chunk 286 optimal weight: 9.9990 chunk 425 optimal weight: 0.0970 chunk 282 optimal weight: 30.0000 chunk 504 optimal weight: 5.9990 chunk 315 optimal weight: 10.0000 chunk 307 optimal weight: 3.9990 chunk 232 optimal weight: 5.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 218 GLN ** 4 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 161 ASN ** 5 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 41 GLN 9 77 GLN AM 71 GLN ** AO 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AR 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AR 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AW 48 GLN ** BA 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 GLN I 87 GLN J 97 GLN ** P 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 385 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.5410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 46515 Z= 0.368 Angle : 0.811 12.844 62995 Z= 0.408 Chirality : 0.048 0.393 6948 Planarity : 0.005 0.062 7985 Dihedral : 5.524 74.036 6218 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.99 % Favored : 94.97 % Rotamer: Outliers : 4.95 % Allowed : 25.29 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.75 (0.11), residues: 5563 helix: 0.32 (0.10), residues: 2956 sheet: 0.07 (0.21), residues: 536 loop : -1.81 (0.13), residues: 2071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP i 365 HIS 0.007 0.001 HIS 2 91 PHE 0.032 0.002 PHE 7 6 TYR 0.034 0.002 TYRAU 57 ARG 0.016 0.001 ARG B 65 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1458 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 1217 time to evaluate : 5.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 38 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7111 (ttm-80) REVERT: 0 75 PHE cc_start: 0.9271 (OUTLIER) cc_final: 0.8932 (t80) REVERT: 0 114 PHE cc_start: 0.9006 (t80) cc_final: 0.8760 (t80) REVERT: 0 116 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7770 (mm-30) REVERT: 0 156 LYS cc_start: 0.8975 (ttmm) cc_final: 0.8516 (mttt) REVERT: 0 186 MET cc_start: 0.8224 (tpp) cc_final: 0.7917 (tpp) REVERT: 0 213 LYS cc_start: 0.9481 (ptmt) cc_final: 0.9243 (ptmm) REVERT: 0 218 GLN cc_start: 0.9109 (tm-30) cc_final: 0.8734 (tm-30) REVERT: 1 16 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8659 (mm) REVERT: 1 110 GLU cc_start: 0.8534 (pm20) cc_final: 0.8295 (pm20) REVERT: 1 160 LYS cc_start: 0.9548 (mtmm) cc_final: 0.9285 (mtmm) REVERT: 1 166 TYR cc_start: 0.8644 (OUTLIER) cc_final: 0.8065 (m-80) REVERT: 1 167 LEU cc_start: 0.9451 (mt) cc_final: 0.9098 (tp) REVERT: 1 173 ASP cc_start: 0.8164 (t70) cc_final: 0.7934 (t70) REVERT: 1 188 MET cc_start: 0.8693 (tmm) cc_final: 0.8403 (tmm) REVERT: 1 198 LYS cc_start: 0.9156 (mtpp) cc_final: 0.8347 (mtpp) REVERT: 1 220 MET cc_start: 0.6079 (tpt) cc_final: 0.5732 (mmt) REVERT: 2 29 LYS cc_start: 0.9156 (ttmm) cc_final: 0.8638 (tttp) REVERT: 2 45 GLN cc_start: 0.8170 (pt0) cc_final: 0.7581 (tp-100) REVERT: 2 76 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8318 (mm-30) REVERT: 2 166 TYR cc_start: 0.9378 (OUTLIER) cc_final: 0.8508 (t80) REVERT: 2 188 MET cc_start: 0.8574 (tpp) cc_final: 0.8364 (tpp) REVERT: 2 206 ASP cc_start: 0.8718 (t0) cc_final: 0.8443 (t0) REVERT: 3 116 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8039 (mm-30) REVERT: 3 154 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8479 (mm-30) REVERT: 3 173 ASP cc_start: 0.8614 (t0) cc_final: 0.8346 (t0) REVERT: 3 180 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9265 (mp) REVERT: 3 206 ASP cc_start: 0.8090 (t0) cc_final: 0.7526 (t0) REVERT: 3 215 LEU cc_start: 0.9536 (mt) cc_final: 0.9269 (mt) REVERT: 3 220 MET cc_start: 0.8080 (tpp) cc_final: 0.7593 (tpp) REVERT: 4 26 CYS cc_start: 0.8653 (p) cc_final: 0.8022 (p) REVERT: 4 61 MET cc_start: 0.8762 (ttt) cc_final: 0.8482 (tmm) REVERT: 4 72 TYR cc_start: 0.8354 (t80) cc_final: 0.7923 (t80) REVERT: 4 76 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7238 (mm-30) REVERT: 4 185 MET cc_start: 0.9076 (mmm) cc_final: 0.8782 (mmm) REVERT: 4 188 MET cc_start: 0.8301 (tpp) cc_final: 0.8012 (tpp) REVERT: 5 95 MET cc_start: 0.8651 (tpp) cc_final: 0.8362 (tpp) REVERT: 5 160 MET cc_start: 0.9401 (mpp) cc_final: 0.9057 (mpp) REVERT: 5 164 THR cc_start: 0.8266 (m) cc_final: 0.7643 (p) REVERT: 5 228 LEU cc_start: 0.9410 (tp) cc_final: 0.9122 (tt) REVERT: 5 229 LEU cc_start: 0.9585 (tt) cc_final: 0.9334 (mm) REVERT: 6 10 LYS cc_start: 0.8773 (tppt) cc_final: 0.8354 (tppp) REVERT: 6 14 LEU cc_start: 0.9510 (mt) cc_final: 0.8974 (mt) REVERT: 6 74 TYR cc_start: 0.8819 (t80) cc_final: 0.8211 (t80) REVERT: 7 49 PHE cc_start: 0.8409 (m-80) cc_final: 0.7622 (m-10) REVERT: 7 52 LYS cc_start: 0.7854 (ttmt) cc_final: 0.7515 (tttt) REVERT: 7 74 TYR cc_start: 0.8879 (t80) cc_final: 0.8678 (t80) REVERT: 8 61 PHE cc_start: 0.8437 (OUTLIER) cc_final: 0.7957 (t80) REVERT: 8 76 ARG cc_start: 0.9216 (mtm180) cc_final: 0.8530 (mtt90) REVERT: 8 77 GLN cc_start: 0.8955 (tp40) cc_final: 0.8384 (tm-30) REVERT: 9 13 TYR cc_start: 0.8357 (t80) cc_final: 0.8102 (t80) REVERT: 9 52 LYS cc_start: 0.9412 (ttmm) cc_final: 0.8623 (ttpt) REVERT: 9 61 PHE cc_start: 0.9130 (t80) cc_final: 0.8749 (t80) REVERT: 9 76 ARG cc_start: 0.8821 (ttm110) cc_final: 0.8436 (mtm110) REVERT: AM 83 MET cc_start: 0.8361 (tmm) cc_final: 0.8148 (tmm) REVERT: AM 98 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8760 (mm) REVERT: AN 49 GLN cc_start: 0.9642 (mm-40) cc_final: 0.9438 (mm-40) REVERT: AN 87 LEU cc_start: 0.9456 (mt) cc_final: 0.9004 (mt) REVERT: AO 35 GLN cc_start: 0.8432 (pp30) cc_final: 0.8207 (pp30) REVERT: AO 67 LEU cc_start: 0.9365 (mm) cc_final: 0.9026 (mm) REVERT: AO 69 ILE cc_start: 0.9250 (tp) cc_final: 0.8947 (tp) REVERT: AO 83 MET cc_start: 0.8934 (tpp) cc_final: 0.8666 (tmm) REVERT: AO 99 LEU cc_start: 0.9108 (mm) cc_final: 0.8789 (mm) REVERT: AO 100 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7586 (mmm160) REVERT: AP 25 ASP cc_start: 0.7562 (p0) cc_final: 0.6763 (t70) REVERT: AP 48 LYS cc_start: 0.8991 (ttmm) cc_final: 0.8698 (tppp) REVERT: AP 77 TYR cc_start: 0.8882 (t80) cc_final: 0.8621 (t80) REVERT: AQ 19 ILE cc_start: 0.8601 (mp) cc_final: 0.7756 (mt) REVERT: AQ 53 ASN cc_start: 0.8636 (m-40) cc_final: 0.8238 (m110) REVERT: AQ 67 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9199 (mm) REVERT: AQ 72 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8200 (mp0) REVERT: AQ 96 GLU cc_start: 0.9224 (mm-30) cc_final: 0.9010 (mm-30) REVERT: AQ 99 LEU cc_start: 0.9035 (mt) cc_final: 0.8778 (mp) REVERT: AR 59 ASN cc_start: 0.8999 (t0) cc_final: 0.8782 (t0) REVERT: AR 63 ASP cc_start: 0.8270 (t0) cc_final: 0.7940 (t70) REVERT: AR 72 GLU cc_start: 0.8528 (tp30) cc_final: 0.7856 (tm-30) REVERT: AR 76 ASP cc_start: 0.8629 (m-30) cc_final: 0.7217 (m-30) REVERT: AR 87 LEU cc_start: 0.9413 (mm) cc_final: 0.9040 (pp) REVERT: AR 96 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7900 (tm-30) REVERT: AR 100 ARG cc_start: 0.8276 (ttp-110) cc_final: 0.7987 (ttp-110) REVERT: AS 51 LEU cc_start: 0.9676 (tt) cc_final: 0.9463 (pp) REVERT: AS 70 ASP cc_start: 0.8210 (m-30) cc_final: 0.7840 (m-30) REVERT: AT 28 THR cc_start: 0.8238 (p) cc_final: 0.8020 (p) REVERT: AT 47 TYR cc_start: 0.9190 (t80) cc_final: 0.8578 (t80) REVERT: AT 53 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7225 (mt-10) REVERT: AT 61 GLN cc_start: 0.9172 (pp30) cc_final: 0.8887 (pp30) REVERT: AU 38 PRO cc_start: 0.6313 (Cg_endo) cc_final: 0.6073 (Cg_exo) REVERT: AU 52 SER cc_start: 0.9243 (m) cc_final: 0.8718 (p) REVERT: AU 80 ARG cc_start: 0.7954 (ptm-80) cc_final: 0.7661 (ttm170) REVERT: AV 22 ASN cc_start: 0.6765 (p0) cc_final: 0.6565 (p0) REVERT: AV 47 TYR cc_start: 0.9104 (t80) cc_final: 0.8615 (t80) REVERT: AV 69 LYS cc_start: 0.9503 (tttt) cc_final: 0.9109 (tttt) REVERT: AW 23 LEU cc_start: 0.8884 (tp) cc_final: 0.8660 (tt) REVERT: AW 47 TYR cc_start: 0.8670 (t80) cc_final: 0.8386 (t80) REVERT: AW 54 TYR cc_start: 0.7928 (t80) cc_final: 0.7649 (t80) REVERT: AW 58 ARG cc_start: 0.8755 (mmt180) cc_final: 0.8111 (mmt180) REVERT: AW 61 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8179 (pp30) REVERT: AW 62 SER cc_start: 0.9105 (t) cc_final: 0.8550 (t) REVERT: AW 70 ASP cc_start: 0.9294 (m-30) cc_final: 0.9000 (m-30) REVERT: AW 79 PHE cc_start: 0.8658 (OUTLIER) cc_final: 0.8169 (t80) REVERT: AY 50 LYS cc_start: 0.7522 (mmmt) cc_final: 0.7238 (ptpp) REVERT: AY 61 GLN cc_start: 0.8357 (pt0) cc_final: 0.7740 (pt0) REVERT: AY 79 PHE cc_start: 0.8911 (m-80) cc_final: 0.8591 (m-80) REVERT: AZ 63 ASN cc_start: 0.9214 (m-40) cc_final: 0.8768 (m-40) REVERT: AZ 72 ASP cc_start: 0.9099 (p0) cc_final: 0.8583 (p0) REVERT: B 62 MET cc_start: 0.8442 (tpp) cc_final: 0.8181 (tpp) REVERT: BA 79 PHE cc_start: 0.8906 (m-80) cc_final: 0.7983 (m-80) REVERT: BB 16 PHE cc_start: 0.6891 (OUTLIER) cc_final: 0.6606 (m-10) REVERT: BB 75 ILE cc_start: 0.9354 (pt) cc_final: 0.9031 (pt) REVERT: BB 78 ASN cc_start: 0.8734 (t0) cc_final: 0.8376 (t0) REVERT: BD 59 ASN cc_start: 0.6818 (OUTLIER) cc_final: 0.6165 (m110) REVERT: C 93 TYR cc_start: 0.8379 (t80) cc_final: 0.8075 (t80) REVERT: C 165 MET cc_start: 0.7824 (mmm) cc_final: 0.7369 (tpt) REVERT: F 107 MET cc_start: 0.8814 (tmm) cc_final: 0.7902 (tmm) REVERT: G 167 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7502 (t0) REVERT: H 108 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.8002 (ptp-170) REVERT: H 157 ASP cc_start: 0.7725 (p0) cc_final: 0.7306 (p0) REVERT: I 87 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7950 (mt0) REVERT: K 107 MET cc_start: 0.8016 (tmm) cc_final: 0.7728 (tmm) REVERT: L 67 LYS cc_start: 0.8393 (mptt) cc_final: 0.8078 (mmtt) REVERT: N 38 LYS cc_start: 0.8511 (pttt) cc_final: 0.8057 (pttt) REVERT: O 105 SER cc_start: 0.8851 (m) cc_final: 0.8332 (t) REVERT: P 76 ASP cc_start: 0.7647 (t0) cc_final: 0.7330 (t0) REVERT: S 369 ARG cc_start: 0.7839 (mmt90) cc_final: 0.7355 (mmt90) REVERT: U 376 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7469 (mm-30) REVERT: b 379 ILE cc_start: 0.8993 (mm) cc_final: 0.8622 (mm) REVERT: c 381 MET cc_start: 0.7537 (pmm) cc_final: 0.7290 (pmm) REVERT: e 387 TYR cc_start: 0.8154 (t80) cc_final: 0.7813 (t80) REVERT: f 371 PHE cc_start: 0.8156 (m-80) cc_final: 0.7900 (m-80) REVERT: g 366 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8248 (pp) REVERT: i 371 PHE cc_start: 0.8420 (m-80) cc_final: 0.7827 (m-10) REVERT: j 366 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8905 (pp) outliers start: 241 outliers final: 176 residues processed: 1333 average time/residue: 0.5694 time to fit residues: 1231.4824 Evaluate side-chains 1372 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1176 time to evaluate : 5.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 38 ARG Chi-restraints excluded: chain 0 residue 75 PHE Chi-restraints excluded: chain 0 residue 81 THR Chi-restraints excluded: chain 0 residue 105 LYS Chi-restraints excluded: chain 0 residue 107 SER Chi-restraints excluded: chain 0 residue 166 TYR Chi-restraints excluded: chain 0 residue 170 VAL Chi-restraints excluded: chain 0 residue 188 MET Chi-restraints excluded: chain 0 residue 211 LEU Chi-restraints excluded: chain 1 residue 16 LEU Chi-restraints excluded: chain 1 residue 72 TYR Chi-restraints excluded: chain 1 residue 85 ILE Chi-restraints excluded: chain 1 residue 94 GLU Chi-restraints excluded: chain 1 residue 103 LEU Chi-restraints excluded: chain 1 residue 166 TYR Chi-restraints excluded: chain 1 residue 170 VAL Chi-restraints excluded: chain 1 residue 186 MET Chi-restraints excluded: chain 1 residue 211 LEU Chi-restraints excluded: chain 1 residue 221 ASP Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 2 residue 57 LEU Chi-restraints excluded: chain 2 residue 83 ASN Chi-restraints excluded: chain 2 residue 84 ASP Chi-restraints excluded: chain 2 residue 160 LYS Chi-restraints excluded: chain 2 residue 165 LEU Chi-restraints excluded: chain 2 residue 166 TYR Chi-restraints excluded: chain 2 residue 172 VAL Chi-restraints excluded: chain 2 residue 201 LEU Chi-restraints excluded: chain 3 residue 50 MET Chi-restraints excluded: chain 3 residue 83 ASN Chi-restraints excluded: chain 3 residue 85 ILE Chi-restraints excluded: chain 3 residue 166 TYR Chi-restraints excluded: chain 3 residue 171 VAL Chi-restraints excluded: chain 3 residue 180 LEU Chi-restraints excluded: chain 4 residue 23 SER Chi-restraints excluded: chain 4 residue 51 THR Chi-restraints excluded: chain 4 residue 215 LEU Chi-restraints excluded: chain 5 residue 10 HIS Chi-restraints excluded: chain 5 residue 12 LEU Chi-restraints excluded: chain 5 residue 68 VAL Chi-restraints excluded: chain 5 residue 129 LEU Chi-restraints excluded: chain 5 residue 149 VAL Chi-restraints excluded: chain 5 residue 177 VAL Chi-restraints excluded: chain 5 residue 182 LEU Chi-restraints excluded: chain 5 residue 237 ASP Chi-restraints excluded: chain 6 residue 18 LEU Chi-restraints excluded: chain 7 residue 2 ASP Chi-restraints excluded: chain 7 residue 42 LEU Chi-restraints excluded: chain 8 residue 3 ASP Chi-restraints excluded: chain 8 residue 14 LEU Chi-restraints excluded: chain 8 residue 15 VAL Chi-restraints excluded: chain 8 residue 16 LEU Chi-restraints excluded: chain 8 residue 57 CYS Chi-restraints excluded: chain 8 residue 61 PHE Chi-restraints excluded: chain 8 residue 69 GLU Chi-restraints excluded: chain 9 residue 15 VAL Chi-restraints excluded: chain 9 residue 19 SER Chi-restraints excluded: chain 9 residue 44 GLU Chi-restraints excluded: chain 9 residue 51 ILE Chi-restraints excluded: chain 9 residue 63 LEU Chi-restraints excluded: chain 9 residue 69 GLU Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain AM residue 98 LEU Chi-restraints excluded: chain AN residue 74 ILE Chi-restraints excluded: chain AO residue 50 THR Chi-restraints excluded: chain AO residue 86 THR Chi-restraints excluded: chain AO residue 87 LEU Chi-restraints excluded: chain AO residue 88 THR Chi-restraints excluded: chain AO residue 95 VAL Chi-restraints excluded: chain AO residue 98 LEU Chi-restraints excluded: chain AO residue 100 ARG Chi-restraints excluded: chain AP residue 19 ILE Chi-restraints excluded: chain AP residue 34 LEU Chi-restraints excluded: chain AP residue 75 SER Chi-restraints excluded: chain AP residue 86 THR Chi-restraints excluded: chain AP residue 98 LEU Chi-restraints excluded: chain AQ residue 21 SER Chi-restraints excluded: chain AQ residue 57 ASP Chi-restraints excluded: chain AQ residue 67 LEU Chi-restraints excluded: chain AQ residue 69 ILE Chi-restraints excluded: chain AQ residue 72 GLU Chi-restraints excluded: chain AQ residue 83 MET Chi-restraints excluded: chain AQ residue 88 THR Chi-restraints excluded: chain AQ residue 97 THR Chi-restraints excluded: chain AR residue 34 LEU Chi-restraints excluded: chain AR residue 42 ILE Chi-restraints excluded: chain AR residue 92 VAL Chi-restraints excluded: chain AS residue 47 TYR Chi-restraints excluded: chain AS residue 67 VAL Chi-restraints excluded: chain AS residue 79 PHE Chi-restraints excluded: chain AT residue 52 SER Chi-restraints excluded: chain AU residue 31 LEU Chi-restraints excluded: chain AU residue 64 THR Chi-restraints excluded: chain AU residue 67 VAL Chi-restraints excluded: chain AV residue 28 THR Chi-restraints excluded: chain AV residue 31 LEU Chi-restraints excluded: chain AV residue 53 GLU Chi-restraints excluded: chain AV residue 62 SER Chi-restraints excluded: chain AW residue 61 GLN Chi-restraints excluded: chain AW residue 64 THR Chi-restraints excluded: chain AW residue 75 ILE Chi-restraints excluded: chain AW residue 79 PHE Chi-restraints excluded: chain AX residue 21 ASP Chi-restraints excluded: chain AX residue 44 LEU Chi-restraints excluded: chain AX residue 71 ILE Chi-restraints excluded: chain AY residue 63 ASN Chi-restraints excluded: chain AY residue 65 VAL Chi-restraints excluded: chain AY residue 76 ILE Chi-restraints excluded: chain AZ residue 68 PHE Chi-restraints excluded: chain AZ residue 75 ILE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain BA residue 20 VAL Chi-restraints excluded: chain BA residue 77 GLN Chi-restraints excluded: chain BB residue 16 PHE Chi-restraints excluded: chain BB residue 54 TYR Chi-restraints excluded: chain BD residue 59 ASN Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 108 ARG Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 108 ARG Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 116 ASN Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain J residue 71 ASN Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain L residue 38 LYS Chi-restraints excluded: chain L residue 40 ASP Chi-restraints excluded: chain L residue 68 ILE Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 116 ASN Chi-restraints excluded: chain L residue 132 TYR Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 47 ASP Chi-restraints excluded: chain M residue 91 ILE Chi-restraints excluded: chain M residue 101 ILE Chi-restraints excluded: chain M residue 105 SER Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 78 ASN Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 61 LYS Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 149 VAL Chi-restraints excluded: chain Q residue 42 LEU Chi-restraints excluded: chain R residue 365 TRP Chi-restraints excluded: chain R residue 366 LEU Chi-restraints excluded: chain S residue 379 ILE Chi-restraints excluded: chain V residue 370 SER Chi-restraints excluded: chain Y residue 367 LYS Chi-restraints excluded: chain Z residue 367 LYS Chi-restraints excluded: chain a residue 366 LEU Chi-restraints excluded: chain b residue 366 LEU Chi-restraints excluded: chain c residue 376 GLU Chi-restraints excluded: chain e residue 366 LEU Chi-restraints excluded: chain f residue 392 LEU Chi-restraints excluded: chain g residue 366 LEU Chi-restraints excluded: chain i residue 379 ILE Chi-restraints excluded: chain j residue 366 LEU Chi-restraints excluded: chain m residue 390 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 311 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 301 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 320 optimal weight: 0.8980 chunk 343 optimal weight: 0.9980 chunk 249 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 chunk 396 optimal weight: 9.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 113 GLN ** 3 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 218 GLN ** 4 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 77 GLN ** AO 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AR 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AR 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 61 GLN AW 48 GLN ** BC 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN L 71 ASN L 97 GLN ** N 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.5532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 46515 Z= 0.211 Angle : 0.774 14.604 62995 Z= 0.377 Chirality : 0.046 0.300 6948 Planarity : 0.005 0.062 7985 Dihedral : 5.293 73.388 6214 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.16 % Favored : 95.78 % Rotamer: Outliers : 3.70 % Allowed : 27.15 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.11), residues: 5563 helix: 0.41 (0.10), residues: 2998 sheet: 0.63 (0.23), residues: 456 loop : -1.71 (0.13), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP i 365 HIS 0.008 0.001 HIS X 385 PHE 0.031 0.001 PHE 8 49 TYR 0.033 0.002 TYRAY 47 ARG 0.012 0.001 ARG c 369 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1452 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1272 time to evaluate : 5.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 38 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.7529 (ttm-80) REVERT: 0 75 PHE cc_start: 0.9253 (OUTLIER) cc_final: 0.8918 (t80) REVERT: 0 116 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7686 (mm-30) REVERT: 0 156 LYS cc_start: 0.8908 (ttmm) cc_final: 0.8579 (mttm) REVERT: 0 186 MET cc_start: 0.8322 (tpp) cc_final: 0.7635 (tpp) REVERT: 1 16 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8539 (mm) REVERT: 1 110 GLU cc_start: 0.8553 (pm20) cc_final: 0.8325 (pm20) REVERT: 1 160 LYS cc_start: 0.9524 (mtmm) cc_final: 0.9273 (mtmm) REVERT: 1 166 TYR cc_start: 0.8510 (OUTLIER) cc_final: 0.7929 (m-80) REVERT: 1 167 LEU cc_start: 0.9424 (mt) cc_final: 0.9070 (tp) REVERT: 1 173 ASP cc_start: 0.8110 (t70) cc_final: 0.7869 (t70) REVERT: 1 188 MET cc_start: 0.8724 (tmm) cc_final: 0.8463 (tmm) REVERT: 1 220 MET cc_start: 0.6076 (tpt) cc_final: 0.5739 (mmt) REVERT: 2 29 LYS cc_start: 0.9120 (ttmm) cc_final: 0.8602 (tttp) REVERT: 2 45 GLN cc_start: 0.7931 (pt0) cc_final: 0.7430 (tp-100) REVERT: 2 76 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8276 (mm-30) REVERT: 2 166 TYR cc_start: 0.9318 (OUTLIER) cc_final: 0.8485 (t80) REVERT: 2 188 MET cc_start: 0.8534 (tpp) cc_final: 0.8138 (tpp) REVERT: 2 206 ASP cc_start: 0.8524 (t0) cc_final: 0.8298 (t0) REVERT: 3 107 SER cc_start: 0.8258 (t) cc_final: 0.7902 (p) REVERT: 3 116 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8133 (mm-30) REVERT: 3 154 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8515 (mm-30) REVERT: 3 173 ASP cc_start: 0.8576 (t0) cc_final: 0.8299 (t0) REVERT: 3 206 ASP cc_start: 0.8307 (t0) cc_final: 0.7770 (t0) REVERT: 3 215 LEU cc_start: 0.9509 (mt) cc_final: 0.9240 (mt) REVERT: 3 220 MET cc_start: 0.7564 (tpp) cc_final: 0.7121 (tpp) REVERT: 4 26 CYS cc_start: 0.8576 (p) cc_final: 0.7935 (p) REVERT: 4 185 MET cc_start: 0.9097 (mmm) cc_final: 0.8778 (mmm) REVERT: 4 188 MET cc_start: 0.8323 (tpp) cc_final: 0.7955 (tpp) REVERT: 5 95 MET cc_start: 0.8541 (tpp) cc_final: 0.8241 (tpp) REVERT: 5 131 MET cc_start: 0.8468 (ttm) cc_final: 0.8259 (ttm) REVERT: 5 160 MET cc_start: 0.9413 (mpp) cc_final: 0.8935 (mpp) REVERT: 5 228 LEU cc_start: 0.9401 (tp) cc_final: 0.9113 (tt) REVERT: 6 10 LYS cc_start: 0.8745 (tppt) cc_final: 0.8393 (tppp) REVERT: 6 14 LEU cc_start: 0.9522 (mt) cc_final: 0.8950 (mt) REVERT: 6 67 TYR cc_start: 0.7539 (m-80) cc_final: 0.7224 (m-80) REVERT: 6 74 TYR cc_start: 0.8802 (t80) cc_final: 0.8187 (t80) REVERT: 7 18 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9086 (mt) REVERT: 7 49 PHE cc_start: 0.8300 (m-80) cc_final: 0.7493 (m-80) REVERT: 7 52 LYS cc_start: 0.7698 (ttmt) cc_final: 0.7268 (tttt) REVERT: 7 74 TYR cc_start: 0.8850 (t80) cc_final: 0.8609 (t80) REVERT: 8 52 LYS cc_start: 0.9123 (ttmt) cc_final: 0.8826 (mtmt) REVERT: 8 61 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.7992 (t80) REVERT: 8 76 ARG cc_start: 0.9155 (mtm180) cc_final: 0.8478 (mtt90) REVERT: 8 77 GLN cc_start: 0.8983 (tp40) cc_final: 0.8387 (tm-30) REVERT: 8 81 LEU cc_start: 0.9319 (tp) cc_final: 0.9058 (tp) REVERT: 9 52 LYS cc_start: 0.9346 (ttmm) cc_final: 0.8583 (ttpt) REVERT: 9 61 PHE cc_start: 0.9048 (t80) cc_final: 0.8668 (t80) REVERT: 9 74 TYR cc_start: 0.8751 (t80) cc_final: 0.8029 (t80) REVERT: 9 76 ARG cc_start: 0.8673 (ttm110) cc_final: 0.8334 (mtm110) REVERT: A 62 MET cc_start: 0.7832 (ttm) cc_final: 0.7534 (ttp) REVERT: A 164 THR cc_start: 0.9475 (p) cc_final: 0.9234 (t) REVERT: AM 98 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8742 (mm) REVERT: AN 87 LEU cc_start: 0.9410 (mt) cc_final: 0.8940 (mt) REVERT: AO 35 GLN cc_start: 0.8389 (pp30) cc_final: 0.8180 (pp30) REVERT: AO 49 GLN cc_start: 0.8673 (tp-100) cc_final: 0.8029 (tp-100) REVERT: AO 67 LEU cc_start: 0.9351 (mm) cc_final: 0.9003 (mm) REVERT: AO 69 ILE cc_start: 0.9245 (tp) cc_final: 0.8958 (tp) REVERT: AO 83 MET cc_start: 0.8894 (tpp) cc_final: 0.8619 (tmm) REVERT: AO 99 LEU cc_start: 0.9087 (mm) cc_final: 0.8728 (mm) REVERT: AP 18 ASN cc_start: 0.9129 (p0) cc_final: 0.8752 (p0) REVERT: AP 25 ASP cc_start: 0.7533 (p0) cc_final: 0.6781 (t70) REVERT: AP 58 PRO cc_start: 0.8107 (Cg_exo) cc_final: 0.7495 (Cg_endo) REVERT: AP 66 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7978 (mp0) REVERT: AP 96 GLU cc_start: 0.8861 (tp30) cc_final: 0.8588 (tt0) REVERT: AQ 53 ASN cc_start: 0.8596 (m-40) cc_final: 0.8184 (m110) REVERT: AQ 67 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9153 (mm) REVERT: AQ 69 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.7664 (tp) REVERT: AQ 72 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8095 (mp0) REVERT: AQ 96 GLU cc_start: 0.9212 (mm-30) cc_final: 0.9004 (mm-30) REVERT: AQ 99 LEU cc_start: 0.9035 (mt) cc_final: 0.8692 (mp) REVERT: AR 48 LYS cc_start: 0.8732 (tmtt) cc_final: 0.8437 (tmtt) REVERT: AR 63 ASP cc_start: 0.8187 (t0) cc_final: 0.7812 (t70) REVERT: AR 72 GLU cc_start: 0.8503 (tp30) cc_final: 0.7827 (tm-30) REVERT: AR 76 ASP cc_start: 0.8591 (m-30) cc_final: 0.7373 (m-30) REVERT: AR 84 VAL cc_start: 0.8877 (m) cc_final: 0.8571 (p) REVERT: AR 87 LEU cc_start: 0.9245 (mm) cc_final: 0.9003 (pp) REVERT: AR 96 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7934 (tm-30) REVERT: AS 51 LEU cc_start: 0.9688 (tt) cc_final: 0.9470 (pp) REVERT: AS 54 TYR cc_start: 0.8784 (t80) cc_final: 0.8573 (t80) REVERT: AT 47 TYR cc_start: 0.9160 (t80) cc_final: 0.8594 (t80) REVERT: AT 61 GLN cc_start: 0.9128 (pp30) cc_final: 0.8798 (pp30) REVERT: AU 38 PRO cc_start: 0.6327 (Cg_endo) cc_final: 0.6075 (Cg_exo) REVERT: AU 48 GLN cc_start: 0.8355 (mm-40) cc_final: 0.8075 (mm110) REVERT: AU 52 SER cc_start: 0.9154 (m) cc_final: 0.8675 (p) REVERT: AU 80 ARG cc_start: 0.7913 (ptm-80) cc_final: 0.7583 (ttm170) REVERT: AV 47 TYR cc_start: 0.8848 (t80) cc_final: 0.8421 (t80) REVERT: AV 53 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8175 (mp0) REVERT: AV 69 LYS cc_start: 0.9438 (tttt) cc_final: 0.9064 (tttt) REVERT: AW 23 LEU cc_start: 0.8851 (tp) cc_final: 0.8616 (tt) REVERT: AW 47 TYR cc_start: 0.8623 (t80) cc_final: 0.8405 (t80) REVERT: AW 58 ARG cc_start: 0.8852 (mmt180) cc_final: 0.8138 (mmm160) REVERT: AW 61 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8173 (pp30) REVERT: AW 62 SER cc_start: 0.9140 (t) cc_final: 0.8734 (t) REVERT: AW 66 LYS cc_start: 0.9086 (tppt) cc_final: 0.8751 (tppt) REVERT: AW 70 ASP cc_start: 0.9281 (m-30) cc_final: 0.9021 (m-30) REVERT: AY 50 LYS cc_start: 0.7476 (mmmt) cc_final: 0.7235 (ptpp) REVERT: AY 61 GLN cc_start: 0.8339 (pt0) cc_final: 0.7930 (pt0) REVERT: AY 79 PHE cc_start: 0.8829 (m-80) cc_final: 0.8493 (m-80) REVERT: AZ 63 ASN cc_start: 0.9105 (m-40) cc_final: 0.8597 (m-40) REVERT: BA 79 PHE cc_start: 0.9008 (m-80) cc_final: 0.8058 (m-80) REVERT: BB 70 ASP cc_start: 0.9116 (t0) cc_final: 0.8851 (p0) REVERT: BB 75 ILE cc_start: 0.9319 (pt) cc_final: 0.9058 (pt) REVERT: BD 59 ASN cc_start: 0.6741 (OUTLIER) cc_final: 0.6142 (m110) REVERT: C 67 LYS cc_start: 0.8352 (mmmm) cc_final: 0.8144 (mmmm) REVERT: C 165 MET cc_start: 0.7518 (mmm) cc_final: 0.7297 (tpp) REVERT: F 62 MET cc_start: 0.8074 (tmm) cc_final: 0.7868 (tmm) REVERT: F 107 MET cc_start: 0.8850 (tmm) cc_final: 0.8164 (tmm) REVERT: G 167 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7569 (t0) REVERT: H 108 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7935 (ptp-170) REVERT: H 167 ASP cc_start: 0.7518 (p0) cc_final: 0.6492 (p0) REVERT: H 168 LYS cc_start: 0.9240 (mmmt) cc_final: 0.8372 (mmtt) REVERT: I 87 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7721 (mt0) REVERT: I 107 MET cc_start: 0.8749 (tpp) cc_final: 0.8450 (tpt) REVERT: I 166 MET cc_start: 0.8905 (mmm) cc_final: 0.8558 (tpp) REVERT: L 67 LYS cc_start: 0.8326 (mptt) cc_final: 0.7977 (mmtt) REVERT: N 38 LYS cc_start: 0.8230 (pttt) cc_final: 0.7990 (pttt) REVERT: O 105 SER cc_start: 0.8695 (m) cc_final: 0.8173 (t) REVERT: P 76 ASP cc_start: 0.7496 (t0) cc_final: 0.7191 (t0) REVERT: P 108 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.8113 (ptp-170) REVERT: T 381 MET cc_start: 0.7962 (tmm) cc_final: 0.7662 (tmm) REVERT: b 379 ILE cc_start: 0.8943 (mm) cc_final: 0.8537 (mm) REVERT: e 387 TYR cc_start: 0.8038 (t80) cc_final: 0.7708 (t80) REVERT: g 366 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8262 (pp) REVERT: i 371 PHE cc_start: 0.8269 (m-80) cc_final: 0.7680 (m-10) REVERT: j 366 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8822 (pp) REVERT: n 381 MET cc_start: 0.7589 (mmm) cc_final: 0.7295 (mmt) outliers start: 180 outliers final: 124 residues processed: 1371 average time/residue: 0.5786 time to fit residues: 1289.9879 Evaluate side-chains 1350 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1206 time to evaluate : 5.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 21 ILE Chi-restraints excluded: chain 0 residue 38 ARG Chi-restraints excluded: chain 0 residue 75 PHE Chi-restraints excluded: chain 0 residue 81 THR Chi-restraints excluded: chain 0 residue 105 LYS Chi-restraints excluded: chain 0 residue 166 TYR Chi-restraints excluded: chain 0 residue 170 VAL Chi-restraints excluded: chain 0 residue 188 MET Chi-restraints excluded: chain 0 residue 211 LEU Chi-restraints excluded: chain 1 residue 16 LEU Chi-restraints excluded: chain 1 residue 72 TYR Chi-restraints excluded: chain 1 residue 84 ASP Chi-restraints excluded: chain 1 residue 85 ILE Chi-restraints excluded: chain 1 residue 103 LEU Chi-restraints excluded: chain 1 residue 166 TYR Chi-restraints excluded: chain 1 residue 186 MET Chi-restraints excluded: chain 1 residue 211 LEU Chi-restraints excluded: chain 1 residue 221 ASP Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 2 residue 83 ASN Chi-restraints excluded: chain 2 residue 84 ASP Chi-restraints excluded: chain 2 residue 164 TYR Chi-restraints excluded: chain 2 residue 166 TYR Chi-restraints excluded: chain 2 residue 172 VAL Chi-restraints excluded: chain 2 residue 201 LEU Chi-restraints excluded: chain 3 residue 36 MET Chi-restraints excluded: chain 3 residue 64 MET Chi-restraints excluded: chain 3 residue 83 ASN Chi-restraints excluded: chain 3 residue 85 ILE Chi-restraints excluded: chain 4 residue 23 SER Chi-restraints excluded: chain 5 residue 10 HIS Chi-restraints excluded: chain 5 residue 12 LEU Chi-restraints excluded: chain 5 residue 68 VAL Chi-restraints excluded: chain 5 residue 182 LEU Chi-restraints excluded: chain 6 residue 18 LEU Chi-restraints excluded: chain 7 residue 2 ASP Chi-restraints excluded: chain 7 residue 18 LEU Chi-restraints excluded: chain 7 residue 42 LEU Chi-restraints excluded: chain 8 residue 3 ASP Chi-restraints excluded: chain 8 residue 16 LEU Chi-restraints excluded: chain 8 residue 51 ILE Chi-restraints excluded: chain 8 residue 57 CYS Chi-restraints excluded: chain 8 residue 61 PHE Chi-restraints excluded: chain 8 residue 72 LEU Chi-restraints excluded: chain 9 residue 15 VAL Chi-restraints excluded: chain 9 residue 19 SER Chi-restraints excluded: chain 9 residue 44 GLU Chi-restraints excluded: chain 9 residue 51 ILE Chi-restraints excluded: chain 9 residue 63 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain AM residue 98 LEU Chi-restraints excluded: chain AO residue 19 ILE Chi-restraints excluded: chain AO residue 86 THR Chi-restraints excluded: chain AO residue 87 LEU Chi-restraints excluded: chain AO residue 88 THR Chi-restraints excluded: chain AO residue 95 VAL Chi-restraints excluded: chain AP residue 34 LEU Chi-restraints excluded: chain AP residue 66 GLU Chi-restraints excluded: chain AP residue 75 SER Chi-restraints excluded: chain AP residue 86 THR Chi-restraints excluded: chain AP residue 98 LEU Chi-restraints excluded: chain AQ residue 21 SER Chi-restraints excluded: chain AQ residue 57 ASP Chi-restraints excluded: chain AQ residue 67 LEU Chi-restraints excluded: chain AQ residue 69 ILE Chi-restraints excluded: chain AQ residue 97 THR Chi-restraints excluded: chain AR residue 34 LEU Chi-restraints excluded: chain AR residue 92 VAL Chi-restraints excluded: chain AS residue 47 TYR Chi-restraints excluded: chain AS residue 67 VAL Chi-restraints excluded: chain AT residue 52 SER Chi-restraints excluded: chain AU residue 31 LEU Chi-restraints excluded: chain AU residue 64 THR Chi-restraints excluded: chain AU residue 67 VAL Chi-restraints excluded: chain AV residue 28 THR Chi-restraints excluded: chain AV residue 53 GLU Chi-restraints excluded: chain AV residue 62 SER Chi-restraints excluded: chain AW residue 61 GLN Chi-restraints excluded: chain AW residue 75 ILE Chi-restraints excluded: chain AX residue 21 ASP Chi-restraints excluded: chain AX residue 44 LEU Chi-restraints excluded: chain AX residue 71 ILE Chi-restraints excluded: chain AY residue 76 ILE Chi-restraints excluded: chain AZ residue 68 PHE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain BA residue 20 VAL Chi-restraints excluded: chain BA residue 77 GLN Chi-restraints excluded: chain BB residue 54 TYR Chi-restraints excluded: chain BD residue 59 ASN Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 108 ARG Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 108 ARG Chi-restraints excluded: chain H residue 116 ASN Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain I residue 87 GLN Chi-restraints excluded: chain J residue 71 ASN Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain L residue 38 LYS Chi-restraints excluded: chain L residue 68 ILE Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 116 ASN Chi-restraints excluded: chain L residue 132 TYR Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 47 ASP Chi-restraints excluded: chain M residue 105 SER Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 78 ASN Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 108 ARG Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 149 VAL Chi-restraints excluded: chain R residue 365 TRP Chi-restraints excluded: chain R residue 366 LEU Chi-restraints excluded: chain S residue 381 MET Chi-restraints excluded: chain V residue 370 SER Chi-restraints excluded: chain Y residue 367 LYS Chi-restraints excluded: chain Z residue 367 LYS Chi-restraints excluded: chain b residue 366 LEU Chi-restraints excluded: chain c residue 376 GLU Chi-restraints excluded: chain e residue 366 LEU Chi-restraints excluded: chain g residue 366 LEU Chi-restraints excluded: chain j residue 366 LEU Chi-restraints excluded: chain m residue 390 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 458 optimal weight: 6.9990 chunk 482 optimal weight: 8.9990 chunk 440 optimal weight: 3.9990 chunk 469 optimal weight: 6.9990 chunk 282 optimal weight: 20.0000 chunk 204 optimal weight: 8.9990 chunk 368 optimal weight: 5.9990 chunk 144 optimal weight: 0.0170 chunk 424 optimal weight: 3.9990 chunk 444 optimal weight: 3.9990 chunk 468 optimal weight: 2.9990 overall best weight: 3.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 218 GLN ** 4 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 37 GLN ** AO 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AR 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AR 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 61 GLN AW 48 GLN ** BC 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 GLN M 123 ASN ** N 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.5710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 46515 Z= 0.309 Angle : 0.820 15.047 62995 Z= 0.405 Chirality : 0.048 0.330 6948 Planarity : 0.005 0.063 7985 Dihedral : 5.328 72.592 6214 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.06 % Favored : 94.92 % Rotamer: Outliers : 3.91 % Allowed : 27.22 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.53 (0.11), residues: 5563 helix: 0.43 (0.10), residues: 2997 sheet: 0.66 (0.23), residues: 456 loop : -1.71 (0.13), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP i 365 HIS 0.005 0.001 HIS 2 91 PHE 0.031 0.002 PHE 7 6 TYR 0.036 0.002 TYRAY 47 ARG 0.013 0.001 ARG c 369 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1389 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 1199 time to evaluate : 5.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 38 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.7622 (ttm-80) REVERT: 0 75 PHE cc_start: 0.9267 (OUTLIER) cc_final: 0.8933 (t80) REVERT: 0 116 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7728 (mm-30) REVERT: 0 156 LYS cc_start: 0.8766 (ttmm) cc_final: 0.8418 (mttt) REVERT: 0 186 MET cc_start: 0.8243 (tpp) cc_final: 0.8030 (tpp) REVERT: 0 187 MET cc_start: 0.8229 (ptp) cc_final: 0.8002 (pmm) REVERT: 1 16 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8774 (mm) REVERT: 1 110 GLU cc_start: 0.8565 (pm20) cc_final: 0.8315 (pm20) REVERT: 1 160 LYS cc_start: 0.9577 (mtmm) cc_final: 0.9283 (mtmm) REVERT: 1 166 TYR cc_start: 0.8549 (OUTLIER) cc_final: 0.7989 (m-80) REVERT: 1 167 LEU cc_start: 0.9419 (mt) cc_final: 0.9069 (tp) REVERT: 1 173 ASP cc_start: 0.8187 (t70) cc_final: 0.7913 (t70) REVERT: 1 188 MET cc_start: 0.8735 (tmm) cc_final: 0.8461 (tmm) REVERT: 1 198 LYS cc_start: 0.9191 (mtpp) cc_final: 0.8434 (mtpp) REVERT: 1 220 MET cc_start: 0.6134 (tpt) cc_final: 0.5756 (mmt) REVERT: 2 29 LYS cc_start: 0.9140 (ttmm) cc_final: 0.8660 (tttp) REVERT: 2 45 GLN cc_start: 0.8083 (pt0) cc_final: 0.7574 (tp-100) REVERT: 2 76 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8285 (mm-30) REVERT: 2 166 TYR cc_start: 0.9334 (OUTLIER) cc_final: 0.8303 (t80) REVERT: 2 188 MET cc_start: 0.8452 (tpp) cc_final: 0.7833 (tpp) REVERT: 2 206 ASP cc_start: 0.8709 (t0) cc_final: 0.8439 (t0) REVERT: 3 68 MET cc_start: 0.8015 (ppp) cc_final: 0.7787 (ppp) REVERT: 3 116 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8357 (mm-30) REVERT: 3 154 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8605 (mm-30) REVERT: 3 206 ASP cc_start: 0.8096 (t0) cc_final: 0.7521 (t0) REVERT: 3 215 LEU cc_start: 0.9510 (mt) cc_final: 0.9244 (mt) REVERT: 3 220 MET cc_start: 0.7494 (tpp) cc_final: 0.7045 (tpp) REVERT: 4 26 CYS cc_start: 0.8517 (p) cc_final: 0.7957 (p) REVERT: 4 76 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7811 (mm-30) REVERT: 4 160 LYS cc_start: 0.9397 (tptt) cc_final: 0.9077 (tppt) REVERT: 4 164 TYR cc_start: 0.8501 (m-80) cc_final: 0.8273 (m-80) REVERT: 4 185 MET cc_start: 0.8997 (mmm) cc_final: 0.8591 (mmm) REVERT: 4 218 GLN cc_start: 0.8779 (mm-40) cc_final: 0.8575 (tp-100) REVERT: 5 95 MET cc_start: 0.8613 (tpp) cc_final: 0.8346 (tpp) REVERT: 5 131 MET cc_start: 0.8531 (ttm) cc_final: 0.8330 (ttm) REVERT: 5 160 MET cc_start: 0.9399 (mpp) cc_final: 0.8960 (mpp) REVERT: 5 164 THR cc_start: 0.7290 (m) cc_final: 0.6524 (p) REVERT: 5 196 GLU cc_start: 0.9086 (tm-30) cc_final: 0.8759 (tm-30) REVERT: 5 228 LEU cc_start: 0.9457 (tp) cc_final: 0.9141 (tt) REVERT: 5 229 LEU cc_start: 0.9602 (tt) cc_final: 0.9297 (mm) REVERT: 6 10 LYS cc_start: 0.8767 (tppt) cc_final: 0.8377 (tppp) REVERT: 6 14 LEU cc_start: 0.9511 (mt) cc_final: 0.8938 (mt) REVERT: 6 67 TYR cc_start: 0.7478 (m-80) cc_final: 0.7160 (m-80) REVERT: 6 74 TYR cc_start: 0.8845 (t80) cc_final: 0.8239 (t80) REVERT: 7 18 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9116 (mt) REVERT: 7 49 PHE cc_start: 0.8395 (m-80) cc_final: 0.7617 (m-80) REVERT: 7 52 LYS cc_start: 0.7813 (ttmt) cc_final: 0.7365 (tttt) REVERT: 7 76 ARG cc_start: 0.8154 (mtm-85) cc_final: 0.7863 (mtm-85) REVERT: 8 52 LYS cc_start: 0.9155 (ttmt) cc_final: 0.8826 (mtmt) REVERT: 8 76 ARG cc_start: 0.9189 (mtm180) cc_final: 0.8510 (mtt90) REVERT: 8 77 GLN cc_start: 0.8949 (tp40) cc_final: 0.8383 (tm-30) REVERT: 9 13 TYR cc_start: 0.8363 (t80) cc_final: 0.8143 (t80) REVERT: 9 52 LYS cc_start: 0.9337 (ttmm) cc_final: 0.8554 (ttpt) REVERT: 9 61 PHE cc_start: 0.9137 (t80) cc_final: 0.8739 (t80) REVERT: A 62 MET cc_start: 0.7889 (ttm) cc_final: 0.7670 (ttp) REVERT: A 100 TYR cc_start: 0.7897 (m-80) cc_final: 0.7624 (m-10) REVERT: A 164 THR cc_start: 0.9518 (p) cc_final: 0.9292 (t) REVERT: AM 98 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8748 (mm) REVERT: AN 87 LEU cc_start: 0.9447 (mt) cc_final: 0.9015 (mt) REVERT: AO 67 LEU cc_start: 0.9356 (mm) cc_final: 0.9010 (mm) REVERT: AO 69 ILE cc_start: 0.9279 (tp) cc_final: 0.9021 (tp) REVERT: AO 83 MET cc_start: 0.8914 (tpp) cc_final: 0.8633 (tmm) REVERT: AO 99 LEU cc_start: 0.9111 (mm) cc_final: 0.8712 (mm) REVERT: AP 18 ASN cc_start: 0.9151 (p0) cc_final: 0.8769 (p0) REVERT: AP 25 ASP cc_start: 0.7541 (p0) cc_final: 0.6731 (t70) REVERT: AP 48 LYS cc_start: 0.9128 (tppp) cc_final: 0.8910 (tppp) REVERT: AP 66 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7843 (mp0) REVERT: AQ 67 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9172 (mm) REVERT: AQ 72 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8193 (mp0) REVERT: AQ 96 GLU cc_start: 0.9220 (mm-30) cc_final: 0.9006 (mm-30) REVERT: AQ 99 LEU cc_start: 0.8907 (mt) cc_final: 0.8636 (mp) REVERT: AR 63 ASP cc_start: 0.8240 (t0) cc_final: 0.7918 (t70) REVERT: AR 72 GLU cc_start: 0.8817 (tp30) cc_final: 0.8334 (tp30) REVERT: AR 76 ASP cc_start: 0.8253 (m-30) cc_final: 0.7668 (m-30) REVERT: AR 84 VAL cc_start: 0.8854 (m) cc_final: 0.8560 (p) REVERT: AR 87 LEU cc_start: 0.9259 (mm) cc_final: 0.9005 (pp) REVERT: AR 96 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7905 (tm-30) REVERT: AS 50 LYS cc_start: 0.8892 (tptt) cc_final: 0.8322 (tttt) REVERT: AS 51 LEU cc_start: 0.9675 (tt) cc_final: 0.9437 (pp) REVERT: AT 47 TYR cc_start: 0.9178 (t80) cc_final: 0.8433 (t80) REVERT: AT 48 GLN cc_start: 0.8950 (tp40) cc_final: 0.7824 (tp40) REVERT: AT 61 GLN cc_start: 0.9196 (pp30) cc_final: 0.8882 (pp30) REVERT: AU 38 PRO cc_start: 0.6277 (Cg_endo) cc_final: 0.6010 (Cg_exo) REVERT: AU 48 GLN cc_start: 0.8364 (mm-40) cc_final: 0.8138 (mm110) REVERT: AU 52 SER cc_start: 0.9167 (m) cc_final: 0.8701 (p) REVERT: AU 54 TYR cc_start: 0.8858 (t80) cc_final: 0.8639 (t80) REVERT: AU 80 ARG cc_start: 0.7980 (ptm-80) cc_final: 0.7650 (ttm170) REVERT: AV 47 TYR cc_start: 0.8868 (t80) cc_final: 0.8516 (t80) REVERT: AV 53 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8246 (mp0) REVERT: AV 69 LYS cc_start: 0.9459 (tttt) cc_final: 0.9104 (tttt) REVERT: AW 47 TYR cc_start: 0.8653 (t80) cc_final: 0.8395 (t80) REVERT: AW 58 ARG cc_start: 0.8852 (mmt180) cc_final: 0.7682 (mtp180) REVERT: AW 61 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8116 (pp30) REVERT: AW 62 SER cc_start: 0.9156 (t) cc_final: 0.8675 (t) REVERT: AW 66 LYS cc_start: 0.9150 (tppt) cc_final: 0.8806 (tppt) REVERT: AW 70 ASP cc_start: 0.9316 (m-30) cc_final: 0.9057 (m-30) REVERT: AY 50 LYS cc_start: 0.7517 (mmmt) cc_final: 0.7250 (ptpp) REVERT: AY 61 GLN cc_start: 0.8372 (pt0) cc_final: 0.7970 (pt0) REVERT: AY 79 PHE cc_start: 0.8934 (m-80) cc_final: 0.8608 (m-80) REVERT: AZ 63 ASN cc_start: 0.9117 (m-40) cc_final: 0.8650 (m-40) REVERT: AZ 66 LYS cc_start: 0.8874 (pttt) cc_final: 0.8635 (pttm) REVERT: B 55 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7369 (tt0) REVERT: B 124 ASN cc_start: 0.8916 (OUTLIER) cc_final: 0.8684 (t0) REVERT: B 155 TYR cc_start: 0.8245 (t80) cc_final: 0.7832 (t80) REVERT: BA 79 PHE cc_start: 0.9001 (m-80) cc_final: 0.8025 (m-80) REVERT: BB 70 ASP cc_start: 0.9213 (t0) cc_final: 0.8884 (p0) REVERT: BB 75 ILE cc_start: 0.9314 (pt) cc_final: 0.9045 (pt) REVERT: BD 59 ASN cc_start: 0.6830 (OUTLIER) cc_final: 0.6270 (m110) REVERT: C 67 LYS cc_start: 0.8543 (mmmm) cc_final: 0.8242 (mmmm) REVERT: F 107 MET cc_start: 0.8839 (tmm) cc_final: 0.7650 (tmm) REVERT: G 55 GLU cc_start: 0.7270 (mp0) cc_final: 0.6867 (mt-10) REVERT: G 167 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7551 (t0) REVERT: H 108 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7977 (ptp-170) REVERT: I 100 TYR cc_start: 0.8675 (m-80) cc_final: 0.8363 (m-10) REVERT: I 166 MET cc_start: 0.8947 (mmm) cc_final: 0.8616 (tpp) REVERT: J 103 ASP cc_start: 0.7789 (p0) cc_final: 0.7512 (p0) REVERT: L 67 LYS cc_start: 0.8379 (mptt) cc_final: 0.8026 (mmtt) REVERT: N 38 LYS cc_start: 0.8391 (pttt) cc_final: 0.8101 (pttt) REVERT: O 47 ASP cc_start: 0.8038 (p0) cc_final: 0.7829 (p0) REVERT: O 105 SER cc_start: 0.8764 (m) cc_final: 0.8307 (t) REVERT: P 76 ASP cc_start: 0.7570 (t0) cc_final: 0.7215 (t0) REVERT: P 108 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8325 (ptp-170) REVERT: S 369 ARG cc_start: 0.7793 (mmt90) cc_final: 0.7512 (mmt90) REVERT: b 379 ILE cc_start: 0.9045 (mm) cc_final: 0.8622 (mm) REVERT: e 387 TYR cc_start: 0.8188 (t80) cc_final: 0.7917 (t80) REVERT: g 366 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8321 (pp) REVERT: i 371 PHE cc_start: 0.8331 (m-80) cc_final: 0.7907 (m-10) REVERT: j 366 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8840 (pp) REVERT: n 381 MET cc_start: 0.7653 (mmm) cc_final: 0.7367 (mmt) outliers start: 190 outliers final: 150 residues processed: 1305 average time/residue: 0.5636 time to fit residues: 1194.5598 Evaluate side-chains 1348 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1181 time to evaluate : 5.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 21 ILE Chi-restraints excluded: chain 0 residue 38 ARG Chi-restraints excluded: chain 0 residue 75 PHE Chi-restraints excluded: chain 0 residue 81 THR Chi-restraints excluded: chain 0 residue 105 LYS Chi-restraints excluded: chain 0 residue 166 TYR Chi-restraints excluded: chain 0 residue 170 VAL Chi-restraints excluded: chain 0 residue 188 MET Chi-restraints excluded: chain 0 residue 211 LEU Chi-restraints excluded: chain 1 residue 16 LEU Chi-restraints excluded: chain 1 residue 72 TYR Chi-restraints excluded: chain 1 residue 84 ASP Chi-restraints excluded: chain 1 residue 85 ILE Chi-restraints excluded: chain 1 residue 103 LEU Chi-restraints excluded: chain 1 residue 166 TYR Chi-restraints excluded: chain 1 residue 170 VAL Chi-restraints excluded: chain 1 residue 186 MET Chi-restraints excluded: chain 1 residue 211 LEU Chi-restraints excluded: chain 1 residue 221 ASP Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 2 residue 57 LEU Chi-restraints excluded: chain 2 residue 83 ASN Chi-restraints excluded: chain 2 residue 84 ASP Chi-restraints excluded: chain 2 residue 160 LYS Chi-restraints excluded: chain 2 residue 166 TYR Chi-restraints excluded: chain 2 residue 172 VAL Chi-restraints excluded: chain 2 residue 201 LEU Chi-restraints excluded: chain 3 residue 83 ASN Chi-restraints excluded: chain 3 residue 85 ILE Chi-restraints excluded: chain 4 residue 23 SER Chi-restraints excluded: chain 4 residue 215 LEU Chi-restraints excluded: chain 5 residue 10 HIS Chi-restraints excluded: chain 5 residue 12 LEU Chi-restraints excluded: chain 5 residue 68 VAL Chi-restraints excluded: chain 5 residue 149 VAL Chi-restraints excluded: chain 5 residue 182 LEU Chi-restraints excluded: chain 6 residue 18 LEU Chi-restraints excluded: chain 7 residue 2 ASP Chi-restraints excluded: chain 7 residue 18 LEU Chi-restraints excluded: chain 7 residue 42 LEU Chi-restraints excluded: chain 8 residue 3 ASP Chi-restraints excluded: chain 8 residue 16 LEU Chi-restraints excluded: chain 8 residue 57 CYS Chi-restraints excluded: chain 8 residue 72 LEU Chi-restraints excluded: chain 9 residue 15 VAL Chi-restraints excluded: chain 9 residue 19 SER Chi-restraints excluded: chain 9 residue 44 GLU Chi-restraints excluded: chain 9 residue 51 ILE Chi-restraints excluded: chain 9 residue 63 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain AM residue 98 LEU Chi-restraints excluded: chain AN residue 75 SER Chi-restraints excluded: chain AO residue 86 THR Chi-restraints excluded: chain AO residue 87 LEU Chi-restraints excluded: chain AO residue 88 THR Chi-restraints excluded: chain AO residue 95 VAL Chi-restraints excluded: chain AO residue 98 LEU Chi-restraints excluded: chain AP residue 33 LEU Chi-restraints excluded: chain AP residue 34 LEU Chi-restraints excluded: chain AP residue 75 SER Chi-restraints excluded: chain AP residue 86 THR Chi-restraints excluded: chain AP residue 98 LEU Chi-restraints excluded: chain AQ residue 19 ILE Chi-restraints excluded: chain AQ residue 21 SER Chi-restraints excluded: chain AQ residue 57 ASP Chi-restraints excluded: chain AQ residue 67 LEU Chi-restraints excluded: chain AQ residue 69 ILE Chi-restraints excluded: chain AQ residue 83 MET Chi-restraints excluded: chain AQ residue 88 THR Chi-restraints excluded: chain AQ residue 97 THR Chi-restraints excluded: chain AR residue 34 LEU Chi-restraints excluded: chain AR residue 42 ILE Chi-restraints excluded: chain AR residue 92 VAL Chi-restraints excluded: chain AS residue 47 TYR Chi-restraints excluded: chain AS residue 67 VAL Chi-restraints excluded: chain AT residue 52 SER Chi-restraints excluded: chain AU residue 31 LEU Chi-restraints excluded: chain AU residue 64 THR Chi-restraints excluded: chain AU residue 67 VAL Chi-restraints excluded: chain AV residue 28 THR Chi-restraints excluded: chain AV residue 31 LEU Chi-restraints excluded: chain AV residue 53 GLU Chi-restraints excluded: chain AV residue 62 SER Chi-restraints excluded: chain AW residue 61 GLN Chi-restraints excluded: chain AW residue 75 ILE Chi-restraints excluded: chain AX residue 21 ASP Chi-restraints excluded: chain AX residue 44 LEU Chi-restraints excluded: chain AX residue 71 ILE Chi-restraints excluded: chain AY residue 63 ASN Chi-restraints excluded: chain AY residue 76 ILE Chi-restraints excluded: chain AZ residue 54 TYR Chi-restraints excluded: chain AZ residue 68 PHE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain BA residue 20 VAL Chi-restraints excluded: chain BA residue 77 GLN Chi-restraints excluded: chain BB residue 51 LEU Chi-restraints excluded: chain BB residue 54 TYR Chi-restraints excluded: chain BD residue 59 ASN Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain F residue 108 ARG Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 108 ARG Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 116 ASN Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain J residue 71 ASN Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain L residue 38 LYS Chi-restraints excluded: chain L residue 68 ILE Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 116 ASN Chi-restraints excluded: chain L residue 132 TYR Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 47 ASP Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 78 ASN Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 61 LYS Chi-restraints excluded: chain O residue 99 ILE Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 108 ARG Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 149 VAL Chi-restraints excluded: chain Q residue 42 LEU Chi-restraints excluded: chain R residue 365 TRP Chi-restraints excluded: chain R residue 366 LEU Chi-restraints excluded: chain S residue 381 MET Chi-restraints excluded: chain T residue 392 LEU Chi-restraints excluded: chain V residue 370 SER Chi-restraints excluded: chain Y residue 367 LYS Chi-restraints excluded: chain Z residue 367 LYS Chi-restraints excluded: chain a residue 366 LEU Chi-restraints excluded: chain b residue 366 LEU Chi-restraints excluded: chain c residue 376 GLU Chi-restraints excluded: chain e residue 366 LEU Chi-restraints excluded: chain g residue 366 LEU Chi-restraints excluded: chain i residue 379 ILE Chi-restraints excluded: chain j residue 366 LEU Chi-restraints excluded: chain m residue 390 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 308 optimal weight: 0.9990 chunk 496 optimal weight: 0.7980 chunk 303 optimal weight: 0.8980 chunk 235 optimal weight: 30.0000 chunk 345 optimal weight: 6.9990 chunk 521 optimal weight: 4.9990 chunk 479 optimal weight: 2.9990 chunk 414 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 320 optimal weight: 3.9990 chunk 254 optimal weight: 7.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 218 GLN ** 5 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 77 GLN ** AO 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AR 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AR 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.5807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 46515 Z= 0.209 Angle : 0.810 15.950 62995 Z= 0.393 Chirality : 0.047 0.347 6948 Planarity : 0.005 0.061 7985 Dihedral : 5.205 74.379 6214 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.02 % Favored : 95.95 % Rotamer: Outliers : 2.86 % Allowed : 28.20 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.41 (0.11), residues: 5563 helix: 0.53 (0.10), residues: 2993 sheet: 0.69 (0.23), residues: 465 loop : -1.66 (0.13), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRPBA 5 HIS 0.004 0.001 HIS G 75 PHE 0.032 0.001 PHE 8 49 TYR 0.041 0.002 TYRAY 47 ARG 0.014 0.001 ARG c 369 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1384 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1245 time to evaluate : 5.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 38 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7576 (ttm-80) REVERT: 0 75 PHE cc_start: 0.9247 (OUTLIER) cc_final: 0.8941 (t80) REVERT: 0 116 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7669 (mm-30) REVERT: 0 156 LYS cc_start: 0.8692 (ttmm) cc_final: 0.8309 (mttt) REVERT: 0 186 MET cc_start: 0.8216 (tpp) cc_final: 0.7940 (tpp) REVERT: 0 187 MET cc_start: 0.8208 (ptp) cc_final: 0.7987 (pmm) REVERT: 1 16 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8741 (mm) REVERT: 1 110 GLU cc_start: 0.8577 (pm20) cc_final: 0.8349 (pm20) REVERT: 1 160 LYS cc_start: 0.9586 (mtmm) cc_final: 0.9288 (mtmm) REVERT: 1 166 TYR cc_start: 0.8502 (OUTLIER) cc_final: 0.8006 (m-80) REVERT: 1 167 LEU cc_start: 0.9423 (mt) cc_final: 0.9093 (tp) REVERT: 1 173 ASP cc_start: 0.8129 (t70) cc_final: 0.7857 (t70) REVERT: 1 220 MET cc_start: 0.6131 (tpt) cc_final: 0.5759 (mmt) REVERT: 2 29 LYS cc_start: 0.9197 (ttmm) cc_final: 0.8950 (tttp) REVERT: 2 45 GLN cc_start: 0.7957 (pt0) cc_final: 0.7565 (tp-100) REVERT: 2 76 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8257 (mm-30) REVERT: 2 166 TYR cc_start: 0.9299 (OUTLIER) cc_final: 0.8385 (t80) REVERT: 2 188 MET cc_start: 0.8400 (tpp) cc_final: 0.7794 (tpp) REVERT: 2 206 ASP cc_start: 0.8693 (t0) cc_final: 0.8465 (t0) REVERT: 3 68 MET cc_start: 0.7977 (ppp) cc_final: 0.7701 (ppp) REVERT: 3 116 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8269 (mm-30) REVERT: 3 154 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8479 (mm-30) REVERT: 3 206 ASP cc_start: 0.8075 (t0) cc_final: 0.7483 (t0) REVERT: 3 215 LEU cc_start: 0.9497 (mt) cc_final: 0.9229 (mt) REVERT: 3 220 MET cc_start: 0.7463 (tpp) cc_final: 0.7022 (tpp) REVERT: 4 26 CYS cc_start: 0.8454 (p) cc_final: 0.7899 (p) REVERT: 4 64 MET cc_start: 0.8938 (mmt) cc_final: 0.8671 (mmm) REVERT: 4 160 LYS cc_start: 0.9357 (tptt) cc_final: 0.8999 (tppt) REVERT: 4 164 TYR cc_start: 0.8397 (m-80) cc_final: 0.8181 (m-80) REVERT: 4 185 MET cc_start: 0.9097 (mmm) cc_final: 0.8555 (mmm) REVERT: 4 218 GLN cc_start: 0.8722 (mm-40) cc_final: 0.8506 (tp-100) REVERT: 5 95 MET cc_start: 0.8509 (tpp) cc_final: 0.8230 (tpp) REVERT: 5 131 MET cc_start: 0.8458 (ttm) cc_final: 0.8245 (ttm) REVERT: 5 160 MET cc_start: 0.9375 (mpp) cc_final: 0.8906 (mpp) REVERT: 5 228 LEU cc_start: 0.9401 (tp) cc_final: 0.9124 (tt) REVERT: 5 229 LEU cc_start: 0.9543 (tt) cc_final: 0.9242 (mm) REVERT: 6 10 LYS cc_start: 0.9022 (tppt) cc_final: 0.8717 (tppp) REVERT: 6 14 LEU cc_start: 0.9499 (mt) cc_final: 0.8924 (mt) REVERT: 6 67 TYR cc_start: 0.7493 (m-80) cc_final: 0.7203 (m-80) REVERT: 6 74 TYR cc_start: 0.8807 (t80) cc_final: 0.8162 (t80) REVERT: 7 18 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9079 (mt) REVERT: 7 49 PHE cc_start: 0.8297 (m-80) cc_final: 0.7517 (m-80) REVERT: 7 52 LYS cc_start: 0.7681 (ttmt) cc_final: 0.7269 (tttt) REVERT: 7 76 ARG cc_start: 0.8213 (mtm-85) cc_final: 0.7671 (mtm-85) REVERT: 8 76 ARG cc_start: 0.9162 (mtm180) cc_final: 0.8468 (mtt90) REVERT: 8 77 GLN cc_start: 0.8980 (tp40) cc_final: 0.8388 (tm-30) REVERT: 8 81 LEU cc_start: 0.9340 (tp) cc_final: 0.9100 (tp) REVERT: 9 52 LYS cc_start: 0.9309 (ttmm) cc_final: 0.8523 (ttpt) REVERT: 9 66 TRP cc_start: 0.9041 (t60) cc_final: 0.8772 (t60) REVERT: 9 74 TYR cc_start: 0.8718 (t80) cc_final: 0.8039 (t80) REVERT: A 62 MET cc_start: 0.7766 (ttm) cc_final: 0.7533 (ttp) REVERT: A 100 TYR cc_start: 0.7837 (m-80) cc_final: 0.7533 (m-10) REVERT: AM 98 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8707 (mm) REVERT: AN 87 LEU cc_start: 0.9398 (mt) cc_final: 0.8946 (mt) REVERT: AO 49 GLN cc_start: 0.8668 (tp-100) cc_final: 0.7990 (tp-100) REVERT: AO 67 LEU cc_start: 0.9357 (mm) cc_final: 0.9016 (mm) REVERT: AO 69 ILE cc_start: 0.9294 (tp) cc_final: 0.9086 (tp) REVERT: AO 83 MET cc_start: 0.8879 (tpp) cc_final: 0.8594 (tmm) REVERT: AO 99 LEU cc_start: 0.9083 (mm) cc_final: 0.8700 (mm) REVERT: AP 18 ASN cc_start: 0.9114 (p0) cc_final: 0.8764 (p0) REVERT: AP 25 ASP cc_start: 0.7492 (p0) cc_final: 0.6754 (t70) REVERT: AP 66 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7855 (mp0) REVERT: AQ 67 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9159 (mm) REVERT: AQ 96 GLU cc_start: 0.9167 (mm-30) cc_final: 0.8937 (mm-30) REVERT: AQ 99 LEU cc_start: 0.8995 (mt) cc_final: 0.8665 (mp) REVERT: AR 48 LYS cc_start: 0.8696 (tmtt) cc_final: 0.8410 (tmtt) REVERT: AR 63 ASP cc_start: 0.8130 (t0) cc_final: 0.7787 (t70) REVERT: AR 72 GLU cc_start: 0.9003 (tp30) cc_final: 0.8528 (tp30) REVERT: AR 76 ASP cc_start: 0.8292 (m-30) cc_final: 0.7644 (m-30) REVERT: AR 84 VAL cc_start: 0.8792 (m) cc_final: 0.8484 (p) REVERT: AR 87 LEU cc_start: 0.9225 (mm) cc_final: 0.8989 (pp) REVERT: AR 96 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7939 (tm-30) REVERT: AS 50 LYS cc_start: 0.8864 (tptt) cc_final: 0.8318 (tttt) REVERT: AS 51 LEU cc_start: 0.9684 (tt) cc_final: 0.9441 (pp) REVERT: AS 58 ARG cc_start: 0.8373 (mmm-85) cc_final: 0.7774 (mmt90) REVERT: AT 47 TYR cc_start: 0.9157 (t80) cc_final: 0.8456 (t80) REVERT: AT 48 GLN cc_start: 0.8865 (tp40) cc_final: 0.8053 (tp40) REVERT: AT 61 GLN cc_start: 0.9151 (pp30) cc_final: 0.8802 (pp30) REVERT: AU 38 PRO cc_start: 0.6274 (Cg_endo) cc_final: 0.6019 (Cg_exo) REVERT: AU 52 SER cc_start: 0.9128 (m) cc_final: 0.8672 (p) REVERT: AU 61 GLN cc_start: 0.8745 (mt0) cc_final: 0.8490 (mt0) REVERT: AU 80 ARG cc_start: 0.7926 (ptm-80) cc_final: 0.7612 (ttm170) REVERT: AV 47 TYR cc_start: 0.8884 (t80) cc_final: 0.8511 (t80) REVERT: AV 54 TYR cc_start: 0.8538 (t80) cc_final: 0.8132 (t80) REVERT: AV 61 GLN cc_start: 0.8705 (tp40) cc_final: 0.8034 (tm-30) REVERT: AV 69 LYS cc_start: 0.9544 (tttt) cc_final: 0.9177 (tttt) REVERT: AW 47 TYR cc_start: 0.8565 (t80) cc_final: 0.8329 (t80) REVERT: AW 58 ARG cc_start: 0.8735 (mmt180) cc_final: 0.8087 (mmt180) REVERT: AW 61 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8118 (pp30) REVERT: AW 62 SER cc_start: 0.9193 (t) cc_final: 0.8797 (t) REVERT: AW 66 LYS cc_start: 0.9154 (tppt) cc_final: 0.8827 (tppt) REVERT: AY 50 LYS cc_start: 0.7490 (mmmt) cc_final: 0.7243 (ptpp) REVERT: AY 61 GLN cc_start: 0.8277 (pt0) cc_final: 0.7878 (pt0) REVERT: AY 79 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.8537 (m-80) REVERT: AZ 63 ASN cc_start: 0.9151 (m-40) cc_final: 0.8456 (m-40) REVERT: B 155 TYR cc_start: 0.8140 (t80) cc_final: 0.7735 (t80) REVERT: BA 8 TYR cc_start: 0.8548 (t80) cc_final: 0.8280 (t80) REVERT: BA 79 PHE cc_start: 0.8990 (m-80) cc_final: 0.7970 (m-80) REVERT: BB 70 ASP cc_start: 0.9159 (t0) cc_final: 0.8822 (p0) REVERT: BB 75 ILE cc_start: 0.9307 (pt) cc_final: 0.9044 (pt) REVERT: BD 59 ASN cc_start: 0.6754 (OUTLIER) cc_final: 0.6233 (m-40) REVERT: C 157 ASP cc_start: 0.6656 (p0) cc_final: 0.6171 (p0) REVERT: D 114 LEU cc_start: 0.8665 (mm) cc_final: 0.8381 (tp) REVERT: F 107 MET cc_start: 0.8919 (tmm) cc_final: 0.8206 (tmm) REVERT: G 167 ASP cc_start: 0.7900 (OUTLIER) cc_final: 0.7527 (t0) REVERT: H 108 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7883 (ptp-170) REVERT: H 167 ASP cc_start: 0.7603 (p0) cc_final: 0.6784 (p0) REVERT: I 166 MET cc_start: 0.8906 (mmm) cc_final: 0.8567 (tpp) REVERT: J 103 ASP cc_start: 0.7643 (p0) cc_final: 0.7355 (p0) REVERT: N 38 LYS cc_start: 0.8133 (pttt) cc_final: 0.7809 (pttt) REVERT: O 105 SER cc_start: 0.8613 (m) cc_final: 0.8182 (t) REVERT: P 76 ASP cc_start: 0.7432 (t0) cc_final: 0.7086 (t0) REVERT: P 108 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.8040 (ptp-170) REVERT: S 369 ARG cc_start: 0.7596 (mmt90) cc_final: 0.7133 (mmt90) REVERT: U 376 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7648 (mm-30) REVERT: b 379 ILE cc_start: 0.8976 (mm) cc_final: 0.8516 (mm) REVERT: g 366 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8228 (pp) REVERT: j 366 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8714 (pp) outliers start: 139 outliers final: 114 residues processed: 1321 average time/residue: 0.5768 time to fit residues: 1241.8728 Evaluate side-chains 1331 residues out of total 4894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1201 time to evaluate : 5.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 21 ILE Chi-restraints excluded: chain 0 residue 38 ARG Chi-restraints excluded: chain 0 residue 75 PHE Chi-restraints excluded: chain 0 residue 81 THR Chi-restraints excluded: chain 0 residue 170 VAL Chi-restraints excluded: chain 0 residue 188 MET Chi-restraints excluded: chain 0 residue 211 LEU Chi-restraints excluded: chain 1 residue 16 LEU Chi-restraints excluded: chain 1 residue 72 TYR Chi-restraints excluded: chain 1 residue 84 ASP Chi-restraints excluded: chain 1 residue 85 ILE Chi-restraints excluded: chain 1 residue 103 LEU Chi-restraints excluded: chain 1 residue 166 TYR Chi-restraints excluded: chain 1 residue 186 MET Chi-restraints excluded: chain 1 residue 221 ASP Chi-restraints excluded: chain 2 residue 28 VAL Chi-restraints excluded: chain 2 residue 83 ASN Chi-restraints excluded: chain 2 residue 84 ASP Chi-restraints excluded: chain 2 residue 90 LYS Chi-restraints excluded: chain 2 residue 166 TYR Chi-restraints excluded: chain 2 residue 172 VAL Chi-restraints excluded: chain 2 residue 201 LEU Chi-restraints excluded: chain 3 residue 83 ASN Chi-restraints excluded: chain 3 residue 85 ILE Chi-restraints excluded: chain 4 residue 23 SER Chi-restraints excluded: chain 4 residue 215 LEU Chi-restraints excluded: chain 5 residue 10 HIS Chi-restraints excluded: chain 5 residue 12 LEU Chi-restraints excluded: chain 5 residue 68 VAL Chi-restraints excluded: chain 5 residue 179 GLN Chi-restraints excluded: chain 5 residue 182 LEU Chi-restraints excluded: chain 6 residue 18 LEU Chi-restraints excluded: chain 7 residue 2 ASP Chi-restraints excluded: chain 7 residue 18 LEU Chi-restraints excluded: chain 7 residue 42 LEU Chi-restraints excluded: chain 8 residue 3 ASP Chi-restraints excluded: chain 8 residue 57 CYS Chi-restraints excluded: chain 8 residue 72 LEU Chi-restraints excluded: chain 9 residue 15 VAL Chi-restraints excluded: chain 9 residue 19 SER Chi-restraints excluded: chain 9 residue 44 GLU Chi-restraints excluded: chain 9 residue 51 ILE Chi-restraints excluded: chain 9 residue 63 LEU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain AM residue 98 LEU Chi-restraints excluded: chain AN residue 75 SER Chi-restraints excluded: chain AO residue 86 THR Chi-restraints excluded: chain AO residue 88 THR Chi-restraints excluded: chain AO residue 95 VAL Chi-restraints excluded: chain AP residue 33 LEU Chi-restraints excluded: chain AP residue 34 LEU Chi-restraints excluded: chain AP residue 75 SER Chi-restraints excluded: chain AP residue 98 LEU Chi-restraints excluded: chain AQ residue 19 ILE Chi-restraints excluded: chain AQ residue 21 SER Chi-restraints excluded: chain AQ residue 57 ASP Chi-restraints excluded: chain AQ residue 67 LEU Chi-restraints excluded: chain AQ residue 69 ILE Chi-restraints excluded: chain AR residue 34 LEU Chi-restraints excluded: chain AR residue 92 VAL Chi-restraints excluded: chain AS residue 47 TYR Chi-restraints excluded: chain AT residue 52 SER Chi-restraints excluded: chain AU residue 31 LEU Chi-restraints excluded: chain AU residue 64 THR Chi-restraints excluded: chain AU residue 67 VAL Chi-restraints excluded: chain AV residue 28 THR Chi-restraints excluded: chain AV residue 31 LEU Chi-restraints excluded: chain AV residue 62 SER Chi-restraints excluded: chain AW residue 61 GLN Chi-restraints excluded: chain AW residue 75 ILE Chi-restraints excluded: chain AX residue 44 LEU Chi-restraints excluded: chain AX residue 71 ILE Chi-restraints excluded: chain AY residue 76 ILE Chi-restraints excluded: chain AY residue 79 PHE Chi-restraints excluded: chain AZ residue 54 TYR Chi-restraints excluded: chain BA residue 20 VAL Chi-restraints excluded: chain BA residue 77 GLN Chi-restraints excluded: chain BB residue 51 LEU Chi-restraints excluded: chain BD residue 59 ASN Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain E residue 379 ILE Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 78 ASN Chi-restraints excluded: chain F residue 108 ARG Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 108 ARG Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 116 ASN Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain K residue 126 LEU Chi-restraints excluded: chain L residue 38 LYS Chi-restraints excluded: chain L residue 68 ILE Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 132 TYR Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 47 ASP Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 78 ASN Chi-restraints excluded: chain N residue 91 ILE Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 108 ARG Chi-restraints excluded: chain P residue 111 VAL Chi-restraints excluded: chain P residue 149 VAL Chi-restraints excluded: chain R residue 366 LEU Chi-restraints excluded: chain S residue 381 MET Chi-restraints excluded: chain V residue 370 SER Chi-restraints excluded: chain Z residue 367 LYS Chi-restraints excluded: chain a residue 366 LEU Chi-restraints excluded: chain b residue 366 LEU Chi-restraints excluded: chain c residue 376 GLU Chi-restraints excluded: chain g residue 366 LEU Chi-restraints excluded: chain j residue 366 LEU Chi-restraints excluded: chain m residue 390 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 329 optimal weight: 0.0570 chunk 441 optimal weight: 0.6980 chunk 127 optimal weight: 7.9990 chunk 382 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 115 optimal weight: 0.5980 chunk 415 optimal weight: 5.9990 chunk 173 optimal weight: 0.0040 chunk 426 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 76 optimal weight: 0.0570 overall best weight: 0.2828 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 218 GLN 4 45 GLN ** 5 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AN 15 GLN A AO 18 ASN ** AO 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AQ 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AR 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AR 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AT 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AU 48 GLN AX 63 ASN ** BC 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 GLN I 87 GLN M 161 ASN ** N 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.095924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.070745 restraints weight = 243909.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.073379 restraints weight = 107087.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.075250 restraints weight = 65034.317| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.5923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 46515 Z= 0.205 Angle : 0.811 15.798 62995 Z= 0.391 Chirality : 0.047 0.337 6948 Planarity : 0.005 0.060 7985 Dihedral : 5.084 75.205 6214 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.07 % Favored : 95.91 % Rotamer: Outliers : 2.58 % Allowed : 28.67 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.37 (0.11), residues: 5563 helix: 0.55 (0.10), residues: 2989 sheet: 0.92 (0.23), residues: 456 loop : -1.64 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRPBA 5 HIS 0.007 0.001 HIS Q 75 PHE 0.032 0.001 PHE 8 49 TYR 0.044 0.002 TYR e 387 ARG 0.014 0.001 ARG B 65 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17724.84 seconds wall clock time: 315 minutes 3.76 seconds (18903.76 seconds total)