Starting phenix.real_space_refine on Wed Feb 21 01:21:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzk_0557/02_2024/6nzk_0557_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzk_0557/02_2024/6nzk_0557.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzk_0557/02_2024/6nzk_0557.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzk_0557/02_2024/6nzk_0557.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzk_0557/02_2024/6nzk_0557_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzk_0557/02_2024/6nzk_0557_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.111 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 183 5.16 5 C 18300 2.51 5 N 4596 2.21 5 O 6189 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 42": "OD1" <-> "OD2" Residue "A TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 160": "OE1" <-> "OE2" Residue "A TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 210": "OD1" <-> "OD2" Residue "A TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 538": "OD1" <-> "OD2" Residue "A TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 579": "NH1" <-> "NH2" Residue "A PHE 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 789": "OD1" <-> "OD2" Residue "A TYR 798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 806": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 843": "OE1" <-> "OE2" Residue "A TYR 844": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 847": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 896": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 931": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 946": "OD1" <-> "OD2" Residue "A TYR 971": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 993": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1051": "OE1" <-> "OE2" Residue "A PHE 1064": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 42": "OD1" <-> "OD2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 160": "OE1" <-> "OE2" Residue "B TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 186": "OE1" <-> "OE2" Residue "B PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 210": "OD1" <-> "OD2" Residue "B TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 538": "OD1" <-> "OD2" Residue "B TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 579": "NH1" <-> "NH2" Residue "B PHE 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 789": "OD1" <-> "OD2" Residue "B TYR 798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 806": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 843": "OE1" <-> "OE2" Residue "B TYR 844": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 847": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 896": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 931": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 946": "OD1" <-> "OD2" Residue "B TYR 971": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 993": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1051": "OE1" <-> "OE2" Residue "B PHE 1064": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 42": "OD1" <-> "OD2" Residue "C TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 160": "OE1" <-> "OE2" Residue "C TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "C PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 210": "OD1" <-> "OD2" Residue "C TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 538": "OD1" <-> "OD2" Residue "C TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 579": "NH1" <-> "NH2" Residue "C PHE 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 789": "OD1" <-> "OD2" Residue "C TYR 798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 806": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 843": "OE1" <-> "OE2" Residue "C TYR 844": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 847": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 896": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 931": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 946": "OD1" <-> "OD2" Residue "C TYR 971": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 981": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 993": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1051": "OE1" <-> "OE2" Residue "C PHE 1064": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1230": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29268 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 9150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9150 Classifications: {'peptide': 1175} Link IDs: {'PCIS': 4, 'PTRANS': 46, 'TRANS': 1124} Chain breaks: 5 Chain: "B" Number of atoms: 9150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9150 Classifications: {'peptide': 1175} Link IDs: {'PCIS': 4, 'PTRANS': 46, 'TRANS': 1124} Chain breaks: 5 Chain: "C" Number of atoms: 9150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9150 Classifications: {'peptide': 1175} Link IDs: {'PCIS': 4, 'PTRANS': 46, 'TRANS': 1124} Chain breaks: 5 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 95 Unusual residues: {'MJJ': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 95 Unusual residues: {'MJJ': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 95 Unusual residues: {'MJJ': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 132 Classifications: {'water': 132} Link IDs: {None: 131} Chain: "B" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 132 Classifications: {'water': 132} Link IDs: {None: 131} Chain: "C" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 132 Classifications: {'water': 132} Link IDs: {None: 131} Time building chain proxies: 15.48, per 1000 atoms: 0.53 Number of scatterers: 29268 At special positions: 0 Unit cell: (147, 153.3, 162.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 183 16.00 O 6189 8.00 N 4596 7.00 C 18300 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=63, symmetry=0 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 169 " distance=2.05 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 197 " distance=2.05 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 256 " distance=2.03 Simple disulfide: pdb=" SG CYS A 290 " - pdb=" SG CYS A 300 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 368 " distance=2.03 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 439 " distance=2.04 Simple disulfide: pdb=" SG CYS A 398 " - pdb=" SG CYS A 614 " distance=2.14 Simple disulfide: pdb=" SG CYS A 491 " - pdb=" SG CYS A 561 " distance=2.04 Simple disulfide: pdb=" SG CYS A 499 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 576 " distance=2.02 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 548 " distance=2.02 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 578 " distance=2.03 Simple disulfide: pdb=" SG CYS A 591 " - pdb=" SG CYS A 597 " distance=2.04 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 683 " distance=2.03 Simple disulfide: pdb=" SG CYS A 708 " - pdb=" SG CYS A 733 " distance=2.04 Simple disulfide: pdb=" SG CYS A 748 " - pdb=" SG CYS A 757 " distance=2.05 Simple disulfide: pdb=" SG CYS A 826 " - pdb=" SG CYS A 848 " distance=2.14 Simple disulfide: pdb=" SG CYS A 831 " - pdb=" SG CYS A 837 " distance=2.03 Simple disulfide: pdb=" SG CYS A 938 " - pdb=" SG CYS A 949 " distance=2.09 Simple disulfide: pdb=" SG CYS A1126 " - pdb=" SG CYS A1137 " distance=2.03 Simple disulfide: pdb=" SG CYS A1176 " - pdb=" SG CYS A1221 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 169 " distance=2.05 Simple disulfide: pdb=" SG CYS B 164 " - pdb=" SG CYS B 197 " distance=2.05 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 256 " distance=2.03 Simple disulfide: pdb=" SG CYS B 290 " - pdb=" SG CYS B 300 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 368 " distance=2.03 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 439 " distance=2.04 Simple disulfide: pdb=" SG CYS B 398 " - pdb=" SG CYS B 614 " distance=2.14 Simple disulfide: pdb=" SG CYS B 491 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS B 499 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 576 " distance=2.02 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 548 " distance=2.02 Simple disulfide: pdb=" SG CYS B 571 " - pdb=" SG CYS B 578 " distance=2.03 Simple disulfide: pdb=" SG CYS B 591 " - pdb=" SG CYS B 597 " distance=2.04 Simple disulfide: pdb=" SG CYS B 630 " - pdb=" SG CYS B 683 " distance=2.03 Simple disulfide: pdb=" SG CYS B 708 " - pdb=" SG CYS B 733 " distance=2.04 Simple disulfide: pdb=" SG CYS B 748 " - pdb=" SG CYS B 757 " distance=2.05 Simple disulfide: pdb=" SG CYS B 826 " - pdb=" SG CYS B 848 " distance=2.14 Simple disulfide: pdb=" SG CYS B 831 " - pdb=" SG CYS B 837 " distance=2.03 Simple disulfide: pdb=" SG CYS B 938 " - pdb=" SG CYS B 949 " distance=2.09 Simple disulfide: pdb=" SG CYS B1126 " - pdb=" SG CYS B1137 " distance=2.03 Simple disulfide: pdb=" SG CYS B1176 " - pdb=" SG CYS B1221 " distance=2.03 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 169 " distance=2.05 Simple disulfide: pdb=" SG CYS C 164 " - pdb=" SG CYS C 197 " distance=2.05 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 256 " distance=2.03 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 300 " distance=2.03 Simple disulfide: pdb=" SG CYS C 343 " - pdb=" SG CYS C 368 " distance=2.03 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 439 " distance=2.04 Simple disulfide: pdb=" SG CYS C 398 " - pdb=" SG CYS C 614 " distance=2.14 Simple disulfide: pdb=" SG CYS C 491 " - pdb=" SG CYS C 561 " distance=2.04 Simple disulfide: pdb=" SG CYS C 499 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS C 576 " distance=2.02 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 548 " distance=2.02 Simple disulfide: pdb=" SG CYS C 571 " - pdb=" SG CYS C 578 " distance=2.03 Simple disulfide: pdb=" SG CYS C 591 " - pdb=" SG CYS C 597 " distance=2.04 Simple disulfide: pdb=" SG CYS C 630 " - pdb=" SG CYS C 683 " distance=2.03 Simple disulfide: pdb=" SG CYS C 708 " - pdb=" SG CYS C 733 " distance=2.04 Simple disulfide: pdb=" SG CYS C 748 " - pdb=" SG CYS C 757 " distance=2.04 Simple disulfide: pdb=" SG CYS C 826 " - pdb=" SG CYS C 848 " distance=2.14 Simple disulfide: pdb=" SG CYS C 831 " - pdb=" SG CYS C 837 " distance=2.03 Simple disulfide: pdb=" SG CYS C 938 " - pdb=" SG CYS C 949 " distance=2.09 Simple disulfide: pdb=" SG CYS C1126 " - pdb=" SG CYS C1137 " distance=2.03 Simple disulfide: pdb=" SG CYS C1176 " - pdb=" SG CYS C1221 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA J 3 " - " MAN J 4 " " BMA P 3 " - " MAN P 4 " " BMA T 3 " - " MAN T 4 " " BMA Z 3 " - " MAN Z 4 " " BMA d 3 " - " MAN d 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " NAG-ASN " NAG A3197 " - " ASN A 59 " " NAG A3198 " - " ASN A 146 " " NAG A3199 " - " ASN A 675 " " NAG A3200 " - " ASN A 695 " " NAG A3201 " - " ASN A 714 " " NAG B3197 " - " ASN B 59 " " NAG B3198 " - " ASN B 146 " " NAG B3199 " - " ASN B 675 " " NAG B3200 " - " ASN B 695 " " NAG B3201 " - " ASN B 714 " " NAG C3197 " - " ASN C 59 " " NAG C3198 " - " ASN C 146 " " NAG C3199 " - " ASN C 675 " " NAG C3200 " - " ASN C 695 " " NAG C3201 " - " ASN C 714 " " NAG D 1 " - " ASN A 133 " " NAG E 1 " - " ASN A 202 " " NAG F 1 " - " ASN A1224 " " NAG G 1 " - " ASN A 371 " " NAG H 1 " - " ASN A 449 " " NAG I 1 " - " ASN A 648 " " NAG J 1 " - " ASN A 739 " " NAG K 1 " - " ASN A 788 " " NAG L 1 " - " ASN A 937 " " NAG M 1 " - " ASN A1194 " " NAG N 1 " - " ASN B 133 " " NAG O 1 " - " ASN B 202 " " NAG P 1 " - " ASN B1224 " " NAG Q 1 " - " ASN B 371 " " NAG R 1 " - " ASN B 449 " " NAG S 1 " - " ASN B 648 " " NAG T 1 " - " ASN B 739 " " NAG U 1 " - " ASN B 788 " " NAG V 1 " - " ASN B 937 " " NAG W 1 " - " ASN B1194 " " NAG X 1 " - " ASN C 133 " " NAG Y 1 " - " ASN C 202 " " NAG Z 1 " - " ASN C1224 " " NAG a 1 " - " ASN C 371 " " NAG b 1 " - " ASN C 449 " " NAG c 1 " - " ASN C 648 " " NAG d 1 " - " ASN C 739 " " NAG e 1 " - " ASN C 788 " " NAG f 1 " - " ASN C 937 " " NAG g 1 " - " ASN C1194 " Time building additional restraints: 14.00 Conformation dependent library (CDL) restraints added in 5.7 seconds 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6588 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 84 helices and 51 sheets defined 23.0% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.21 Creating SS restraints... Processing helix chain 'A' and resid 88 through 91 Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 345 through 349 Processing helix chain 'A' and resid 372 through 378 removed outlier: 4.228A pdb=" N SER A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 396 removed outlier: 4.819A pdb=" N TYR A 395 " --> pdb=" O ALA A 392 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 396 " --> pdb=" O LYS A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 417 Processing helix chain 'A' and resid 424 through 428 Processing helix chain 'A' and resid 447 through 449 No H-bonds generated for 'chain 'A' and resid 447 through 449' Processing helix chain 'A' and resid 459 through 463 Processing helix chain 'A' and resid 468 through 471 No H-bonds generated for 'chain 'A' and resid 468 through 471' Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 580 through 582 No H-bonds generated for 'chain 'A' and resid 580 through 582' Processing helix chain 'A' and resid 708 through 714 Processing helix chain 'A' and resid 826 through 830 Processing helix chain 'A' and resid 835 through 874 removed outlier: 3.608A pdb=" N VAL A 842 " --> pdb=" O LYS A 838 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU A 843 " --> pdb=" O SER A 839 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N TYR A 844 " --> pdb=" O GLN A 840 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N SER A 846 " --> pdb=" O VAL A 842 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N PHE A 847 " --> pdb=" O GLU A 843 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS A 848 " --> pdb=" O TYR A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 884 Processing helix chain 'A' and resid 915 through 922 Processing helix chain 'A' and resid 928 through 936 Processing helix chain 'A' and resid 947 through 953 Processing helix chain 'A' and resid 965 through 979 removed outlier: 3.999A pdb=" N SER A 979 " --> pdb=" O ALA A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 987 No H-bonds generated for 'chain 'A' and resid 985 through 987' Processing helix chain 'A' and resid 992 through 1003 removed outlier: 3.724A pdb=" N LEU A1003 " --> pdb=" O ARG A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1010 No H-bonds generated for 'chain 'A' and resid 1007 through 1010' Processing helix chain 'A' and resid 1014 through 1032 removed outlier: 3.827A pdb=" N PHE A1032 " --> pdb=" O ILE A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1061 removed outlier: 4.178A pdb=" N GLN A1059 " --> pdb=" O ASN A1055 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU A1060 " --> pdb=" O LEU A1056 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N SER A1061 " --> pdb=" O LEU A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1077 Processing helix chain 'A' and resid 1080 through 1125 Processing helix chain 'A' and resid 1212 through 1214 No H-bonds generated for 'chain 'A' and resid 1212 through 1214' Processing helix chain 'B' and resid 88 through 91 Processing helix chain 'B' and resid 294 through 301 Processing helix chain 'B' and resid 345 through 349 Processing helix chain 'B' and resid 372 through 378 removed outlier: 4.228A pdb=" N SER B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 396 removed outlier: 4.818A pdb=" N TYR B 395 " --> pdb=" O ALA B 392 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY B 396 " --> pdb=" O LYS B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 417 Processing helix chain 'B' and resid 424 through 428 Processing helix chain 'B' and resid 447 through 449 No H-bonds generated for 'chain 'B' and resid 447 through 449' Processing helix chain 'B' and resid 459 through 463 Processing helix chain 'B' and resid 468 through 471 No H-bonds generated for 'chain 'B' and resid 468 through 471' Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 580 through 582 No H-bonds generated for 'chain 'B' and resid 580 through 582' Processing helix chain 'B' and resid 708 through 714 Processing helix chain 'B' and resid 826 through 830 Processing helix chain 'B' and resid 835 through 874 removed outlier: 3.608A pdb=" N VAL B 842 " --> pdb=" O LYS B 838 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU B 843 " --> pdb=" O SER B 839 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N TYR B 844 " --> pdb=" O GLN B 840 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N SER B 846 " --> pdb=" O VAL B 842 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N PHE B 847 " --> pdb=" O GLU B 843 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS B 848 " --> pdb=" O TYR B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 881 through 884 Processing helix chain 'B' and resid 915 through 922 Processing helix chain 'B' and resid 928 through 936 Processing helix chain 'B' and resid 947 through 953 Processing helix chain 'B' and resid 965 through 979 removed outlier: 4.000A pdb=" N SER B 979 " --> pdb=" O ALA B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 987 No H-bonds generated for 'chain 'B' and resid 985 through 987' Processing helix chain 'B' and resid 992 through 1003 removed outlier: 3.724A pdb=" N LEU B1003 " --> pdb=" O ARG B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1010 No H-bonds generated for 'chain 'B' and resid 1007 through 1010' Processing helix chain 'B' and resid 1014 through 1032 removed outlier: 3.827A pdb=" N PHE B1032 " --> pdb=" O ILE B1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 1037 through 1061 removed outlier: 4.178A pdb=" N GLN B1059 " --> pdb=" O ASN B1055 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU B1060 " --> pdb=" O LEU B1056 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N SER B1061 " --> pdb=" O LEU B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1071 through 1077 Processing helix chain 'B' and resid 1080 through 1125 Processing helix chain 'B' and resid 1212 through 1214 No H-bonds generated for 'chain 'B' and resid 1212 through 1214' Processing helix chain 'C' and resid 88 through 91 Processing helix chain 'C' and resid 294 through 301 Processing helix chain 'C' and resid 345 through 349 Processing helix chain 'C' and resid 372 through 378 removed outlier: 4.228A pdb=" N SER C 377 " --> pdb=" O SER C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 396 removed outlier: 4.819A pdb=" N TYR C 395 " --> pdb=" O ALA C 392 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY C 396 " --> pdb=" O LYS C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 417 Processing helix chain 'C' and resid 424 through 428 Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 459 through 463 Processing helix chain 'C' and resid 468 through 471 No H-bonds generated for 'chain 'C' and resid 468 through 471' Processing helix chain 'C' and resid 568 through 570 No H-bonds generated for 'chain 'C' and resid 568 through 570' Processing helix chain 'C' and resid 580 through 582 No H-bonds generated for 'chain 'C' and resid 580 through 582' Processing helix chain 'C' and resid 708 through 714 Processing helix chain 'C' and resid 826 through 830 Processing helix chain 'C' and resid 835 through 874 removed outlier: 3.607A pdb=" N VAL C 842 " --> pdb=" O LYS C 838 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU C 843 " --> pdb=" O SER C 839 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N TYR C 844 " --> pdb=" O GLN C 840 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N SER C 846 " --> pdb=" O VAL C 842 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N PHE C 847 " --> pdb=" O GLU C 843 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS C 848 " --> pdb=" O TYR C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 881 through 884 Processing helix chain 'C' and resid 915 through 922 Processing helix chain 'C' and resid 928 through 936 Processing helix chain 'C' and resid 947 through 953 Processing helix chain 'C' and resid 965 through 979 removed outlier: 3.999A pdb=" N SER C 979 " --> pdb=" O ALA C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 987 No H-bonds generated for 'chain 'C' and resid 985 through 987' Processing helix chain 'C' and resid 992 through 1003 removed outlier: 3.724A pdb=" N LEU C1003 " --> pdb=" O ARG C 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 1007 through 1010 No H-bonds generated for 'chain 'C' and resid 1007 through 1010' Processing helix chain 'C' and resid 1014 through 1032 removed outlier: 3.826A pdb=" N PHE C1032 " --> pdb=" O ILE C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1037 through 1061 removed outlier: 4.178A pdb=" N GLN C1059 " --> pdb=" O ASN C1055 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU C1060 " --> pdb=" O LEU C1056 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N SER C1061 " --> pdb=" O LEU C1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 1071 through 1077 Processing helix chain 'C' and resid 1080 through 1125 Processing helix chain 'C' and resid 1212 through 1214 No H-bonds generated for 'chain 'C' and resid 1212 through 1214' Processing sheet with id= A, first strand: chain 'A' and resid 60 through 69 Processing sheet with id= B, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.697A pdb=" N GLY A 157 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR A 199 " --> pdb=" O VAL A 163 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 264 through 268 removed outlier: 5.513A pdb=" N PHE A 227 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N PHE A 236 " --> pdb=" O PHE A 227 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 110 through 114 Processing sheet with id= E, first strand: chain 'A' and resid 173 through 175 No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 310 through 313 Processing sheet with id= G, first strand: chain 'A' and resid 331 through 335 removed outlier: 3.634A pdb=" N ALA A 331 " --> pdb=" O CYS A 630 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR A 677 " --> pdb=" O VAL A 647 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N TYR A 667 " --> pdb=" O ILE A 680 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU A 659 " --> pdb=" O TYR A 667 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 353 through 355 removed outlier: 5.957A pdb=" N SER A 451 " --> pdb=" O VAL A 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'A' and resid 361 through 366 removed outlier: 3.580A pdb=" N SER A 438 " --> pdb=" O ASN A 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ASN A 444 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ALA A 381 " --> pdb=" O ASN A 444 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 484 through 488 Processing sheet with id= K, first strand: chain 'A' and resid 491 through 493 removed outlier: 4.330A pdb=" N CYS A 491 " --> pdb=" O SER A 553 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 774 through 778 removed outlier: 3.555A pdb=" N GLY A 753 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL A 758 " --> pdb=" O THR A 751 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N THR A 751 " --> pdb=" O VAL A 758 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 806 through 816 Processing sheet with id= N, first strand: chain 'A' and resid 821 through 824 removed outlier: 4.223A pdb=" N LYS A 821 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 1182 through 1185 Processing sheet with id= P, first strand: chain 'A' and resid 1188 through 1193 Processing sheet with id= Q, first strand: chain 'A' and resid 798 through 805 removed outlier: 6.544A pdb=" N LYS A1165 " --> pdb=" O SER A 804 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 60 through 69 Processing sheet with id= S, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.697A pdb=" N GLY B 157 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR B 199 " --> pdb=" O VAL B 163 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 264 through 268 removed outlier: 5.514A pdb=" N PHE B 227 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N PHE B 236 " --> pdb=" O PHE B 227 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 110 through 114 Processing sheet with id= V, first strand: chain 'B' and resid 173 through 175 No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'B' and resid 310 through 313 Processing sheet with id= X, first strand: chain 'B' and resid 331 through 335 removed outlier: 3.634A pdb=" N ALA B 331 " --> pdb=" O CYS B 630 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N THR B 677 " --> pdb=" O VAL B 647 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N TYR B 667 " --> pdb=" O ILE B 680 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU B 659 " --> pdb=" O TYR B 667 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 353 through 355 removed outlier: 5.956A pdb=" N SER B 451 " --> pdb=" O VAL B 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'B' and resid 361 through 366 removed outlier: 3.580A pdb=" N SER B 438 " --> pdb=" O ASN B 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ASN B 444 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ALA B 381 " --> pdb=" O ASN B 444 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 484 through 488 Processing sheet with id= AB, first strand: chain 'B' and resid 491 through 493 removed outlier: 4.330A pdb=" N CYS B 491 " --> pdb=" O SER B 553 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 774 through 778 removed outlier: 3.555A pdb=" N GLY B 753 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL B 758 " --> pdb=" O THR B 751 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N THR B 751 " --> pdb=" O VAL B 758 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'B' and resid 806 through 816 Processing sheet with id= AE, first strand: chain 'B' and resid 821 through 824 removed outlier: 4.223A pdb=" N LYS B 821 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'B' and resid 1182 through 1185 Processing sheet with id= AG, first strand: chain 'B' and resid 1188 through 1193 Processing sheet with id= AH, first strand: chain 'B' and resid 798 through 805 removed outlier: 6.543A pdb=" N LYS B1165 " --> pdb=" O SER B 804 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 60 through 69 Processing sheet with id= AJ, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.697A pdb=" N GLY C 157 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR C 199 " --> pdb=" O VAL C 163 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'C' and resid 264 through 268 removed outlier: 5.513A pdb=" N PHE C 227 " --> pdb=" O PHE C 236 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N PHE C 236 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'C' and resid 110 through 114 Processing sheet with id= AM, first strand: chain 'C' and resid 173 through 175 No H-bonds generated for sheet with id= AM Processing sheet with id= AN, first strand: chain 'C' and resid 310 through 313 Processing sheet with id= AO, first strand: chain 'C' and resid 331 through 335 removed outlier: 3.635A pdb=" N ALA C 331 " --> pdb=" O CYS C 630 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N THR C 677 " --> pdb=" O VAL C 647 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N TYR C 667 " --> pdb=" O ILE C 680 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU C 659 " --> pdb=" O TYR C 667 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'C' and resid 353 through 355 removed outlier: 5.957A pdb=" N SER C 451 " --> pdb=" O VAL C 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= AP Processing sheet with id= AQ, first strand: chain 'C' and resid 361 through 366 removed outlier: 3.579A pdb=" N SER C 438 " --> pdb=" O ASN C 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ASN C 444 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ALA C 381 " --> pdb=" O ASN C 444 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'C' and resid 484 through 488 Processing sheet with id= AS, first strand: chain 'C' and resid 491 through 493 removed outlier: 4.330A pdb=" N CYS C 491 " --> pdb=" O SER C 553 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'C' and resid 774 through 778 removed outlier: 3.555A pdb=" N GLY C 753 " --> pdb=" O TYR C 756 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL C 758 " --> pdb=" O THR C 751 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N THR C 751 " --> pdb=" O VAL C 758 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'C' and resid 806 through 816 Processing sheet with id= AV, first strand: chain 'C' and resid 821 through 824 removed outlier: 4.223A pdb=" N LYS C 821 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'C' and resid 1182 through 1185 Processing sheet with id= AX, first strand: chain 'C' and resid 1188 through 1193 Processing sheet with id= AY, first strand: chain 'C' and resid 798 through 805 removed outlier: 6.543A pdb=" N LYS C1165 " --> pdb=" O SER C 804 " (cutoff:3.500A) 996 hydrogen bonds defined for protein. 2772 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: 13.06 Time building geometry restraints manager: 14.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 7501 1.32 - 1.46: 9819 1.46 - 1.60: 11939 1.60 - 1.73: 24 1.73 - 1.87: 216 Bond restraints: 29499 Sorted by residual: bond pdb=" CB HIS C 215 " pdb=" CG HIS C 215 " ideal model delta sigma weight residual 1.497 1.388 0.109 1.40e-02 5.10e+03 6.09e+01 bond pdb=" CB HIS A 215 " pdb=" CG HIS A 215 " ideal model delta sigma weight residual 1.497 1.388 0.109 1.40e-02 5.10e+03 6.09e+01 bond pdb=" CB HIS B 215 " pdb=" CG HIS B 215 " ideal model delta sigma weight residual 1.497 1.388 0.109 1.40e-02 5.10e+03 6.09e+01 bond pdb=" CB ASN B 444 " pdb=" CG ASN B 444 " ideal model delta sigma weight residual 1.516 1.349 0.167 2.50e-02 1.60e+03 4.48e+01 bond pdb=" CB ASN C 444 " pdb=" CG ASN C 444 " ideal model delta sigma weight residual 1.516 1.349 0.167 2.50e-02 1.60e+03 4.48e+01 ... (remaining 29494 not shown) Histogram of bond angle deviations from ideal: 97.83 - 105.09: 717 105.09 - 112.35: 13902 112.35 - 119.60: 11348 119.60 - 126.86: 14003 126.86 - 134.12: 200 Bond angle restraints: 40170 Sorted by residual: angle pdb=" N ASP A 893 " pdb=" CA ASP A 893 " pdb=" C ASP A 893 " ideal model delta sigma weight residual 113.56 127.61 -14.05 1.39e+00 5.18e-01 1.02e+02 angle pdb=" N ASP C 893 " pdb=" CA ASP C 893 " pdb=" C ASP C 893 " ideal model delta sigma weight residual 113.56 127.60 -14.04 1.39e+00 5.18e-01 1.02e+02 angle pdb=" N ASP B 893 " pdb=" CA ASP B 893 " pdb=" C ASP B 893 " ideal model delta sigma weight residual 113.56 127.58 -14.02 1.39e+00 5.18e-01 1.02e+02 angle pdb=" N THR B 134 " pdb=" CA THR B 134 " pdb=" C THR B 134 " ideal model delta sigma weight residual 114.56 102.52 12.04 1.27e+00 6.20e-01 8.98e+01 angle pdb=" N THR C 134 " pdb=" CA THR C 134 " pdb=" C THR C 134 " ideal model delta sigma weight residual 114.56 102.53 12.03 1.27e+00 6.20e-01 8.97e+01 ... (remaining 40165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.20: 18059 22.20 - 44.41: 541 44.41 - 66.61: 120 66.61 - 88.81: 138 88.81 - 111.01: 84 Dihedral angle restraints: 18942 sinusoidal: 8637 harmonic: 10305 Sorted by residual: dihedral pdb=" CB CYS C 491 " pdb=" SG CYS C 491 " pdb=" SG CYS C 561 " pdb=" CB CYS C 561 " ideal model delta sinusoidal sigma weight residual -86.00 -124.55 38.55 1 1.00e+01 1.00e-02 2.09e+01 dihedral pdb=" CB CYS A 491 " pdb=" SG CYS A 491 " pdb=" SG CYS A 561 " pdb=" CB CYS A 561 " ideal model delta sinusoidal sigma weight residual -86.00 -124.52 38.52 1 1.00e+01 1.00e-02 2.09e+01 dihedral pdb=" CB CYS B 491 " pdb=" SG CYS B 491 " pdb=" SG CYS B 561 " pdb=" CB CYS B 561 " ideal model delta sinusoidal sigma weight residual -86.00 -124.51 38.51 1 1.00e+01 1.00e-02 2.09e+01 ... (remaining 18939 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 3008 0.098 - 0.195: 1405 0.195 - 0.293: 352 0.293 - 0.390: 68 0.390 - 0.488: 15 Chirality restraints: 4848 Sorted by residual: chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.18e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.16e+02 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.14e+02 ... (remaining 4845 not shown) Planarity restraints: 5067 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 648 " -0.049 2.00e-02 2.50e+03 5.14e-02 3.31e+01 pdb=" CG ASN B 648 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN B 648 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN B 648 " 0.081 2.00e-02 2.50e+03 pdb=" C1 NAG S 1 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 648 " 0.049 2.00e-02 2.50e+03 5.13e-02 3.29e+01 pdb=" CG ASN A 648 " -0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN A 648 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 648 " -0.081 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 648 " -0.049 2.00e-02 2.50e+03 5.10e-02 3.25e+01 pdb=" CG ASN C 648 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN C 648 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN C 648 " 0.080 2.00e-02 2.50e+03 pdb=" C1 NAG c 1 " -0.060 2.00e-02 2.50e+03 ... (remaining 5064 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 396 2.61 - 3.18: 25951 3.18 - 3.75: 47332 3.75 - 4.33: 70993 4.33 - 4.90: 112119 Nonbonded interactions: 256791 Sorted by model distance: nonbonded pdb=" O HOH A5095 " pdb=" O HOH B5118 " model vdw 2.033 2.440 nonbonded pdb=" O HOH A5118 " pdb=" O HOH C5095 " model vdw 2.033 2.440 nonbonded pdb=" O HOH B5095 " pdb=" O HOH C5118 " model vdw 2.034 2.440 nonbonded pdb=" O ARG C 687 " pdb=" O HOH C5057 " model vdw 2.143 2.440 nonbonded pdb=" O ARG A 687 " pdb=" O HOH A5057 " model vdw 2.143 2.440 ... (remaining 256786 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'g' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'P' selection = chain 'T' selection = chain 'Z' selection = chain 'd' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'c' selection = chain 'e' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.990 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: 0.020 Extract box with map and model: 14.440 Check model and map are aligned: 0.450 Set scattering table: 0.260 Process input model: 82.980 Find NCS groups from input model: 2.100 Set up NCS constraints: 0.490 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: 0.000 Load rotamer database and sin/cos tables:13.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 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 : 0.025 0.167 29499 Z= 1.655 Angle : 1.829 19.979 40170 Z= 1.182 Chirality : 0.116 0.488 4848 Planarity : 0.009 0.047 5022 Dihedral : 16.034 111.014 12165 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.63 % Favored : 98.28 % Rotamer: Outliers : 0.39 % Allowed : 0.98 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.13), residues: 3489 helix: -0.42 (0.16), residues: 765 sheet: 1.10 (0.17), residues: 801 loop : 0.50 (0.13), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.009 TRP C 460 HIS 0.009 0.002 HIS C1142 PHE 0.049 0.007 PHE C 713 TYR 0.073 0.010 TYR A 75 ARG 0.010 0.001 ARG C 999 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 555 time to evaluate : 3.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 TYR cc_start: 0.8325 (m-80) cc_final: 0.8116 (m-80) REVERT: A 681 ARG cc_start: 0.8332 (mtp85) cc_final: 0.8061 (mtp85) REVERT: A 698 GLU cc_start: 0.8077 (pt0) cc_final: 0.7865 (pt0) REVERT: A 725 ASN cc_start: 0.7795 (p0) cc_final: 0.7475 (p0) REVERT: A 738 TYR cc_start: 0.7957 (p90) cc_final: 0.7540 (p90) REVERT: A 884 LYS cc_start: 0.8358 (mttt) cc_final: 0.7445 (mmtm) REVERT: A 1015 LYS cc_start: 0.8549 (ttmm) cc_final: 0.8190 (tptp) REVERT: A 1026 TYR cc_start: 0.7850 (t80) cc_final: 0.7250 (t80) REVERT: B 156 GLN cc_start: 0.8001 (mm-40) cc_final: 0.7680 (tp40) REVERT: B 698 GLU cc_start: 0.8119 (pt0) cc_final: 0.7900 (pt0) REVERT: B 725 ASN cc_start: 0.7678 (p0) cc_final: 0.7423 (p0) REVERT: B 857 GLU cc_start: 0.7660 (tt0) cc_final: 0.7452 (tt0) REVERT: B 884 LYS cc_start: 0.8247 (mttt) cc_final: 0.7565 (mptt) REVERT: B 1015 LYS cc_start: 0.8483 (ttmm) cc_final: 0.8135 (tptp) REVERT: C 155 LEU cc_start: 0.7838 (mt) cc_final: 0.7628 (mp) REVERT: C 698 GLU cc_start: 0.8124 (pt0) cc_final: 0.7873 (pt0) REVERT: C 884 LYS cc_start: 0.8354 (mttt) cc_final: 0.7922 (mttp) REVERT: C 1015 LYS cc_start: 0.8532 (ttmm) cc_final: 0.8126 (tptp) REVERT: C 1063 ARG cc_start: 0.8304 (mtt180) cc_final: 0.8093 (mtp180) outliers start: 12 outliers final: 1 residues processed: 561 average time/residue: 1.2014 time to fit residues: 805.9208 Evaluate side-chains 319 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 318 time to evaluate : 3.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 624 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 296 optimal weight: 0.9990 chunk 266 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 179 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 275 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 167 optimal weight: 0.9990 chunk 204 optimal weight: 2.9990 chunk 318 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN A 248 HIS A 380 GLN A 482 ASN A 593 GLN A 641 GLN A 801 GLN ** A 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1029 GLN A1036 ASN A1059 GLN A1062 ASN A1104 GLN ** A1139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS B 248 HIS B 380 GLN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 ASN ** B 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 801 GLN ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1029 GLN B1036 ASN B1059 GLN B1062 ASN C 182 ASN ** C 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 HIS C 387 ASN C 482 ASN C 581 GLN ** C 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 GLN C 850 ASN ** C 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1029 GLN C1036 ASN C1059 GLN C1062 ASN C1104 GLN C1192 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 29499 Z= 0.276 Angle : 0.724 24.952 40170 Z= 0.364 Chirality : 0.051 0.515 4848 Planarity : 0.004 0.031 5022 Dihedral : 12.619 75.485 6029 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.51 % Allowed : 6.75 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.13), residues: 3489 helix: 0.96 (0.19), residues: 759 sheet: 0.69 (0.17), residues: 792 loop : 0.24 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 460 HIS 0.005 0.001 HIS A 215 PHE 0.020 0.002 PHE B 91 TYR 0.019 0.002 TYR C 738 ARG 0.005 0.001 ARG B1170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 393 time to evaluate : 3.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7398 (t70) REVERT: A 519 ILE cc_start: 0.8908 (mt) cc_final: 0.8672 (mm) REVERT: A 567 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7924 (tttt) REVERT: A 681 ARG cc_start: 0.8424 (mtp85) cc_final: 0.8115 (mtp85) REVERT: A 738 TYR cc_start: 0.7668 (p90) cc_final: 0.7370 (p90) REVERT: A 792 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7046 (mt-10) REVERT: A 884 LYS cc_start: 0.8172 (mttt) cc_final: 0.7346 (mmtm) REVERT: A 1015 LYS cc_start: 0.8475 (ttmm) cc_final: 0.8104 (tptp) REVERT: B 156 GLN cc_start: 0.7988 (mm-40) cc_final: 0.7609 (tp40) REVERT: B 185 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7250 (mtpt) REVERT: B 698 GLU cc_start: 0.8191 (pt0) cc_final: 0.7933 (pt0) REVERT: B 792 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7217 (mp0) REVERT: B 884 LYS cc_start: 0.8132 (mttt) cc_final: 0.7427 (mptt) REVERT: B 1015 LYS cc_start: 0.8392 (ttmm) cc_final: 0.7992 (tptp) REVERT: B 1084 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7487 (mt-10) REVERT: C 95 PHE cc_start: 0.8003 (m-80) cc_final: 0.7785 (m-80) REVERT: C 792 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7392 (mp0) REVERT: C 884 LYS cc_start: 0.8179 (mttt) cc_final: 0.7668 (mptt) REVERT: C 1015 LYS cc_start: 0.8384 (ttmm) cc_final: 0.8017 (tptp) outliers start: 77 outliers final: 26 residues processed: 442 average time/residue: 1.0984 time to fit residues: 593.0612 Evaluate side-chains 345 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 313 time to evaluate : 3.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 567 LYS Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 866 GLN Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 551 THR Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 783 THR Chi-restraints excluded: chain C residue 792 GLU Chi-restraints excluded: chain C residue 856 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 177 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 265 optimal weight: 0.8980 chunk 217 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 319 optimal weight: 3.9990 chunk 344 optimal weight: 0.9980 chunk 284 optimal weight: 2.9990 chunk 316 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 256 optimal weight: 0.0570 overall best weight: 1.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN A 482 ASN A 593 GLN ** A 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 850 ASN A1092 ASN B 182 ASN B 257 ASN B 387 ASN B 482 ASN ** B 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 GLN ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1019 ASN ** B1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 HIS C 387 ASN C 482 ASN C 593 GLN C 641 GLN ** C 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1019 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 29499 Z= 0.377 Angle : 0.711 21.132 40170 Z= 0.359 Chirality : 0.052 0.646 4848 Planarity : 0.004 0.042 5022 Dihedral : 9.395 71.070 6029 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.54 % Allowed : 8.74 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.14), residues: 3489 helix: 0.85 (0.19), residues: 774 sheet: 0.17 (0.17), residues: 813 loop : 0.01 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 188 HIS 0.004 0.001 HIS C 560 PHE 0.017 0.002 PHE B 889 TYR 0.019 0.002 TYR C 217 ARG 0.005 0.001 ARG A1170 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 350 time to evaluate : 3.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.7749 (OUTLIER) cc_final: 0.7528 (t70) REVERT: A 244 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.6533 (ppp) REVERT: A 567 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8166 (tttt) REVERT: A 681 ARG cc_start: 0.8364 (mtp85) cc_final: 0.8069 (mtp85) REVERT: A 738 TYR cc_start: 0.7744 (p90) cc_final: 0.7406 (p90) REVERT: A 792 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7071 (mt-10) REVERT: A 884 LYS cc_start: 0.8248 (mttt) cc_final: 0.7491 (mmtm) REVERT: A 1015 LYS cc_start: 0.8402 (ttmm) cc_final: 0.8045 (tptp) REVERT: B 156 GLN cc_start: 0.7995 (mm-40) cc_final: 0.7668 (tp40) REVERT: B 884 LYS cc_start: 0.8280 (mttt) cc_final: 0.7575 (mptt) REVERT: B 1015 LYS cc_start: 0.8389 (ttmm) cc_final: 0.7987 (tptp) REVERT: C 95 PHE cc_start: 0.8084 (m-80) cc_final: 0.7860 (m-80) REVERT: C 440 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8002 (mp10) REVERT: C 552 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8313 (tptp) REVERT: C 792 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7218 (mp0) REVERT: C 1015 LYS cc_start: 0.8422 (ttmm) cc_final: 0.7993 (tptp) outliers start: 78 outliers final: 43 residues processed: 396 average time/residue: 1.1079 time to fit residues: 536.5601 Evaluate side-chains 369 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 319 time to evaluate : 3.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 567 LYS Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 866 GLN Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1196 THR Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 444 ASN Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 567 LYS Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain B residue 1196 THR Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain C residue 444 ASN Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 552 LYS Chi-restraints excluded: chain C residue 567 LYS Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 783 THR Chi-restraints excluded: chain C residue 792 GLU Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 1175 LEU Chi-restraints excluded: chain C residue 1208 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 315 optimal weight: 0.9980 chunk 240 optimal weight: 2.9990 chunk 165 optimal weight: 0.1980 chunk 35 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 320 optimal weight: 0.9980 chunk 339 optimal weight: 0.6980 chunk 167 optimal weight: 3.9990 chunk 303 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 ASN A 593 GLN ** A 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 ASN ** B 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1019 ASN ** C 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 456 ASN C 593 GLN C 598 ASN C1058 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29499 Z= 0.275 Angle : 0.621 13.833 40170 Z= 0.315 Chirality : 0.048 0.415 4848 Planarity : 0.004 0.036 5022 Dihedral : 7.965 71.140 6029 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.67 % Allowed : 9.69 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.14), residues: 3489 helix: 1.04 (0.19), residues: 768 sheet: 0.11 (0.17), residues: 783 loop : -0.08 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 460 HIS 0.004 0.001 HIS C 560 PHE 0.017 0.002 PHE B 889 TYR 0.017 0.002 TYR C 217 ARG 0.003 0.000 ARG B1170 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 342 time to evaluate : 3.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.7521 (t70) REVERT: A 681 ARG cc_start: 0.8362 (mtp85) cc_final: 0.8132 (mtp85) REVERT: A 738 TYR cc_start: 0.7618 (p90) cc_final: 0.7301 (p90) REVERT: A 792 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7140 (mt-10) REVERT: A 884 LYS cc_start: 0.8348 (mttt) cc_final: 0.7517 (mmtm) REVERT: A 1015 LYS cc_start: 0.8342 (ttmm) cc_final: 0.8002 (tptp) REVERT: B 156 GLN cc_start: 0.8001 (mm-40) cc_final: 0.7672 (tp40) REVERT: B 792 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7169 (mp0) REVERT: B 884 LYS cc_start: 0.8359 (mttt) cc_final: 0.7542 (mptt) REVERT: B 1015 LYS cc_start: 0.8369 (ttmm) cc_final: 0.7937 (tptp) REVERT: C 125 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8412 (tp) REVERT: C 183 HIS cc_start: 0.6409 (m90) cc_final: 0.6167 (m90) REVERT: C 244 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.6786 (pp-130) REVERT: C 440 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8014 (mp10) REVERT: C 552 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8289 (tptp) REVERT: C 792 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7249 (mp0) REVERT: C 813 GLU cc_start: 0.8354 (tt0) cc_final: 0.8055 (pt0) REVERT: C 1011 SER cc_start: 0.8859 (p) cc_final: 0.8550 (m) REVERT: C 1015 LYS cc_start: 0.8411 (ttmm) cc_final: 0.7994 (tptp) outliers start: 82 outliers final: 41 residues processed: 387 average time/residue: 1.0842 time to fit residues: 515.9600 Evaluate side-chains 364 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 315 time to evaluate : 3.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1198 MET Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 444 ASN Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 552 LYS Chi-restraints excluded: chain C residue 567 LYS Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 792 GLU Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 1175 LEU Chi-restraints excluded: chain C residue 1208 GLU Chi-restraints excluded: chain C residue 1233 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 282 optimal weight: 0.0020 chunk 192 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 252 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 289 optimal weight: 0.9980 chunk 234 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 304 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 ASN A 482 ASN A 593 GLN ** A 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1019 ASN A1036 ASN B 257 ASN B 482 ASN B 641 GLN ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1019 ASN C 482 ASN C 598 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 29499 Z= 0.254 Angle : 0.601 10.622 40170 Z= 0.307 Chirality : 0.047 0.392 4848 Planarity : 0.004 0.037 5022 Dihedral : 7.487 69.492 6029 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.45 % Allowed : 10.08 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.14), residues: 3489 helix: 1.12 (0.19), residues: 768 sheet: 0.08 (0.17), residues: 795 loop : -0.11 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 460 HIS 0.004 0.001 HIS A 215 PHE 0.018 0.002 PHE C 889 TYR 0.016 0.002 TYR C 136 ARG 0.003 0.000 ARG B1170 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 326 time to evaluate : 3.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7533 (t70) REVERT: A 244 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.6456 (ppp) REVERT: A 681 ARG cc_start: 0.8441 (mtp85) cc_final: 0.8221 (mtp85) REVERT: A 738 TYR cc_start: 0.7592 (p90) cc_final: 0.7226 (p90) REVERT: A 792 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7135 (mt-10) REVERT: A 884 LYS cc_start: 0.8384 (mttt) cc_final: 0.7885 (mptp) REVERT: A 1015 LYS cc_start: 0.8357 (ttmm) cc_final: 0.7930 (tptp) REVERT: B 156 GLN cc_start: 0.7971 (mm-40) cc_final: 0.7654 (tp40) REVERT: B 792 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: B 884 LYS cc_start: 0.8328 (mttt) cc_final: 0.7729 (mptt) REVERT: B 1015 LYS cc_start: 0.8358 (ttmm) cc_final: 0.7975 (tptp) REVERT: C 125 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8420 (tp) REVERT: C 244 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7478 (pp-130) REVERT: C 440 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8062 (mp10) REVERT: C 552 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8267 (tptp) REVERT: C 792 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: C 813 GLU cc_start: 0.8339 (tt0) cc_final: 0.8073 (pt0) REVERT: C 1011 SER cc_start: 0.8820 (p) cc_final: 0.8560 (m) REVERT: C 1015 LYS cc_start: 0.8433 (ttmm) cc_final: 0.8016 (tptp) outliers start: 75 outliers final: 45 residues processed: 368 average time/residue: 1.0939 time to fit residues: 496.8595 Evaluate side-chains 368 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 314 time to evaluate : 3.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1198 MET Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 444 ASN Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 706 ILE Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 552 LYS Chi-restraints excluded: chain C residue 567 LYS Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain C residue 792 GLU Chi-restraints excluded: chain C residue 839 SER Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 1175 LEU Chi-restraints excluded: chain C residue 1208 GLU Chi-restraints excluded: chain C residue 1233 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 114 optimal weight: 0.9980 chunk 305 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 199 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 339 optimal weight: 0.5980 chunk 281 optimal weight: 3.9990 chunk 157 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 112 optimal weight: 0.4980 chunk 178 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN A 183 HIS A 482 ASN A 593 GLN A 840 GLN B 257 ASN B 387 ASN B 482 ASN ** B 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1019 ASN C 641 GLN C 725 ASN C1019 ASN C1092 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29499 Z= 0.222 Angle : 0.569 8.089 40170 Z= 0.293 Chirality : 0.046 0.386 4848 Planarity : 0.004 0.036 5022 Dihedral : 6.983 68.691 6027 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.28 % Allowed : 10.57 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.27 (0.14), residues: 3489 helix: 1.23 (0.20), residues: 768 sheet: 0.07 (0.17), residues: 795 loop : -0.11 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 460 HIS 0.003 0.001 HIS A 215 PHE 0.019 0.002 PHE B 889 TYR 0.017 0.002 TYR C 136 ARG 0.007 0.000 ARG B1170 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 335 time to evaluate : 3.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7524 (t70) REVERT: A 244 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.6565 (ppp) REVERT: A 681 ARG cc_start: 0.8441 (mtp85) cc_final: 0.8217 (mtp85) REVERT: A 738 TYR cc_start: 0.7435 (p90) cc_final: 0.7209 (p90) REVERT: A 792 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7129 (mt-10) REVERT: A 884 LYS cc_start: 0.8385 (mttt) cc_final: 0.7885 (mptp) REVERT: A 1011 SER cc_start: 0.8718 (p) cc_final: 0.8458 (m) REVERT: A 1015 LYS cc_start: 0.8363 (ttmm) cc_final: 0.7949 (tptp) REVERT: B 156 GLN cc_start: 0.7969 (mm-40) cc_final: 0.7706 (tp40) REVERT: B 204 THR cc_start: 0.8605 (t) cc_final: 0.8214 (m) REVERT: B 792 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7052 (mp0) REVERT: B 884 LYS cc_start: 0.8307 (mttt) cc_final: 0.7841 (mptt) REVERT: B 1015 LYS cc_start: 0.8322 (ttmm) cc_final: 0.7976 (tptp) REVERT: C 125 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8426 (tp) REVERT: C 244 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7479 (pp-130) REVERT: C 440 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8018 (mp10) REVERT: C 552 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8346 (tptp) REVERT: C 792 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7258 (mp0) REVERT: C 813 GLU cc_start: 0.8334 (tt0) cc_final: 0.8126 (pt0) REVERT: C 1015 LYS cc_start: 0.8397 (ttmm) cc_final: 0.7976 (tptp) outliers start: 70 outliers final: 44 residues processed: 376 average time/residue: 1.0623 time to fit residues: 492.8790 Evaluate side-chains 364 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 311 time to evaluate : 3.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1198 MET Chi-restraints excluded: chain A residue 1221 CYS Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 444 ASN Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 552 LYS Chi-restraints excluded: chain C residue 567 LYS Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain C residue 792 GLU Chi-restraints excluded: chain C residue 839 SER Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 885 ASP Chi-restraints excluded: chain C residue 1175 LEU Chi-restraints excluded: chain C residue 1208 GLU Chi-restraints excluded: chain C residue 1233 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 327 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 193 optimal weight: 0.8980 chunk 248 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 285 optimal weight: 2.9990 chunk 189 optimal weight: 0.7980 chunk 338 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 206 optimal weight: 0.5980 chunk 156 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 ASN A 593 GLN A 890 ASN B 598 ASN ** B 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1019 ASN ** C 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 29499 Z= 0.330 Angle : 0.626 9.015 40170 Z= 0.322 Chirality : 0.048 0.474 4848 Planarity : 0.004 0.038 5022 Dihedral : 6.970 65.916 6027 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.54 % Allowed : 11.02 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.14), residues: 3489 helix: 1.06 (0.19), residues: 768 sheet: -0.07 (0.17), residues: 825 loop : -0.17 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 188 HIS 0.005 0.001 HIS A 215 PHE 0.020 0.002 PHE B 889 TYR 0.021 0.002 TYR C 136 ARG 0.007 0.001 ARG B1170 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 315 time to evaluate : 4.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.6445 (ppp) REVERT: A 681 ARG cc_start: 0.8467 (mtp85) cc_final: 0.8243 (mtp85) REVERT: A 738 TYR cc_start: 0.7637 (p90) cc_final: 0.7283 (p90) REVERT: A 792 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7100 (mt-10) REVERT: A 884 LYS cc_start: 0.8406 (mttt) cc_final: 0.7874 (mptp) REVERT: A 1015 LYS cc_start: 0.8365 (ttmm) cc_final: 0.7924 (tptp) REVERT: B 156 GLN cc_start: 0.7962 (mm-40) cc_final: 0.7698 (tp40) REVERT: B 204 THR cc_start: 0.8614 (t) cc_final: 0.8219 (m) REVERT: B 792 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7002 (mp0) REVERT: B 884 LYS cc_start: 0.8326 (mttt) cc_final: 0.7860 (mptt) REVERT: B 1015 LYS cc_start: 0.8369 (ttmm) cc_final: 0.7987 (tptp) REVERT: C 125 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8448 (tp) REVERT: C 244 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.6945 (pp-130) REVERT: C 440 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8111 (mp10) REVERT: C 552 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8432 (tptp) REVERT: C 792 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7231 (mp0) REVERT: C 1015 LYS cc_start: 0.8434 (ttmm) cc_final: 0.7995 (tptp) outliers start: 78 outliers final: 53 residues processed: 362 average time/residue: 1.1140 time to fit residues: 496.2253 Evaluate side-chains 363 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 302 time to evaluate : 3.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 790 SER Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1198 MET Chi-restraints excluded: chain A residue 1221 CYS Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain C residue 444 ASN Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 552 LYS Chi-restraints excluded: chain C residue 567 LYS Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 792 GLU Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 885 ASP Chi-restraints excluded: chain C residue 1175 LEU Chi-restraints excluded: chain C residue 1208 GLU Chi-restraints excluded: chain C residue 1233 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 209 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 chunk 202 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 215 optimal weight: 2.9990 chunk 230 optimal weight: 0.9990 chunk 167 optimal weight: 5.9990 chunk 31 optimal weight: 0.1980 chunk 265 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 ASN A 593 GLN A 606 HIS B 444 ASN ** B 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1019 ASN C 598 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29499 Z= 0.200 Angle : 0.562 8.869 40170 Z= 0.290 Chirality : 0.046 0.556 4848 Planarity : 0.004 0.037 5022 Dihedral : 6.645 66.153 6027 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.35 % Allowed : 11.45 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.14), residues: 3489 helix: 1.27 (0.20), residues: 768 sheet: 0.01 (0.17), residues: 795 loop : -0.14 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 460 HIS 0.003 0.001 HIS A 490 PHE 0.021 0.002 PHE C 889 TYR 0.018 0.001 TYR C 136 ARG 0.007 0.000 ARG B1170 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 323 time to evaluate : 3.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.6555 (ppp) REVERT: A 681 ARG cc_start: 0.8453 (mtp85) cc_final: 0.8224 (mtp85) REVERT: A 738 TYR cc_start: 0.7424 (p90) cc_final: 0.7202 (p90) REVERT: A 792 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7092 (mt-10) REVERT: A 884 LYS cc_start: 0.8400 (mttt) cc_final: 0.7949 (mptp) REVERT: A 1011 SER cc_start: 0.8737 (p) cc_final: 0.8476 (m) REVERT: A 1015 LYS cc_start: 0.8362 (ttmm) cc_final: 0.7938 (tptp) REVERT: B 156 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7665 (tp40) REVERT: B 204 THR cc_start: 0.8598 (t) cc_final: 0.8222 (m) REVERT: B 792 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7001 (mp0) REVERT: B 884 LYS cc_start: 0.8340 (mttt) cc_final: 0.7879 (mptt) REVERT: B 1015 LYS cc_start: 0.8328 (ttmm) cc_final: 0.7978 (tptp) REVERT: C 125 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8418 (tp) REVERT: C 440 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8038 (mp10) REVERT: C 552 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8434 (tptp) REVERT: C 1015 LYS cc_start: 0.8415 (ttmm) cc_final: 0.7994 (tptp) outliers start: 72 outliers final: 43 residues processed: 367 average time/residue: 1.0672 time to fit residues: 482.1317 Evaluate side-chains 357 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 308 time to evaluate : 3.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1198 MET Chi-restraints excluded: chain A residue 1221 CYS Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 706 ILE Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain B residue 1233 LEU Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 552 LYS Chi-restraints excluded: chain C residue 567 LYS Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain C residue 839 SER Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 885 ASP Chi-restraints excluded: chain C residue 1175 LEU Chi-restraints excluded: chain C residue 1208 GLU Chi-restraints excluded: chain C residue 1233 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 307 optimal weight: 1.9990 chunk 324 optimal weight: 0.0040 chunk 295 optimal weight: 1.9990 chunk 315 optimal weight: 0.9980 chunk 189 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 247 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 284 optimal weight: 0.7980 chunk 298 optimal weight: 0.6980 chunk 314 optimal weight: 1.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 ASN A 482 ASN A 593 GLN B 380 GLN B 482 ASN ** B 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1019 ASN ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN C 593 GLN C 598 ASN ** C 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1019 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29499 Z= 0.217 Angle : 0.570 9.259 40170 Z= 0.292 Chirality : 0.046 0.570 4848 Planarity : 0.004 0.037 5022 Dihedral : 6.449 65.885 6027 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.22 % Allowed : 11.58 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.14), residues: 3489 helix: 1.31 (0.20), residues: 768 sheet: -0.01 (0.17), residues: 795 loop : -0.13 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 460 HIS 0.004 0.001 HIS A 215 PHE 0.021 0.002 PHE C 889 TYR 0.018 0.002 TYR C 136 ARG 0.008 0.000 ARG A1170 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 316 time to evaluate : 3.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 GLN cc_start: 0.7846 (mm-40) cc_final: 0.7342 (tm-30) REVERT: A 244 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.6545 (ppp) REVERT: A 681 ARG cc_start: 0.8499 (mtp85) cc_final: 0.8264 (mtp85) REVERT: A 738 TYR cc_start: 0.7389 (p90) cc_final: 0.7173 (p90) REVERT: A 792 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7058 (mt-10) REVERT: A 884 LYS cc_start: 0.8405 (mttt) cc_final: 0.7963 (mptp) REVERT: A 1011 SER cc_start: 0.8723 (p) cc_final: 0.8499 (m) REVERT: A 1015 LYS cc_start: 0.8379 (ttmm) cc_final: 0.7939 (tptp) REVERT: B 156 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7728 (tp40) REVERT: B 204 THR cc_start: 0.8604 (t) cc_final: 0.8227 (m) REVERT: B 541 THR cc_start: 0.7320 (m) cc_final: 0.7096 (p) REVERT: B 792 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.6997 (mp0) REVERT: B 884 LYS cc_start: 0.8350 (mttt) cc_final: 0.7877 (mptt) REVERT: B 1015 LYS cc_start: 0.8335 (ttmm) cc_final: 0.7989 (tptp) REVERT: C 125 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8438 (tp) REVERT: C 244 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7286 (pp-130) REVERT: C 440 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8099 (mp10) REVERT: C 552 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8401 (tptp) REVERT: C 792 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7189 (mp0) REVERT: C 1015 LYS cc_start: 0.8418 (ttmm) cc_final: 0.7995 (tptp) outliers start: 68 outliers final: 51 residues processed: 356 average time/residue: 1.1065 time to fit residues: 484.3838 Evaluate side-chains 364 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 305 time to evaluate : 3.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1198 MET Chi-restraints excluded: chain A residue 1221 CYS Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 706 ILE Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain B residue 1233 LEU Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 552 LYS Chi-restraints excluded: chain C residue 567 LYS Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain C residue 792 GLU Chi-restraints excluded: chain C residue 839 SER Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 885 ASP Chi-restraints excluded: chain C residue 1175 LEU Chi-restraints excluded: chain C residue 1208 GLU Chi-restraints excluded: chain C residue 1233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 207 optimal weight: 0.2980 chunk 333 optimal weight: 3.9990 chunk 203 optimal weight: 0.7980 chunk 158 optimal weight: 0.5980 chunk 231 optimal weight: 0.8980 chunk 349 optimal weight: 0.3980 chunk 321 optimal weight: 0.9990 chunk 278 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 215 optimal weight: 0.4980 chunk 170 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 ASN A 482 ASN A 593 GLN B 606 HIS ** B 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1019 ASN ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1019 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29499 Z= 0.182 Angle : 0.546 9.670 40170 Z= 0.281 Chirality : 0.046 0.528 4848 Planarity : 0.004 0.038 5022 Dihedral : 6.204 66.239 6027 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.96 % Allowed : 12.07 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.14), residues: 3489 helix: 1.45 (0.20), residues: 765 sheet: 0.05 (0.18), residues: 774 loop : -0.14 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 460 HIS 0.003 0.001 HIS A 490 PHE 0.020 0.001 PHE B 889 TYR 0.017 0.001 TYR B 136 ARG 0.007 0.000 ARG B1170 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 317 time to evaluate : 3.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 GLN cc_start: 0.7874 (mm-40) cc_final: 0.7359 (tm-30) REVERT: A 244 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.6544 (ppp) REVERT: A 681 ARG cc_start: 0.8489 (mtp85) cc_final: 0.8252 (mtp85) REVERT: A 738 TYR cc_start: 0.7319 (p90) cc_final: 0.7103 (p90) REVERT: A 792 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7016 (mt-10) REVERT: A 884 LYS cc_start: 0.8401 (mttt) cc_final: 0.7974 (mptp) REVERT: A 1015 LYS cc_start: 0.8388 (ttmm) cc_final: 0.7946 (tptp) REVERT: B 204 THR cc_start: 0.8612 (t) cc_final: 0.8231 (m) REVERT: B 792 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.6966 (mp0) REVERT: B 884 LYS cc_start: 0.8347 (mttt) cc_final: 0.7819 (mptt) REVERT: B 1015 LYS cc_start: 0.8324 (ttmm) cc_final: 0.7964 (tptp) REVERT: C 125 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8436 (tp) REVERT: C 244 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7014 (pp-130) REVERT: C 440 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.7992 (mp10) REVERT: C 790 SER cc_start: 0.8561 (OUTLIER) cc_final: 0.8325 (m) REVERT: C 792 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: C 1015 LYS cc_start: 0.8387 (ttmm) cc_final: 0.7968 (tptp) outliers start: 60 outliers final: 43 residues processed: 351 average time/residue: 1.1241 time to fit residues: 486.9891 Evaluate side-chains 356 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 305 time to evaluate : 3.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 792 GLU Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1198 MET Chi-restraints excluded: chain A residue 1221 CYS Chi-restraints excluded: chain A residue 1233 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 40 THR Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 569 ASP Chi-restraints excluded: chain B residue 706 ILE Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain B residue 1233 LEU Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain C residue 484 ASP Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 567 LYS Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain C residue 790 SER Chi-restraints excluded: chain C residue 792 GLU Chi-restraints excluded: chain C residue 839 SER Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 885 ASP Chi-restraints excluded: chain C residue 1175 LEU Chi-restraints excluded: chain C residue 1208 GLU Chi-restraints excluded: chain C residue 1233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 221 optimal weight: 2.9990 chunk 296 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 256 optimal weight: 0.4980 chunk 41 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 278 optimal weight: 3.9990 chunk 116 optimal weight: 8.9990 chunk 286 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 ASN A 482 ASN A 593 GLN B 27 ASN B 482 ASN ** B 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1019 ASN ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1019 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.141570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.117196 restraints weight = 29819.265| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.47 r_work: 0.3020 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29499 Z= 0.212 Angle : 0.559 9.921 40170 Z= 0.287 Chirality : 0.046 0.439 4848 Planarity : 0.004 0.038 5022 Dihedral : 6.052 65.563 6027 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.86 % Allowed : 12.30 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.14), residues: 3489 helix: 1.38 (0.20), residues: 768 sheet: -0.02 (0.17), residues: 795 loop : -0.14 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 188 HIS 0.004 0.001 HIS A 215 PHE 0.020 0.002 PHE B 889 TYR 0.015 0.001 TYR B 136 ARG 0.007 0.000 ARG B1170 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9303.13 seconds wall clock time: 167 minutes 41.43 seconds (10061.43 seconds total)