Starting phenix.real_space_refine on Wed Feb 21 02:44:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sb3_24968/02_2024/7sb3_24968_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sb3_24968/02_2024/7sb3_24968.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sb3_24968/02_2024/7sb3_24968.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sb3_24968/02_2024/7sb3_24968.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sb3_24968/02_2024/7sb3_24968_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sb3_24968/02_2024/7sb3_24968_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 18691 2.51 5 N 4797 2.21 5 O 5774 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 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 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 542": "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 PHE 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 737": "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 PHE 805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 824": "OD1" <-> "OD2" Residue "J TYR 833": "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 920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 930": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 934": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 980": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 992": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 997": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 1020": "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 "J TYR 1229": "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 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 188": "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 302": "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 PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 407": "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 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 484": "OD1" <-> "OD2" Residue "A TYR 487": "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 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 726": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 804": "OE1" <-> "OE2" 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 888": "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 PHE 980": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 992": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 997": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1020": "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 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1207": "OE1" <-> "OE2" 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 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 99": "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 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 175": "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 ASP 332": "OD1" <-> "OD2" 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 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 487": "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 TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 725": "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 TYR 997": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1020": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1031": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1063": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1229": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29451 Number of models: 1 Model: "" Number of chains: 22 Chain: "J" Number of atoms: 9198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1183, 9198 Classifications: {'peptide': 1183} Link IDs: {'PTRANS': 51, 'TRANS': 1131} Chain breaks: 5 Chain: "A" Number of atoms: 9168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1178, 9168 Classifications: {'peptide': 1178} Link IDs: {'PTRANS': 51, 'TRANS': 1126} Chain breaks: 6 Chain: "B" Number of atoms: 9185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1182, 9185 Classifications: {'peptide': 1182} Link IDs: {'PTRANS': 53, 'TRANS': 1128} Chain breaks: 5 Chain: "H" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 555 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'TRANS': 110} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 333 Unresolved non-hydrogen dihedrals: 111 Planarities with less than four sites: {'UNK:plan-1': 111} Unresolved non-hydrogen planarities: 111 Chain: "L" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 510 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'TRANS': 101} Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 306 Unresolved non-hydrogen dihedrals: 102 Planarities with less than four sites: {'UNK:plan-1': 102} Unresolved non-hydrogen planarities: 102 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 162 Unusual residues: {'8Z9': 2, 'NAG': 9} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" 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 dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 15.21, per 1000 atoms: 0.52 Number of scatterers: 29451 At special positions: 0 Unit cell: (151.41, 177.16, 166.86, 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 5774 8.00 N 4797 7.00 C 18691 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=2.03 Simple disulfide: pdb=" SG CYS J 168 " - pdb=" SG CYS J 201 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS J 343 " - pdb=" SG CYS J 368 " distance=2.09 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=2.03 Simple disulfide: pdb=" SG CYS J 491 " - pdb=" SG CYS J 561 " distance=2.03 Simple disulfide: pdb=" SG CYS J 499 " - pdb=" SG CYS J 522 " distance=2.04 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=2.04 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=2.13 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=2.02 Simple disulfide: pdb=" SG CYS J 825 " - pdb=" SG CYS J 847 " distance=2.02 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=2.10 Simple disulfide: pdb=" SG CYS J1125 " - pdb=" SG CYS J1136 " distance=2.03 Simple disulfide: pdb=" SG CYS J1175 " - pdb=" SG CYS J1220 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 260 " distance=2.03 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=2.05 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=2.04 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 576 " distance=2.02 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 548 " distance=2.03 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 578 " distance=2.04 Simple disulfide: pdb=" SG CYS A 591 " - pdb=" SG CYS A 597 " distance=2.09 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 683 " distance=2.09 Simple disulfide: pdb=" SG CYS A 708 " - pdb=" SG CYS A 732 " distance=2.04 Simple disulfide: pdb=" SG CYS A 747 " - pdb=" SG CYS A 756 " distance=2.02 Simple disulfide: pdb=" SG CYS A 825 " - pdb=" SG CYS A 847 " distance=2.10 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=2.08 Simple disulfide: pdb=" SG CYS A1125 " - pdb=" SG CYS A1136 " distance=2.03 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=2.16 Simple disulfide: pdb=" SG CYS B 168 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 260 " distance=2.03 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 571 " - pdb=" SG CYS B 578 " distance=2.04 Simple disulfide: pdb=" SG CYS B 591 " - pdb=" SG CYS B 597 " distance=2.06 Simple disulfide: pdb=" SG CYS B 630 " - pdb=" SG CYS B 683 " distance=2.10 Simple disulfide: pdb=" SG CYS B 708 " - pdb=" SG CYS B 732 " distance=2.04 Simple disulfide: pdb=" SG CYS B 747 " - pdb=" SG CYS B 756 " distance=2.02 Simple disulfide: pdb=" SG CYS B 825 " - pdb=" SG CYS B 847 " distance=2.10 Simple disulfide: pdb=" SG CYS B 830 " - pdb=" SG CYS B 836 " distance=2.03 Simple disulfide: pdb=" SG CYS B 937 " - pdb=" SG CYS B 948 " distance=2.04 Simple disulfide: pdb=" SG CYS B1125 " - pdb=" SG CYS B1136 " distance=2.03 Simple disulfide: pdb=" SG CYS B1175 " - pdb=" SG CYS B1220 " distance=2.06 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 F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " 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 P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " NAG-ASN " NAG A1401 " - " ASN A 212 " " NAG A1402 " - " ASN A 449 " " NAG A1403 " - " ASN A 713 " " NAG A1404 " - " ASN A 787 " " NAG A1405 " - " ASN A 936 " " NAG A1406 " - " ASN A1193 " " NAG A1407 " - " ASN A 675 " " NAG A1408 " - " ASN A 648 " " NAG A1409 " - " ASN A1223 " " NAG B1401 " - " ASN B 137 " " NAG B1402 " - " ASN B 212 " " NAG B1403 " - " ASN B 449 " " NAG B1404 " - " ASN B 713 " " NAG B1405 " - " ASN B 787 " " NAG B1406 " - " ASN B 695 " " NAG B1407 " - " ASN B 648 " " NAG B1408 " - " ASN B 936 " " NAG B1409 " - " ASN B1223 " " NAG C 1 " - " ASN J 137 " " NAG D 1 " - " ASN J 371 " " NAG E 1 " - " ASN J 738 " " NAG F 1 " - " ASN J 206 " " NAG G 1 " - " ASN A 137 " " NAG I 1 " - " ASN A 371 " " 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 J1193 " " NAG J1407 " - " ASN J 675 " " NAG J1408 " - " ASN J 695 " " NAG J1409 " - " ASN J 648 " " NAG K 1 " - " ASN A 738 " " NAG M 1 " - " ASN A 206 " " NAG N 1 " - " ASN A 695 " " NAG O 1 " - " ASN B 371 " " NAG P 1 " - " ASN B 738 " " NAG Q 1 " - " ASN B1193 " " NAG R 1 " - " ASN B 206 " " NAG S 1 " - " ASN B 675 " Time building additional restraints: 11.85 Conformation dependent library (CDL) restraints added in 5.1 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: 7044 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 91 helices and 53 sheets defined 23.0% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.53 Creating SS restraints... Processing helix chain 'J' and resid 92 through 94 No H-bonds generated for 'chain 'J' and resid 92 through 94' Processing helix chain 'J' and resid 182 through 184 No H-bonds generated for 'chain 'J' and resid 182 through 184' 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 378 removed outlier: 4.125A 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 424 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 462 through 464 No H-bonds generated for 'chain 'J' and resid 462 through 464' 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 826 through 829 No H-bonds generated for 'chain 'J' and resid 826 through 829' Processing helix chain 'J' and resid 834 through 842 removed outlier: 4.095A pdb=" N GLU J 842 " --> pdb=" O SER J 838 " (cutoff:3.500A) Processing helix chain 'J' and resid 844 through 873 removed outlier: 4.090A pdb=" N ASN J 849 " --> pdb=" O PHE J 846 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE J 850 " --> pdb=" O CYS J 847 " (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 933 Processing helix chain 'J' and resid 946 through 953 removed outlier: 3.519A pdb=" N LYS J 953 " --> pdb=" O VAL J 949 " (cutoff:3.500A) Processing helix chain 'J' and resid 964 through 978 removed outlier: 3.615A pdb=" N ALA J 977 " --> pdb=" O ALA J 973 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N SER J 978 " --> pdb=" O ALA J 974 " (cutoff:3.500A) Processing helix chain 'J' and resid 985 through 988 removed outlier: 3.779A pdb=" N GLY J 988 " --> pdb=" O ALA J 985 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 985 through 988' Processing helix chain 'J' and resid 991 through 1002 removed outlier: 3.581A pdb=" N LEU J1002 " --> pdb=" O ARG J 998 " (cutoff:3.500A) Processing helix chain 'J' and resid 1006 through 1030 removed outlier: 3.546A pdb=" N GLN J1011 " --> pdb=" O ASP J1007 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN J1013 " --> pdb=" O LEU J1009 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LYS J1014 " --> pdb=" O SER J1010 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU J1015 " --> pdb=" O GLN J1011 " (cutoff:3.500A) Processing helix chain 'J' and resid 1036 through 1060 removed outlier: 3.852A pdb=" N LEU J1059 " --> pdb=" O LEU J1055 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER J1060 " --> pdb=" O LEU J1056 " (cutoff:3.500A) Processing helix chain 'J' and resid 1070 through 1076 removed outlier: 3.568A pdb=" N SER J1075 " --> pdb=" O GLN J1071 " (cutoff:3.500A) Processing helix chain 'J' and resid 1079 through 1124 removed outlier: 4.910A 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 264 through 266 No H-bonds generated for 'chain 'A' and resid 264 through 266' Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' 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: 5.024A pdb=" N SER A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) removed outlier: 3.567A 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 424 through 427 No H-bonds generated for 'chain 'A' and resid 424 through 427' 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 464 removed outlier: 3.579A pdb=" N PHE A 464 " --> pdb=" O TRP A 460 " (cutoff:3.500A) 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 475 through 477 No H-bonds generated for 'chain 'A' and resid 475 through 477' Processing helix chain 'A' and resid 539 through 541 No H-bonds generated for 'chain 'A' and resid 539 through 541' 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 711 No H-bonds generated for 'chain 'A' and resid 708 through 711' Processing helix chain 'A' and resid 825 through 829 Processing helix chain 'A' and resid 834 through 872 removed outlier: 3.880A pdb=" N GLN A 839 " --> pdb=" O ALA A 835 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N GLU A 842 " --> pdb=" O SER A 838 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N TYR A 843 " --> pdb=" O GLN A 839 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N SER A 845 " --> pdb=" O VAL A 841 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N PHE A 846 " --> pdb=" O GLU A 842 " (cutoff:3.500A) removed outlier: 4.000A 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 921 Processing helix chain 'A' and resid 927 through 936 removed outlier: 3.521A pdb=" N ASN A 935 " --> pdb=" O VAL A 931 " (cutoff:3.500A) removed outlier: 3.971A 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 979 removed outlier: 4.110A pdb=" N SER A 978 " --> pdb=" O ALA A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1002 removed outlier: 3.727A 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 1037 through 1058 removed outlier: 4.185A pdb=" N ALA A1047 " --> pdb=" O ALA A1043 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN A1048 " --> pdb=" O VAL A1044 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N GLU A1050 " --> pdb=" O ASN A1046 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLN A1058 " --> pdb=" O ASN A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1076 Processing helix chain 'A' and resid 1079 through 1124 removed outlier: 4.967A pdb=" N ALA A1084 " --> pdb=" O PRO A1080 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR A1109 " --> pdb=" O LEU A1105 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A1110 " --> pdb=" O SER A1106 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 94 No H-bonds generated for 'chain 'B' and resid 92 through 94' Processing helix chain 'B' and resid 302 through 309 Processing helix chain 'B' and resid 346 through 349 No H-bonds generated for 'chain 'B' and resid 346 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: 5.085A pdb=" N SER B 377 " --> pdb=" O SER B 373 " (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 460 through 463 No H-bonds generated for 'chain 'B' and resid 460 through 463' Processing helix chain 'B' and resid 468 through 471 No H-bonds generated for 'chain 'B' and resid 468 through 471' Processing helix chain 'B' and resid 475 through 477 No H-bonds generated for 'chain 'B' and resid 475 through 477' Processing helix chain 'B' and resid 539 through 541 No H-bonds generated for 'chain 'B' and resid 539 through 541' 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 829 Processing helix chain 'B' and resid 834 through 873 removed outlier: 3.712A pdb=" N VAL B 841 " --> pdb=" O LYS B 837 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLU B 842 " --> pdb=" O SER B 838 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR B 843 " --> pdb=" O GLN B 839 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N SER B 845 " --> pdb=" O VAL B 841 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N PHE B 846 " --> pdb=" O GLU B 842 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS B 847 " --> pdb=" O TYR B 843 " (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 933 Processing helix chain 'B' and resid 946 through 953 Processing helix chain 'B' and resid 964 through 979 removed outlier: 3.541A pdb=" N THR B 975 " --> pdb=" O THR B 971 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER B 978 " --> pdb=" O ALA B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1002 removed outlier: 3.739A pdb=" N GLN B 996 " --> pdb=" O TYR B 992 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU B1002 " --> pdb=" O ARG B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1006 through 1030 removed outlier: 3.891A pdb=" N GLN B1013 " --> pdb=" O LEU B1009 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LYS B1014 " --> pdb=" O SER B1010 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU B1015 " --> pdb=" O GLN B1011 " (cutoff:3.500A) Processing helix chain 'B' and resid 1036 through 1059 removed outlier: 3.522A pdb=" N VAL B1044 " --> pdb=" O LYS B1040 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B1045 " --> pdb=" O ILE B1041 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU B1059 " --> pdb=" O LEU B1055 " (cutoff:3.500A) Processing helix chain 'B' and resid 1070 through 1076 Processing helix chain 'B' and resid 1079 through 1124 removed outlier: 5.052A pdb=" N ALA B1084 " --> pdb=" O PRO B1080 " (cutoff:3.500A) Processing helix chain 'B' and resid 1211 through 1213 No H-bonds generated for 'chain 'B' and resid 1211 through 1213' Processing helix chain 'L' and resid 60 through 62 No H-bonds generated for 'chain 'L' and resid 60 through 62' Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing sheet with id= A, first strand: chain 'J' and resid 65 through 73 Processing sheet with id= B, first strand: chain 'J' and resid 272 through 276 removed outlier: 3.518A pdb=" N PHE J 242 " --> pdb=" O ALA J 229 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'J' and resid 114 through 118 Processing sheet with id= D, first strand: chain 'J' and resid 252 through 256 removed outlier: 4.211A pdb=" N ALA J 128 " --> pdb=" O MET J 256 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY J 161 " --> pdb=" O TYR J 209 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'J' and resid 318 through 321 Processing sheet with id= F, first strand: chain 'J' and resid 332 through 335 removed outlier: 8.208A pdb=" N VAL J 333 " --> pdb=" O CYS J 630 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASN J 632 " --> pdb=" O VAL J 333 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N ARG J 335 " --> pdb=" O ASN J 632 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASP J 634 " --> pdb=" O ARG J 335 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N TYR J 667 " --> pdb=" O ILE J 680 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU J 659 " --> pdb=" O TYR J 667 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 353 through 355 removed outlier: 6.020A pdb=" N SER J 451 " --> pdb=" O VAL J 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'J' and resid 361 through 365 removed outlier: 3.963A pdb=" N SER J 401 " --> pdb=" O HIS J 606 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ASN J 444 " --> pdb=" O ALA J 381 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ALA J 381 " --> pdb=" O ASN J 444 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'J' and resid 484 through 488 Processing sheet with id= J, first strand: chain 'J' and resid 491 through 494 removed outlier: 4.410A pdb=" N CYS J 491 " --> pdb=" O SER J 553 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'J' and resid 755 through 759 Processing sheet with id= L, first strand: chain 'J' and resid 805 through 815 removed outlier: 3.504A pdb=" N ILE J1143 " --> pdb=" O PHE J1158 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N TYR J1160 " --> pdb=" O HIS J1141 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N HIS J1141 " --> pdb=" O TYR J1160 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'J' and resid 820 through 823 removed outlier: 4.117A pdb=" N LYS J 820 " --> pdb=" O LEU J 958 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'J' and resid 1174 through 1176 Processing sheet with id= O, first strand: chain 'J' and resid 1187 through 1192 Processing sheet with id= P, first strand: chain 'J' and resid 797 through 804 removed outlier: 6.531A pdb=" N LYS J1164 " --> pdb=" O SER J 803 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 29 through 31 Processing sheet with id= R, first strand: chain 'A' and resid 64 through 73 Processing sheet with id= S, first strand: chain 'A' and resid 272 through 276 removed outlier: 5.536A pdb=" N PHE A 231 " --> pdb=" O PHE A 240 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N PHE A 240 " --> pdb=" O PHE A 231 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'A' and resid 114 through 118 Processing sheet with id= U, first strand: chain 'A' and resid 252 through 255 removed outlier: 4.010A pdb=" N GLY A 161 " --> pdb=" O TYR A 209 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'A' and resid 318 through 321 Processing sheet with id= W, first strand: chain 'A' and resid 324 through 326 Processing sheet with id= X, first strand: chain 'A' and resid 331 through 335 removed outlier: 4.055A pdb=" N ALA A 331 " --> pdb=" O CYS A 630 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N TYR A 667 " --> pdb=" O ILE A 680 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU A 659 " --> pdb=" O TYR A 667 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.070A pdb=" N SER A 451 " --> pdb=" O VAL A 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'A' and resid 361 through 365 removed outlier: 3.992A pdb=" N SER A 401 " --> pdb=" O HIS A 606 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ASN A 444 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ALA A 381 " --> pdb=" O ASN A 444 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'A' and resid 484 through 488 Processing sheet with id= AB, first strand: chain 'A' and resid 773 through 777 removed outlier: 5.737A pdb=" N VAL A 757 " --> pdb=" O THR A 750 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N THR A 750 " --> pdb=" O VAL A 757 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'A' and resid 805 through 815 removed outlier: 3.554A pdb=" N ILE A1143 " --> pdb=" O PHE A1158 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N TYR A1160 " --> pdb=" O HIS A1141 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N HIS A1141 " --> pdb=" O TYR A1160 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'A' and resid 820 through 823 removed outlier: 4.292A pdb=" N LYS A 820 " --> pdb=" O LEU A 958 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'A' and resid 1174 through 1176 Processing sheet with id= AF, first strand: chain 'A' and resid 1187 through 1192 Processing sheet with id= AG, first strand: chain 'A' and resid 41 through 44 removed outlier: 6.503A pdb=" N TYR A 79 " --> pdb=" O THR A 42 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'A' and resid 797 through 804 removed outlier: 6.516A pdb=" N LYS A1164 " --> pdb=" O SER A 803 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'B' and resid 29 through 31 Processing sheet with id= AJ, first strand: chain 'B' and resid 64 through 72 removed outlier: 3.856A pdb=" N ASN B 294 " --> pdb=" O ALA B 285 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'B' and resid 272 through 276 removed outlier: 5.512A pdb=" N PHE B 231 " --> pdb=" O PHE B 240 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N PHE B 240 " --> pdb=" O PHE B 231 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'B' and resid 116 through 118 Processing sheet with id= AM, first strand: chain 'B' and resid 252 through 255 Processing sheet with id= AN, first strand: chain 'B' and resid 318 through 321 removed outlier: 3.574A pdb=" N CYS B 732 " --> pdb=" O PHE B 703 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'B' and resid 332 through 335 removed outlier: 8.068A pdb=" N VAL B 333 " --> pdb=" O CYS B 630 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASN B 632 " --> pdb=" O VAL B 333 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N ARG B 335 " --> pdb=" O ASN B 632 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASP B 634 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N THR B 677 " --> pdb=" O VAL B 647 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N TYR B 667 " --> pdb=" O ILE B 680 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU B 659 " --> pdb=" O TYR B 667 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'B' and resid 353 through 355 removed outlier: 6.155A pdb=" N SER B 451 " --> pdb=" O VAL B 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= AP Processing sheet with id= AQ, first strand: chain 'B' and resid 361 through 365 removed outlier: 3.561A pdb=" N SER B 401 " --> pdb=" O HIS B 606 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ASN B 444 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ALA B 381 " --> pdb=" O ASN B 444 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'B' and resid 484 through 488 Processing sheet with id= AS, first strand: chain 'B' and resid 755 through 759 Processing sheet with id= AT, first strand: chain 'B' and resid 797 through 802 Processing sheet with id= AU, first strand: chain 'B' and resid 805 through 815 Processing sheet with id= AV, first strand: chain 'B' and resid 820 through 823 removed outlier: 4.286A pdb=" N LYS B 820 " --> pdb=" O LEU B 958 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'B' and resid 1225 through 1227 Processing sheet with id= AX, first strand: chain 'B' and resid 1187 through 1192 Processing sheet with id= AY, first strand: chain 'H' and resid 21 through 23 Processing sheet with id= AZ, first strand: chain 'H' and resid 43 through 45 Processing sheet with id= BA, first strand: chain 'L' and resid 34 through 38 955 hydrogen bonds defined for protein. 2607 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: 12.99 Time building geometry restraints manager: 12.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 7714 1.33 - 1.47: 9841 1.47 - 1.61: 12282 1.61 - 1.75: 16 1.75 - 1.89: 230 Bond restraints: 30083 Sorted by residual: bond pdb=" CB PHE A 669 " pdb=" CG PHE A 669 " ideal model delta sigma weight residual 1.502 1.350 0.152 2.30e-02 1.89e+03 4.38e+01 bond pdb=" CB HIS A 193 " pdb=" CG HIS A 193 " ideal model delta sigma weight residual 1.497 1.406 0.091 1.40e-02 5.10e+03 4.20e+01 bond pdb=" CB HIS J 219 " pdb=" CG HIS J 219 " ideal model delta sigma weight residual 1.497 1.412 0.085 1.40e-02 5.10e+03 3.73e+01 bond pdb=" CB HIS A 219 " pdb=" CG HIS A 219 " ideal model delta sigma weight residual 1.497 1.412 0.085 1.40e-02 5.10e+03 3.68e+01 bond pdb=" CB HIS A 483 " pdb=" CG HIS A 483 " ideal model delta sigma weight residual 1.497 1.416 0.081 1.40e-02 5.10e+03 3.38e+01 ... (remaining 30078 not shown) Histogram of bond angle deviations from ideal: 97.65 - 104.99: 642 104.99 - 112.34: 14095 112.34 - 119.68: 11904 119.68 - 127.02: 14145 127.02 - 134.37: 183 Bond angle restraints: 40969 Sorted by residual: angle pdb=" N PRO A 981 " pdb=" CA PRO A 981 " pdb=" C PRO A 981 " ideal model delta sigma weight residual 110.70 122.80 -12.10 1.22e+00 6.72e-01 9.84e+01 angle pdb=" N PHE J 240 " pdb=" CA PHE J 240 " pdb=" C PHE J 240 " ideal model delta sigma weight residual 111.33 123.13 -11.80 1.21e+00 6.83e-01 9.51e+01 angle pdb=" C LYS J 473 " pdb=" N PRO J 474 " pdb=" CA PRO J 474 " ideal model delta sigma weight residual 119.76 128.89 -9.13 1.03e+00 9.43e-01 7.86e+01 angle pdb=" C PRO B 959 " pdb=" N PRO B 960 " pdb=" CA PRO B 960 " ideal model delta sigma weight residual 120.03 128.54 -8.51 9.90e-01 1.02e+00 7.39e+01 angle pdb=" C ALA J 314 " pdb=" N PRO J 315 " pdb=" CA PRO J 315 " ideal model delta sigma weight residual 119.66 125.88 -6.22 7.30e-01 1.88e+00 7.26e+01 ... (remaining 40964 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.75: 18085 21.75 - 43.49: 402 43.49 - 65.23: 137 65.23 - 86.98: 23 86.98 - 108.72: 8 Dihedral angle restraints: 18655 sinusoidal: 7669 harmonic: 10986 Sorted by residual: dihedral pdb=" CB CYS B 21 " pdb=" SG CYS B 21 " pdb=" SG CYS B 173 " pdb=" CB CYS B 173 " ideal model delta sinusoidal sigma weight residual 93.00 44.86 48.14 1 1.00e+01 1.00e-02 3.19e+01 dihedral pdb=" CA UNK L 30 " pdb=" C UNK L 30 " pdb=" N UNK L 31 " pdb=" CA UNK L 31 " ideal model delta harmonic sigma weight residual -180.00 -152.83 -27.17 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" C TRP A 460 " pdb=" N TRP A 460 " pdb=" CA TRP A 460 " pdb=" CB TRP A 460 " ideal model delta harmonic sigma weight residual -122.60 -135.61 13.01 0 2.50e+00 1.60e-01 2.71e+01 ... (remaining 18652 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 3622 0.104 - 0.207: 1059 0.207 - 0.311: 118 0.311 - 0.415: 15 0.415 - 0.519: 3 Chirality restraints: 4817 Sorted by residual: chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.51e+01 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.43e+01 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.21e+01 ... (remaining 4814 not shown) Planarity restraints: 5270 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1405 " -0.333 2.00e-02 2.50e+03 2.82e-01 9.96e+02 pdb=" C7 NAG B1405 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG B1405 " -0.184 2.00e-02 2.50e+03 pdb=" N2 NAG B1405 " 0.492 2.00e-02 2.50e+03 pdb=" O7 NAG B1405 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1403 " -0.228 2.00e-02 2.50e+03 1.90e-01 4.52e+02 pdb=" C7 NAG B1403 " 0.063 2.00e-02 2.50e+03 pdb=" C8 NAG B1403 " -0.161 2.00e-02 2.50e+03 pdb=" N2 NAG B1403 " 0.314 2.00e-02 2.50e+03 pdb=" O7 NAG B1403 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 936 " -0.063 2.00e-02 2.50e+03 1.29e-01 1.67e+02 pdb=" C ASN B 936 " 0.223 2.00e-02 2.50e+03 pdb=" O ASN B 936 " -0.085 2.00e-02 2.50e+03 pdb=" N CYS B 937 " -0.075 2.00e-02 2.50e+03 ... (remaining 5267 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 8939 2.82 - 3.34: 26555 3.34 - 3.86: 48584 3.86 - 4.38: 57627 4.38 - 4.90: 94253 Nonbonded interactions: 235958 Sorted by model distance: nonbonded pdb=" N ASN B 935 " pdb=" O ASN B 935 " model vdw 2.294 2.496 nonbonded pdb=" N ASN J 935 " pdb=" O ASN J 935 " model vdw 2.307 2.496 nonbonded pdb=" N ASN A 371 " pdb=" OD1 ASN A 371 " model vdw 2.319 2.520 nonbonded pdb=" NZ LYS J 85 " pdb=" OG1 THR J 87 " model vdw 2.343 2.520 nonbonded pdb=" N ASN A1046 " pdb=" O ASN A1046 " model vdw 2.345 2.496 ... (remaining 235953 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 23 or resid 25 or resid 39 through 761 or resid \ 771 through 901 or resid 910 through 1232 or resid 1401 through 1408)) selection = (chain 'B' and (resid 15 through 23 or resid 29 or resid 39 through 151 or resid \ 159 through 195 or resid 199 through 505 or resid 517 through 901 or resid 910 \ through 1232 or resid 1402 through 1409)) selection = (chain 'J' and (resid 15 through 23 or resid 25 or resid 39 through 151 or resid \ 159 through 195 or resid 199 through 505 or resid 517 through 761 or resid 771 \ through 901 or resid 910 through 1232 or resid 1402 through 1409)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } ncs_group { reference = (chain 'H' and resid 13 through 114) 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: 4.050 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: 0.000 Extract box with map and model: 9.970 Check model and map are aligned: 0.420 Set scattering table: 0.280 Process input model: 79.410 Find NCS groups from input model: 2.590 Set up NCS constraints: 0.510 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 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 : 0.019 0.152 30083 Z= 1.207 Angle : 1.743 13.349 40969 Z= 1.160 Chirality : 0.093 0.519 4817 Planarity : 0.010 0.282 5229 Dihedral : 10.581 108.724 11422 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.36 % Allowed : 0.71 % Favored : 98.93 % Cbeta Deviations : 0.11 % 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: 0.19 (0.13), residues: 3505 helix: -0.68 (0.16), residues: 816 sheet: 0.94 (0.16), residues: 806 loop : 0.28 (0.14), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.008 TRP A 655 HIS 0.012 0.002 HIS B 177 PHE 0.030 0.005 PHE J 542 TYR 0.067 0.008 TYR B 667 ARG 0.007 0.001 ARG J1093 *********************** 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 386 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 375 time to evaluate : 3.312 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 REVERT: J 389 ILE cc_start: 0.8754 (mm) cc_final: 0.8542 (tt) REVERT: A 938 THR cc_start: 0.8584 (p) cc_final: 0.8362 (p) REVERT: B 444 ASN cc_start: 0.7826 (m-40) cc_final: 0.7188 (m-40) REVERT: B 886 VAL cc_start: 0.8308 (t) cc_final: 0.8035 (p) outliers start: 11 outliers final: 7 residues processed: 386 average time/residue: 0.4269 time to fit residues: 261.1287 Evaluate side-chains 146 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 139 time to evaluate : 3.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 695 ASN Chi-restraints excluded: chain B residue 787 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 315 optimal weight: 1.9990 chunk 283 optimal weight: 7.9990 chunk 157 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 191 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 293 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 178 optimal weight: 2.9990 chunk 218 optimal weight: 0.9990 chunk 339 optimal weight: 0.8980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 187 HIS J 219 HIS ** J 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 724 ASN ** J 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 800 GLN J1011 GLN J1091 ASN J1103 GLN J1147 GLN A 252 HIS A 418 GLN ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 724 ASN A 777 ASN A 849 ASN A1061 ASN A1071 GLN A1138 ASN B 31 ASN B 252 HIS B 418 GLN B 849 ASN B 865 GLN ** B 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1103 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30083 Z= 0.198 Angle : 0.630 10.782 40969 Z= 0.334 Chirality : 0.045 0.233 4817 Planarity : 0.004 0.050 5229 Dihedral : 7.353 68.932 5264 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.04 % Allowed : 4.12 % Favored : 94.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.14), residues: 3505 helix: 0.85 (0.19), residues: 791 sheet: 0.71 (0.17), residues: 805 loop : 0.15 (0.14), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 273 HIS 0.018 0.001 HIS B 187 PHE 0.019 0.002 PHE A 286 TYR 0.020 0.002 TYR J 667 ARG 0.005 0.001 ARG A 264 *********************** 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 207 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 175 time to evaluate : 3.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.7454 (tpp) cc_final: 0.6827 (tpp) outliers start: 32 outliers final: 17 residues processed: 198 average time/residue: 0.3661 time to fit residues: 123.7343 Evaluate side-chains 135 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 3.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 293 PHE Chi-restraints excluded: chain J residue 344 ASN Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain J residue 1066 ILE Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 1138 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 188 optimal weight: 8.9990 chunk 105 optimal weight: 0.7980 chunk 282 optimal weight: 0.2980 chunk 231 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 340 optimal weight: 0.9980 chunk 367 optimal weight: 40.0000 chunk 303 optimal weight: 2.9990 chunk 337 optimal weight: 5.9990 chunk 115 optimal weight: 0.0370 chunk 272 optimal weight: 8.9990 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 252 HIS J 388 ASN ** J 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1000 ASN ** J1138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 ASN ** A 724 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN A 874 ASN B 777 ASN ** B 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 30083 Z= 0.155 Angle : 0.520 11.787 40969 Z= 0.278 Chirality : 0.042 0.247 4817 Planarity : 0.004 0.042 5229 Dihedral : 6.059 59.085 5260 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.17 % Allowed : 5.09 % Favored : 93.74 % 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: 1.25 (0.19), residues: 796 sheet: 0.77 (0.17), residues: 796 loop : 0.08 (0.14), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 192 HIS 0.007 0.001 HIS B 187 PHE 0.028 0.001 PHE B 268 TYR 0.015 0.001 TYR J 79 ARG 0.005 0.000 ARG A 264 *********************** 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 167 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 131 time to evaluate : 3.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 82 MET cc_start: 0.8742 (mmm) cc_final: 0.8473 (mmt) REVERT: A 122 MET cc_start: 0.7517 (tpp) cc_final: 0.7050 (tpp) outliers start: 36 outliers final: 19 residues processed: 160 average time/residue: 0.3660 time to fit residues: 102.5134 Evaluate side-chains 123 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 3.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 344 ASN Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain J residue 810 MET Chi-restraints excluded: chain J residue 1066 ILE Chi-restraints excluded: chain J residue 1074 LEU Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 188 PHE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 787 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 336 optimal weight: 10.0000 chunk 255 optimal weight: 6.9990 chunk 176 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 162 optimal weight: 0.7980 chunk 228 optimal weight: 7.9990 chunk 341 optimal weight: 6.9990 chunk 361 optimal weight: 30.0000 chunk 178 optimal weight: 1.9990 chunk 323 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 344 ASN ** J 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 219 HIS ** A 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 724 ASN A 996 GLN ** B 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 30083 Z= 0.405 Angle : 0.669 18.253 40969 Z= 0.344 Chirality : 0.047 0.307 4817 Planarity : 0.005 0.054 5229 Dihedral : 6.307 57.808 5260 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.39 % Allowed : 5.38 % Favored : 93.22 % 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: 0.30 (0.14), residues: 3505 helix: 1.13 (0.19), residues: 780 sheet: 0.44 (0.17), residues: 802 loop : -0.23 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 273 HIS 0.015 0.002 HIS B 187 PHE 0.028 0.002 PHE B 268 TYR 0.028 0.002 TYR A1224 ARG 0.006 0.001 ARG B1093 *********************** 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 164 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 121 time to evaluate : 3.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.6963 (OUTLIER) cc_final: 0.6498 (m-30) REVERT: A 122 MET cc_start: 0.7653 (tpp) cc_final: 0.7299 (tpp) outliers start: 43 outliers final: 31 residues processed: 156 average time/residue: 0.3694 time to fit residues: 99.6635 Evaluate side-chains 132 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 100 time to evaluate : 3.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 270 LEU Chi-restraints excluded: chain J residue 333 VAL Chi-restraints excluded: chain J residue 344 ASN Chi-restraints excluded: chain J residue 593 GLN Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain J residue 810 MET Chi-restraints excluded: chain J residue 1066 ILE Chi-restraints excluded: chain J residue 1074 LEU Chi-restraints excluded: chain J residue 1078 ASP Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 192 TRP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 1138 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 301 optimal weight: 0.7980 chunk 205 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 269 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 chunk 308 optimal weight: 0.9990 chunk 249 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 184 optimal weight: 0.8980 chunk 324 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 429 ASN J 444 ASN J 800 GLN ** J 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1138 ASN ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1000 ASN B 874 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30083 Z= 0.199 Angle : 0.525 12.009 40969 Z= 0.275 Chirality : 0.042 0.211 4817 Planarity : 0.004 0.047 5229 Dihedral : 5.706 54.458 5260 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.27 % Allowed : 6.00 % Favored : 92.73 % 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: 0.38 (0.14), residues: 3505 helix: 1.41 (0.20), residues: 771 sheet: 0.45 (0.17), residues: 792 loop : -0.25 (0.14), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 192 HIS 0.011 0.001 HIS B 187 PHE 0.022 0.001 PHE B 268 TYR 0.013 0.001 TYR J 667 ARG 0.004 0.000 ARG B 944 *********************** 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 146 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 107 time to evaluate : 3.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.7592 (tpp) cc_final: 0.7263 (tpp) outliers start: 39 outliers final: 25 residues processed: 142 average time/residue: 0.4088 time to fit residues: 103.4968 Evaluate side-chains 122 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 97 time to evaluate : 3.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 26 ARG Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 333 VAL Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain J residue 1066 ILE Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 192 TRP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 1138 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 121 optimal weight: 5.9990 chunk 325 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 212 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 361 optimal weight: 30.0000 chunk 300 optimal weight: 9.9990 chunk 167 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 119 optimal weight: 20.0000 chunk 189 optimal weight: 3.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 157 ASN J 344 ASN ** J 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1138 ASN A 598 ASN ** A1138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 865 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 30083 Z= 0.388 Angle : 0.618 12.660 40969 Z= 0.320 Chirality : 0.045 0.310 4817 Planarity : 0.004 0.048 5229 Dihedral : 6.060 54.600 5260 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.52 % Allowed : 6.13 % Favored : 92.35 % 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: 0.17 (0.14), residues: 3505 helix: 1.25 (0.19), residues: 777 sheet: 0.36 (0.17), residues: 802 loop : -0.43 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 655 HIS 0.011 0.001 HIS B 187 PHE 0.023 0.002 PHE B 268 TYR 0.019 0.002 TYR A1224 ARG 0.006 0.001 ARG B1093 *********************** 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 153 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 106 time to evaluate : 3.448 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: A 119 ASP cc_start: 0.7076 (OUTLIER) cc_final: 0.6747 (m-30) REVERT: A 122 MET cc_start: 0.7614 (tpp) cc_final: 0.7341 (tpp) outliers start: 47 outliers final: 35 residues processed: 147 average time/residue: 0.3711 time to fit residues: 95.4711 Evaluate side-chains 132 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 96 time to evaluate : 3.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 219 HIS Chi-restraints excluded: chain J residue 333 VAL Chi-restraints excluded: chain J residue 344 ASN Chi-restraints excluded: chain J residue 593 GLN Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 734 VAL Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain J residue 810 MET Chi-restraints excluded: chain J residue 846 PHE Chi-restraints excluded: chain J residue 1066 ILE Chi-restraints excluded: chain J residue 1074 LEU Chi-restraints excluded: chain J residue 1078 ASP Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1222 VAL Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 192 TRP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 1138 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 348 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 206 optimal weight: 9.9990 chunk 264 optimal weight: 0.9990 chunk 204 optimal weight: 6.9990 chunk 304 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 chunk 360 optimal weight: 40.0000 chunk 225 optimal weight: 3.9990 chunk 219 optimal weight: 4.9990 chunk 166 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1138 ASN A 598 ASN ** A1138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN B 533 ASN B 865 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 30083 Z= 0.291 Angle : 0.553 12.326 40969 Z= 0.289 Chirality : 0.043 0.224 4817 Planarity : 0.004 0.048 5229 Dihedral : 5.880 55.466 5260 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.05 % Favored : 96.92 % Rotamer: Outliers : 1.52 % Allowed : 6.62 % Favored : 91.86 % 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: 0.18 (0.14), residues: 3505 helix: 1.37 (0.20), residues: 778 sheet: 0.35 (0.18), residues: 792 loop : -0.46 (0.14), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 460 HIS 0.010 0.001 HIS B 187 PHE 0.030 0.001 PHE B 268 TYR 0.013 0.001 TYR A 71 ARG 0.005 0.000 ARG B 944 *********************** 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 154 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 107 time to evaluate : 3.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 82 MET cc_start: 0.8993 (mmm) cc_final: 0.8675 (mmt) REVERT: A 122 MET cc_start: 0.7581 (tpp) cc_final: 0.7331 (tpp) outliers start: 47 outliers final: 34 residues processed: 146 average time/residue: 0.4124 time to fit residues: 106.4132 Evaluate side-chains 132 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 98 time to evaluate : 3.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 219 HIS Chi-restraints excluded: chain J residue 248 MET Chi-restraints excluded: chain J residue 542 PHE Chi-restraints excluded: chain J residue 593 GLN Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 734 VAL Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain J residue 810 MET Chi-restraints excluded: chain J residue 846 PHE Chi-restraints excluded: chain J residue 847 CYS Chi-restraints excluded: chain J residue 1066 ILE Chi-restraints excluded: chain J residue 1074 LEU Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 192 TRP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 689 SER Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 1138 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 223 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 215 optimal weight: 0.0470 chunk 108 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 229 optimal weight: 2.9990 chunk 245 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 283 optimal weight: 20.0000 overall best weight: 1.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN ** A1138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 874 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30083 Z= 0.206 Angle : 0.517 13.286 40969 Z= 0.270 Chirality : 0.042 0.202 4817 Planarity : 0.004 0.047 5229 Dihedral : 5.588 54.632 5260 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.17 % Allowed : 6.81 % Favored : 92.02 % 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: 0.25 (0.14), residues: 3505 helix: 1.49 (0.20), residues: 779 sheet: 0.43 (0.18), residues: 783 loop : -0.46 (0.14), residues: 1943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 460 HIS 0.009 0.001 HIS B 187 PHE 0.019 0.001 PHE A 286 TYR 0.013 0.001 TYR B 221 ARG 0.005 0.000 ARG B 944 *********************** 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 143 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 107 time to evaluate : 3.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 873 MET cc_start: 0.8366 (mmm) cc_final: 0.8077 (mmt) REVERT: A 122 MET cc_start: 0.7525 (tpp) cc_final: 0.7253 (tpp) outliers start: 36 outliers final: 31 residues processed: 138 average time/residue: 0.3766 time to fit residues: 90.8826 Evaluate side-chains 130 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 99 time to evaluate : 3.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 219 HIS Chi-restraints excluded: chain J residue 542 PHE Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 734 VAL Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain J residue 810 MET Chi-restraints excluded: chain J residue 846 PHE Chi-restraints excluded: chain J residue 847 CYS Chi-restraints excluded: chain J residue 1066 ILE Chi-restraints excluded: chain J residue 1074 LEU Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 192 TRP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 1138 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 327 optimal weight: 5.9990 chunk 345 optimal weight: 5.9990 chunk 315 optimal weight: 5.9990 chunk 335 optimal weight: 5.9990 chunk 202 optimal weight: 7.9990 chunk 146 optimal weight: 0.7980 chunk 263 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 303 optimal weight: 6.9990 chunk 317 optimal weight: 4.9990 chunk 334 optimal weight: 1.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 344 ASN ** J 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 800 GLN ** J 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 HIS ** A 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 30083 Z= 0.270 Angle : 0.535 12.729 40969 Z= 0.279 Chirality : 0.042 0.206 4817 Planarity : 0.004 0.048 5229 Dihedral : 5.642 55.548 5260 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.23 % Allowed : 7.01 % Favored : 91.76 % 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: 0.19 (0.14), residues: 3505 helix: 1.47 (0.20), residues: 778 sheet: 0.37 (0.18), residues: 791 loop : -0.51 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 460 HIS 0.008 0.001 HIS B 187 PHE 0.017 0.001 PHE A 286 TYR 0.013 0.001 TYR J 667 ARG 0.003 0.000 ARG B 944 *********************** 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 141 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 103 time to evaluate : 3.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.7533 (tpp) cc_final: 0.7247 (tpp) outliers start: 38 outliers final: 35 residues processed: 137 average time/residue: 0.3665 time to fit residues: 87.1104 Evaluate side-chains 134 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 99 time to evaluate : 3.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 219 HIS Chi-restraints excluded: chain J residue 333 VAL Chi-restraints excluded: chain J residue 344 ASN Chi-restraints excluded: chain J residue 542 PHE Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 734 VAL Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain J residue 810 MET Chi-restraints excluded: chain J residue 846 PHE Chi-restraints excluded: chain J residue 847 CYS Chi-restraints excluded: chain J residue 1066 ILE Chi-restraints excluded: chain J residue 1074 LEU Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1078 ASP Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 192 TRP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 1138 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 220 optimal weight: 0.0020 chunk 355 optimal weight: 20.0000 chunk 216 optimal weight: 3.9990 chunk 168 optimal weight: 6.9990 chunk 246 optimal weight: 5.9990 chunk 372 optimal weight: 20.0000 chunk 342 optimal weight: 2.9990 chunk 296 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 229 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 344 ASN ** J 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 ASN ** A1138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30083 Z= 0.241 Angle : 0.527 12.771 40969 Z= 0.275 Chirality : 0.042 0.202 4817 Planarity : 0.004 0.048 5229 Dihedral : 5.585 55.177 5260 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.10 % Allowed : 7.27 % Favored : 91.63 % 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: 0.17 (0.14), residues: 3505 helix: 1.44 (0.20), residues: 786 sheet: 0.36 (0.18), residues: 791 loop : -0.52 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 460 HIS 0.008 0.001 HIS B 187 PHE 0.019 0.001 PHE A 286 TYR 0.012 0.001 TYR B 221 ARG 0.010 0.000 ARG B 264 ********************** 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 137 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 103 time to evaluate : 3.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 82 MET cc_start: 0.8930 (mmm) cc_final: 0.8606 (mmt) REVERT: J 873 MET cc_start: 0.8369 (mmm) cc_final: 0.8075 (mmt) REVERT: A 122 MET cc_start: 0.7533 (tpp) cc_final: 0.7257 (tpp) outliers start: 34 outliers final: 34 residues processed: 133 average time/residue: 0.3574 time to fit residues: 84.8317 Evaluate side-chains 134 residues out of total 3083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 100 time to evaluate : 3.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 219 HIS Chi-restraints excluded: chain J residue 344 ASN Chi-restraints excluded: chain J residue 542 PHE Chi-restraints excluded: chain J residue 645 VAL Chi-restraints excluded: chain J residue 734 VAL Chi-restraints excluded: chain J residue 787 ASN Chi-restraints excluded: chain J residue 810 MET Chi-restraints excluded: chain J residue 846 PHE Chi-restraints excluded: chain J residue 847 CYS Chi-restraints excluded: chain J residue 1066 ILE Chi-restraints excluded: chain J residue 1074 LEU Chi-restraints excluded: chain A residue 301 ASP Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 787 ASN Chi-restraints excluded: chain A residue 1066 ILE Chi-restraints excluded: chain A residue 1078 ASP Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 192 TRP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 353 SER Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain B residue 787 ASN Chi-restraints excluded: chain B residue 1138 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 235 optimal weight: 0.0570 chunk 316 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 273 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 chunk 297 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 305 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 54 optimal weight: 0.4980 overall best weight: 1.0300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 344 ASN ** J 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 598 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.065202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.050471 restraints weight = 83207.185| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 2.93 r_work: 0.2566 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.125 30083 Z= 0.220 Angle : 0.640 59.192 40969 Z= 0.354 Chirality : 0.042 0.379 4817 Planarity : 0.004 0.049 5229 Dihedral : 5.590 55.179 5260 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.25 % Favored : 96.72 % Rotamer: Outliers : 1.20 % Allowed : 7.30 % Favored : 91.50 % 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: 0.18 (0.14), residues: 3505 helix: 1.45 (0.20), residues: 786 sheet: 0.36 (0.18), residues: 791 loop : -0.52 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 460 HIS 0.007 0.001 HIS B 187 PHE 0.018 0.001 PHE A 286 TYR 0.012 0.001 TYR B 221 ARG 0.007 0.000 ARG B 264 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4802.09 seconds wall clock time: 89 minutes 53.64 seconds (5393.64 seconds total)