Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 05:09:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzk_0557/04_2023/6nzk_0557_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzk_0557/04_2023/6nzk_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_0557/04_2023/6nzk_0557.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzk_0557/04_2023/6nzk_0557.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzk_0557/04_2023/6nzk_0557_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzk_0557/04_2023/6nzk_0557_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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: 15.66, per 1000 atoms: 0.54 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: 14.03 Conformation dependent library (CDL) restraints added in 4.4 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: 4.97 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: 12.56 Time building geometry restraints manager: 14.94 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 - 17.70: 16059 17.70 - 35.40: 513 35.40 - 53.10: 108 53.10 - 70.80: 36 70.80 - 88.50: 21 Dihedral angle restraints: 16737 sinusoidal: 6432 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 16734 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: 3.120 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: 15.280 Check model and map are aligned: 0.410 Set scattering table: 0.260 Process input model: 78.470 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.430 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:12.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.800 ------------------------------------------------------------------------------- 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 : 10.375 88.503 9960 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 % 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 *********************** 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 : 3.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 1 residues processed: 561 average time/residue: 1.2207 time to fit residues: 820.7981 Evaluate side-chains 315 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 314 time to evaluate : 3.749 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 4.9492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 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 725 ASN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 HIS B 380 GLN B 387 ASN ** 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 725 ASN 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 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN C 581 GLN ** C 598 ASN ** 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: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 29499 Z= 0.272 Angle : 0.707 24.714 40170 Z= 0.360 Chirality : 0.050 0.482 4848 Planarity : 0.004 0.031 5022 Dihedral : 5.801 33.177 3822 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 2.58 % 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: 0.98 (0.19), residues: 759 sheet: 0.71 (0.17), residues: 792 loop : 0.23 (0.13), residues: 1938 *********************** 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 462 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 383 time to evaluate : 3.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 25 residues processed: 430 average time/residue: 1.1516 time to fit residues: 605.5353 Evaluate side-chains 336 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 311 time to evaluate : 3.309 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 13 residues processed: 12 average time/residue: 0.2811 time to fit residues: 10.6765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 177 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 265 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 319 optimal weight: 0.2980 chunk 344 optimal weight: 2.9990 chunk 284 optimal weight: 2.9990 chunk 316 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 256 optimal weight: 0.8980 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 183 HIS B 598 ASN B 641 GLN ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 HIS C 387 ASN C 482 ASN ** C 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 GLN ** C 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1019 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.084 29499 Z= 0.383 Angle : 0.709 22.571 40170 Z= 0.358 Chirality : 0.050 0.655 4848 Planarity : 0.004 0.038 5022 Dihedral : 5.798 31.444 3822 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer Outliers : 2.74 % 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: 0.27 (0.14), residues: 3489 helix: 0.84 (0.19), residues: 774 sheet: 0.17 (0.17), residues: 813 loop : 0.01 (0.13), residues: 1902 *********************** 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 431 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 347 time to evaluate : 3.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 84 outliers final: 43 residues processed: 391 average time/residue: 1.1485 time to fit residues: 550.3847 Evaluate side-chains 355 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 312 time to evaluate : 3.319 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 22 residues processed: 22 average time/residue: 0.5126 time to fit residues: 21.3476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 315 optimal weight: 0.6980 chunk 240 optimal weight: 1.9990 chunk 165 optimal weight: 6.9990 chunk 35 optimal weight: 0.0670 chunk 152 optimal weight: 2.9990 chunk 214 optimal weight: 0.9990 chunk 320 optimal weight: 0.7980 chunk 339 optimal weight: 0.6980 chunk 167 optimal weight: 0.6980 chunk 303 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 ** A 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 ASN ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1019 ASN B1036 ASN C 444 ASN C 456 ASN C 593 GLN C 641 GLN C 725 ASN C1058 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.086 29499 Z= 0.197 Angle : 0.591 20.336 40170 Z= 0.296 Chirality : 0.046 0.387 4848 Planarity : 0.004 0.036 5022 Dihedral : 5.297 32.083 3822 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer Outliers : 2.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.38 (0.14), residues: 3489 helix: 1.22 (0.20), residues: 765 sheet: 0.19 (0.17), residues: 795 loop : -0.03 (0.14), residues: 1929 *********************** 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 429 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 354 time to evaluate : 3.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 40 residues processed: 393 average time/residue: 1.0625 time to fit residues: 515.6806 Evaluate side-chains 360 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 320 time to evaluate : 3.336 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 21 residues processed: 19 average time/residue: 0.4797 time to fit residues: 18.4672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 282 optimal weight: 0.0970 chunk 192 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 252 optimal weight: 0.7980 chunk 139 optimal weight: 0.9980 chunk 289 optimal weight: 0.8980 chunk 234 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 chunk 304 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS ** 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 387 ASN B 482 ASN B 598 ASN B 736 ASN ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1019 ASN B1036 ASN ** C 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 29499 Z= 0.269 Angle : 0.617 18.977 40170 Z= 0.311 Chirality : 0.047 0.383 4848 Planarity : 0.004 0.035 5022 Dihedral : 5.338 30.038 3822 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 2.35 % 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: 0.28 (0.14), residues: 3489 helix: 1.16 (0.20), residues: 768 sheet: 0.08 (0.17), residues: 783 loop : -0.08 (0.14), residues: 1938 *********************** 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 404 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 332 time to evaluate : 3.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 47 residues processed: 372 average time/residue: 1.0912 time to fit residues: 504.4591 Evaluate side-chains 366 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 319 time to evaluate : 3.437 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 25 residues processed: 23 average time/residue: 0.4853 time to fit residues: 22.0158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 114 optimal weight: 0.9990 chunk 305 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 339 optimal weight: 0.5980 chunk 281 optimal weight: 3.9990 chunk 157 optimal weight: 0.8980 chunk 28 optimal weight: 0.0010 chunk 112 optimal weight: 0.0370 chunk 178 optimal weight: 2.9990 overall best weight: 0.5066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 ASN A 456 ASN A 482 ASN A 593 GLN A 840 GLN A1019 ASN B 257 ASN ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1019 ASN B1036 ASN B1104 GLN C 598 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 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= 0.179 Angle : 0.558 14.150 40170 Z= 0.284 Chirality : 0.045 0.376 4848 Planarity : 0.003 0.037 5022 Dihedral : 5.080 30.171 3822 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer Outliers : 1.79 % 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: 0.38 (0.14), residues: 3489 helix: 1.34 (0.20), residues: 768 sheet: 0.10 (0.17), residues: 795 loop : -0.04 (0.14), residues: 1926 *********************** 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 392 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 337 time to evaluate : 3.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 33 residues processed: 370 average time/residue: 1.1263 time to fit residues: 525.8318 Evaluate side-chains 340 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 307 time to evaluate : 3.350 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 21 residues processed: 12 average time/residue: 0.5089 time to fit residues: 13.8584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 327 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 285 optimal weight: 0.0040 chunk 189 optimal weight: 0.4980 chunk 338 optimal weight: 1.9990 chunk 211 optimal weight: 0.0670 chunk 206 optimal weight: 0.5980 chunk 156 optimal weight: 3.9990 overall best weight: 0.6332 ------------------------------------------------------------------------------- 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 482 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 B1036 ASN ** B1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2940 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= 0.202 Angle : 0.569 11.334 40170 Z= 0.290 Chirality : 0.046 0.428 4848 Planarity : 0.004 0.037 5022 Dihedral : 5.056 29.355 3822 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer Outliers : 1.66 % 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: 0.38 (0.14), residues: 3489 helix: 1.38 (0.20), residues: 768 sheet: 0.10 (0.17), residues: 795 loop : -0.05 (0.14), residues: 1926 *********************** 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 371 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 320 time to evaluate : 3.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 38 residues processed: 355 average time/residue: 1.1173 time to fit residues: 493.1858 Evaluate side-chains 346 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 308 time to evaluate : 3.255 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 25 residues processed: 13 average time/residue: 0.4596 time to fit residues: 13.5677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 209 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 215 optimal weight: 0.8980 chunk 230 optimal weight: 0.7980 chunk 167 optimal weight: 0.0370 chunk 31 optimal weight: 2.9990 chunk 265 optimal weight: 3.9990 overall best weight: 0.9060 ------------------------------------------------------------------------------- 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 444 ASN B 482 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 B1036 ASN C 482 ASN ** C 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 29499 Z= 0.255 Angle : 0.591 9.669 40170 Z= 0.302 Chirality : 0.046 0.481 4848 Planarity : 0.004 0.037 5022 Dihedral : 5.181 33.857 3822 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 2.02 % 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: 0.28 (0.14), residues: 3489 helix: 1.30 (0.20), residues: 768 sheet: -0.02 (0.17), residues: 825 loop : -0.09 (0.14), residues: 1896 *********************** 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 378 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 316 time to evaluate : 3.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 37 residues processed: 360 average time/residue: 1.1123 time to fit residues: 498.2200 Evaluate side-chains 353 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 316 time to evaluate : 3.048 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 26 residues processed: 11 average time/residue: 0.5047 time to fit residues: 13.0545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0570 chunk 295 optimal weight: 0.9990 chunk 315 optimal weight: 0.6980 chunk 189 optimal weight: 0.6980 chunk 137 optimal weight: 0.6980 chunk 247 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 284 optimal weight: 4.9990 chunk 298 optimal weight: 0.7980 chunk 314 optimal weight: 2.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 B 387 ASN ** B 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1019 ASN B1036 ASN ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 29499 Z= 0.193 Angle : 0.567 9.682 40170 Z= 0.289 Chirality : 0.045 0.447 4848 Planarity : 0.004 0.039 5022 Dihedral : 5.052 36.470 3822 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 1.47 % 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: 1.40 (0.20), residues: 768 sheet: 0.10 (0.18), residues: 774 loop : -0.14 (0.14), residues: 1947 *********************** 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 365 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 320 time to evaluate : 3.732 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 34 residues processed: 355 average time/residue: 1.1087 time to fit residues: 488.6779 Evaluate side-chains 338 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 304 time to evaluate : 4.046 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 29 residues processed: 5 average time/residue: 0.3254 time to fit residues: 7.2818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 207 optimal weight: 5.9990 chunk 333 optimal weight: 3.9990 chunk 203 optimal weight: 0.0980 chunk 158 optimal weight: 0.0870 chunk 231 optimal weight: 0.8980 chunk 349 optimal weight: 0.8980 chunk 321 optimal weight: 0.8980 chunk 278 optimal weight: 4.9990 chunk 28 optimal weight: 0.0000 chunk 215 optimal weight: 0.9980 chunk 170 optimal weight: 0.9990 overall best weight: 0.3962 ------------------------------------------------------------------------------- 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 B 482 ASN B 606 HIS ** B 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1019 ASN B1036 ASN ** C 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 29499 Z= 0.158 Angle : 0.535 9.539 40170 Z= 0.273 Chirality : 0.044 0.386 4848 Planarity : 0.003 0.040 5022 Dihedral : 4.857 37.637 3822 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 1.24 % 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: 0.39 (0.14), residues: 3489 helix: 1.55 (0.20), residues: 765 sheet: 0.13 (0.18), residues: 774 loop : -0.14 (0.14), residues: 1950 ********************** 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 369 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 331 time to evaluate : 3.216 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 29 residues processed: 362 average time/residue: 1.0705 time to fit residues: 485.6785 Evaluate side-chains 337 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 308 time to evaluate : 3.292 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 26 residues processed: 3 average time/residue: 0.3469 time to fit residues: 6.2607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 221 optimal weight: 0.6980 chunk 296 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 256 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 278 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 286 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 B 482 ASN ** B 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1019 ASN B1036 ASN ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 ASN C 482 ASN ** C 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1092 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.140088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.115594 restraints weight = 29994.962| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.43 r_work: 0.3014 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 29499 Z= 0.286 Angle : 0.616 11.226 40170 Z= 0.314 Chirality : 0.047 0.492 4848 Planarity : 0.004 0.037 5022 Dihedral : 5.162 38.083 3822 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 1.53 % 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: 0.22 (0.14), residues: 3489 helix: 1.30 (0.20), residues: 768 sheet: -0.10 (0.17), residues: 813 loop : -0.13 (0.14), residues: 1908 =============================================================================== Job complete usr+sys time: 9104.41 seconds wall clock time: 164 minutes 4.99 seconds (9844.99 seconds total)