Starting phenix.real_space_refine (version: dev) on Thu Apr 7 19:48:29 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzk_0557/04_2022/6nzk_0557_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzk_0557/04_2022/6nzk_0557.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzk_0557/04_2022/6nzk_0557_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzk_0557/04_2022/6nzk_0557_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzk_0557/04_2022/6nzk_0557_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzk_0557/04_2022/6nzk_0557.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzk_0557/04_2022/6nzk_0557.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzk_0557/04_2022/6nzk_0557_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzk_0557/04_2022/6nzk_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 Convert atoms to be neutral 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-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 29268 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 9150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9150 Classifications: {'peptide': 1175} Link IDs: {'PTRANS': 46, 'TRANS': 1124, 'PCIS': 4} 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: {'PTRANS': 46, 'TRANS': 1124, 'PCIS': 4} 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: {'PTRANS': 46, 'TRANS': 1124, 'PCIS': 4} Chain breaks: 5 Chain: "A" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 474 Unusual residues: {'BMA': 7, 'NAG': 25, 'MJJ': 1, 'MAN': 2} Classifications: {'undetermined': 35} Link IDs: {None: 34} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 34 Chain: "B" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 474 Unusual residues: {'BMA': 7, 'NAG': 25, 'MJJ': 1, 'MAN': 2} Classifications: {'undetermined': 35} Link IDs: {None: 34} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 34 Chain: "C" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 474 Unusual residues: {'BMA': 7, 'NAG': 25, 'MJJ': 1, 'MAN': 2} Classifications: {'undetermined': 35} Link IDs: {None: 34} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 34 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: 16.41, per 1000 atoms: 0.56 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 A2226 " - " MAN A2227 " " BMA A2741 " - " MAN A2742 " " BMA B2226 " - " MAN B2227 " " BMA B2741 " - " MAN B2742 " " BMA C2226 " - " MAN C2227 " " BMA C2741 " - " MAN C2742 " BETA1-4 " NAG A2133 " - " NAG A2134 " " NAG A2134 " - " BMA A2135 " " NAG A2202 " - " NAG A2203 " " NAG A2203 " - " BMA A2204 " " NAG A2224 " - " NAG A2225 " " NAG A2225 " - " BMA A2226 " " NAG A2371 " - " NAG A2372 " " NAG A2372 " - " BMA A2373 " " NAG A2449 " - " NAG A2450 " " NAG A2450 " - " BMA A2451 " " NAG A2648 " - " NAG A2649 " " NAG A2739 " - " NAG A2740 " " NAG A2740 " - " BMA A2741 " " NAG A2788 " - " NAG A2789 " " NAG A2937 " - " NAG A2938 " " NAG A3194 " - " NAG A3195 " " NAG A3195 " - " BMA A3196 " " NAG B2133 " - " NAG B2134 " " NAG B2134 " - " BMA B2135 " " NAG B2202 " - " NAG B2203 " " NAG B2203 " - " BMA B2204 " " NAG B2224 " - " NAG B2225 " " NAG B2225 " - " BMA B2226 " " NAG B2371 " - " NAG B2372 " " NAG B2372 " - " BMA B2373 " " NAG B2449 " - " NAG B2450 " " NAG B2450 " - " BMA B2451 " " NAG B2648 " - " NAG B2649 " " NAG B2739 " - " NAG B2740 " " NAG B2740 " - " BMA B2741 " " NAG B2788 " - " NAG B2789 " " NAG B2937 " - " NAG B2938 " " NAG B3194 " - " NAG B3195 " " NAG B3195 " - " BMA B3196 " " NAG C2133 " - " NAG C2134 " " NAG C2134 " - " BMA C2135 " " NAG C2202 " - " NAG C2203 " " NAG C2203 " - " BMA C2204 " " NAG C2224 " - " NAG C2225 " " NAG C2225 " - " BMA C2226 " " NAG C2371 " - " NAG C2372 " " NAG C2372 " - " BMA C2373 " " NAG C2449 " - " NAG C2450 " " NAG C2450 " - " BMA C2451 " " NAG C2648 " - " NAG C2649 " " NAG C2739 " - " NAG C2740 " " NAG C2740 " - " BMA C2741 " " NAG C2788 " - " NAG C2789 " " NAG C2937 " - " NAG C2938 " " NAG C3194 " - " NAG C3195 " " NAG C3195 " - " BMA C3196 " NAG-ASN " NAG A2133 " - " ASN A 133 " " NAG A2202 " - " ASN A 202 " " NAG A2224 " - " ASN A1224 " " NAG A2371 " - " ASN A 371 " " NAG A2449 " - " ASN A 449 " " NAG A2648 " - " ASN A 648 " " NAG A2739 " - " ASN A 739 " " NAG A2788 " - " ASN A 788 " " NAG A2937 " - " ASN A 937 " " NAG A3194 " - " ASN A1194 " " 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 B2133 " - " ASN B 133 " " NAG B2202 " - " ASN B 202 " " NAG B2224 " - " ASN B1224 " " NAG B2371 " - " ASN B 371 " " NAG B2449 " - " ASN B 449 " " NAG B2648 " - " ASN B 648 " " NAG B2739 " - " ASN B 739 " " NAG B2788 " - " ASN B 788 " " NAG B2937 " - " ASN B 937 " " NAG B3194 " - " ASN B1194 " " 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 C2133 " - " ASN C 133 " " NAG C2202 " - " ASN C 202 " " NAG C2224 " - " ASN C1224 " " NAG C2371 " - " ASN C 371 " " NAG C2449 " - " ASN C 449 " " NAG C2648 " - " ASN C 648 " " NAG C2739 " - " ASN C 739 " " NAG C2788 " - " ASN C 788 " " NAG C2937 " - " ASN C 937 " " NAG C3194 " - " ASN C1194 " " 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 " Time building additional restraints: 14.57 Conformation dependent library (CDL) restraints added in 4.2 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: 5.11 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: 12.07 Time building geometry restraints manager: 15.24 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: 16827 17.70 - 35.40: 543 35.40 - 53.10: 108 53.10 - 70.80: 36 70.80 - 88.50: 21 Dihedral angle restraints: 17535 sinusoidal: 7230 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 17532 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.008: 4830 1.008 - 2.016: 0 2.016 - 3.024: 0 3.024 - 4.032: 0 4.032 - 5.040: 3 Chirality restraints: 4833 Sorted by residual: chirality pdb=" C2 MJJ B9999 " pdb=" C1 MJJ B9999 " pdb=" C3 MJJ B9999 " pdb=" O6 MJJ B9999 " both_signs ideal model delta sigma weight residual False 2.56 -2.48 5.04 2.00e-01 2.50e+01 6.35e+02 chirality pdb=" C2 MJJ C9999 " pdb=" C1 MJJ C9999 " pdb=" C3 MJJ C9999 " pdb=" O6 MJJ C9999 " both_signs ideal model delta sigma weight residual False 2.56 -2.48 5.04 2.00e-01 2.50e+01 6.35e+02 chirality pdb=" C2 MJJ A9999 " pdb=" C1 MJJ A9999 " pdb=" C3 MJJ A9999 " pdb=" O6 MJJ A9999 " both_signs ideal model delta sigma weight residual False 2.56 -2.48 5.04 2.00e-01 2.50e+01 6.34e+02 ... (remaining 4830 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 B2648 " -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 A2648 " 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 C2648 " -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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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. 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: 5.120 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: 15.960 Check model and map are aligned: 0.450 Convert atoms to be neutral: 0.250 Process input model: 77.770 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:10.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 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= 1.648 Angle : 1.797 15.944 40170 Z= 1.215 Chirality : 0.169 5.040 4833 Planarity : 0.009 0.047 5022 Dihedral : 10.374 88.503 10758 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 : 3.403 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: 1.2171 time to fit residues: 822.2973 Evaluate side-chains 314 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 313 time to evaluate : 3.297 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 4.2537 ------------------------------------------------------------------------------- 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: 1.9990 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 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 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: 0.8532 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 29499 Z= 0.290 Angle : 0.781 24.123 40170 Z= 0.389 Chirality : 0.073 2.111 4833 Planarity : 0.004 0.033 5022 Dihedral : 6.572 40.741 4620 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.54 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: 0.97 (0.19), residues: 759 sheet: 0.70 (0.17), residues: 795 loop : 0.24 (0.13), residues: 1935 *********************** 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 458 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 379 time to evaluate : 3.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 29 residues processed: 425 average time/residue: 1.0729 time to fit residues: 560.8644 Evaluate side-chains 339 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 310 time to evaluate : 3.408 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 16 residues processed: 13 average time/residue: 0.2917 time to fit residues: 11.4053 ------------------------------------------------------------------------------- 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: 3.9990 chunk 98 optimal weight: 2.9990 chunk 265 optimal weight: 2.9990 chunk 217 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 319 optimal weight: 3.9990 chunk 344 optimal weight: 1.9990 chunk 284 optimal weight: 1.9990 chunk 316 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 256 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN A 387 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 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1104 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 850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1019 ASN C1092 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.077 29499 Z= 0.506 Angle : 0.847 24.101 40170 Z= 0.418 Chirality : 0.074 2.018 4833 Planarity : 0.005 0.056 5022 Dihedral : 6.901 41.288 4620 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer Outliers : 2.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.03 (0.13), residues: 3489 helix: 0.57 (0.19), residues: 774 sheet: 0.08 (0.17), residues: 816 loop : -0.13 (0.13), residues: 1899 *********************** 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 434 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 343 time to evaluate : 3.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 52 residues processed: 393 average time/residue: 1.0929 time to fit residues: 527.7083 Evaluate side-chains 357 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 305 time to evaluate : 3.460 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 52 outliers final: 30 residues processed: 24 average time/residue: 0.4640 time to fit residues: 21.1782 ------------------------------------------------------------------------------- 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: 0.9980 chunk 240 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 214 optimal weight: 3.9990 chunk 320 optimal weight: 1.9990 chunk 339 optimal weight: 0.5980 chunk 167 optimal weight: 0.9980 chunk 303 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 890 ASN B 257 ASN ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1019 ASN B1104 GLN C 444 ASN C 456 ASN C 593 GLN C 598 ASN C 641 GLN C 850 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.095 29499 Z= 0.270 Angle : 0.730 23.846 40170 Z= 0.351 Chirality : 0.071 2.014 4833 Planarity : 0.004 0.037 5022 Dihedral : 6.524 41.915 4620 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer Outliers : 3.00 % 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: 0.15 (0.14), residues: 3489 helix: 0.96 (0.19), residues: 768 sheet: 0.04 (0.17), residues: 798 loop : -0.14 (0.14), residues: 1923 *********************** 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 432 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 340 time to evaluate : 3.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 92 outliers final: 47 residues processed: 395 average time/residue: 1.1017 time to fit residues: 537.9745 Evaluate side-chains 364 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 317 time to evaluate : 3.195 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 47 outliers final: 27 residues processed: 21 average time/residue: 0.4000 time to fit residues: 17.9529 ------------------------------------------------------------------------------- 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: 0.9980 chunk 192 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 252 optimal weight: 0.7980 chunk 139 optimal weight: 0.5980 chunk 289 optimal weight: 1.9990 chunk 234 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 304 optimal weight: 0.0270 chunk 85 optimal weight: 3.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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 A 606 HIS ** A 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 ASN B 257 ASN B 482 ASN B 641 GLN ** B 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1019 ASN B1092 ASN C 482 ASN C 598 ASN C 725 ASN C1058 GLN C1104 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 29499 Z= 0.217 Angle : 0.700 23.086 40170 Z= 0.334 Chirality : 0.068 2.000 4833 Planarity : 0.004 0.038 5022 Dihedral : 6.262 41.817 4620 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 2.51 % 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: 0.26 (0.14), residues: 3489 helix: 1.18 (0.20), residues: 768 sheet: 0.05 (0.17), residues: 798 loop : -0.09 (0.14), residues: 1923 *********************** 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 415 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 338 time to evaluate : 3.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 45 residues processed: 385 average time/residue: 1.0381 time to fit residues: 497.0469 Evaluate side-chains 355 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 310 time to evaluate : 3.166 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 27 residues processed: 18 average time/residue: 0.3929 time to fit residues: 15.2757 ------------------------------------------------------------------------------- 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: 0.6980 chunk 305 optimal weight: 0.2980 chunk 67 optimal weight: 5.9990 chunk 199 optimal weight: 2.9990 chunk 83 optimal weight: 0.4980 chunk 339 optimal weight: 0.5980 chunk 281 optimal weight: 0.4980 chunk 157 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 112 optimal weight: 0.5980 chunk 178 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 387 ASN ** B 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1019 ASN C 598 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2887 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= 0.189 Angle : 0.675 23.300 40170 Z= 0.321 Chirality : 0.067 1.982 4833 Planarity : 0.004 0.049 5022 Dihedral : 6.049 41.550 4620 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 2.05 % 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: 0.35 (0.14), residues: 3489 helix: 1.34 (0.20), residues: 768 sheet: 0.07 (0.17), residues: 798 loop : -0.06 (0.14), residues: 1923 *********************** 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 398 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 335 time to evaluate : 3.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 42 residues processed: 378 average time/residue: 1.0456 time to fit residues: 498.4866 Evaluate side-chains 353 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 311 time to evaluate : 3.234 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 42 outliers final: 30 residues processed: 13 average time/residue: 0.6069 time to fit residues: 15.6403 ------------------------------------------------------------------------------- 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: 1.9990 chunk 38 optimal weight: 0.0770 chunk 193 optimal weight: 0.7980 chunk 248 optimal weight: 0.9990 chunk 192 optimal weight: 2.9990 chunk 285 optimal weight: 1.9990 chunk 189 optimal weight: 0.0870 chunk 338 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 overall best weight: 0.7920 ------------------------------------------------------------------------------- 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 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1019 ASN C 482 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.096 29499 Z= 0.244 Angle : 0.703 23.349 40170 Z= 0.342 Chirality : 0.069 1.970 4833 Planarity : 0.004 0.051 5022 Dihedral : 6.088 41.469 4620 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.03 % 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: 0.30 (0.14), residues: 3489 helix: 1.31 (0.20), residues: 768 sheet: 0.01 (0.17), residues: 786 loop : -0.09 (0.14), residues: 1935 *********************** 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 391 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 325 time to evaluate : 3.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 44 residues processed: 371 average time/residue: 1.1171 time to fit residues: 515.0256 Evaluate side-chains 364 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 320 time to evaluate : 3.444 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 31 residues processed: 15 average time/residue: 0.4842 time to fit residues: 15.5105 ------------------------------------------------------------------------------- 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: 0.5980 chunk 135 optimal weight: 0.8980 chunk 202 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 215 optimal weight: 0.9980 chunk 230 optimal weight: 0.8980 chunk 167 optimal weight: 4.9990 chunk 31 optimal weight: 0.0670 chunk 265 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 156 GLN A 482 ASN A 593 GLN B 444 ASN B 482 ASN ** B 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1019 ASN ** C 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.119 29499 Z= 0.211 Angle : 0.692 23.461 40170 Z= 0.335 Chirality : 0.068 1.967 4833 Planarity : 0.004 0.039 5022 Dihedral : 6.420 113.935 4620 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 2.12 % 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: 0.32 (0.14), residues: 3489 helix: 1.40 (0.20), residues: 768 sheet: 0.00 (0.17), residues: 807 loop : -0.10 (0.14), residues: 1914 *********************** 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 387 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 322 time to evaluate : 3.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 42 residues processed: 371 average time/residue: 1.0311 time to fit residues: 478.9799 Evaluate side-chains 353 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 311 time to evaluate : 3.346 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 42 outliers final: 32 residues processed: 11 average time/residue: 0.5610 time to fit residues: 13.6069 ------------------------------------------------------------------------------- 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: 0.6980 chunk 324 optimal weight: 0.7980 chunk 295 optimal weight: 3.9990 chunk 315 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 247 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 284 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 chunk 314 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1019 ASN ** C 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.294 29499 Z= 0.327 Angle : 0.754 23.525 40170 Z= 0.379 Chirality : 0.069 1.956 4833 Planarity : 0.004 0.042 5022 Dihedral : 6.556 112.488 4620 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 1.89 % 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: 0.17 (0.14), residues: 3489 helix: 1.24 (0.19), residues: 768 sheet: -0.15 (0.17), residues: 816 loop : -0.15 (0.14), residues: 1905 *********************** 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: 58 poor density : 307 time to evaluate : 3.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 42 residues processed: 349 average time/residue: 1.0750 time to fit residues: 462.6683 Evaluate side-chains 346 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 304 time to evaluate : 3.225 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 33 residues processed: 12 average time/residue: 0.4847 time to fit residues: 13.0038 ------------------------------------------------------------------------------- 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: 0.6980 chunk 333 optimal weight: 4.9990 chunk 203 optimal weight: 0.9990 chunk 158 optimal weight: 0.3980 chunk 231 optimal weight: 0.9990 chunk 349 optimal weight: 0.9990 chunk 321 optimal weight: 0.6980 chunk 278 optimal weight: 3.9990 chunk 28 optimal weight: 0.0980 chunk 215 optimal weight: 0.9990 chunk 170 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1019 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.381 29499 Z= 0.260 Angle : 0.778 48.706 40170 Z= 0.381 Chirality : 0.068 1.963 4833 Planarity : 0.004 0.111 5022 Dihedral : 6.418 112.101 4620 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 1.21 % 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: 0.22 (0.14), residues: 3489 helix: 1.37 (0.20), residues: 768 sheet: -0.14 (0.17), residues: 828 loop : -0.14 (0.14), residues: 1893 ********************** 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 353 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 316 time to evaluate : 3.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 33 residues processed: 348 average time/residue: 1.0573 time to fit residues: 459.1863 Evaluate side-chains 341 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 308 time to evaluate : 3.152 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 31 residues processed: 4 average time/residue: 0.3913 time to fit residues: 6.5279 ------------------------------------------------------------------------------- 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: 0.5980 chunk 296 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 256 optimal weight: 0.9980 chunk 41 optimal weight: 0.4980 chunk 77 optimal weight: 0.6980 chunk 278 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 286 optimal weight: 4.9990 chunk 35 optimal weight: 0.3980 chunk 51 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 ASN A 593 GLN B 482 ASN ** B 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1019 ASN C 482 ASN ** C 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.142170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.117830 restraints weight = 29837.101| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.45 r_work: 0.3176 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 1.38 restraints_weight: 0.2500 r_work: 0.3114 rms_B_bonded: 1.69 restraints_weight: 0.1250 r_work: 0.3056 rms_B_bonded: 2.35 restraints_weight: 0.0625 r_work: 0.2953 rms_B_bonded: 3.76 restraints_weight: 0.0312 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.488 29499 Z= 0.295 Angle : 0.763 37.119 40170 Z= 0.383 Chirality : 0.067 1.953 4833 Planarity : 0.004 0.056 5022 Dihedral : 6.326 112.043 4620 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer Outliers : 1.44 % Cbeta Deviations : 0.03 % 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: 0.23 (0.14), residues: 3489 helix: 1.43 (0.20), residues: 765 sheet: -0.08 (0.17), residues: 798 loop : -0.19 (0.14), residues: 1926 =============================================================================== Job complete usr+sys time: 8238.45 seconds wall clock time: 148 minutes 54.88 seconds (8934.88 seconds total)