Starting phenix.real_space_refine (version: dev) on Mon Feb 27 08:12:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbx_24991/02_2023/7sbx_24991_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbx_24991/02_2023/7sbx_24991.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbx_24991/02_2023/7sbx_24991.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbx_24991/02_2023/7sbx_24991.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbx_24991/02_2023/7sbx_24991_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbx_24991/02_2023/7sbx_24991_updated.pdb" } resolution = 3.0 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= 0.000 sd= 0.004 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 Process input model Symmetric amino acids flipped Residue "J TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 223": "OE1" <-> "OE2" Residue "J PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 726": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 737": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 804": "OE1" <-> "OE2" Residue "J PHE 805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 843": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 930": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 934": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 980": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 1020": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 1031": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 1063": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 1151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 1158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 1188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 1189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 320": "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 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 583": "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 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 726": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 737": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 843": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 930": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 934": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 942": "OE1" <-> "OE2" Residue "A TYR 952": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 980": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 992": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1020": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1031": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1063": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 320": "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 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 583": "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 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 726": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 737": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 843": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 930": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 934": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 952": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 980": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 992": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1020": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1031": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1063": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1229": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 29599 Number of models: 1 Model: "" Number of chains: 27 Chain: "J" Number of atoms: 9152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1176, 9152 Classifications: {'peptide': 1176} Link IDs: {'PTRANS': 51, 'TRANS': 1124} Chain breaks: 6 Chain: "A" Number of atoms: 9204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1184, 9204 Classifications: {'peptide': 1184} Link IDs: {'PTRANS': 52, 'TRANS': 1131} Chain breaks: 5 Chain: "B" Number of atoms: 9197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1183, 9197 Classifications: {'peptide': 1183} Link IDs: {'PTRANS': 52, 'TRANS': 1130} Chain breaks: 5 Chain: "H" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 605 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 121} Link IDs: {'TRANS': 120} Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 121 Planarities with less than four sites: {'UNK:plan-1': 121} Unresolved non-hydrogen planarities: 121 Chain: "L" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 525 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'TRANS': 104} Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 315 Unresolved non-hydrogen dihedrals: 105 Planarities with less than four sites: {'UNK:plan-1': 105} Unresolved non-hydrogen planarities: 105 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 144 Unusual residues: {'8Z9': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 148 Unusual residues: {'8Z9': 2, 'NAG': 8} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 17.22, per 1000 atoms: 0.58 Number of scatterers: 29599 At special positions: 0 Unit cell: (150.38, 149.35, 197.76, 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 189 16.00 O 5814 8.00 N 4816 7.00 C 18780 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=63, symmetry=0 Simple disulfide: pdb=" SG CYS J 21 " - pdb=" SG CYS J 173 " distance=2.04 Simple disulfide: pdb=" SG CYS J 168 " - pdb=" SG CYS J 201 " distance=2.03 Simple disulfide: pdb=" SG CYS J 180 " - pdb=" SG CYS J 260 " distance=2.03 Simple disulfide: pdb=" SG CYS J 298 " - pdb=" SG CYS J 308 " distance=2.03 Simple disulfide: pdb=" SG CYS J 343 " - pdb=" SG CYS J 368 " distance=2.11 Simple disulfide: pdb=" SG CYS J 386 " - pdb=" SG CYS J 439 " distance=2.04 Simple disulfide: pdb=" SG CYS J 398 " - pdb=" SG CYS J 614 " distance=2.08 Simple disulfide: pdb=" SG CYS J 491 " - pdb=" SG CYS J 561 " distance=2.10 Simple disulfide: pdb=" SG CYS J 499 " - pdb=" SG CYS J 522 " distance=2.03 Simple disulfide: pdb=" SG CYS J 501 " - pdb=" SG CYS J 576 " distance=2.02 Simple disulfide: pdb=" SG CYS J 535 " - pdb=" SG CYS J 548 " distance=2.03 Simple disulfide: pdb=" SG CYS J 571 " - pdb=" SG CYS J 578 " distance=2.03 Simple disulfide: pdb=" SG CYS J 591 " - pdb=" SG CYS J 597 " distance=2.04 Simple disulfide: pdb=" SG CYS J 630 " - pdb=" SG CYS J 683 " distance=2.05 Simple disulfide: pdb=" SG CYS J 708 " - pdb=" SG CYS J 732 " distance=2.04 Simple disulfide: pdb=" SG CYS J 747 " - pdb=" SG CYS J 756 " distance=2.04 Simple disulfide: pdb=" SG CYS J 825 " - pdb=" SG CYS J 847 " distance=2.13 Simple disulfide: pdb=" SG CYS J 830 " - pdb=" SG CYS J 836 " distance=2.03 Simple disulfide: pdb=" SG CYS J 937 " - pdb=" SG CYS J 948 " distance=2.06 Simple disulfide: pdb=" SG CYS J1125 " - pdb=" SG CYS J1136 " distance=2.02 Simple disulfide: pdb=" SG CYS J1175 " - pdb=" SG CYS J1220 " distance=2.03 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 173 " distance=2.03 Simple disulfide: pdb=" SG CYS A 168 " - pdb=" SG CYS A 201 " distance=2.04 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 260 " distance=2.04 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 368 " distance=2.09 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 398 " - pdb=" SG CYS A 614 " distance=2.05 Simple disulfide: pdb=" SG CYS A 491 " - pdb=" SG CYS A 561 " distance=2.03 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=1.70 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 548 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 683 " distance=2.05 Simple disulfide: pdb=" SG CYS A 708 " - pdb=" SG CYS A 732 " distance=2.05 Simple disulfide: pdb=" SG CYS A 747 " - pdb=" SG CYS A 756 " distance=2.04 Simple disulfide: pdb=" SG CYS A 825 " - pdb=" SG CYS A 847 " distance=2.12 Simple disulfide: pdb=" SG CYS A 830 " - pdb=" SG CYS A 836 " distance=2.03 Simple disulfide: pdb=" SG CYS A 937 " - pdb=" SG CYS A 948 " distance=2.09 Simple disulfide: pdb=" SG CYS A1125 " - pdb=" SG CYS A1136 " distance=2.01 Simple disulfide: pdb=" SG CYS A1175 " - pdb=" SG CYS A1220 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 173 " distance=2.04 Simple disulfide: pdb=" SG CYS B 168 " - pdb=" SG CYS B 201 " distance=2.04 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 260 " distance=2.04 Simple disulfide: pdb=" SG CYS B 298 " - pdb=" SG CYS B 308 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 368 " distance=2.08 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 439 " distance=2.03 Simple disulfide: pdb=" SG CYS B 398 " - pdb=" SG CYS B 614 " distance=2.08 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=2.03 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=2.05 Simple disulfide: pdb=" SG CYS B 630 " - pdb=" SG CYS B 683 " distance=2.06 Simple disulfide: pdb=" SG CYS B 708 " - pdb=" SG CYS B 732 " distance=2.05 Simple disulfide: pdb=" SG CYS B 747 " - pdb=" SG CYS B 756 " distance=2.04 Simple disulfide: pdb=" SG CYS B 825 " - pdb=" SG CYS B 847 " distance=2.02 Simple disulfide: pdb=" SG CYS B 830 " - pdb=" SG CYS B 836 " distance=2.04 Simple disulfide: pdb=" SG CYS B 937 " - pdb=" SG CYS B 948 " distance=2.07 Simple disulfide: pdb=" SG CYS B1125 " - pdb=" SG CYS B1136 " distance=2.02 Simple disulfide: pdb=" SG CYS B1175 " - pdb=" SG CYS B1220 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1401 " - " ASN A 212 " " NAG A1402 " - " ASN A 713 " " NAG A1403 " - " ASN A 787 " " NAG A1404 " - " ASN A 936 " " NAG A1405 " - " ASN A 695 " " NAG A1406 " - " ASN A 648 " " NAG A1407 " - " ASN A 449 " " NAG A1408 " - " ASN A1223 " " NAG B1401 " - " ASN B 212 " " NAG B1402 " - " ASN B 713 " " NAG B1403 " - " ASN B 787 " " NAG B1404 " - " ASN B 695 " " NAG B1405 " - " ASN B 648 " " NAG C 1 " - " ASN J 137 " " NAG D 1 " - " ASN J 371 " " NAG E 1 " - " ASN J 738 " " NAG F 1 " - " ASN J1193 " " NAG G 1 " - " ASN J 206 " " NAG I 1 " - " ASN A 137 " " NAG J1401 " - " ASN J 212 " " NAG J1402 " - " ASN J 449 " " NAG J1403 " - " ASN J 713 " " NAG J1404 " - " ASN J 787 " " NAG J1405 " - " ASN J 936 " " NAG J1406 " - " ASN J 675 " " NAG J1407 " - " ASN J 695 " " NAG J1408 " - " ASN J 648 " " NAG J1409 " - " ASN J 63 " " NAG K 1 " - " ASN A 371 " " NAG M 1 " - " ASN A 738 " " NAG N 1 " - " ASN A1193 " " NAG O 1 " - " ASN A 206 " " NAG P 1 " - " ASN A 675 " " NAG Q 1 " - " ASN B 137 " " NAG R 1 " - " ASN B 371 " " NAG S 1 " - " ASN B 449 " " NAG T 1 " - " ASN B 738 " " NAG U 1 " - " ASN B 936 " " NAG V 1 " - " ASN B1193 " " NAG W 1 " - " ASN B 206 " " NAG X 1 " - " ASN B 675 " Time building additional restraints: 12.72 Conformation dependent library (CDL) restraints added in 4.1 seconds 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7066 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 86 helices and 59 sheets defined 23.0% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.65 Creating SS restraints... Processing helix chain 'J' and resid 264 through 266 No H-bonds generated for 'chain 'J' and resid 264 through 266' Processing helix chain 'J' and resid 302 through 309 Processing helix chain 'J' and resid 345 through 349 Processing helix chain 'J' and resid 357 through 359 No H-bonds generated for 'chain 'J' and resid 357 through 359' Processing helix chain 'J' and resid 372 through 377 removed outlier: 4.502A pdb=" N SER J 377 " --> pdb=" O SER J 373 " (cutoff:3.500A) Processing helix chain 'J' and resid 391 through 393 No H-bonds generated for 'chain 'J' and resid 391 through 393' Processing helix chain 'J' and resid 414 through 417 Processing helix chain 'J' and resid 425 through 428 No H-bonds generated for 'chain 'J' and resid 425 through 428' Processing helix chain 'J' and resid 447 through 449 No H-bonds generated for 'chain 'J' and resid 447 through 449' Processing helix chain 'J' and resid 459 through 464 removed outlier: 3.917A pdb=" N PHE J 464 " --> pdb=" O TRP J 460 " (cutoff:3.500A) Processing helix chain 'J' and resid 468 through 471 No H-bonds generated for 'chain 'J' and resid 468 through 471' Processing helix chain 'J' and resid 539 through 541 No H-bonds generated for 'chain 'J' and resid 539 through 541' Processing helix chain 'J' and resid 568 through 570 No H-bonds generated for 'chain 'J' and resid 568 through 570' Processing helix chain 'J' and resid 580 through 582 No H-bonds generated for 'chain 'J' and resid 580 through 582' Processing helix chain 'J' and resid 708 through 713 Processing helix chain 'J' and resid 825 through 829 Processing helix chain 'J' and resid 834 through 873 removed outlier: 3.598A pdb=" N VAL J 841 " --> pdb=" O LYS J 837 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLU J 842 " --> pdb=" O SER J 838 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N TYR J 843 " --> pdb=" O GLN J 839 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N SER J 845 " --> pdb=" O VAL J 841 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N PHE J 846 " --> pdb=" O GLU J 842 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS J 847 " --> pdb=" O TYR J 843 " (cutoff:3.500A) Processing helix chain 'J' and resid 880 through 883 Processing helix chain 'J' and resid 914 through 921 Processing helix chain 'J' and resid 927 through 936 removed outlier: 3.722A pdb=" N ASN J 936 " --> pdb=" O ALA J 932 " (cutoff:3.500A) Processing helix chain 'J' and resid 946 through 952 Processing helix chain 'J' and resid 964 through 979 removed outlier: 4.292A pdb=" N SER J 978 " --> pdb=" O ALA J 974 " (cutoff:3.500A) Processing helix chain 'J' and resid 984 through 986 No H-bonds generated for 'chain 'J' and resid 984 through 986' Processing helix chain 'J' and resid 991 through 1002 removed outlier: 3.761A pdb=" N LEU J1002 " --> pdb=" O ARG J 998 " (cutoff:3.500A) Processing helix chain 'J' and resid 1006 through 1030 removed outlier: 3.939A pdb=" N GLN J1013 " --> pdb=" O LEU J1009 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LYS J1014 " --> pdb=" O SER J1010 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU J1015 " --> pdb=" O GLN J1011 " (cutoff:3.500A) Processing helix chain 'J' and resid 1036 through 1060 removed outlier: 4.095A pdb=" N ALA J1047 " --> pdb=" O ALA J1043 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASN J1048 " --> pdb=" O VAL J1044 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N GLU J1050 " --> pdb=" O ASN J1046 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN J1058 " --> pdb=" O ASN J1054 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU J1059 " --> pdb=" O LEU J1055 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N SER J1060 " --> pdb=" O LEU J1056 " (cutoff:3.500A) Processing helix chain 'J' and resid 1070 through 1076 Processing helix chain 'J' and resid 1079 through 1124 removed outlier: 4.781A pdb=" N ALA J1084 " --> pdb=" O PRO J1080 " (cutoff:3.500A) Processing helix chain 'J' and resid 1211 through 1213 No H-bonds generated for 'chain 'J' and resid 1211 through 1213' Processing helix chain 'A' and resid 92 through 95 Processing helix chain 'A' and resid 264 through 266 No H-bonds generated for 'chain 'A' and resid 264 through 266' Processing helix chain 'A' and resid 302 through 309 Processing helix chain 'A' and resid 345 through 349 Processing helix chain 'A' and resid 357 through 359 No H-bonds generated for 'chain 'A' and resid 357 through 359' Processing helix chain 'A' and resid 372 through 378 removed outlier: 5.096A pdb=" N SER A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A 378 " --> pdb=" O SER A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 393 No H-bonds generated for 'chain 'A' and resid 391 through 393' Processing helix chain 'A' and resid 414 through 417 Processing helix chain 'A' and resid 425 through 428 No H-bonds generated for 'chain 'A' and resid 425 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 713 Processing helix chain 'A' and resid 825 through 829 Processing helix chain 'A' and resid 834 through 873 removed outlier: 4.576A pdb=" N GLU A 842 " --> pdb=" O SER A 838 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N TYR A 843 " --> pdb=" O GLN A 839 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N SER A 845 " --> pdb=" O VAL A 841 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N PHE A 846 " --> pdb=" O GLU A 842 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N CYS A 847 " --> pdb=" O TYR A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 883 Processing helix chain 'A' and resid 914 through 920 Processing helix chain 'A' and resid 927 through 936 removed outlier: 3.712A pdb=" N ASN A 936 " --> pdb=" O ALA A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 952 Processing helix chain 'A' and resid 964 through 978 removed outlier: 4.003A pdb=" N SER A 978 " --> pdb=" O ALA A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 986 No H-bonds generated for 'chain 'A' and resid 984 through 986' Processing helix chain 'A' and resid 991 through 1002 removed outlier: 3.707A pdb=" N LEU A1002 " --> pdb=" O ARG A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1011 Processing helix chain 'A' and resid 1013 through 1030 Processing helix chain 'A' and resid 1036 through 1060 removed outlier: 3.965A pdb=" N LEU A1059 " --> pdb=" O LEU A1055 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER A1060 " --> pdb=" O LEU A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1076 Processing helix chain 'A' and resid 1079 through 1124 removed outlier: 4.706A pdb=" N ALA A1084 " --> pdb=" O PRO A1080 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 95 Processing helix chain 'B' and resid 302 through 309 Processing helix chain 'B' and resid 345 through 349 Processing helix chain 'B' and resid 357 through 359 No H-bonds generated for 'chain 'B' and resid 357 through 359' Processing helix chain 'B' and resid 372 through 378 removed outlier: 4.313A pdb=" N SER B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE B 378 " --> pdb=" O SER B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 393 No H-bonds generated for 'chain 'B' and resid 391 through 393' Processing helix chain 'B' and resid 414 through 417 Processing helix chain 'B' and resid 425 through 428 No H-bonds generated for 'chain 'B' and resid 425 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 464 removed outlier: 3.805A pdb=" N PHE B 464 " --> pdb=" O TRP B 460 " (cutoff:3.500A) 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 713 Processing helix chain 'B' and resid 825 through 830 Processing helix chain 'B' and resid 834 through 873 removed outlier: 3.589A pdb=" N VAL B 841 " --> pdb=" O LYS B 837 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLU B 842 " --> pdb=" O SER B 838 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N TYR B 843 " --> pdb=" O GLN B 839 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N SER B 845 " --> pdb=" O VAL B 841 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N PHE B 846 " --> pdb=" O GLU B 842 " (cutoff:3.500A) Processing helix chain 'B' and resid 880 through 883 Processing helix chain 'B' and resid 914 through 921 Processing helix chain 'B' and resid 927 through 936 removed outlier: 3.991A pdb=" N ASN B 936 " --> pdb=" O ALA B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 952 Processing helix chain 'B' and resid 964 through 978 removed outlier: 3.995A pdb=" N SER B 978 " --> pdb=" O ALA B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 986 No H-bonds generated for 'chain 'B' and resid 984 through 986' Processing helix chain 'B' and resid 991 through 1002 removed outlier: 3.703A pdb=" N LEU B1002 " --> pdb=" O ARG B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1006 through 1011 Processing helix chain 'B' and resid 1013 through 1030 Processing helix chain 'B' and resid 1036 through 1060 removed outlier: 3.504A pdb=" N GLN B1058 " --> pdb=" O ASN B1054 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU B1059 " --> pdb=" O LEU B1055 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N SER B1060 " --> pdb=" O LEU B1056 " (cutoff:3.500A) Processing helix chain 'B' and resid 1070 through 1076 Processing helix chain 'B' and resid 1079 through 1124 removed outlier: 4.834A pdb=" N ALA B1084 " --> pdb=" O PRO B1080 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'J' and resid 29 through 31 Processing sheet with id= B, first strand: chain 'J' and resid 42 through 44 Processing sheet with id= C, first strand: chain 'J' and resid 65 through 73 removed outlier: 3.526A pdb=" N ASN J 294 " --> pdb=" O ALA J 285 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'J' and resid 272 through 276 removed outlier: 5.507A pdb=" N PHE J 231 " --> pdb=" O PHE J 240 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N PHE J 240 " --> pdb=" O PHE J 231 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'J' and resid 114 through 118 Processing sheet with id= F, first strand: chain 'J' and resid 252 through 255 removed outlier: 3.989A pdb=" N GLY J 161 " --> pdb=" O TYR J 209 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 177 through 179 No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'J' and resid 318 through 321 Processing sheet with id= I, first strand: chain 'J' and resid 331 through 335 removed outlier: 4.028A pdb=" N ALA J 331 " --> pdb=" O CYS J 630 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N THR J 677 " --> pdb=" O VAL J 647 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N TYR J 667 " --> pdb=" O ILE J 680 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU J 659 " --> pdb=" O TYR J 667 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'J' and resid 361 through 366 removed outlier: 3.952A pdb=" N SER J 401 " --> pdb=" O HIS J 606 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASN J 444 " --> pdb=" O ALA J 381 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ALA J 381 " --> pdb=" O ASN J 444 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'J' and resid 484 through 488 Processing sheet with id= L, first strand: chain 'J' and resid 773 through 777 removed outlier: 3.511A pdb=" N GLY J 752 " --> pdb=" O TYR J 755 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL J 757 " --> pdb=" O THR J 750 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N THR J 750 " --> pdb=" O VAL J 757 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'J' and resid 805 through 815 Processing sheet with id= N, first strand: chain 'J' and resid 820 through 823 removed outlier: 4.097A pdb=" N LYS J 820 " --> pdb=" O LEU J 958 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'J' and resid 1174 through 1176 Processing sheet with id= P, first strand: chain 'J' and resid 1187 through 1192 Processing sheet with id= Q, first strand: chain 'J' and resid 797 through 804 removed outlier: 6.497A pdb=" N LYS J1164 " --> pdb=" O SER J 803 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 29 through 31 Processing sheet with id= S, first strand: chain 'A' and resid 42 through 44 Processing sheet with id= T, first strand: chain 'A' and resid 64 through 73 removed outlier: 3.576A pdb=" N ASN A 294 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'A' and resid 272 through 276 removed outlier: 5.477A pdb=" N PHE A 231 " --> pdb=" O PHE A 240 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N PHE A 240 " --> pdb=" O PHE A 231 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'A' and resid 114 through 118 Processing sheet with id= W, first strand: chain 'A' and resid 252 through 255 removed outlier: 3.741A pdb=" N GLY A 161 " --> pdb=" O TYR A 209 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'A' and resid 177 through 179 No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'A' and resid 318 through 321 Processing sheet with id= Z, first strand: chain 'A' and resid 331 through 335 removed outlier: 4.124A pdb=" N ALA A 331 " --> pdb=" O CYS A 630 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N THR A 677 " --> pdb=" O VAL A 647 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N TYR A 667 " --> pdb=" O ILE A 680 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU A 659 " --> pdb=" O TYR A 667 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.082A pdb=" N SER A 451 " --> pdb=" O VAL A 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'A' and resid 361 through 365 removed outlier: 6.455A pdb=" N ASN A 444 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ALA A 381 " --> pdb=" O ASN A 444 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'A' and resid 484 through 488 Processing sheet with id= AD, first strand: chain 'A' and resid 773 through 777 removed outlier: 6.448A pdb=" N VAL A 757 " --> pdb=" O THR A 750 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N THR A 750 " --> pdb=" O VAL A 757 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'A' and resid 805 through 815 Processing sheet with id= AF, first strand: chain 'A' and resid 820 through 823 removed outlier: 4.130A pdb=" N LYS A 820 " --> pdb=" O LEU A 958 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'A' and resid 1225 through 1227 Processing sheet with id= AH, first strand: chain 'A' and resid 1187 through 1192 Processing sheet with id= AI, first strand: chain 'A' and resid 797 through 804 removed outlier: 6.544A pdb=" N LYS A1164 " --> pdb=" O SER A 803 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'B' and resid 29 through 31 Processing sheet with id= AK, first strand: chain 'B' and resid 42 through 44 Processing sheet with id= AL, first strand: chain 'B' and resid 64 through 73 removed outlier: 3.804A pdb=" N ASN B 294 " --> pdb=" O ALA B 285 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'B' and resid 272 through 276 removed outlier: 5.506A pdb=" N PHE B 231 " --> pdb=" O PHE B 240 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N PHE B 240 " --> pdb=" O PHE B 231 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'B' and resid 114 through 118 Processing sheet with id= AO, first strand: chain 'B' and resid 252 through 255 removed outlier: 3.850A pdb=" N GLY B 161 " --> pdb=" O TYR B 209 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'B' and resid 177 through 179 No H-bonds generated for sheet with id= AP Processing sheet with id= AQ, first strand: chain 'B' and resid 318 through 321 Processing sheet with id= AR, first strand: chain 'B' and resid 331 through 335 removed outlier: 4.067A pdb=" N ALA B 331 " --> pdb=" O CYS B 630 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N THR B 677 " --> pdb=" O VAL B 647 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N TYR B 667 " --> pdb=" O ILE B 680 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU B 659 " --> pdb=" O TYR B 667 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'B' and resid 353 through 355 removed outlier: 6.218A pdb=" N SER B 451 " --> pdb=" O VAL B 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= AS Processing sheet with id= AT, first strand: chain 'B' and resid 361 through 366 removed outlier: 6.520A pdb=" N ASN B 444 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ALA B 381 " --> pdb=" O ASN B 444 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'B' and resid 484 through 488 Processing sheet with id= AV, first strand: chain 'B' and resid 492 through 494 Processing sheet with id= AW, first strand: chain 'B' and resid 773 through 777 removed outlier: 3.511A pdb=" N GLY B 752 " --> pdb=" O TYR B 755 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL B 757 " --> pdb=" O THR B 750 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N THR B 750 " --> pdb=" O VAL B 757 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'B' and resid 805 through 815 Processing sheet with id= AY, first strand: chain 'B' and resid 820 through 823 removed outlier: 4.136A pdb=" N LYS B 820 " --> pdb=" O LEU B 958 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'B' and resid 1225 through 1227 Processing sheet with id= BA, first strand: chain 'B' and resid 1187 through 1192 Processing sheet with id= BB, first strand: chain 'B' and resid 797 through 804 removed outlier: 6.526A pdb=" N LYS B1164 " --> pdb=" O SER B 803 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'H' and resid 3 through 8 Processing sheet with id= BD, first strand: chain 'H' and resid 118 through 121 removed outlier: 11.716A pdb=" N UNK H 32 " --> pdb=" O UNK H 53 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N UNK H 53 " --> pdb=" O UNK H 32 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N UNK H 38 " --> pdb=" O UNK H 47 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N UNK H 47 " --> pdb=" O UNK H 38 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N UNK H 40 " --> pdb=" O UNK H 45 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N UNK H 45 " --> pdb=" O UNK H 40 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N UNK H 56 " --> pdb=" O UNK H 52 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'H' and resid 99 through 102 Processing sheet with id= BF, first strand: chain 'L' and resid 17 through 20 Processing sheet with id= BG, first strand: chain 'L' and resid 87 through 92 removed outlier: 5.847A pdb=" N UNK L 41 " --> pdb=" O UNK L 49 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N UNK L 49 " --> pdb=" O UNK L 41 " (cutoff:3.500A) 1043 hydrogen bonds defined for protein. 2904 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: 14.54 Time building geometry restraints manager: 13.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 6651 1.32 - 1.45: 9552 1.45 - 1.58: 13779 1.58 - 1.72: 9 1.72 - 1.85: 240 Bond restraints: 30231 Sorted by residual: bond pdb=" CB HIS A 219 " pdb=" CG HIS A 219 " ideal model delta sigma weight residual 1.497 1.403 0.094 1.40e-02 5.10e+03 4.54e+01 bond pdb=" CB HIS B 219 " pdb=" CG HIS B 219 " ideal model delta sigma weight residual 1.497 1.406 0.091 1.40e-02 5.10e+03 4.24e+01 bond pdb=" CB HIS J 219 " pdb=" CG HIS J 219 " ideal model delta sigma weight residual 1.497 1.409 0.088 1.40e-02 5.10e+03 3.97e+01 bond pdb=" C3 NAG J1405 " pdb=" C4 NAG J1405 " ideal model delta sigma weight residual 1.523 1.584 -0.061 1.00e-02 1.00e+04 3.66e+01 bond pdb=" CB HIS J 490 " pdb=" CG HIS J 490 " ideal model delta sigma weight residual 1.497 1.415 0.082 1.40e-02 5.10e+03 3.45e+01 ... (remaining 30226 not shown) Histogram of bond angle deviations from ideal: 96.87 - 104.31: 479 104.31 - 111.74: 13179 111.74 - 119.18: 11481 119.18 - 126.61: 15816 126.61 - 134.04: 216 Bond angle restraints: 41171 Sorted by residual: angle pdb=" C GLN A 160 " pdb=" N GLY A 161 " pdb=" CA GLY A 161 " ideal model delta sigma weight residual 122.18 113.95 8.23 6.90e-01 2.10e+00 1.42e+02 angle pdb=" N PRO J 981 " pdb=" CA PRO J 981 " pdb=" C PRO J 981 " ideal model delta sigma weight residual 110.70 122.70 -12.00 1.22e+00 6.72e-01 9.67e+01 angle pdb=" N PRO A 981 " pdb=" CA PRO A 981 " pdb=" C PRO A 981 " ideal model delta sigma weight residual 110.70 122.59 -11.89 1.22e+00 6.72e-01 9.49e+01 angle pdb=" N PRO B 981 " pdb=" CA PRO B 981 " pdb=" C PRO B 981 " ideal model delta sigma weight residual 110.70 122.56 -11.86 1.22e+00 6.72e-01 9.45e+01 angle pdb=" N PRO A 575 " pdb=" CA PRO A 575 " pdb=" C PRO A 575 " ideal model delta sigma weight residual 111.19 96.87 14.32 1.57e+00 4.06e-01 8.32e+01 ... (remaining 41166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.56: 17342 19.56 - 39.12: 388 39.12 - 58.69: 128 58.69 - 78.25: 33 78.25 - 97.81: 6 Dihedral angle restraints: 17897 sinusoidal: 6876 harmonic: 11021 Sorted by residual: dihedral pdb=" CB CYS J 535 " pdb=" SG CYS J 535 " pdb=" SG CYS J 548 " pdb=" CB CYS J 548 " ideal model delta sinusoidal sigma weight residual 93.00 150.85 -57.85 1 1.00e+01 1.00e-02 4.49e+01 dihedral pdb=" CA UNK L 13 " pdb=" C UNK L 13 " pdb=" N UNK L 14 " pdb=" CA UNK L 14 " ideal model delta harmonic sigma weight residual 180.00 150.40 29.60 0 5.00e+00 4.00e-02 3.51e+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 -132.57 46.57 1 1.00e+01 1.00e-02 3.00e+01 ... (remaining 17894 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 3727 0.113 - 0.226: 1002 0.226 - 0.339: 111 0.339 - 0.451: 17 0.451 - 0.564: 3 Chirality restraints: 4860 Sorted by residual: chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.24e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.18e+01 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.05e+01 ... (remaining 4857 not shown) Planarity restraints: 5287 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1403 " 0.304 2.00e-02 2.50e+03 2.56e-01 8.19e+02 pdb=" C7 NAG A1403 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG A1403 " 0.188 2.00e-02 2.50e+03 pdb=" N2 NAG A1403 " -0.439 2.00e-02 2.50e+03 pdb=" O7 NAG A1403 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1406 " 0.214 2.00e-02 2.50e+03 1.82e-01 4.15e+02 pdb=" C7 NAG A1406 " -0.057 2.00e-02 2.50e+03 pdb=" C8 NAG A1406 " 0.150 2.00e-02 2.50e+03 pdb=" N2 NAG A1406 " -0.307 2.00e-02 2.50e+03 pdb=" O7 NAG A1406 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 1 " -0.216 2.00e-02 2.50e+03 1.80e-01 4.03e+02 pdb=" C7 NAG R 1 " 0.060 2.00e-02 2.50e+03 pdb=" C8 NAG R 1 " -0.155 2.00e-02 2.50e+03 pdb=" N2 NAG R 1 " 0.294 2.00e-02 2.50e+03 pdb=" O7 NAG R 1 " 0.018 2.00e-02 2.50e+03 ... (remaining 5284 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 8277 2.79 - 3.32: 26758 3.32 - 3.85: 49598 3.85 - 4.37: 60501 4.37 - 4.90: 99869 Nonbonded interactions: 245003 Sorted by model distance: nonbonded pdb=" OG SER B 374 " pdb=" O6 NAG R 1 " model vdw 2.267 2.440 nonbonded pdb=" N ASN J1046 " pdb=" O ASN J1046 " model vdw 2.282 2.496 nonbonded pdb=" N ASN B 371 " pdb=" OD1 ASN B 371 " model vdw 2.284 2.520 nonbonded pdb=" N ASN J 371 " pdb=" OD1 ASN J 371 " model vdw 2.309 2.520 nonbonded pdb=" N ASN A 371 " pdb=" OD1 ASN A 371 " model vdw 2.314 2.520 ... (remaining 244998 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 33 or resid 38 through 150 or resid 159 through \ 474 or resid 480 through 504 or resid 517 through 761 or resid 771 through 903 \ or resid 910 through 1233 or resid 1401 through 1405)) selection = (chain 'B' and (resid 15 through 474 or resid 480 through 504 or resid 517 throu \ gh 761 or resid 771 through 903 or resid 910 through 1233 or resid 1401 through \ 1405)) selection = (chain 'J' and (resid 15 through 150 or resid 159 through 1233 or resid 1401 thr \ ough 1405)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'G' selection = chain 'O' } ncs_group { reference = (chain 'H' and resid 18 through 122) selection = chain 'L' } 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 189 5.16 5 C 18780 2.51 5 N 4816 2.21 5 O 5814 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: 1.520 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: 0.040 Extract box with map and model: 11.330 Check model and map are aligned: 0.460 Process input model: 80.130 Find NCS groups from input model: 2.700 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Set scattering table: 0.270 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:14.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9072 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 : 0.023 0.124 30231 Z= 1.477 Angle : 1.683 14.317 41171 Z= 1.150 Chirality : 0.099 0.564 4860 Planarity : 0.010 0.256 5246 Dihedral : 10.175 97.810 10642 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 1.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.54 (0.13), residues: 3505 helix: -0.26 (0.16), residues: 813 sheet: 0.89 (0.17), residues: 847 loop : 0.57 (0.14), residues: 1845 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 305 time to evaluate : 3.592 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: 8 outliers final: 6 residues processed: 313 average time/residue: 1.6690 time to fit residues: 605.1102 Evaluate side-chains 130 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 124 time to evaluate : 3.542 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 4.5689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 316 optimal weight: 1.9990 chunk 284 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 293 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 218 optimal weight: 0.8980 chunk 340 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 219 HIS J 418 GLN J 839 GLN J 849 ASN J 950 GLN J1103 GLN J1141 HIS A 219 HIS A 252 HIS A 849 ASN A1103 GLN A1138 ASN B 160 GLN B 219 HIS B 252 HIS ** B 483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 849 ASN B1103 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9037 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 30231 Z= 0.189 Angle : 0.579 6.623 41171 Z= 0.322 Chirality : 0.045 0.327 4860 Planarity : 0.004 0.049 5246 Dihedral : 6.341 72.927 4470 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer Outliers : 1.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.07 (0.14), residues: 3505 helix: 1.49 (0.19), residues: 805 sheet: 0.85 (0.17), residues: 801 loop : 0.42 (0.14), residues: 1899 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 190 time to evaluate : 3.550 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: 36 outliers final: 17 residues processed: 217 average time/residue: 1.4661 time to fit residues: 378.0158 Evaluate side-chains 142 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 125 time to evaluate : 3.444 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 16 residues processed: 1 average time/residue: 0.4040 time to fit residues: 5.1845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 189 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 283 optimal weight: 20.0000 chunk 231 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 341 optimal weight: 6.9990 chunk 368 optimal weight: 10.0000 chunk 303 optimal weight: 4.9990 chunk 338 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 273 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 32 ASN J 171 ASN J 777 ASN J 849 ASN J 950 GLN J1103 GLN A 421 ASN A 532 HIS B 777 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9125 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.054 30231 Z= 0.478 Angle : 0.636 7.405 41171 Z= 0.350 Chirality : 0.049 0.349 4860 Planarity : 0.005 0.052 5246 Dihedral : 6.268 67.734 4470 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer Outliers : 1.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.58 (0.14), residues: 3505 helix: 1.48 (0.19), residues: 806 sheet: 0.40 (0.17), residues: 791 loop : -0.02 (0.14), residues: 1908 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 140 time to evaluate : 3.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 25 residues processed: 186 average time/residue: 1.6332 time to fit residues: 357.6693 Evaluate side-chains 146 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 121 time to evaluate : 3.515 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 19 residues processed: 6 average time/residue: 1.2176 time to fit residues: 13.7175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 337 optimal weight: 1.9990 chunk 256 optimal weight: 0.6980 chunk 177 optimal weight: 0.7980 chunk 37 optimal weight: 0.1980 chunk 162 optimal weight: 6.9990 chunk 229 optimal weight: 0.9990 chunk 342 optimal weight: 4.9990 chunk 362 optimal weight: 20.0000 chunk 178 optimal weight: 3.9990 chunk 324 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 ASN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9070 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.051 30231 Z= 0.153 Angle : 0.492 6.960 41171 Z= 0.270 Chirality : 0.043 0.383 4860 Planarity : 0.004 0.046 5246 Dihedral : 5.601 73.056 4470 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.76 (0.14), residues: 3505 helix: 1.85 (0.20), residues: 795 sheet: 0.55 (0.17), residues: 782 loop : -0.02 (0.14), residues: 1928 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 151 time to evaluate : 3.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 20 residues processed: 182 average time/residue: 1.5750 time to fit residues: 339.4227 Evaluate side-chains 146 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 126 time to evaluate : 3.931 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 16 residues processed: 4 average time/residue: 1.0212 time to fit residues: 9.6446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 301 optimal weight: 4.9990 chunk 205 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 269 optimal weight: 5.9990 chunk 149 optimal weight: 0.1980 chunk 309 optimal weight: 20.0000 chunk 250 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 185 optimal weight: 4.9990 chunk 325 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 HIS A 745 GLN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 849 ASN B 536 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9107 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 30231 Z= 0.313 Angle : 0.537 6.687 41171 Z= 0.294 Chirality : 0.044 0.299 4860 Planarity : 0.004 0.053 5246 Dihedral : 5.662 76.374 4470 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.61 (0.14), residues: 3505 helix: 1.84 (0.20), residues: 799 sheet: 0.35 (0.17), residues: 786 loop : -0.13 (0.14), residues: 1920 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 131 time to evaluate : 3.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 28 residues processed: 168 average time/residue: 1.6189 time to fit residues: 321.1424 Evaluate side-chains 152 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 124 time to evaluate : 3.408 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 25 residues processed: 3 average time/residue: 0.7044 time to fit residues: 7.3733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 121 optimal weight: 2.9990 chunk 326 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 212 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 362 optimal weight: 20.0000 chunk 301 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 30 optimal weight: 0.0870 chunk 120 optimal weight: 4.9990 chunk 190 optimal weight: 0.1980 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 745 GLN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9079 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 30231 Z= 0.157 Angle : 0.475 6.666 41171 Z= 0.261 Chirality : 0.042 0.357 4860 Planarity : 0.004 0.050 5246 Dihedral : 5.361 79.176 4470 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.71 (0.14), residues: 3505 helix: 2.01 (0.20), residues: 790 sheet: 0.51 (0.17), residues: 787 loop : -0.14 (0.14), residues: 1928 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 130 time to evaluate : 3.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 29 residues processed: 166 average time/residue: 1.5338 time to fit residues: 303.1836 Evaluate side-chains 155 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 126 time to evaluate : 3.622 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 23 residues processed: 6 average time/residue: 0.5051 time to fit residues: 9.2808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 349 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 206 optimal weight: 5.9990 chunk 264 optimal weight: 1.9990 chunk 205 optimal weight: 0.7980 chunk 305 optimal weight: 7.9990 chunk 202 optimal weight: 6.9990 chunk 361 optimal weight: 20.0000 chunk 226 optimal weight: 6.9990 chunk 220 optimal weight: 1.9990 chunk 166 optimal weight: 0.4980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 HIS A 745 GLN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9087 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 30231 Z= 0.204 Angle : 0.484 6.646 41171 Z= 0.265 Chirality : 0.043 0.367 4860 Planarity : 0.004 0.052 5246 Dihedral : 5.309 82.394 4470 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 1.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.68 (0.14), residues: 3505 helix: 2.05 (0.20), residues: 784 sheet: 0.46 (0.17), residues: 796 loop : -0.17 (0.14), residues: 1925 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 128 time to evaluate : 3.869 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: 49 outliers final: 32 residues processed: 170 average time/residue: 1.5997 time to fit residues: 323.5493 Evaluate side-chains 158 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 126 time to evaluate : 3.573 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 28 residues processed: 4 average time/residue: 0.4155 time to fit residues: 7.4473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 223 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 215 optimal weight: 0.2980 chunk 108 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 229 optimal weight: 6.9990 chunk 246 optimal weight: 0.6980 chunk 178 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 284 optimal weight: 9.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 745 GLN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9100 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 30231 Z= 0.258 Angle : 0.502 7.037 41171 Z= 0.275 Chirality : 0.043 0.343 4860 Planarity : 0.004 0.055 5246 Dihedral : 5.392 85.015 4470 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.64 (0.14), residues: 3505 helix: 2.04 (0.20), residues: 781 sheet: 0.46 (0.17), residues: 796 loop : -0.23 (0.14), residues: 1928 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 132 time to evaluate : 3.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 29 residues processed: 169 average time/residue: 1.5194 time to fit residues: 307.7308 Evaluate side-chains 151 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 122 time to evaluate : 4.386 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 26 residues processed: 3 average time/residue: 0.4669 time to fit residues: 7.0014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 328 optimal weight: 0.0770 chunk 346 optimal weight: 1.9990 chunk 315 optimal weight: 0.5980 chunk 336 optimal weight: 2.9990 chunk 202 optimal weight: 8.9990 chunk 146 optimal weight: 0.0870 chunk 264 optimal weight: 0.0980 chunk 103 optimal weight: 1.9990 chunk 304 optimal weight: 6.9990 chunk 318 optimal weight: 0.9990 chunk 335 optimal weight: 4.9990 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 HIS A 745 GLN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1138 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9056 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 30231 Z= 0.124 Angle : 0.462 7.949 41171 Z= 0.253 Chirality : 0.041 0.284 4860 Planarity : 0.004 0.050 5246 Dihedral : 5.034 85.246 4470 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer Outliers : 1.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.72 (0.14), residues: 3505 helix: 2.10 (0.20), residues: 782 sheet: 0.58 (0.17), residues: 805 loop : -0.22 (0.14), residues: 1918 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 144 time to evaluate : 3.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 27 residues processed: 181 average time/residue: 1.5025 time to fit residues: 324.5408 Evaluate side-chains 152 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 125 time to evaluate : 3.517 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 25 residues processed: 2 average time/residue: 0.3966 time to fit residues: 6.2267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 221 optimal weight: 4.9990 chunk 356 optimal weight: 20.0000 chunk 217 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 chunk 247 optimal weight: 0.9980 chunk 373 optimal weight: 30.0000 chunk 343 optimal weight: 5.9990 chunk 297 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 229 optimal weight: 4.9990 chunk 182 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1053 ASN A 724 ASN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9119 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.065 30231 Z= 0.408 Angle : 0.559 8.362 41171 Z= 0.305 Chirality : 0.046 0.387 4860 Planarity : 0.005 0.062 5246 Dihedral : 5.504 88.679 4470 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.48 (0.14), residues: 3505 helix: 1.93 (0.20), residues: 780 sheet: 0.36 (0.17), residues: 799 loop : -0.34 (0.14), residues: 1926 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7010 Ramachandran restraints generated. 3505 Oldfield, 0 Emsley, 3505 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 125 time to evaluate : 3.573 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: 37 outliers final: 31 residues processed: 157 average time/residue: 1.6132 time to fit residues: 301.3553 Evaluate side-chains 151 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 120 time to evaluate : 3.557 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 28 residues processed: 3 average time/residue: 0.4996 time to fit residues: 7.1435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 236 optimal weight: 0.9990 chunk 316 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 274 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 297 optimal weight: 1.9990 chunk 124 optimal weight: 0.0870 chunk 305 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 745 GLN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.081915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.061791 restraints weight = 57969.051| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 2.47 r_work: 0.2574 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2445 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9087 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 30231 Z= 0.153 Angle : 0.480 8.266 41171 Z= 0.263 Chirality : 0.042 0.309 4860 Planarity : 0.004 0.053 5246 Dihedral : 5.173 87.704 4470 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.62 (0.14), residues: 3505 helix: 2.05 (0.20), residues: 783 sheet: 0.60 (0.17), residues: 795 loop : -0.34 (0.14), residues: 1927 =============================================================================== Job complete usr+sys time: 7109.74 seconds wall clock time: 130 minutes 21.10 seconds (7821.10 seconds total)