Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 08:59:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbx_24991/04_2023/7sbx_24991_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbx_24991/04_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_24991/04_2023/7sbx_24991.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbx_24991/04_2023/7sbx_24991.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbx_24991/04_2023/7sbx_24991_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbx_24991/04_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 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. 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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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 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 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: 15.14, per 1000 atoms: 0.51 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: 13.14 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: 5.28 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: 12.85 Time building geometry restraints manager: 14.03 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=" C1 NAG U 2 " pdb=" O5 NAG U 2 " ideal model delta sigma weight residual 1.406 1.547 -0.141 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C1 NAG B1405 " pdb=" O5 NAG B1405 " ideal model delta sigma weight residual 1.406 1.546 -0.140 2.00e-02 2.50e+03 4.87e+01 bond pdb=" C1 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.406 1.545 -0.139 2.00e-02 2.50e+03 4.86e+01 bond pdb=" C1 NAG B1401 " pdb=" O5 NAG B1401 " ideal model delta sigma weight residual 1.406 1.545 -0.139 2.00e-02 2.50e+03 4.86e+01 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.545 -0.139 2.00e-02 2.50e+03 4.83e+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: 16962 19.56 - 39.12: 388 39.12 - 58.69: 128 58.69 - 78.25: 33 78.25 - 97.81: 6 Dihedral angle restraints: 17517 sinusoidal: 6496 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 17514 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 3692 0.113 - 0.226: 1032 0.226 - 0.339: 115 0.339 - 0.451: 16 0.451 - 0.564: 5 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 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: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 11.270 Check model and map are aligned: 0.460 Set scattering table: 0.270 Process input model: 76.290 Find NCS groups from input model: 2.360 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 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 0.141 30231 Z= 1.490 Angle : 1.695 14.317 41171 Z= 1.134 Chirality : 0.101 0.564 4860 Planarity : 0.010 0.256 5246 Dihedral : 10.176 97.810 10262 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 : 3.687 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: 1.5783 time to fit residues: 575.2786 Evaluate side-chains 130 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 124 time to evaluate : 3.355 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 4.4497 ------------------------------------------------------------------------------- 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 849 ASN B1103 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 30231 Z= 0.184 Angle : 0.591 6.490 41171 Z= 0.322 Chirality : 0.044 0.282 4860 Planarity : 0.004 0.050 5246 Dihedral : 6.203 72.980 4090 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer Outliers : 1.23 % 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: 1.08 (0.14), residues: 3505 helix: 1.49 (0.19), residues: 806 sheet: 0.87 (0.17), residues: 801 loop : 0.42 (0.14), residues: 1898 *********************** 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 227 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 189 time to evaluate : 3.325 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: 38 outliers final: 18 residues processed: 218 average time/residue: 1.4047 time to fit residues: 364.6167 Evaluate side-chains 145 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 127 time to evaluate : 3.407 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 17 residues processed: 1 average time/residue: 0.4082 time to fit residues: 5.0798 ------------------------------------------------------------------------------- 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: 1.9990 chunk 105 optimal weight: 2.9990 chunk 283 optimal weight: 20.0000 chunk 231 optimal weight: 4.9990 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: 4.9990 chunk 116 optimal weight: 0.0070 chunk 273 optimal weight: 5.9990 overall best weight: 3.0006 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 ASN A 532 HIS ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.061 30231 Z= 0.378 Angle : 0.616 7.791 41171 Z= 0.332 Chirality : 0.047 0.275 4860 Planarity : 0.005 0.052 5246 Dihedral : 5.939 67.536 4090 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer Outliers : 1.82 % 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: 0.70 (0.14), residues: 3505 helix: 1.66 (0.19), residues: 798 sheet: 0.42 (0.17), residues: 798 loop : 0.06 (0.14), residues: 1909 *********************** 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 207 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 151 time to evaluate : 3.651 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: 56 outliers final: 24 residues processed: 194 average time/residue: 1.5276 time to fit residues: 349.1659 Evaluate side-chains 149 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 125 time to evaluate : 3.323 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 20 residues processed: 4 average time/residue: 1.2687 time to fit residues: 10.3913 ------------------------------------------------------------------------------- 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: 0.8980 chunk 256 optimal weight: 0.6980 chunk 177 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 229 optimal weight: 3.9990 chunk 342 optimal weight: 4.9990 chunk 362 optimal weight: 20.0000 chunk 178 optimal weight: 5.9990 chunk 324 optimal weight: 7.9990 chunk 97 optimal weight: 0.2980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 32 ASN A 527 ASN A 532 HIS ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.2651 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= 0.147 Angle : 0.497 6.454 41171 Z= 0.268 Chirality : 0.042 0.265 4860 Planarity : 0.004 0.047 5246 Dihedral : 5.308 74.178 4090 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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: 0.81 (0.14), residues: 3505 helix: 1.88 (0.20), residues: 801 sheet: 0.58 (0.17), residues: 782 loop : 0.02 (0.14), residues: 1922 *********************** 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 191 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 146 time to evaluate : 3.434 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: 177 average time/residue: 1.4733 time to fit residues: 311.4885 Evaluate side-chains 148 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 3.568 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 16 residues processed: 4 average time/residue: 0.9174 time to fit residues: 9.2198 ------------------------------------------------------------------------------- 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: 2.9990 chunk 205 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 269 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 309 optimal weight: 8.9990 chunk 250 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 185 optimal weight: 3.9990 chunk 325 optimal weight: 0.1980 chunk 91 optimal weight: 0.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J1053 ASN A 532 HIS A 745 GLN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 849 ASN A1035 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 30231 Z= 0.245 Angle : 0.519 6.570 41171 Z= 0.279 Chirality : 0.044 0.275 4860 Planarity : 0.004 0.053 5246 Dihedral : 5.259 77.102 4090 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer Outliers : 1.65 % 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: 1.88 (0.20), residues: 804 sheet: 0.54 (0.17), residues: 780 loop : -0.09 (0.14), residues: 1921 *********************** 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 183 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 132 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 revert: symmetry clash outliers start: 51 outliers final: 29 residues processed: 168 average time/residue: 1.5571 time to fit residues: 311.3477 Evaluate side-chains 156 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 127 time to evaluate : 3.394 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 24 residues processed: 5 average time/residue: 0.5693 time to fit residues: 8.6166 ------------------------------------------------------------------------------- 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: 3.9990 chunk 326 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 212 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 362 optimal weight: 20.0000 chunk 301 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 190 optimal weight: 0.0870 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 32 ASN A 532 HIS A 745 GLN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 30231 Z= 0.195 Angle : 0.491 6.767 41171 Z= 0.264 Chirality : 0.042 0.255 4860 Planarity : 0.004 0.051 5246 Dihedral : 5.088 81.154 4090 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % 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: 0.74 (0.14), residues: 3505 helix: 1.99 (0.20), residues: 796 sheet: 0.55 (0.17), residues: 791 loop : -0.13 (0.14), residues: 1918 *********************** 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 184 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 131 time to evaluate : 3.439 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: 53 outliers final: 30 residues processed: 170 average time/residue: 1.4712 time to fit residues: 299.1253 Evaluate side-chains 154 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 124 time to evaluate : 3.401 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 25 residues processed: 5 average time/residue: 0.3703 time to fit residues: 7.6154 ------------------------------------------------------------------------------- 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: 4.9990 chunk 40 optimal weight: 4.9990 chunk 206 optimal weight: 4.9990 chunk 264 optimal weight: 0.9980 chunk 205 optimal weight: 0.7980 chunk 305 optimal weight: 7.9990 chunk 202 optimal weight: 7.9990 chunk 361 optimal weight: 20.0000 chunk 226 optimal weight: 8.9990 chunk 220 optimal weight: 0.6980 chunk 166 optimal weight: 1.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 30231 Z= 0.252 Angle : 0.515 6.864 41171 Z= 0.276 Chirality : 0.043 0.265 4860 Planarity : 0.004 0.055 5246 Dihedral : 5.146 85.102 4090 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer Outliers : 1.82 % 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: 0.66 (0.14), residues: 3505 helix: 2.09 (0.20), residues: 779 sheet: 0.45 (0.17), residues: 810 loop : -0.22 (0.14), residues: 1916 *********************** 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 183 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 127 time to evaluate : 3.086 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: 56 outliers final: 36 residues processed: 176 average time/residue: 1.4845 time to fit residues: 317.2090 Evaluate side-chains 162 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 126 time to evaluate : 3.408 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 31 residues processed: 5 average time/residue: 0.4375 time to fit residues: 8.1387 ------------------------------------------------------------------------------- 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: 3.9990 chunk 144 optimal weight: 5.9990 chunk 215 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 229 optimal weight: 6.9990 chunk 246 optimal weight: 1.9990 chunk 178 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 284 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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** B 461 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 30231 Z= 0.341 Angle : 0.559 7.292 41171 Z= 0.298 Chirality : 0.045 0.256 4860 Planarity : 0.004 0.058 5246 Dihedral : 5.405 86.077 4090 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 1.69 % 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: 785 sheet: 0.36 (0.17), residues: 792 loop : -0.34 (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 182 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 130 time to evaluate : 3.397 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: 52 outliers final: 35 residues processed: 173 average time/residue: 1.5149 time to fit residues: 311.9318 Evaluate side-chains 157 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 122 time to evaluate : 3.232 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 31 residues processed: 4 average time/residue: 0.4059 time to fit residues: 7.0687 ------------------------------------------------------------------------------- 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: 0.9980 chunk 346 optimal weight: 2.9990 chunk 315 optimal weight: 1.9990 chunk 336 optimal weight: 0.9990 chunk 202 optimal weight: 7.9990 chunk 146 optimal weight: 0.2980 chunk 264 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 304 optimal weight: 5.9990 chunk 318 optimal weight: 4.9990 chunk 335 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 HIS ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1138 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 30231 Z= 0.166 Angle : 0.495 7.895 41171 Z= 0.266 Chirality : 0.042 0.235 4860 Planarity : 0.004 0.052 5246 Dihedral : 4.999 86.979 4090 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer Outliers : 1.27 % 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: 2.12 (0.20), residues: 776 sheet: 0.51 (0.17), residues: 800 loop : -0.31 (0.14), residues: 1929 *********************** 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 166 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 127 time to evaluate : 3.991 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: 39 outliers final: 30 residues processed: 162 average time/residue: 1.5876 time to fit residues: 307.9590 Evaluate side-chains 152 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 122 time to evaluate : 3.365 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 29 residues processed: 1 average time/residue: 0.4432 time to fit residues: 5.1428 ------------------------------------------------------------------------------- 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: 5.9990 chunk 247 optimal weight: 7.9990 chunk 373 optimal weight: 30.0000 chunk 343 optimal weight: 0.0470 chunk 297 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 229 optimal weight: 5.9990 chunk 182 optimal weight: 4.9990 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.064 30231 Z= 0.428 Angle : 0.597 7.458 41171 Z= 0.317 Chirality : 0.046 0.265 4860 Planarity : 0.005 0.063 5246 Dihedral : 5.477 88.936 4090 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % 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: 0.36 (0.14), residues: 3505 helix: 1.87 (0.20), residues: 780 sheet: 0.34 (0.17), residues: 792 loop : -0.46 (0.14), residues: 1933 ********************** 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 172 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 127 time to evaluate : 3.382 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: 45 outliers final: 30 residues processed: 165 average time/residue: 1.5113 time to fit residues: 297.8549 Evaluate side-chains 151 residues out of total 3082 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 121 time to evaluate : 3.415 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 28 residues processed: 2 average time/residue: 0.4211 time to fit residues: 6.0218 ------------------------------------------------------------------------------- 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: 7.9990 chunk 316 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 274 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 297 optimal weight: 1.9990 chunk 124 optimal weight: 0.0040 chunk 305 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 overall best weight: 1.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 HIS ** 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 = 0.3086 r_free = 0.3086 target = 0.081032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.060920 restraints weight = 58009.692| |-----------------------------------------------------------------------------| r_work (start): 0.2679 rms_B_bonded: 2.45 r_work: 0.2554 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2426 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 30231 Z= 0.192 Angle : 0.507 8.736 41171 Z= 0.270 Chirality : 0.043 0.228 4860 Planarity : 0.004 0.053 5246 Dihedral : 5.050 87.212 4090 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 1.27 % 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: 0.52 (0.14), residues: 3505 helix: 2.07 (0.20), residues: 778 sheet: 0.47 (0.17), residues: 803 loop : -0.41 (0.14), residues: 1924 =============================================================================== Job complete usr+sys time: 7052.62 seconds wall clock time: 128 minutes 12.08 seconds (7692.08 seconds total)