Starting phenix.real_space_refine on Sun Mar 17 20:48:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqn_11369/03_2024/6zqn_11369_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqn_11369/03_2024/6zqn_11369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqn_11369/03_2024/6zqn_11369.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqn_11369/03_2024/6zqn_11369.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqn_11369/03_2024/6zqn_11369_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqn_11369/03_2024/6zqn_11369_trim_updated.pdb" } resolution = 4.0 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= 0.017 sd= 1.103 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: 7 Type Number sf(0) Gaussians P 23 5.49 5 Mg 5 5.21 5 S 154 5.16 5 C 25602 2.51 5 N 6752 2.21 5 O 7544 1.98 5 H 40551 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 26": "OE1" <-> "OE2" Residue "A PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 154": "OD1" <-> "OD2" Residue "A ARG 219": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 238": "OD1" <-> "OD2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 291": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "A PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 373": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 426": "OE1" <-> "OE2" Residue "A TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 452": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 484": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 486": "OD1" <-> "OD2" Residue "B GLU 14": "OE1" <-> "OE2" Residue "B ASP 24": "OD1" <-> "OD2" Residue "B ARG 45": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 50": "OE1" <-> "OE2" Residue "B GLU 51": "OE1" <-> "OE2" Residue "B ASP 69": "OD1" <-> "OD2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 269": "OD1" <-> "OD2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 297": "OD1" <-> "OD2" Residue "B PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "B ARG 373": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 393": "OE1" <-> "OE2" Residue "B GLU 399": "OE1" <-> "OE2" Residue "B TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 508": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "C PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 79": "OD1" <-> "OD2" Residue "C ARG 143": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 144": "OE1" <-> "OE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 297": "OD1" <-> "OD2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "C TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 393": "OE1" <-> "OE2" Residue "C ARG 398": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 440": "OE1" <-> "OE2" Residue "C TYR 452": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "D GLU 67": "OE1" <-> "OE2" Residue "D ASP 77": "OD1" <-> "OD2" Residue "D GLU 104": "OE1" <-> "OE2" Residue "D PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 125": "OE1" <-> "OE2" Residue "D GLU 129": "OE1" <-> "OE2" Residue "D GLU 131": "OE1" <-> "OE2" Residue "D PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 192": "OE1" <-> "OE2" Residue "D GLU 199": "OE1" <-> "OE2" Residue "D ASP 210": "OD1" <-> "OD2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 267": "OE1" <-> "OE2" Residue "D TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 288": "OD1" <-> "OD2" Residue "D PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 349": "OD1" <-> "OD2" Residue "D GLU 366": "OE1" <-> "OE2" Residue "D PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 465": "OE1" <-> "OE2" Residue "D GLU 476": "OE1" <-> "OE2" Residue "E GLU 48": "OE1" <-> "OE2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 131": "OE1" <-> "OE2" Residue "E ASP 141": "OD1" <-> "OD2" Residue "E TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 256": "OD1" <-> "OD2" Residue "E TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 330": "OD1" <-> "OD2" Residue "E GLU 366": "OE1" <-> "OE2" Residue "E PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 436": "OE1" <-> "OE2" Residue "E PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 448": "OE1" <-> "OE2" Residue "E TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 471": "OD1" <-> "OD2" Residue "F PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 27": "OE1" <-> "OE2" Residue "F GLU 37": "OE1" <-> "OE2" Residue "F GLU 42": "OE1" <-> "OE2" Residue "F GLU 55": "OE1" <-> "OE2" Residue "F GLU 104": "OE1" <-> "OE2" Residue "F PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 119": "OE1" <-> "OE2" Residue "F ASP 141": "OD1" <-> "OD2" Residue "F TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 195": "OD1" <-> "OD2" Residue "F GLU 202": "OE1" <-> "OE2" Residue "F PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 250": "OD1" <-> "OD2" Residue "F PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 256": "OD1" <-> "OD2" Residue "F PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 359": "OD1" <-> "OD2" Residue "F ASP 380": "OD1" <-> "OD2" Residue "F PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 436": "OE1" <-> "OE2" Residue "F PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 465": "OE1" <-> "OE2" Residue "F ASP 471": "OD1" <-> "OD2" Residue "G ARG 9": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 56": "OD1" <-> "OD2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 133": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 157": "OE1" <-> "OE2" Residue "G PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 174": "OE1" <-> "OE2" Residue "G ASP 195": "OD1" <-> "OD2" Residue "G ASP 199": "OD1" <-> "OD2" Residue "G ARG 202": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 224": "OE1" <-> "OE2" Residue "G GLU 261": "OE1" <-> "OE2" Residue "G GLU 264": "OE1" <-> "OE2" Residue "H PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 68": "OE1" <-> "OE2" Residue "H TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 96": "OE1" <-> "OE2" Residue "H ASP 104": "OD1" <-> "OD2" Residue "H ASP 124": "OD1" <-> "OD2" Residue "H GLU 136": "OE1" <-> "OE2" Residue "H GLU 139": "OE1" <-> "OE2" Residue "I ARG 5": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 24": "OD1" <-> "OD2" Residue "J PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 25": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 31": "OE1" <-> "OE2" Residue "J TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 52": "OE1" <-> "OE2" Residue "K ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 58": "OE1" <-> "OE2" Residue "L ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ASP 1": "OD1" <-> "OD2" Residue "M TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N GLU 58": "OE1" <-> "OE2" Residue "P PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 1": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S GLU 76": "OE1" <-> "OE2" Residue "S ARG 94": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S GLU 133": "OE1" <-> "OE2" Residue "S ARG 165": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S ASP 172": "OD1" <-> "OD2" Residue "O PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "8 ASP 5": "OD1" <-> "OD2" Residue "8 PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "8 PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "8 TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 3": "OE1" <-> "OE2" Residue "a PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ARG 36": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ARG 159": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ASP 224": "OD1" <-> "OD2" Residue "d PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d GLU 46": "OE1" <-> "OE2" Residue "d GLU 102": "OE1" <-> "OE2" Residue "d ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f ASP 27": "OD1" <-> "OD2" Residue "f ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f ARG 73": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f ARG 84": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g ARG 25": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g GLU 81": "OE1" <-> "OE2" Residue "g ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "j TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ARG 121": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ARG 129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 141": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "k TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "k PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e GLU 52": "OE1" <-> "OE2" Residue "Q ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 80631 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 7741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 7741 Classifications: {'peptide': 501} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 482} Chain: "B" Number of atoms: 7760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 7760 Classifications: {'peptide': 502} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 483} Chain breaks: 1 Chain: "C" Number of atoms: 7488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 7488 Classifications: {'peptide': 483} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 464} Chain breaks: 1 Chain: "D" Number of atoms: 7163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 7163 Classifications: {'peptide': 469} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 444} Chain: "E" Number of atoms: 7132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 7132 Classifications: {'peptide': 467} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 442} Chain: "F" Number of atoms: 7131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 7131 Classifications: {'peptide': 467} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 442} Chain: "G" Number of atoms: 4300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 4300 Classifications: {'peptide': 272} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 266} Chain: "H" Number of atoms: 1940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1940 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "I" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 764 Classifications: {'peptide': 47} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 46} Chain: "J" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 731 Classifications: {'peptide': 47} Link IDs: {'TRANS': 46} Chain: "K" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1077 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1077 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 1060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1060 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1077 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 2989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 2989 Classifications: {'peptide': 187} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 178} Chain: "O" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1077 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "8" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 696 Classifications: {'peptide': 41} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 37} Chain: "a" Number of atoms: 3611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3611 Classifications: {'peptide': 226} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 213} Chain: "d" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 2549 Classifications: {'peptide': 155} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 143} Chain: "f" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1411 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "g" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1291 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "j" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 828 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "b" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3456 Classifications: {'peptide': 209} Modifications used: {'NH2': 1} Link IDs: {'PTRANS': 7, 'TRANS': 201} Chain: "h" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1009 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 5, 'TRANS': 56} Chain: "k" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 596 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "e" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 951 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 3, 'TRANS': 52} Chain: "Q" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1077 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "f" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 172 Unusual residues: {'CDL': 1, 'LHG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Chain: "b" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 161 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 39 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 26.04, per 1000 atoms: 0.32 Number of scatterers: 80631 At special positions: 0 Unit cell: (154.056, 141.48, 252.568, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 154 16.00 P 23 15.00 Mg 5 11.99 O 7544 8.00 N 6752 7.00 C 25602 6.00 H 40551 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 53.91 Conformation dependent library (CDL) restraints added in 6.6 seconds 10158 Ramachandran restraints generated. 5079 Oldfield, 0 Emsley, 5079 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9438 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 188 helices and 25 sheets defined 52.1% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.43 Creating SS restraints... Processing helix chain 'A' and resid 9 through 17 removed outlier: 3.865A pdb=" N GLU A 14 " --> pdb=" O SER A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 175 through 191 removed outlier: 3.649A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LYS A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ARG A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N PHE A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 222 Processing helix chain 'A' and resid 240 through 260 Proline residue: A 247 - end of helix removed outlier: 3.897A pdb=" N PHE A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 285 Processing helix chain 'A' and resid 291 through 293 No H-bonds generated for 'chain 'A' and resid 291 through 293' Processing helix chain 'A' and resid 300 through 306 removed outlier: 3.592A pdb=" N LEU A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 381 through 403 removed outlier: 4.095A pdb=" N THR A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL A 400 " --> pdb=" O GLN A 396 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ALA A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N PHE A 403 " --> pdb=" O GLU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 428 removed outlier: 3.910A pdb=" N ARG A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 449 Processing helix chain 'A' and resid 458 through 473 removed outlier: 4.753A pdb=" N THR A 462 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE A 473 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 485 Processing helix chain 'A' and resid 491 through 506 Processing helix chain 'B' and resid 9 through 16 removed outlier: 4.110A pdb=" N GLU B 14 " --> pdb=" O SER B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 21 No H-bonds generated for 'chain 'B' and resid 19 through 21' Processing helix chain 'B' and resid 79 through 81 No H-bonds generated for 'chain 'B' and resid 79 through 81' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 175 through 184 Processing helix chain 'B' and resid 210 through 223 removed outlier: 3.614A pdb=" N ALA B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 260 Proline residue: B 247 - end of helix removed outlier: 4.119A pdb=" N PHE B 257 " --> pdb=" O MET B 253 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN B 260 " --> pdb=" O TYR B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 285 Processing helix chain 'B' and resid 300 through 306 removed outlier: 3.607A pdb=" N ARG B 304 " --> pdb=" O TYR B 300 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 354 through 358 Processing helix chain 'B' and resid 375 through 377 No H-bonds generated for 'chain 'B' and resid 375 through 377' Processing helix chain 'B' and resid 381 through 400 removed outlier: 4.486A pdb=" N THR B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU B 399 " --> pdb=" O ALA B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 428 Processing helix chain 'B' and resid 438 through 449 Processing helix chain 'B' and resid 458 through 475 removed outlier: 3.740A pdb=" N ILE B 461 " --> pdb=" O PRO B 458 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR B 462 " --> pdb=" O SER B 459 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLU B 465 " --> pdb=" O THR B 462 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN B 475 " --> pdb=" O VAL B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 486 Processing helix chain 'B' and resid 491 through 507 removed outlier: 4.086A pdb=" N GLY B 507 " --> pdb=" O ASN B 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 151 through 154 No H-bonds generated for 'chain 'C' and resid 151 through 154' Processing helix chain 'C' and resid 175 through 190 removed outlier: 3.520A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LYS C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ARG C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N PHE C 189 " --> pdb=" O ASN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 223 removed outlier: 3.706A pdb=" N ALA C 223 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 259 Proline residue: C 247 - end of helix removed outlier: 4.013A pdb=" N PHE C 257 " --> pdb=" O MET C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 284 Processing helix chain 'C' and resid 291 through 293 No H-bonds generated for 'chain 'C' and resid 291 through 293' Processing helix chain 'C' and resid 298 through 308 removed outlier: 3.796A pdb=" N HIS C 302 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ARG C 308 " --> pdb=" O ARG C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 356 through 359 No H-bonds generated for 'chain 'C' and resid 356 through 359' Processing helix chain 'C' and resid 375 through 378 Processing helix chain 'C' and resid 381 through 399 removed outlier: 4.023A pdb=" N VAL C 386 " --> pdb=" O ALA C 382 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N THR C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 428 Processing helix chain 'C' and resid 438 through 449 Processing helix chain 'C' and resid 461 through 474 Processing helix chain 'C' and resid 477 through 486 Processing helix chain 'C' and resid 491 through 506 Processing helix chain 'D' and resid 123 through 125 No H-bonds generated for 'chain 'D' and resid 123 through 125' Processing helix chain 'D' and resid 138 through 143 Processing helix chain 'D' and resid 162 through 173 Processing helix chain 'D' and resid 190 through 203 removed outlier: 3.561A pdb=" N ASN D 194 " --> pdb=" O THR D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 229 No H-bonds generated for 'chain 'D' and resid 226 through 229' Processing helix chain 'D' and resid 232 through 245 Processing helix chain 'D' and resid 260 through 269 removed outlier: 3.732A pdb=" N VAL D 268 " --> pdb=" O ALA D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 293 removed outlier: 3.787A pdb=" N MET D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 315 No H-bonds generated for 'chain 'D' and resid 313 through 315' Processing helix chain 'D' and resid 320 through 328 removed outlier: 4.729A pdb=" N ALA D 327 " --> pdb=" O ALA D 323 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N HIS D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 340 No H-bonds generated for 'chain 'D' and resid 337 through 340' Processing helix chain 'D' and resid 360 through 363 No H-bonds generated for 'chain 'D' and resid 360 through 363' Processing helix chain 'D' and resid 365 through 391 removed outlier: 3.928A pdb=" N ASP D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE D 390 " --> pdb=" O ASP D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 413 Processing helix chain 'D' and resid 434 through 446 Processing helix chain 'D' and resid 454 through 456 No H-bonds generated for 'chain 'D' and resid 454 through 456' Processing helix chain 'D' and resid 463 through 475 Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 138 through 143 Processing helix chain 'E' and resid 163 through 176 Processing helix chain 'E' and resid 190 through 203 Processing helix chain 'E' and resid 226 through 228 No H-bonds generated for 'chain 'E' and resid 226 through 228' Processing helix chain 'E' and resid 234 through 247 removed outlier: 3.629A pdb=" N PHE E 243 " --> pdb=" O VAL E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 271 Processing helix chain 'E' and resid 285 through 293 removed outlier: 3.862A pdb=" N MET E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 315 No H-bonds generated for 'chain 'E' and resid 313 through 315' Processing helix chain 'E' and resid 320 through 325 Processing helix chain 'E' and resid 338 through 341 No H-bonds generated for 'chain 'E' and resid 338 through 341' Processing helix chain 'E' and resid 365 through 390 removed outlier: 3.723A pdb=" N ASP E 386 " --> pdb=" O LYS E 382 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE E 387 " --> pdb=" O SER E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 395 No H-bonds generated for 'chain 'E' and resid 393 through 395' Processing helix chain 'E' and resid 398 through 414 removed outlier: 4.365A pdb=" N THR E 403 " --> pdb=" O GLU E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 425 removed outlier: 4.106A pdb=" N VAL E 423 " --> pdb=" O VAL E 420 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR E 425 " --> pdb=" O GLU E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 445 Processing helix chain 'E' and resid 454 through 456 No H-bonds generated for 'chain 'E' and resid 454 through 456' Processing helix chain 'E' and resid 463 through 473 Processing helix chain 'F' and resid 123 through 125 No H-bonds generated for 'chain 'F' and resid 123 through 125' Processing helix chain 'F' and resid 138 through 143 Processing helix chain 'F' and resid 162 through 173 Processing helix chain 'F' and resid 190 through 203 Processing helix chain 'F' and resid 226 through 229 No H-bonds generated for 'chain 'F' and resid 226 through 229' Processing helix chain 'F' and resid 232 through 245 Processing helix chain 'F' and resid 260 through 267 Processing helix chain 'F' and resid 285 through 293 removed outlier: 3.769A pdb=" N MET F 292 " --> pdb=" O ASP F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 315 No H-bonds generated for 'chain 'F' and resid 313 through 315' Processing helix chain 'F' and resid 320 through 328 removed outlier: 4.778A pdb=" N ALA F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N HIS F 328 " --> pdb=" O THR F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 342 removed outlier: 3.737A pdb=" N LEU F 342 " --> pdb=" O ALA F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 363 No H-bonds generated for 'chain 'F' and resid 360 through 363' Processing helix chain 'F' and resid 365 through 388 removed outlier: 4.586A pdb=" N ASP F 386 " --> pdb=" O LYS F 382 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ILE F 387 " --> pdb=" O SER F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 395 No H-bonds generated for 'chain 'F' and resid 393 through 395' Processing helix chain 'F' and resid 398 through 414 Processing helix chain 'F' and resid 419 through 421 No H-bonds generated for 'chain 'F' and resid 419 through 421' Processing helix chain 'F' and resid 434 through 445 Processing helix chain 'F' and resid 454 through 456 No H-bonds generated for 'chain 'F' and resid 454 through 456' Processing helix chain 'F' and resid 463 through 474 Processing helix chain 'G' and resid 3 through 54 Proline residue: G 40 - end of helix removed outlier: 4.172A pdb=" N VAL G 43 " --> pdb=" O LYS G 39 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N TYR G 52 " --> pdb=" O SER G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 99 Processing helix chain 'G' and resid 110 through 117 Processing helix chain 'G' and resid 138 through 149 Processing helix chain 'G' and resid 181 through 186 Processing helix chain 'G' and resid 188 through 190 No H-bonds generated for 'chain 'G' and resid 188 through 190' Processing helix chain 'G' and resid 200 through 270 removed outlier: 3.953A pdb=" N ALA G 210 " --> pdb=" O GLU G 206 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU G 248 " --> pdb=" O ASP G 244 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 102 No H-bonds generated for 'chain 'H' and resid 100 through 102' Processing helix chain 'H' and resid 105 through 118 Processing helix chain 'H' and resid 125 through 145 Processing helix chain 'I' and resid 3 through 7 Processing helix chain 'I' and resid 11 through 25 Processing helix chain 'I' and resid 28 through 35 removed outlier: 3.957A pdb=" N ALA I 32 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ASN I 33 " --> pdb=" O GLU I 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 21 through 53 removed outlier: 3.975A pdb=" N GLN J 27 " --> pdb=" O GLY J 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 37 removed outlier: 4.582A pdb=" N VAL K 16 " --> pdb=" O GLY K 12 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLY K 17 " --> pdb=" O ALA K 13 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N VAL K 18 " --> pdb=" O ALA K 14 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ALA K 19 " --> pdb=" O THR K 15 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLY K 20 " --> pdb=" O VAL K 16 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER K 21 " --> pdb=" O GLY K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 72 removed outlier: 4.045A pdb=" N MET K 60 " --> pdb=" O LEU K 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 38 removed outlier: 3.771A pdb=" N VAL L 16 " --> pdb=" O GLY L 12 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY L 17 " --> pdb=" O ALA L 13 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL L 18 " --> pdb=" O ALA L 14 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ALA L 19 " --> pdb=" O THR L 15 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLY L 20 " --> pdb=" O VAL L 16 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER L 21 " --> pdb=" O GLY L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 46 through 72 removed outlier: 4.239A pdb=" N MET L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 38 removed outlier: 4.356A pdb=" N PHE M 8 " --> pdb=" O THR M 4 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL M 16 " --> pdb=" O GLY M 12 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N GLY M 17 " --> pdb=" O ALA M 13 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N VAL M 18 " --> pdb=" O ALA M 14 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ALA M 19 " --> pdb=" O THR M 15 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLY M 20 " --> pdb=" O VAL M 16 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER M 21 " --> pdb=" O GLY M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 71 Processing helix chain 'N' and resid 2 through 14 Processing helix chain 'N' and resid 16 through 38 removed outlier: 4.820A pdb=" N GLY N 20 " --> pdb=" O GLY N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 72 removed outlier: 4.232A pdb=" N MET N 60 " --> pdb=" O LEU N 56 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYS N 64 " --> pdb=" O MET N 60 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 37 removed outlier: 4.387A pdb=" N VAL P 16 " --> pdb=" O GLY P 12 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLY P 17 " --> pdb=" O ALA P 13 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL P 18 " --> pdb=" O ALA P 14 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ALA P 19 " --> pdb=" O THR P 15 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLY P 20 " --> pdb=" O VAL P 16 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER P 21 " --> pdb=" O GLY P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 73 removed outlier: 3.548A pdb=" N LEU P 52 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER P 57 " --> pdb=" O PHE P 54 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE P 71 " --> pdb=" O ALA P 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 3 through 38 removed outlier: 4.627A pdb=" N VAL R 16 " --> pdb=" O GLY R 12 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLY R 17 " --> pdb=" O ALA R 13 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL R 18 " --> pdb=" O ALA R 14 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ALA R 19 " --> pdb=" O THR R 15 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY R 20 " --> pdb=" O VAL R 16 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER R 21 " --> pdb=" O GLY R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 73 removed outlier: 4.426A pdb=" N MET R 60 " --> pdb=" O LEU R 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 27 Processing helix chain 'S' and resid 32 through 45 removed outlier: 3.542A pdb=" N GLN S 44 " --> pdb=" O LEU S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 54 Processing helix chain 'S' and resid 62 through 76 Processing helix chain 'S' and resid 80 through 92 Processing helix chain 'S' and resid 95 through 113 Proline residue: S 99 - end of helix removed outlier: 3.718A pdb=" N ILE S 102 " --> pdb=" O PRO S 99 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER S 103 " --> pdb=" O ALA S 100 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER S 110 " --> pdb=" O THR S 107 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL S 111 " --> pdb=" O MET S 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 128 through 140 removed outlier: 4.101A pdb=" N SER S 140 " --> pdb=" O THR S 136 " (cutoff:3.500A) Processing helix chain 'S' and resid 175 through 186 Processing helix chain 'O' and resid 3 through 38 removed outlier: 3.564A pdb=" N THR O 15 " --> pdb=" O ALA O 11 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL O 16 " --> pdb=" O GLY O 12 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N GLY O 17 " --> pdb=" O ALA O 13 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N VAL O 18 " --> pdb=" O ALA O 14 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ALA O 19 " --> pdb=" O THR O 15 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY O 20 " --> pdb=" O VAL O 16 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER O 21 " --> pdb=" O GLY O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 72 removed outlier: 4.408A pdb=" N MET O 60 " --> pdb=" O LEU O 56 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N CYS O 64 " --> pdb=" O MET O 60 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU O 65 " --> pdb=" O GLY O 61 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 4 No H-bonds generated for 'chain '8' and resid 2 through 4' Processing helix chain '8' and resid 6 through 21 removed outlier: 4.528A pdb=" N LEU 8 10 " --> pdb=" O SER 8 7 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE 8 21 " --> pdb=" O LEU 8 18 " (cutoff:3.500A) Processing helix chain '8' and resid 24 through 29 Processing helix chain 'a' and resid 7 through 9 No H-bonds generated for 'chain 'a' and resid 7 through 9' Processing helix chain 'a' and resid 19 through 30 Proline residue: a 27 - end of helix Processing helix chain 'a' and resid 41 through 60 removed outlier: 5.142A pdb=" N ILE a 60 " --> pdb=" O GLN a 56 " (cutoff:3.500A) Processing helix chain 'a' and resid 63 through 87 removed outlier: 4.322A pdb=" N TRP a 68 " --> pdb=" O LYS a 64 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR a 69 " --> pdb=" O GLY a 65 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N LEU a 70 " --> pdb=" O GLN a 66 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N MET a 71 " --> pdb=" O THR a 67 " (cutoff:3.500A) Processing helix chain 'a' and resid 94 through 96 No H-bonds generated for 'chain 'a' and resid 94 through 96' Processing helix chain 'a' and resid 98 through 118 Proline residue: a 107 - end of helix Processing helix chain 'a' and resid 122 through 128 removed outlier: 4.667A pdb=" N PHE a 128 " --> pdb=" O SER a 124 " (cutoff:3.500A) Processing helix chain 'a' and resid 135 through 183 Proline residue: a 139 - end of helix removed outlier: 4.202A pdb=" N ILE a 143 " --> pdb=" O MET a 140 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR a 146 " --> pdb=" O ILE a 143 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE a 151 " --> pdb=" O SER a 148 " (cutoff:3.500A) Proline residue: a 153 - end of helix removed outlier: 4.497A pdb=" N THR a 165 " --> pdb=" O ALA a 162 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE a 174 " --> pdb=" O ILE a 171 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 224 removed outlier: 3.584A pdb=" N MET a 208 " --> pdb=" O PHE a 204 " (cutoff:3.500A) Processing helix chain 'd' and resid 12 through 17 removed outlier: 3.663A pdb=" N GLU d 17 " --> pdb=" O VAL d 13 " (cutoff:3.500A) Processing helix chain 'd' and resid 24 through 43 Processing helix chain 'd' and resid 53 through 59 Processing helix chain 'd' and resid 65 through 75 Processing helix chain 'd' and resid 88 through 100 Processing helix chain 'd' and resid 104 through 122 removed outlier: 3.546A pdb=" N ARG d 122 " --> pdb=" O LEU d 118 " (cutoff:3.500A) Processing helix chain 'd' and resid 127 through 129 No H-bonds generated for 'chain 'd' and resid 127 through 129' Processing helix chain 'd' and resid 132 through 138 Processing helix chain 'd' and resid 140 through 142 No H-bonds generated for 'chain 'd' and resid 140 through 142' Processing helix chain 'f' and resid 11 through 13 No H-bonds generated for 'chain 'f' and resid 11 through 13' Processing helix chain 'f' and resid 16 through 25 Proline residue: f 20 - end of helix Processing helix chain 'f' and resid 30 through 48 Processing helix chain 'f' and resid 56 through 74 removed outlier: 4.003A pdb=" N SER f 60 " --> pdb=" O ALA f 57 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N MET f 61 " --> pdb=" O GLY f 58 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU f 63 " --> pdb=" O SER f 60 " (cutoff:3.500A) Processing helix chain 'f' and resid 79 through 81 No H-bonds generated for 'chain 'f' and resid 79 through 81' Processing helix chain 'g' and resid 22 through 36 removed outlier: 4.032A pdb=" N VAL g 35 " --> pdb=" O TYR g 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 42 through 60 Proline residue: g 46 - end of helix removed outlier: 3.753A pdb=" N LYS g 60 " --> pdb=" O ASN g 57 " (cutoff:3.500A) Processing helix chain 'g' and resid 63 through 66 removed outlier: 3.532A pdb=" N GLN g 66 " --> pdb=" O SER g 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 63 through 66' Processing helix chain 'g' and resid 69 through 93 removed outlier: 4.086A pdb=" N PHE g 86 " --> pdb=" O VAL g 82 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TYR g 87 " --> pdb=" O TRP g 83 " (cutoff:3.500A) Processing helix chain 'j' and resid 4 through 9 Processing helix chain 'j' and resid 14 through 18 Processing helix chain 'j' and resid 22 through 47 Processing helix chain 'b' and resid 19 through 29 Proline residue: b 27 - end of helix Processing helix chain 'b' and resid 33 through 48 Processing helix chain 'b' and resid 55 through 119 removed outlier: 5.964A pdb=" N ALA b 76 " --> pdb=" O LYS b 72 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N SER b 77 " --> pdb=" O LYS b 73 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN b 119 " --> pdb=" O GLN b 115 " (cutoff:3.500A) Processing helix chain 'b' and resid 123 through 184 removed outlier: 3.762A pdb=" N HIS b 158 " --> pdb=" O ARG b 154 " (cutoff:3.500A) Processing helix chain 'b' and resid 190 through 208 Processing helix chain 'h' and resid 9 through 26 removed outlier: 4.471A pdb=" N GLY h 26 " --> pdb=" O ARG h 22 " (cutoff:3.500A) Processing helix chain 'h' and resid 33 through 50 Processing helix chain 'k' and resid 14 through 17 No H-bonds generated for 'chain 'k' and resid 14 through 17' Processing helix chain 'k' and resid 23 through 45 Processing helix chain 'e' and resid 8 through 56 Proline residue: e 34 - end of helix Processing helix chain 'Q' and resid 3 through 38 removed outlier: 4.260A pdb=" N VAL Q 16 " --> pdb=" O GLY Q 12 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY Q 17 " --> pdb=" O ALA Q 13 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N VAL Q 18 " --> pdb=" O ALA Q 14 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ALA Q 19 " --> pdb=" O THR Q 15 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLY Q 20 " --> pdb=" O VAL Q 16 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER Q 21 " --> pdb=" O GLY Q 17 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE Q 33 " --> pdb=" O PHE Q 29 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 72 removed outlier: 3.827A pdb=" N MET Q 60 " --> pdb=" O LEU Q 56 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N CYS Q 64 " --> pdb=" O MET Q 60 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 29 through 31 removed outlier: 6.930A pdb=" N VAL A 74 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N SER A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 98 Processing sheet with id= C, first strand: chain 'A' and resid 167 through 169 Processing sheet with id= D, first strand: chain 'A' and resid 199 through 205 removed outlier: 7.486A pdb=" N HIS A 263 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ILE A 202 " --> pdb=" O HIS A 263 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU A 265 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N VAL A 204 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE A 267 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N SER A 320 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ILE A 266 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N THR A 322 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N TYR A 268 " --> pdb=" O THR A 322 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.877A pdb=" N ARG B 40 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ILE B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE B 38 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN B 65 " --> pdb=" O GLY B 72 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL B 74 " --> pdb=" O SER B 63 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N SER B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 98 Processing sheet with id= G, first strand: chain 'B' and resid 164 through 168 removed outlier: 8.123A pdb=" N GLU B 165 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA B 323 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ILE B 167 " --> pdb=" O ALA B 323 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA B 264 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR B 268 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TYR B 200 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ILE B 267 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE B 202 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ASP B 269 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL B 204 " --> pdb=" O ASP B 269 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 87 through 89 removed outlier: 6.616A pdb=" N ARG C 40 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE C 38 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL C 74 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N SER C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 96 through 98 Processing sheet with id= J, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.689A pdb=" N CYS C 201 " --> pdb=" O ILE C 230 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL C 232 " --> pdb=" O CYS C 201 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N TYR C 203 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ALA C 234 " --> pdb=" O TYR C 203 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ALA C 205 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE C 267 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE C 206 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ASP C 269 " --> pdb=" O ILE C 206 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.539A pdb=" N ARG D 59 " --> pdb=" O ALA D 50 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N GLN D 24 " --> pdb=" O ILE D 13 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE D 13 " --> pdb=" O GLN D 24 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 83 through 86 removed outlier: 4.177A pdb=" N GLN D 112 " --> pdb=" O VAL D 86 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 331 through 334 removed outlier: 3.724A pdb=" N ASP D 256 " --> pdb=" O ALA D 184 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.593A pdb=" N ARG E 59 " --> pdb=" O ALA E 50 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N GLN E 24 " --> pdb=" O ILE E 13 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ILE E 13 " --> pdb=" O GLN E 24 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 83 through 85 Processing sheet with id= P, first strand: chain 'E' and resid 151 through 154 removed outlier: 6.148A pdb=" N SER E 306 " --> pdb=" O ILE E 152 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LEU E 154 " --> pdb=" O SER E 306 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLN E 308 " --> pdb=" O LEU E 154 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'E' and resid 183 through 188 Processing sheet with id= R, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.667A pdb=" N ARG F 59 " --> pdb=" O ALA F 50 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N HIS F 52 " --> pdb=" O THR F 57 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N THR F 57 " --> pdb=" O HIS F 52 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N GLN F 24 " --> pdb=" O ILE F 13 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ILE F 13 " --> pdb=" O GLN F 24 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 83 through 85 Processing sheet with id= T, first strand: chain 'F' and resid 216 through 220 removed outlier: 3.680A pdb=" N LEU F 252 " --> pdb=" O TYR F 180 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 103 through 108 removed outlier: 6.623A pdb=" N HIS G 66 " --> pdb=" O LYS G 104 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ILE G 106 " --> pdb=" O HIS G 66 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE G 68 " --> pdb=" O ILE G 106 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N VAL G 108 " --> pdb=" O ILE G 68 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLY G 70 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ASN G 163 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N SER G 170 " --> pdb=" O ARG G 166 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 80 through 84 removed outlier: 6.801A pdb=" N SER H 22 " --> pdb=" O VAL H 26 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL H 26 " --> pdb=" O SER H 22 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 45 through 47 removed outlier: 3.590A pdb=" N GLN H 35 " --> pdb=" O HIS H 66 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL H 64 " --> pdb=" O ASP H 37 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'S' and resid 115 through 117 removed outlier: 6.299A pdb=" N VAL S 147 " --> pdb=" O VAL S 116 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'S' and resid 152 through 154 removed outlier: 8.085A pdb=" N LYS S 153 " --> pdb=" O CYS S 118 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N VAL S 120 " --> pdb=" O LYS S 153 " (cutoff:3.500A) 1972 hydrogen bonds defined for protein. 5370 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: 27.49 Time building geometry restraints manager: 56.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 40530 1.03 - 1.23: 531 1.23 - 1.43: 15673 1.43 - 1.62: 24221 1.62 - 1.82: 301 Bond restraints: 81256 Sorted by residual: bond pdb=" C PHE P 47 " pdb=" O PHE P 47 " ideal model delta sigma weight residual 1.236 1.062 0.174 1.15e-02 7.56e+03 2.30e+02 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.14e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.10e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.09e+01 bond pdb=" C PHE P 47 " pdb=" N SER P 48 " ideal model delta sigma weight residual 1.335 1.249 0.086 1.27e-02 6.20e+03 4.55e+01 ... (remaining 81251 not shown) Histogram of bond angle deviations from ideal: 93.31 - 101.90: 134 101.90 - 110.49: 85602 110.49 - 119.08: 29108 119.08 - 127.67: 32062 127.67 - 136.26: 288 Bond angle restraints: 147194 Sorted by residual: angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 116.89 22.98 1.00e+00 1.00e+00 5.28e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 117.57 22.30 1.00e+00 1.00e+00 4.97e+02 angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 118.53 21.34 1.00e+00 1.00e+00 4.55e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 119.21 17.62 1.00e+00 1.00e+00 3.10e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 119.32 17.51 1.00e+00 1.00e+00 3.07e+02 ... (remaining 147189 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.43: 35693 26.43 - 52.87: 1997 52.87 - 79.30: 324 79.30 - 105.73: 26 105.73 - 132.17: 1 Dihedral angle restraints: 38041 sinusoidal: 21298 harmonic: 16743 Sorted by residual: dihedral pdb=" O2A ADP E 600 " pdb=" O3A ADP E 600 " pdb=" PA ADP E 600 " pdb=" PB ADP E 600 " ideal model delta sinusoidal sigma weight residual 300.00 167.83 132.17 1 2.00e+01 2.50e-03 4.01e+01 dihedral pdb=" CA ARG P 38 " pdb=" C ARG P 38 " pdb=" N ASN P 39 " pdb=" CA ASN P 39 " ideal model delta harmonic sigma weight residual -180.00 -150.10 -29.90 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA MET Q 60 " pdb=" C MET Q 60 " pdb=" N GLY Q 61 " pdb=" CA GLY Q 61 " ideal model delta harmonic sigma weight residual 180.00 153.20 26.80 0 5.00e+00 4.00e-02 2.87e+01 ... (remaining 38038 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 5434 0.064 - 0.127: 866 0.127 - 0.191: 59 0.191 - 0.254: 6 0.254 - 0.318: 3 Chirality restraints: 6368 Sorted by residual: chirality pdb=" CA ALA O 37 " pdb=" N ALA O 37 " pdb=" C ALA O 37 " pdb=" CB ALA O 37 " both_signs ideal model delta sigma weight residual False 2.48 2.17 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CA ASN O 39 " pdb=" N ASN O 39 " pdb=" C ASN O 39 " pdb=" CB ASN O 39 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA SER Q 48 " pdb=" N SER Q 48 " pdb=" C SER Q 48 " pdb=" CB SER Q 48 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 6365 not shown) Planarity restraints: 11888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C23 LHG f 102 " -0.082 2.00e-02 2.50e+03 4.77e-02 2.27e+01 pdb=" C24 LHG f 102 " 0.025 2.00e-02 2.50e+03 pdb=" O10 LHG f 102 " 0.031 2.00e-02 2.50e+03 pdb=" O8 LHG f 102 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE P 47 " 0.022 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" N SER P 48 " -0.069 2.00e-02 2.50e+03 pdb=" CA SER P 48 " 0.017 2.00e-02 2.50e+03 pdb=" H SER P 48 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7 LHG f 102 " -0.062 2.00e-02 2.50e+03 3.57e-02 1.28e+01 pdb=" C8 LHG f 102 " 0.018 2.00e-02 2.50e+03 pdb=" O7 LHG f 102 " 0.019 2.00e-02 2.50e+03 pdb=" O9 LHG f 102 " 0.025 2.00e-02 2.50e+03 ... (remaining 11885 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.03: 1073 2.03 - 2.67: 126643 2.67 - 3.31: 242421 3.31 - 3.96: 309020 3.96 - 4.60: 494684 Nonbonded interactions: 1173841 Sorted by model distance: nonbonded pdb="HD11 ILE R 2 " pdb="HG22 ILE Q 2 " model vdw 1.384 2.440 nonbonded pdb="HH12 ARG P 38 " pdb=" NH1 ARG Q 38 " model vdw 1.396 2.600 nonbonded pdb=" O LEU O 42 " pdb=" H GLN O 44 " model vdw 1.417 1.850 nonbonded pdb=" HZ PHE P 8 " pdb=" HG2 MET Q 75 " model vdw 1.422 2.270 nonbonded pdb="HH12 ARG P 38 " pdb=" CZ ARG Q 38 " model vdw 1.463 2.750 ... (remaining 1173836 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 23 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name \ HG13 or name HG21 or name HG22 or name HG23)) or resid 24 through 403 or (resid \ 410 and (name N or name CA or name C or name O or name CB or name CG or name CD1 \ or name CD2 or name HA or name HB2 or name HB3 or name HG or name HD11 or name \ HD12 or name HD13 or name HD21 or name HD22 or name HD23)) or resid 411 through \ 508 or resid 600 through 601)) selection = (chain 'B' and ((resid 23 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name \ HG13 or name HG21 or name HG22 or name HG23)) or resid 24 through 508 or resid 6 \ 00 through 601)) selection = (chain 'C' and (resid 23 through 403 or resid 410 through 508 or resid 600 throu \ gh 601)) } ncs_group { reference = (chain 'D' and resid 9 through 475) selection = (chain 'E' and (resid 9 through 162 or (resid 163 and (name N or name CA or name \ C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 164 through 475)) selection = (chain 'F' and resid 9 through 475) } ncs_group { reference = chain 'K' selection = chain 'L' selection = (chain 'M' and resid 1 through 74) selection = (chain 'N' and resid 1 through 74) selection = (chain 'O' and resid 1 through 74) selection = chain 'P' selection = (chain 'Q' and resid 1 through 74) selection = (chain 'R' and resid 1 through 74) } 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=0.75 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: 4.670 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: 0.900 Extract box with map and model: 27.510 Check model and map are aligned: 0.870 Set scattering table: 0.570 Process input model: 199.610 Find NCS groups from input model: 2.670 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 239.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 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 : 0.008 0.174 40705 Z= 0.513 Angle : 0.857 22.980 54991 Z= 0.510 Chirality : 0.046 0.318 6368 Planarity : 0.004 0.056 6957 Dihedral : 15.427 132.167 15347 Min Nonbonded Distance : 1.537 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 0.02 % Allowed : 0.57 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.12), residues: 5079 helix: -0.03 (0.10), residues: 2701 sheet: -2.42 (0.21), residues: 539 loop : -1.76 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP d 33 HIS 0.009 0.001 HIS F 367 PHE 0.040 0.002 PHE P 47 TYR 0.026 0.002 TYR P 49 ARG 0.042 0.001 ARG P 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10158 Ramachandran restraints generated. 5079 Oldfield, 0 Emsley, 5079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10158 Ramachandran restraints generated. 5079 Oldfield, 0 Emsley, 5079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Evaluate side-chains 493 residues out of total 4183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 492 time to evaluate : 4.765 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: E 22 ASP cc_start: 0.8416 (m-30) cc_final: 0.8089 (m-30) REVERT: E 168 GLU cc_start: 0.7558 (tp30) cc_final: 0.7135 (tp30) REVERT: F 63 MET cc_start: 0.8208 (mmt) cc_final: 0.7504 (mmt) REVERT: K 44 GLN cc_start: 0.7076 (mp-120) cc_final: 0.6778 (mp10) REVERT: K 54 PHE cc_start: 0.8666 (t80) cc_final: 0.8460 (t80) REVERT: O 51 ILE cc_start: 0.8722 (pt) cc_final: 0.8424 (mm) REVERT: e 55 ARG cc_start: 0.6950 (ttp-170) cc_final: 0.6726 (ttt180) outliers start: 1 outliers final: 0 residues processed: 492 average time/residue: 1.0713 time to fit residues: 870.4694 Evaluate side-chains 401 residues out of total 4183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 401 time to evaluate : 4.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 423 optimal weight: 3.9990 chunk 380 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 256 optimal weight: 3.9990 chunk 203 optimal weight: 0.9980 chunk 393 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 239 optimal weight: 0.9990 chunk 292 optimal weight: 1.9990 chunk 455 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 ASN B 415 GLN G 117 HIS J 51 ASN N 39 ASN ** N 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 59 ASN g 57 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.0601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 40705 Z= 0.257 Angle : 0.571 6.897 54991 Z= 0.302 Chirality : 0.041 0.158 6368 Planarity : 0.004 0.046 6957 Dihedral : 9.556 127.649 6025 Min Nonbonded Distance : 1.699 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 0.45 % Allowed : 5.24 % Favored : 94.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.12), residues: 5079 helix: 0.23 (0.10), residues: 2700 sheet: -2.23 (0.21), residues: 533 loop : -1.57 (0.15), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP d 33 HIS 0.006 0.001 HIS F 367 PHE 0.027 0.001 PHE h 44 TYR 0.014 0.001 TYR h 35 ARG 0.008 0.000 ARG e 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10158 Ramachandran restraints generated. 5079 Oldfield, 0 Emsley, 5079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10158 Ramachandran restraints generated. 5079 Oldfield, 0 Emsley, 5079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Evaluate side-chains 466 residues out of total 4183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 447 time to evaluate : 4.905 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: E 22 ASP cc_start: 0.8357 (m-30) cc_final: 0.8033 (m-30) REVERT: E 168 GLU cc_start: 0.7527 (tp30) cc_final: 0.7115 (tp30) REVERT: F 63 MET cc_start: 0.8234 (mmt) cc_final: 0.7564 (mmt) REVERT: G 195 ASP cc_start: 0.7676 (t70) cc_final: 0.7324 (t0) REVERT: R 3 ASP cc_start: 0.7505 (OUTLIER) cc_final: 0.7052 (t0) REVERT: d 7 LEU cc_start: 0.6714 (mm) cc_final: 0.6483 (mt) REVERT: e 55 ARG cc_start: 0.7045 (ttp-170) cc_final: 0.6840 (ttt180) outliers start: 19 outliers final: 16 residues processed: 459 average time/residue: 1.0334 time to fit residues: 779.7296 Evaluate side-chains 427 residues out of total 4183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 410 time to evaluate : 5.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain R residue 3 ASP Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain a residue 148 SER Chi-restraints excluded: chain d residue 59 ASN Chi-restraints excluded: chain b residue 80 GLU Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 65 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 253 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 379 optimal weight: 5.9990 chunk 310 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 456 optimal weight: 2.9990 chunk 493 optimal weight: 4.9990 chunk 406 optimal weight: 1.9990 chunk 452 optimal weight: 0.4980 chunk 155 optimal weight: 0.8980 chunk 366 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN B 415 GLN G 117 HIS G 211 ASN ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 51 ASN N 39 ASN ** N 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 40705 Z= 0.251 Angle : 0.545 6.771 54991 Z= 0.287 Chirality : 0.040 0.156 6368 Planarity : 0.004 0.042 6957 Dihedral : 8.979 122.793 6025 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.69 % Allowed : 6.91 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.12), residues: 5079 helix: 0.40 (0.10), residues: 2696 sheet: -2.11 (0.22), residues: 520 loop : -1.51 (0.15), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP d 33 HIS 0.008 0.001 HIS C 471 PHE 0.023 0.001 PHE h 44 TYR 0.015 0.001 TYR G 44 ARG 0.003 0.000 ARG E 337 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10158 Ramachandran restraints generated. 5079 Oldfield, 0 Emsley, 5079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10158 Ramachandran restraints generated. 5079 Oldfield, 0 Emsley, 5079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Evaluate side-chains 461 residues out of total 4183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 432 time to evaluate : 4.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 76 LEU cc_start: 0.8720 (mm) cc_final: 0.8126 (tp) REVERT: E 22 ASP cc_start: 0.8196 (m-30) cc_final: 0.7941 (m-30) REVERT: E 168 GLU cc_start: 0.7510 (tp30) cc_final: 0.7162 (tp30) REVERT: F 63 MET cc_start: 0.8253 (mmt) cc_final: 0.7553 (mmt) REVERT: G 195 ASP cc_start: 0.7722 (t70) cc_final: 0.7272 (t0) REVERT: R 3 ASP cc_start: 0.7300 (OUTLIER) cc_final: 0.6842 (t0) REVERT: S 91 GLU cc_start: 0.7343 (pm20) cc_final: 0.7129 (pm20) REVERT: d 7 LEU cc_start: 0.6731 (mm) cc_final: 0.6497 (mt) REVERT: e 55 ARG cc_start: 0.7110 (ttp-170) cc_final: 0.6894 (ttt180) outliers start: 29 outliers final: 18 residues processed: 449 average time/residue: 1.0256 time to fit residues: 760.3191 Evaluate side-chains 426 residues out of total 4183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 407 time to evaluate : 4.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain G residue 211 ASN Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 47 PHE Chi-restraints excluded: chain R residue 3 ASP Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain a residue 148 SER Chi-restraints excluded: chain a residue 220 LEU Chi-restraints excluded: chain b residue 80 GLU Chi-restraints excluded: chain Q residue 16 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 451 optimal weight: 4.9990 chunk 343 optimal weight: 1.9990 chunk 237 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 217 optimal weight: 1.9990 chunk 306 optimal weight: 2.9990 chunk 458 optimal weight: 0.8980 chunk 485 optimal weight: 2.9990 chunk 239 optimal weight: 2.9990 chunk 434 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 415 GLN G 150 ASN ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 51 ASN N 44 GLN ** 8 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 40705 Z= 0.255 Angle : 0.538 6.682 54991 Z= 0.282 Chirality : 0.040 0.155 6368 Planarity : 0.004 0.041 6957 Dihedral : 8.574 118.978 6025 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.79 % Allowed : 8.15 % Favored : 91.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.12), residues: 5079 helix: 0.50 (0.10), residues: 2707 sheet: -2.06 (0.22), residues: 510 loop : -1.45 (0.15), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP d 33 HIS 0.009 0.001 HIS C 476 PHE 0.020 0.001 PHE R 29 TYR 0.020 0.001 TYR G 44 ARG 0.004 0.000 ARG E 337 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10158 Ramachandran restraints generated. 5079 Oldfield, 0 Emsley, 5079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10158 Ramachandran restraints generated. 5079 Oldfield, 0 Emsley, 5079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Evaluate side-chains 465 residues out of total 4183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 432 time to evaluate : 4.752 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: D 76 LEU cc_start: 0.8703 (mm) cc_final: 0.8116 (tp) REVERT: E 22 ASP cc_start: 0.8190 (m-30) cc_final: 0.7942 (m-30) REVERT: E 168 GLU cc_start: 0.7502 (tp30) cc_final: 0.7145 (tp30) REVERT: F 63 MET cc_start: 0.8267 (mmt) cc_final: 0.7565 (mmt) REVERT: G 195 ASP cc_start: 0.7751 (t70) cc_final: 0.7196 (t0) REVERT: R 3 ASP cc_start: 0.7238 (OUTLIER) cc_final: 0.6793 (t0) REVERT: S 91 GLU cc_start: 0.7226 (pm20) cc_final: 0.6961 (pm20) REVERT: O 2 ILE cc_start: 0.8321 (pt) cc_final: 0.7706 (tt) REVERT: d 7 LEU cc_start: 0.6710 (mm) cc_final: 0.6467 (mt) REVERT: e 55 ARG cc_start: 0.7112 (ttp-170) cc_final: 0.6896 (ttt180) outliers start: 33 outliers final: 27 residues processed: 449 average time/residue: 1.0199 time to fit residues: 758.1343 Evaluate side-chains 442 residues out of total 4183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 414 time to evaluate : 4.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 47 PHE Chi-restraints excluded: chain R residue 3 ASP Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain a residue 148 SER Chi-restraints excluded: chain a residue 195 ILE Chi-restraints excluded: chain a residue 220 LEU Chi-restraints excluded: chain d residue 59 ASN Chi-restraints excluded: chain b residue 42 ILE Chi-restraints excluded: chain b residue 80 GLU Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 42 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 404 optimal weight: 3.9990 chunk 275 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 361 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 414 optimal weight: 1.9990 chunk 335 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 247 optimal weight: 2.9990 chunk 435 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 415 GLN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 51 ASN ** 8 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 40705 Z= 0.356 Angle : 0.568 6.862 54991 Z= 0.300 Chirality : 0.042 0.159 6368 Planarity : 0.004 0.043 6957 Dihedral : 8.484 116.566 6025 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 0.96 % Allowed : 9.30 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.12), residues: 5079 helix: 0.47 (0.10), residues: 2708 sheet: -2.13 (0.22), residues: 528 loop : -1.49 (0.15), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP d 33 HIS 0.009 0.001 HIS C 471 PHE 0.021 0.001 PHE R 29 TYR 0.014 0.001 TYR h 35 ARG 0.010 0.000 ARG h 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10158 Ramachandran restraints generated. 5079 Oldfield, 0 Emsley, 5079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10158 Ramachandran restraints generated. 5079 Oldfield, 0 Emsley, 5079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Evaluate side-chains 463 residues out of total 4183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 423 time to evaluate : 4.946 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: E 22 ASP cc_start: 0.8194 (m-30) cc_final: 0.7957 (m-30) REVERT: E 168 GLU cc_start: 0.7466 (tp30) cc_final: 0.7167 (tp30) REVERT: F 63 MET cc_start: 0.8275 (mmt) cc_final: 0.7563 (mmt) REVERT: G 211 ASN cc_start: 0.8719 (m-40) cc_final: 0.8502 (t0) REVERT: R 3 ASP cc_start: 0.7262 (OUTLIER) cc_final: 0.6782 (t0) REVERT: S 91 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6944 (pm20) REVERT: O 2 ILE cc_start: 0.8314 (pt) cc_final: 0.7725 (tt) REVERT: d 7 LEU cc_start: 0.6729 (mm) cc_final: 0.6465 (mt) REVERT: e 55 ARG cc_start: 0.7090 (ttp-170) cc_final: 0.6870 (ttt180) REVERT: Q 60 MET cc_start: 0.8631 (mmm) cc_final: 0.8332 (mmm) outliers start: 40 outliers final: 29 residues processed: 446 average time/residue: 1.0263 time to fit residues: 760.9491 Evaluate side-chains 436 residues out of total 4183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 405 time to evaluate : 4.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 47 PHE Chi-restraints excluded: chain R residue 3 ASP Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain S residue 91 GLU Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain a residue 148 SER Chi-restraints excluded: chain a residue 195 ILE Chi-restraints excluded: chain a residue 220 LEU Chi-restraints excluded: chain d residue 59 ASN Chi-restraints excluded: chain k residue 12 THR Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 42 LEU Chi-restraints excluded: chain Q residue 57 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 163 optimal weight: 1.9990 chunk 436 optimal weight: 0.8980 chunk 95 optimal weight: 0.3980 chunk 284 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 485 optimal weight: 6.9990 chunk 403 optimal weight: 0.9990 chunk 224 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 254 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 415 GLN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 51 ASN ** 8 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 40705 Z= 0.193 Angle : 0.521 6.612 54991 Z= 0.270 Chirality : 0.040 0.154 6368 Planarity : 0.003 0.039 6957 Dihedral : 8.078 109.533 6025 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.84 % Allowed : 9.97 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.12), residues: 5079 helix: 0.68 (0.10), residues: 2707 sheet: -1.94 (0.22), residues: 523 loop : -1.31 (0.15), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP d 33 HIS 0.010 0.001 HIS C 471 PHE 0.020 0.001 PHE R 29 TYR 0.015 0.001 TYR h 35 ARG 0.005 0.000 ARG E 337 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10158 Ramachandran restraints generated. 5079 Oldfield, 0 Emsley, 5079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10158 Ramachandran restraints generated. 5079 Oldfield, 0 Emsley, 5079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Evaluate side-chains 474 residues out of total 4183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 439 time to evaluate : 4.743 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: B 328 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7390 (tt0) REVERT: D 76 LEU cc_start: 0.8684 (mm) cc_final: 0.8126 (tp) REVERT: D 377 ILE cc_start: 0.8962 (tt) cc_final: 0.8666 (tp) REVERT: E 22 ASP cc_start: 0.8037 (m-30) cc_final: 0.7773 (m-30) REVERT: E 168 GLU cc_start: 0.7420 (tp30) cc_final: 0.6951 (tp30) REVERT: F 63 MET cc_start: 0.8244 (mmt) cc_final: 0.7562 (mmt) REVERT: R 3 ASP cc_start: 0.7396 (OUTLIER) cc_final: 0.7037 (t0) REVERT: O 2 ILE cc_start: 0.8254 (pt) cc_final: 0.7648 (tt) REVERT: d 7 LEU cc_start: 0.6732 (mm) cc_final: 0.6456 (mt) REVERT: e 55 ARG cc_start: 0.7224 (ttp-170) cc_final: 0.6914 (ttt180) REVERT: Q 60 MET cc_start: 0.8667 (mmm) cc_final: 0.8406 (mmm) outliers start: 35 outliers final: 25 residues processed: 462 average time/residue: 1.0258 time to fit residues: 791.8809 Evaluate side-chains 441 residues out of total 4183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 414 time to evaluate : 4.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 116 GLN Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 47 PHE Chi-restraints excluded: chain R residue 3 ASP Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain a residue 143 ILE Chi-restraints excluded: chain a residue 195 ILE Chi-restraints excluded: chain d residue 59 ASN Chi-restraints excluded: chain b residue 80 GLU Chi-restraints excluded: chain k residue 12 THR Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 42 LEU Chi-restraints excluded: chain Q residue 57 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 468 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 276 optimal weight: 1.9990 chunk 354 optimal weight: 3.9990 chunk 274 optimal weight: 2.9990 chunk 408 optimal weight: 0.6980 chunk 271 optimal weight: 0.7980 chunk 483 optimal weight: 5.9990 chunk 302 optimal weight: 0.8980 chunk 294 optimal weight: 1.9990 chunk 223 optimal weight: 0.0060 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 ASN B 415 GLN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 51 ASN ** 8 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 56 GLN ** a 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 40705 Z= 0.162 Angle : 0.506 6.830 54991 Z= 0.260 Chirality : 0.039 0.152 6368 Planarity : 0.003 0.042 6957 Dihedral : 7.684 100.425 6025 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.74 % Allowed : 10.66 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.12), residues: 5079 helix: 0.87 (0.10), residues: 2720 sheet: -1.80 (0.22), residues: 544 loop : -1.12 (0.15), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP d 33 HIS 0.009 0.001 HIS C 471 PHE 0.018 0.001 PHE M 54 TYR 0.017 0.001 TYR Q 49 ARG 0.006 0.000 ARG E 337 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10158 Ramachandran restraints generated. 5079 Oldfield, 0 Emsley, 5079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10158 Ramachandran restraints generated. 5079 Oldfield, 0 Emsley, 5079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Evaluate side-chains 483 residues out of total 4183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 452 time to evaluate : 4.783 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: C 301 LEU cc_start: 0.8668 (tt) cc_final: 0.8467 (tt) REVERT: D 76 LEU cc_start: 0.8667 (mm) cc_final: 0.8143 (tp) REVERT: E 22 ASP cc_start: 0.7987 (m-30) cc_final: 0.7748 (m-30) REVERT: E 168 GLU cc_start: 0.7422 (tp30) cc_final: 0.6992 (tp30) REVERT: F 63 MET cc_start: 0.8236 (mmt) cc_final: 0.7541 (mmt) REVERT: F 400 ASP cc_start: 0.6796 (m-30) cc_final: 0.6507 (m-30) REVERT: G 195 ASP cc_start: 0.8000 (t70) cc_final: 0.7516 (t0) REVERT: J 35 ARG cc_start: 0.7709 (ttm-80) cc_final: 0.7439 (mtt-85) REVERT: L 47 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.7158 (m-80) REVERT: R 3 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.7098 (t0) REVERT: O 2 ILE cc_start: 0.8196 (pt) cc_final: 0.7612 (tt) REVERT: a 58 MET cc_start: 0.8187 (mmm) cc_final: 0.7877 (mmm) REVERT: a 209 ILE cc_start: 0.9091 (mt) cc_final: 0.8856 (mm) REVERT: d 7 LEU cc_start: 0.6784 (mm) cc_final: 0.6566 (mt) REVERT: e 55 ARG cc_start: 0.7173 (ttp-170) cc_final: 0.6952 (ttt180) REVERT: Q 60 MET cc_start: 0.8683 (mmm) cc_final: 0.8408 (mmm) outliers start: 31 outliers final: 24 residues processed: 470 average time/residue: 1.0309 time to fit residues: 807.2894 Evaluate side-chains 452 residues out of total 4183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 426 time to evaluate : 4.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain L residue 47 PHE Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 47 PHE Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain R residue 3 ASP Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain a residue 195 ILE Chi-restraints excluded: chain d residue 59 ASN Chi-restraints excluded: chain b residue 80 GLU Chi-restraints excluded: chain k residue 12 THR Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 42 LEU Chi-restraints excluded: chain Q residue 57 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 299 optimal weight: 0.9980 chunk 193 optimal weight: 1.9990 chunk 288 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 95 optimal weight: 0.0000 chunk 93 optimal weight: 0.7980 chunk 307 optimal weight: 1.9990 chunk 329 optimal weight: 7.9990 chunk 239 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 380 optimal weight: 4.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 415 GLN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 51 ASN ** 8 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 131 GLN ** a 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 40705 Z= 0.206 Angle : 0.516 7.293 54991 Z= 0.266 Chirality : 0.040 0.162 6368 Planarity : 0.003 0.041 6957 Dihedral : 7.569 92.568 6025 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.72 % Allowed : 11.28 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.12), residues: 5079 helix: 0.95 (0.10), residues: 2714 sheet: -1.79 (0.22), residues: 538 loop : -1.11 (0.15), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP d 33 HIS 0.011 0.001 HIS C 471 PHE 0.016 0.001 PHE R 29 TYR 0.015 0.001 TYR h 35 ARG 0.005 0.000 ARG E 337 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10158 Ramachandran restraints generated. 5079 Oldfield, 0 Emsley, 5079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10158 Ramachandran restraints generated. 5079 Oldfield, 0 Emsley, 5079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Evaluate side-chains 466 residues out of total 4183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 436 time to evaluate : 4.990 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: B 328 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7375 (tt0) REVERT: D 76 LEU cc_start: 0.8683 (mm) cc_final: 0.8141 (tp) REVERT: E 22 ASP cc_start: 0.7990 (m-30) cc_final: 0.7774 (m-30) REVERT: E 168 GLU cc_start: 0.7414 (tp30) cc_final: 0.7009 (tp30) REVERT: F 63 MET cc_start: 0.8246 (mmt) cc_final: 0.7552 (mmt) REVERT: G 195 ASP cc_start: 0.7987 (t70) cc_final: 0.7484 (t0) REVERT: J 35 ARG cc_start: 0.7711 (ttm-80) cc_final: 0.7430 (mtt-85) REVERT: L 47 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.7231 (m-80) REVERT: L 54 PHE cc_start: 0.8149 (t80) cc_final: 0.7938 (t80) REVERT: R 3 ASP cc_start: 0.7448 (OUTLIER) cc_final: 0.7119 (t0) REVERT: O 2 ILE cc_start: 0.8183 (pt) cc_final: 0.7615 (tt) REVERT: a 209 ILE cc_start: 0.9099 (mt) cc_final: 0.8881 (mm) REVERT: d 7 LEU cc_start: 0.6759 (mm) cc_final: 0.6544 (mt) REVERT: b 164 MET cc_start: 0.8545 (ppp) cc_final: 0.8306 (ppp) REVERT: e 55 ARG cc_start: 0.7223 (ttp-170) cc_final: 0.6930 (ttt180) REVERT: Q 60 MET cc_start: 0.8677 (mmm) cc_final: 0.8420 (mmm) outliers start: 30 outliers final: 24 residues processed: 452 average time/residue: 1.0279 time to fit residues: 777.0061 Evaluate side-chains 451 residues out of total 4183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 424 time to evaluate : 4.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain L residue 47 PHE Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 47 PHE Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain R residue 3 ASP Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain a residue 195 ILE Chi-restraints excluded: chain d residue 59 ASN Chi-restraints excluded: chain b residue 80 GLU Chi-restraints excluded: chain k residue 12 THR Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 57 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 440 optimal weight: 1.9990 chunk 463 optimal weight: 0.8980 chunk 422 optimal weight: 3.9990 chunk 450 optimal weight: 0.1980 chunk 271 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 354 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 chunk 407 optimal weight: 0.9980 chunk 426 optimal weight: 1.9990 chunk 449 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 415 GLN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 51 ASN ** 8 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 40705 Z= 0.209 Angle : 0.518 7.622 54991 Z= 0.267 Chirality : 0.040 0.151 6368 Planarity : 0.003 0.044 6957 Dihedral : 7.462 87.880 6025 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.77 % Allowed : 11.43 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.12), residues: 5079 helix: 0.98 (0.10), residues: 2719 sheet: -1.76 (0.22), residues: 538 loop : -1.07 (0.15), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP d 33 HIS 0.012 0.001 HIS C 471 PHE 0.017 0.001 PHE R 29 TYR 0.024 0.001 TYR Q 49 ARG 0.006 0.000 ARG E 337 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10158 Ramachandran restraints generated. 5079 Oldfield, 0 Emsley, 5079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10158 Ramachandran restraints generated. 5079 Oldfield, 0 Emsley, 5079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Evaluate side-chains 477 residues out of total 4183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 445 time to evaluate : 4.853 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: B 328 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7334 (tt0) REVERT: D 76 LEU cc_start: 0.8679 (mm) cc_final: 0.8156 (tp) REVERT: E 22 ASP cc_start: 0.7989 (m-30) cc_final: 0.7770 (m-30) REVERT: E 168 GLU cc_start: 0.7419 (tp30) cc_final: 0.7019 (tp30) REVERT: F 63 MET cc_start: 0.8229 (mmt) cc_final: 0.7540 (mmt) REVERT: G 195 ASP cc_start: 0.7954 (t70) cc_final: 0.7438 (t0) REVERT: J 35 ARG cc_start: 0.7711 (ttm-80) cc_final: 0.7393 (mtt-85) REVERT: L 47 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.7272 (m-80) REVERT: R 3 ASP cc_start: 0.7437 (OUTLIER) cc_final: 0.7118 (t0) REVERT: O 2 ILE cc_start: 0.8176 (pt) cc_final: 0.7609 (tt) REVERT: a 58 MET cc_start: 0.8165 (mmm) cc_final: 0.7943 (mmm) REVERT: d 7 LEU cc_start: 0.6747 (mm) cc_final: 0.6534 (mt) REVERT: b 164 MET cc_start: 0.8582 (ppp) cc_final: 0.8248 (ppp) REVERT: e 55 ARG cc_start: 0.7243 (ttp-170) cc_final: 0.6978 (ttt180) outliers start: 32 outliers final: 23 residues processed: 462 average time/residue: 0.9977 time to fit residues: 762.8453 Evaluate side-chains 455 residues out of total 4183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 429 time to evaluate : 4.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain L residue 47 PHE Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain R residue 3 ASP Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain a residue 195 ILE Chi-restraints excluded: chain b residue 80 GLU Chi-restraints excluded: chain k residue 12 THR Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 54 PHE Chi-restraints excluded: chain Q residue 57 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 296 optimal weight: 5.9990 chunk 476 optimal weight: 9.9990 chunk 291 optimal weight: 0.9990 chunk 226 optimal weight: 3.9990 chunk 331 optimal weight: 4.9990 chunk 500 optimal weight: 2.9990 chunk 460 optimal weight: 2.9990 chunk 398 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 307 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 415 GLN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 51 ASN ** 8 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 209 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 40705 Z= 0.362 Angle : 0.575 8.041 54991 Z= 0.302 Chirality : 0.042 0.157 6368 Planarity : 0.004 0.042 6957 Dihedral : 7.722 88.035 6025 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.81 % Allowed : 11.59 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.12), residues: 5079 helix: 0.81 (0.10), residues: 2706 sheet: -1.91 (0.22), residues: 548 loop : -1.17 (0.15), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP d 33 HIS 0.010 0.001 HIS C 471 PHE 0.029 0.002 PHE h 44 TYR 0.029 0.001 TYR Q 49 ARG 0.006 0.000 ARG d 122 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10158 Ramachandran restraints generated. 5079 Oldfield, 0 Emsley, 5079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10158 Ramachandran restraints generated. 5079 Oldfield, 0 Emsley, 5079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 176 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Residue THR 163 is missing expected H atoms. Skipping. Evaluate side-chains 453 residues out of total 4183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 419 time to evaluate : 4.950 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: B 328 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7413 (tt0) REVERT: D 76 LEU cc_start: 0.8704 (mm) cc_final: 0.8155 (tp) REVERT: D 167 MET cc_start: 0.8423 (mmm) cc_final: 0.8206 (mmm) REVERT: E 22 ASP cc_start: 0.8131 (m-30) cc_final: 0.7894 (m-30) REVERT: E 168 GLU cc_start: 0.7442 (tp30) cc_final: 0.7184 (tp30) REVERT: F 63 MET cc_start: 0.8257 (mmt) cc_final: 0.7550 (mmt) REVERT: H 104 ASP cc_start: 0.7487 (m-30) cc_final: 0.6850 (p0) REVERT: L 47 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.7246 (m-80) REVERT: R 3 ASP cc_start: 0.7564 (OUTLIER) cc_final: 0.7233 (t0) REVERT: O 2 ILE cc_start: 0.8252 (pt) cc_final: 0.7656 (tt) REVERT: a 58 MET cc_start: 0.8318 (mmm) cc_final: 0.8099 (mmm) REVERT: d 7 LEU cc_start: 0.6651 (mm) cc_final: 0.6368 (mt) REVERT: b 164 MET cc_start: 0.8570 (ppp) cc_final: 0.8176 (ppp) REVERT: e 55 ARG cc_start: 0.7225 (ttp-170) cc_final: 0.6945 (ttt180) REVERT: Q 60 MET cc_start: 0.8736 (mmm) cc_final: 0.8241 (mmm) outliers start: 34 outliers final: 27 residues processed: 435 average time/residue: 1.0390 time to fit residues: 747.9709 Evaluate side-chains 442 residues out of total 4183 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 412 time to evaluate : 4.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 402 LEU Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain I residue 28 THR Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain L residue 47 PHE Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 67 VAL Chi-restraints excluded: chain P residue 60 MET Chi-restraints excluded: chain R residue 3 ASP Chi-restraints excluded: chain R residue 72 LEU Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain a residue 195 ILE Chi-restraints excluded: chain b residue 80 GLU Chi-restraints excluded: chain b residue 124 LEU Chi-restraints excluded: chain k residue 12 THR Chi-restraints excluded: chain Q residue 18 VAL Chi-restraints excluded: chain Q residue 54 PHE Chi-restraints excluded: chain Q residue 57 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 502 random chunks: chunk 316 optimal weight: 0.8980 chunk 424 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 367 optimal weight: 0.4980 chunk 58 optimal weight: 1.9990 chunk 110 optimal weight: 0.4980 chunk 398 optimal weight: 0.7980 chunk 166 optimal weight: 3.9990 chunk 409 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 GLN ** C 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 211 ASN ** H 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.107331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.090899 restraints weight = 229945.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.092797 restraints weight = 140205.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.093678 restraints weight = 94525.045| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 40705 Z= 0.168 Angle : 0.516 8.154 54991 Z= 0.264 Chirality : 0.040 0.154 6368 Planarity : 0.004 0.048 6957 Dihedral : 7.368 83.504 6025 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.67 % Allowed : 11.91 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.12), residues: 5079 helix: 1.04 (0.10), residues: 2707 sheet: -1.77 (0.22), residues: 542 loop : -1.02 (0.15), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP d 33 HIS 0.011 0.001 HIS C 471 PHE 0.025 0.001 PHE h 44 TYR 0.018 0.001 TYR Q 49 ARG 0.006 0.000 ARG h 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13799.30 seconds wall clock time: 241 minutes 2.88 seconds (14462.88 seconds total)