Starting phenix.real_space_refine on Wed Mar 20 05:18:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jw0_22512/03_2024/7jw0_22512.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jw0_22512/03_2024/7jw0_22512.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jw0_22512/03_2024/7jw0_22512.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jw0_22512/03_2024/7jw0_22512.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jw0_22512/03_2024/7jw0_22512.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jw0_22512/03_2024/7jw0_22512.pdb" } resolution = 4.3 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= 0.004 sd= 0.044 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 123 5.16 5 C 16324 2.51 5 N 4778 2.21 5 O 5026 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 26251 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 6270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 6270 Classifications: {'peptide': 1007} Incomplete info: {'truncation_to_alanine': 533} Link IDs: {'PTRANS': 50, 'TRANS': 956} Chain breaks: 9 Unresolved non-hydrogen bonds: 1641 Unresolved non-hydrogen angles: 2121 Unresolved non-hydrogen dihedrals: 1250 Unresolved non-hydrogen chiralities: 219 Planarities with less than four sites: {'GLN:plan1': 30, 'ASP:plan': 42, 'TYR:plan': 13, 'ASN:plan1': 48, 'HIS:plan': 4, 'PHE:plan': 21, 'GLU:plan': 34, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 853 Chain: "L" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1074 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 170} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 199} Unresolved non-hydrogen bonds: 570 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 476 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 2, 'TYR:plan': 11, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 8, 'GLU:plan': 8, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 316 Chain: "H" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1097 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 207} Unresolved non-hydrogen bonds: 574 Unresolved non-hydrogen angles: 750 Unresolved non-hydrogen dihedrals: 488 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 14, 'ASN:plan1': 6, 'TRP:plan': 4, 'ASP:plan': 9, 'PHE:plan': 7, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 314 Chain: "B" Number of atoms: 6237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 6237 Classifications: {'peptide': 1007} Incomplete info: {'truncation_to_alanine': 539} Link IDs: {'PTRANS': 50, 'TRANS': 956} Chain breaks: 9 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1681 Unresolved non-hydrogen angles: 2176 Unresolved non-hydrogen dihedrals: 1292 Unresolved non-hydrogen chiralities: 219 Planarities with less than four sites: {'GLN:plan1': 30, 'ASP:plan': 42, 'TYR:plan': 15, 'ASN:plan1': 48, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 22, 'GLU:plan': 34, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 882 Chain: "C" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1074 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 170} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 199} Unresolved non-hydrogen bonds: 570 Unresolved non-hydrogen angles: 731 Unresolved non-hydrogen dihedrals: 476 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 2, 'TYR:plan': 11, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 8, 'GLU:plan': 8, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 316 Chain: "D" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1097 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 207} Unresolved non-hydrogen bonds: 574 Unresolved non-hydrogen angles: 750 Unresolved non-hydrogen dihedrals: 488 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 14, 'ASN:plan1': 6, 'TRP:plan': 4, 'ASP:plan': 9, 'PHE:plan': 7, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 314 Chain: "E" Number of atoms: 6271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 6271 Classifications: {'peptide': 1007} Incomplete info: {'truncation_to_alanine': 532} Link IDs: {'PTRANS': 50, 'TRANS': 956} Chain breaks: 9 Unresolved non-hydrogen bonds: 1640 Unresolved non-hydrogen angles: 2120 Unresolved non-hydrogen dihedrals: 1249 Unresolved non-hydrogen chiralities: 219 Planarities with less than four sites: {'GLN:plan1': 30, 'ASP:plan': 42, 'TYR:plan': 13, 'ASN:plan1': 48, 'HIS:plan': 4, 'PHE:plan': 21, 'GLU:plan': 34, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 853 Chain: "F" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1077 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 168} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 199} Unresolved non-hydrogen bonds: 567 Unresolved non-hydrogen angles: 727 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 54 Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 2, 'TYR:plan': 11, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 8, 'GLU:plan': 8, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 316 Chain: "G" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1097 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 207} Unresolved non-hydrogen bonds: 574 Unresolved non-hydrogen angles: 750 Unresolved non-hydrogen dihedrals: 488 Unresolved non-hydrogen chiralities: 61 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 14, 'ASN:plan1': 6, 'TRP:plan': 4, 'ASP:plan': 9, 'PHE:plan': 7, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 314 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: "J" 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: 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: "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: 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: "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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "E" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 12.98, per 1000 atoms: 0.49 Number of scatterers: 26251 At special positions: 0 Unit cell: (147, 152.25, 203.7, 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 123 16.00 O 5026 8.00 N 4778 7.00 C 16324 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=1.87 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.08 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.02 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=1.87 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.02 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 203 " distance=2.03 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 136 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=1.87 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.02 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.04 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.08 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.02 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.04 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.04 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 135 " - pdb=" SG CYS F 195 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 95 " distance=2.02 Simple disulfide: pdb=" SG CYS G 147 " - pdb=" SG CYS G 203 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " 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 R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A 717 " " NAG A1311 " - " ASN A1074 " " NAG A1312 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B 717 " " NAG B1311 " - " ASN B1074 " " NAG B1312 " - " ASN B 165 " " NAG E1301 " - " ASN E 61 " " NAG E1302 " - " ASN E 122 " " NAG E1303 " - " ASN E 234 " " NAG E1304 " - " ASN E 282 " " NAG E1305 " - " ASN E 331 " " NAG E1306 " - " ASN E 603 " " NAG E1307 " - " ASN E 616 " " NAG E1308 " - " ASN E 657 " " NAG E1309 " - " ASN E 709 " " NAG E1310 " - " ASN E 717 " " NAG E1311 " - " ASN E1074 " " NAG E1312 " - " ASN E 165 " " NAG I 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG M 1 " - " ASN A 343 " " NAG N 1 " - " ASN A 17 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN B 343 " " NAG S 1 " - " ASN B 17 " " NAG T 1 " - " ASN E 801 " " NAG U 1 " - " ASN E1098 " " NAG V 1 " - " ASN E1134 " " NAG W 1 " - " ASN E 343 " " NAG X 1 " - " ASN E 17 " Time building additional restraints: 9.24 Conformation dependent library (CDL) restraints added in 6.0 seconds 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8040 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 87 sheets defined 20.9% alpha, 36.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.30 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.946A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.345A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.707A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.219A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 941 through 944 removed outlier: 4.052A pdb=" N ALA A 944 " --> pdb=" O THR A 941 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 941 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.826A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.989A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.178A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'L' and resid 122 through 127 Processing helix chain 'L' and resid 185 through 187 No H-bonds generated for 'chain 'L' and resid 185 through 187' Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'H' and resid 134 through 136 No H-bonds generated for 'chain 'H' and resid 134 through 136' Processing helix chain 'H' and resid 163 through 165 No H-bonds generated for 'chain 'H' and resid 163 through 165' Processing helix chain 'H' and resid 194 through 196 No H-bonds generated for 'chain 'H' and resid 194 through 196' Processing helix chain 'H' and resid 209 through 211 No H-bonds generated for 'chain 'H' and resid 209 through 211' Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 365 through 369 Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.945A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.345A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.706A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.219A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 941 through 944 removed outlier: 4.053A pdb=" N ALA B 944 " --> pdb=" O THR B 941 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 941 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.826A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.989A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.178A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'C' and resid 122 through 127 Processing helix chain 'C' and resid 185 through 187 No H-bonds generated for 'chain 'C' and resid 185 through 187' Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'D' and resid 134 through 136 No H-bonds generated for 'chain 'D' and resid 134 through 136' Processing helix chain 'D' and resid 163 through 165 No H-bonds generated for 'chain 'D' and resid 163 through 165' Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 209 through 211 No H-bonds generated for 'chain 'D' and resid 209 through 211' Processing helix chain 'E' and resid 294 through 303 Processing helix chain 'E' and resid 337 through 343 Processing helix chain 'E' and resid 351 through 353 No H-bonds generated for 'chain 'E' and resid 351 through 353' Processing helix chain 'E' and resid 365 through 369 Processing helix chain 'E' and resid 383 through 388 removed outlier: 3.945A pdb=" N ASN E 388 " --> pdb=" O PRO E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.345A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 502 through 505 Processing helix chain 'E' and resid 737 through 744 Processing helix chain 'E' and resid 746 through 754 Processing helix chain 'E' and resid 755 through 757 No H-bonds generated for 'chain 'E' and resid 755 through 757' Processing helix chain 'E' and resid 758 through 783 removed outlier: 3.706A pdb=" N ASP E 775 " --> pdb=" O ALA E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 824 Processing helix chain 'E' and resid 866 through 884 Processing helix chain 'E' and resid 886 through 891 Processing helix chain 'E' and resid 897 through 908 Processing helix chain 'E' and resid 912 through 919 removed outlier: 4.219A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR E 917 " --> pdb=" O GLN E 913 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 939 Processing helix chain 'E' and resid 941 through 944 removed outlier: 4.053A pdb=" N ALA E 944 " --> pdb=" O THR E 941 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 941 through 944' Processing helix chain 'E' and resid 945 through 965 removed outlier: 3.826A pdb=" N VAL E 951 " --> pdb=" O LYS E 947 " (cutoff:3.500A) Processing helix chain 'E' and resid 966 through 968 No H-bonds generated for 'chain 'E' and resid 966 through 968' Processing helix chain 'E' and resid 976 through 982 Processing helix chain 'E' and resid 985 through 1033 removed outlier: 4.989A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) Processing helix chain 'E' and resid 1140 through 1147 removed outlier: 4.178A pdb=" N GLU E1144 " --> pdb=" O PRO E1140 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'F' and resid 122 through 127 Processing helix chain 'F' and resid 185 through 187 No H-bonds generated for 'chain 'F' and resid 185 through 187' Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 86 through 90 Processing helix chain 'G' and resid 134 through 136 No H-bonds generated for 'chain 'G' and resid 134 through 136' Processing helix chain 'G' and resid 163 through 165 No H-bonds generated for 'chain 'G' and resid 163 through 165' Processing helix chain 'G' and resid 194 through 196 No H-bonds generated for 'chain 'G' and resid 194 through 196' Processing helix chain 'G' and resid 209 through 211 No H-bonds generated for 'chain 'G' and resid 209 through 211' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.056A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.543A pdb=" N ALA E 575 " --> pdb=" O GLY E 566 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.895A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG A 273 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 133 through 140 removed outlier: 5.592A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.276A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AA8, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.259A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.599A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.259A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.599A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 551 through 554 removed outlier: 5.994A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.478A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N TYR A 660 " --> pdb=" O SER A 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.478A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.669A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.435A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.449A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.899A pdb=" N ILE A 788 " --> pdb=" O ASN E 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.941A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.526A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.554A pdb=" N ALA L 84 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.554A pdb=" N ALA L 84 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR L 98 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 115 through 119 removed outlier: 4.584A pdb=" N SER L 132 " --> pdb=" O LEU L 182 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU L 182 " --> pdb=" O SER L 132 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N VAL L 134 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU L 180 " --> pdb=" O VAL L 134 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LEU L 136 " --> pdb=" O SER L 178 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N SER L 178 " --> pdb=" O LEU L 136 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ASN L 138 " --> pdb=" O LEU L 176 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU L 176 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 154 through 155 Processing sheet with id=AC8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC9, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.900A pdb=" N MET H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N THR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.942A pdb=" N CYS H 95 " --> pdb=" O TRP H 110 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TRP H 110 " --> pdb=" O CYS H 95 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ARG H 97 " --> pdb=" O ASP H 108 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 127 through 131 removed outlier: 4.821A pdb=" N ALA H 144 " --> pdb=" O VAL H 191 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL H 191 " --> pdb=" O ALA H 144 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLY H 146 " --> pdb=" O VAL H 189 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL H 189 " --> pdb=" O GLY H 146 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N LEU H 148 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N SER H 187 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LYS H 150 " --> pdb=" O LEU H 185 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU H 185 " --> pdb=" O LYS H 150 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 138 through 139 removed outlier: 4.821A pdb=" N ALA H 144 " --> pdb=" O VAL H 191 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL H 191 " --> pdb=" O ALA H 144 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLY H 146 " --> pdb=" O VAL H 189 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL H 189 " --> pdb=" O GLY H 146 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N LEU H 148 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N SER H 187 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LYS H 150 " --> pdb=" O LEU H 185 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU H 185 " --> pdb=" O LYS H 150 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 157 through 161 removed outlier: 4.651A pdb=" N TYR H 201 " --> pdb=" O VAL H 218 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.057A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.895A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AD8, first strand: chain 'B' and resid 133 through 140 removed outlier: 5.591A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.277A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AE2, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.259A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.600A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.259A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.600A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'B' and resid 551 through 554 removed outlier: 5.995A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N PHE B 565 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.478A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N TYR B 660 " --> pdb=" O SER B 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.478A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AF1, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.669A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.435A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.449A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.941A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.527A pdb=" N SER C 67 " --> pdb=" O ASP C 70 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 10 through 13 removed outlier: 3.555A pdb=" N ALA C 84 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLN C 37 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU C 46 " --> pdb=" O GLN C 37 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 10 through 13 removed outlier: 3.555A pdb=" N ALA C 84 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR C 98 " --> pdb=" O GLN C 90 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 115 through 119 removed outlier: 4.584A pdb=" N SER C 132 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU C 182 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N VAL C 134 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU C 180 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LEU C 136 " --> pdb=" O SER C 178 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N SER C 178 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ASN C 138 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU C 176 " --> pdb=" O ASN C 138 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AG1, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AG2, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.899A pdb=" N MET D 34 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N THR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.941A pdb=" N CYS D 95 " --> pdb=" O TRP D 110 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TRP D 110 " --> pdb=" O CYS D 95 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ARG D 97 " --> pdb=" O ASP D 108 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 127 through 131 removed outlier: 4.822A pdb=" N ALA D 144 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL D 191 " --> pdb=" O ALA D 144 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLY D 146 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL D 189 " --> pdb=" O GLY D 146 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU D 148 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N SER D 187 " --> pdb=" O LEU D 148 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N LYS D 150 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU D 185 " --> pdb=" O LYS D 150 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'D' and resid 138 through 139 removed outlier: 4.822A pdb=" N ALA D 144 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL D 191 " --> pdb=" O ALA D 144 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLY D 146 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL D 189 " --> pdb=" O GLY D 146 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU D 148 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N SER D 187 " --> pdb=" O LEU D 148 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N LYS D 150 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU D 185 " --> pdb=" O LYS D 150 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 157 through 161 removed outlier: 4.651A pdb=" N TYR D 201 " --> pdb=" O VAL D 218 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 27 through 30 removed outlier: 8.056A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 47 through 55 removed outlier: 3.895A pdb=" N ASP E 53 " --> pdb=" O ARG E 273 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG E 273 " --> pdb=" O ASP E 53 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N THR E 274 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ASP E 290 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU E 276 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA E 288 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 83 through 85 Processing sheet with id=AH1, first strand: chain 'E' and resid 133 through 140 removed outlier: 5.591A pdb=" N GLN E 134 " --> pdb=" O SER E 161 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL E 159 " --> pdb=" O CYS E 136 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'E' and resid 311 through 319 removed outlier: 5.277A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 325 through 328 Processing sheet with id=AH4, first strand: chain 'E' and resid 348 through 349 removed outlier: 7.259A pdb=" N ALA E 348 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 9.599A pdb=" N ARG E 403 " --> pdb=" O ALA E 348 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'E' and resid 348 through 349 removed outlier: 7.259A pdb=" N ALA E 348 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 9.599A pdb=" N ARG E 403 " --> pdb=" O ALA E 348 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AH7, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AH8, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.477A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N TYR E 660 " --> pdb=" O SER E 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.477A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'E' and resid 711 through 715 removed outlier: 3.669A pdb=" N ALA E1078 " --> pdb=" O PHE E1095 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE E1095 " --> pdb=" O ALA E1078 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'E' and resid 718 through 728 removed outlier: 7.435A pdb=" N GLY E1059 " --> pdb=" O SER E1055 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N SER E1055 " --> pdb=" O GLY E1059 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL E1061 " --> pdb=" O PRO E1053 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU E1063 " --> pdb=" O SER E1051 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N SER E1051 " --> pdb=" O LEU E1063 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL E1065 " --> pdb=" O LEU E1049 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'E' and resid 733 through 736 removed outlier: 4.449A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 4.941A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.527A pdb=" N SER F 67 " --> pdb=" O ASP F 70 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.555A pdb=" N ALA F 84 " --> pdb=" O VAL F 105 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLN F 37 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU F 46 " --> pdb=" O GLN F 37 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.555A pdb=" N ALA F 84 " --> pdb=" O VAL F 105 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR F 98 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'F' and resid 115 through 119 removed outlier: 4.585A pdb=" N SER F 132 " --> pdb=" O LEU F 182 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU F 182 " --> pdb=" O SER F 132 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N VAL F 134 " --> pdb=" O LEU F 180 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N LEU F 180 " --> pdb=" O VAL F 134 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LEU F 136 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N SER F 178 " --> pdb=" O LEU F 136 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ASN F 138 " --> pdb=" O LEU F 176 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU F 176 " --> pdb=" O ASN F 138 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'F' and resid 154 through 155 Processing sheet with id=AJ1, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AJ2, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.900A pdb=" N MET G 34 " --> pdb=" O THR G 50 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N THR G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.941A pdb=" N CYS G 95 " --> pdb=" O TRP G 110 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TRP G 110 " --> pdb=" O CYS G 95 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ARG G 97 " --> pdb=" O ASP G 108 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'G' and resid 127 through 131 removed outlier: 4.821A pdb=" N ALA G 144 " --> pdb=" O VAL G 191 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL G 191 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLY G 146 " --> pdb=" O VAL G 189 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL G 189 " --> pdb=" O GLY G 146 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N LEU G 148 " --> pdb=" O SER G 187 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N SER G 187 " --> pdb=" O LEU G 148 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LYS G 150 " --> pdb=" O LEU G 185 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU G 185 " --> pdb=" O LYS G 150 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'G' and resid 138 through 139 removed outlier: 4.821A pdb=" N ALA G 144 " --> pdb=" O VAL G 191 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL G 191 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLY G 146 " --> pdb=" O VAL G 189 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL G 189 " --> pdb=" O GLY G 146 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N LEU G 148 " --> pdb=" O SER G 187 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N SER G 187 " --> pdb=" O LEU G 148 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LYS G 150 " --> pdb=" O LEU G 185 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU G 185 " --> pdb=" O LYS G 150 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'G' and resid 157 through 161 removed outlier: 4.651A pdb=" N TYR G 201 " --> pdb=" O VAL G 218 " (cutoff:3.500A) 1439 hydrogen bonds defined for protein. 3759 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: 15.16 Time building geometry restraints manager: 10.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7609 1.33 - 1.46: 6954 1.46 - 1.59: 12005 1.59 - 1.72: 3 1.72 - 1.85: 141 Bond restraints: 26712 Sorted by residual: bond pdb=" C ASN E 81 " pdb=" N PRO E 82 " ideal model delta sigma weight residual 1.328 1.381 -0.053 1.26e-02 6.30e+03 1.75e+01 bond pdb=" C ASN B 81 " pdb=" N PRO B 82 " ideal model delta sigma weight residual 1.328 1.381 -0.052 1.26e-02 6.30e+03 1.72e+01 bond pdb=" C ASN A 81 " pdb=" N PRO A 82 " ideal model delta sigma weight residual 1.328 1.380 -0.052 1.26e-02 6.30e+03 1.71e+01 bond pdb=" N PRO G 220 " pdb=" CD PRO G 220 " ideal model delta sigma weight residual 1.473 1.524 -0.051 1.40e-02 5.10e+03 1.31e+01 bond pdb=" N PRO H 220 " pdb=" CD PRO H 220 " ideal model delta sigma weight residual 1.473 1.523 -0.050 1.40e-02 5.10e+03 1.29e+01 ... (remaining 26707 not shown) Histogram of bond angle deviations from ideal: 91.69 - 102.41: 233 102.41 - 113.13: 14517 113.13 - 123.85: 21327 123.85 - 134.57: 819 134.57 - 145.29: 3 Bond angle restraints: 36899 Sorted by residual: angle pdb=" N SER A 939 " pdb=" CA SER A 939 " pdb=" C SER A 939 " ideal model delta sigma weight residual 111.37 145.29 -33.92 1.65e+00 3.67e-01 4.23e+02 angle pdb=" N SER E 939 " pdb=" CA SER E 939 " pdb=" C SER E 939 " ideal model delta sigma weight residual 111.37 145.27 -33.90 1.65e+00 3.67e-01 4.22e+02 angle pdb=" N SER B 939 " pdb=" CA SER B 939 " pdb=" C SER B 939 " ideal model delta sigma weight residual 111.37 145.23 -33.86 1.65e+00 3.67e-01 4.21e+02 angle pdb=" N SER A 940 " pdb=" CA SER A 940 " pdb=" CB SER A 940 " ideal model delta sigma weight residual 110.81 91.69 19.12 1.48e+00 4.57e-01 1.67e+02 angle pdb=" N SER B 940 " pdb=" CA SER B 940 " pdb=" CB SER B 940 " ideal model delta sigma weight residual 110.81 91.71 19.10 1.48e+00 4.57e-01 1.67e+02 ... (remaining 36894 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.31: 16260 21.31 - 42.62: 248 42.62 - 63.93: 27 63.93 - 85.24: 30 85.24 - 106.55: 21 Dihedral angle restraints: 16586 sinusoidal: 4177 harmonic: 12409 Sorted by residual: dihedral pdb=" N SER E 939 " pdb=" C SER E 939 " pdb=" CA SER E 939 " pdb=" CB SER E 939 " ideal model delta harmonic sigma weight residual 122.80 156.52 -33.72 0 2.50e+00 1.60e-01 1.82e+02 dihedral pdb=" N SER A 939 " pdb=" C SER A 939 " pdb=" CA SER A 939 " pdb=" CB SER A 939 " ideal model delta harmonic sigma weight residual 122.80 156.52 -33.72 0 2.50e+00 1.60e-01 1.82e+02 dihedral pdb=" N SER B 939 " pdb=" C SER B 939 " pdb=" CA SER B 939 " pdb=" CB SER B 939 " ideal model delta harmonic sigma weight residual 122.80 156.49 -33.69 0 2.50e+00 1.60e-01 1.82e+02 ... (remaining 16583 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.353: 4615 0.353 - 0.705: 6 0.705 - 1.058: 0 1.058 - 1.410: 0 1.410 - 1.763: 3 Chirality restraints: 4624 Sorted by residual: 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 -2.59 0.19 2.00e-02 2.50e+03 8.70e+01 chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 8.61e+01 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.39e+01 ... (remaining 4621 not shown) Planarity restraints: 5097 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1074 " -0.051 2.00e-02 2.50e+03 5.18e-02 3.36e+01 pdb=" CG ASN A1074 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN A1074 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A1074 " 0.079 2.00e-02 2.50e+03 pdb=" C1 NAG A1311 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E1074 " 0.050 2.00e-02 2.50e+03 5.17e-02 3.34e+01 pdb=" CG ASN E1074 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN E1074 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN E1074 " -0.079 2.00e-02 2.50e+03 pdb=" C1 NAG E1311 " 0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B1074 " -0.050 2.00e-02 2.50e+03 5.17e-02 3.33e+01 pdb=" CG ASN B1074 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN B1074 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN B1074 " 0.078 2.00e-02 2.50e+03 pdb=" C1 NAG B1311 " -0.063 2.00e-02 2.50e+03 ... (remaining 5094 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 13594 3.00 - 3.48: 23236 3.48 - 3.95: 36890 3.95 - 4.43: 39025 4.43 - 4.90: 65328 Nonbonded interactions: 178073 Sorted by model distance: nonbonded pdb=" N PRO A 600 " pdb=" O PRO A 600 " model vdw 2.527 2.496 nonbonded pdb=" N PRO E 600 " pdb=" O PRO E 600 " model vdw 2.527 2.496 nonbonded pdb=" N PRO B 600 " pdb=" O PRO B 600 " model vdw 2.527 2.496 nonbonded pdb=" N GLY E1085 " pdb=" N LYS E1086 " model vdw 2.551 2.560 nonbonded pdb=" N GLY B1085 " pdb=" N LYS B1086 " model vdw 2.551 2.560 ... (remaining 178068 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 422 or (resid 423 through 430 and (name N or na \ me CA or name C or name O or name CB )) or resid 431 or (resid 432 through 444 a \ nd (name N or name CA or name C or name O or name CB )) or (resid 447 through 47 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 476 through \ 1075 or (resid 1076 through 1078 and (name N or name CA or name C or name O or n \ ame CB )) or resid 1079 through 1147 or resid 1301 through 1312)) selection = (chain 'B' and (resid 15 through 365 or (resid 366 through 373 and (name N or na \ me CA or name C or name O or name CB )) or resid 374 through 1075 or (resid 1076 \ through 1078 and (name N or name CA or name C or name O or name CB )) or resid \ 1079 through 1147 or resid 1301 through 1312)) selection = (chain 'E' and (resid 15 through 365 or (resid 366 through 373 and (name N or na \ me CA or name C or name O or name CB )) or resid 374 through 422 or (resid 423 t \ hrough 430 and (name N or name CA or name C or name O or name CB )) or resid 431 \ or (resid 432 through 444 and (name N or name CA or name C or name O or name CB \ )) or (resid 447 through 475 and (name N or name CA or name C or name O or name \ CB )) or resid 476 through 1076 or (resid 1077 through 1078 and (name N or name \ CA or name C or name O or name CB )) or resid 1079 through 1147 or resid 1301 t \ hrough 1312)) } ncs_group { reference = chain 'C' selection = (chain 'F' and (resid 2 through 102 or (resid 103 through 113 and (name N or nam \ e CA or name C or name O or name CB )) or resid 114 through 194 or (resid 195 th \ rough 200 and (name N or name CA or name C or name O or name CB )) or resid 201 \ through 213)) selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' } ncs_group { reference = chain 'M' selection = chain 'R' selection = chain 'W' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.010 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 71.560 Find NCS groups from input model: 1.950 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 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 : 0.010 0.076 26712 Z= 0.729 Angle : 1.535 33.916 36899 Z= 1.034 Chirality : 0.098 1.763 4624 Planarity : 0.005 0.024 5046 Dihedral : 9.597 106.547 8393 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 0.37 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.33 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.12), residues: 4242 helix: -0.01 (0.17), residues: 714 sheet: 1.45 (0.14), residues: 1218 loop : 0.65 (0.13), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.006 TRP B1102 HIS 0.006 0.001 HIS E1083 PHE 0.022 0.003 PHE B 898 TYR 0.029 0.005 TYR A 495 ARG 0.003 0.001 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 2.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 707 TYR cc_start: 0.7400 (t80) cc_final: 0.7059 (t80) REVERT: A 906 PHE cc_start: 0.8785 (m-80) cc_final: 0.8481 (m-10) REVERT: A 1064 HIS cc_start: 0.8172 (m-70) cc_final: 0.7841 (m170) REVERT: A 1095 PHE cc_start: 0.8060 (m-80) cc_final: 0.7541 (m-10) REVERT: B 900 MET cc_start: 0.8596 (mmm) cc_final: 0.8158 (tpp) REVERT: B 1039 ARG cc_start: 0.7479 (mtp180) cc_final: 0.7238 (mmm-85) REVERT: B 1064 HIS cc_start: 0.8379 (m-70) cc_final: 0.8109 (m170) REVERT: B 1095 PHE cc_start: 0.7991 (m-80) cc_final: 0.7457 (m-10) REVERT: E 900 MET cc_start: 0.8679 (mmm) cc_final: 0.8077 (tpp) REVERT: E 1021 SER cc_start: 0.9545 (m) cc_final: 0.9291 (p) REVERT: E 1039 ARG cc_start: 0.7618 (mtp180) cc_final: 0.7341 (mmm-85) REVERT: E 1064 HIS cc_start: 0.8254 (m-70) cc_final: 0.8049 (m170) REVERT: E 1095 PHE cc_start: 0.7904 (m-80) cc_final: 0.7610 (m-10) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.3313 time to fit residues: 153.1023 Evaluate side-chains 128 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 2.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 359 optimal weight: 0.8980 chunk 322 optimal weight: 8.9990 chunk 179 optimal weight: 9.9990 chunk 110 optimal weight: 20.0000 chunk 217 optimal weight: 0.9980 chunk 172 optimal weight: 0.5980 chunk 333 optimal weight: 9.9990 chunk 129 optimal weight: 1.9990 chunk 203 optimal weight: 0.5980 chunk 248 optimal weight: 30.0000 chunk 386 optimal weight: 20.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 26712 Z= 0.199 Angle : 0.568 6.667 36899 Z= 0.311 Chirality : 0.047 0.394 4624 Planarity : 0.004 0.037 5046 Dihedral : 6.354 65.574 5860 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.70 % Favored : 98.23 % Rotamer: Outliers : 0.26 % Allowed : 1.84 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.13), residues: 4242 helix: 1.55 (0.19), residues: 702 sheet: 1.44 (0.14), residues: 1233 loop : 0.58 (0.13), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 886 HIS 0.004 0.001 HIS A1064 PHE 0.024 0.002 PHE A1052 TYR 0.014 0.001 TYR B 707 ARG 0.003 0.000 ARG A1019 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 189 time to evaluate : 3.172 Fit side-chains revert: symmetry clash REVERT: A 707 TYR cc_start: 0.7404 (t80) cc_final: 0.6982 (t80) REVERT: A 1064 HIS cc_start: 0.8363 (m-70) cc_final: 0.7823 (m170) REVERT: A 1072 GLU cc_start: 0.8948 (pm20) cc_final: 0.8519 (pm20) REVERT: B 900 MET cc_start: 0.8505 (mmm) cc_final: 0.7970 (tpp) REVERT: B 1064 HIS cc_start: 0.8472 (m-70) cc_final: 0.7944 (m170) REVERT: B 1095 PHE cc_start: 0.8270 (m-80) cc_final: 0.8060 (m-10) REVERT: E 900 MET cc_start: 0.8316 (mmm) cc_final: 0.7961 (tpp) REVERT: E 1039 ARG cc_start: 0.7652 (mtp180) cc_final: 0.7159 (mtm-85) REVERT: E 1064 HIS cc_start: 0.8338 (m-70) cc_final: 0.8043 (m170) REVERT: E 1072 GLU cc_start: 0.8983 (pm20) cc_final: 0.8523 (pm20) REVERT: E 1095 PHE cc_start: 0.8105 (m-80) cc_final: 0.7897 (m-10) outliers start: 3 outliers final: 0 residues processed: 192 average time/residue: 0.3451 time to fit residues: 110.9238 Evaluate side-chains 112 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 2.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 214 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 321 optimal weight: 20.0000 chunk 263 optimal weight: 40.0000 chunk 106 optimal weight: 30.0000 chunk 387 optimal weight: 20.0000 chunk 418 optimal weight: 1.9990 chunk 345 optimal weight: 1.9990 chunk 384 optimal weight: 20.0000 chunk 132 optimal weight: 40.0000 chunk 310 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1023 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** E 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1023 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.164 26712 Z= 0.415 Angle : 0.677 10.408 36899 Z= 0.369 Chirality : 0.049 0.342 4624 Planarity : 0.005 0.075 5046 Dihedral : 5.705 52.711 5860 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.37 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % 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: 0.92 (0.13), residues: 4242 helix: 1.37 (0.20), residues: 681 sheet: 1.09 (0.14), residues: 1254 loop : 0.19 (0.13), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 886 HIS 0.013 0.003 HIS E1048 PHE 0.037 0.003 PHE E 192 TYR 0.029 0.003 TYR B 269 ARG 0.006 0.001 ARG E1014 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 2.905 Fit side-chains REVERT: A 781 VAL cc_start: 0.9464 (t) cc_final: 0.9169 (p) REVERT: A 900 MET cc_start: 0.8236 (mmt) cc_final: 0.7724 (mmt) REVERT: A 1083 HIS cc_start: 0.7963 (t-90) cc_final: 0.7755 (t-90) REVERT: B 707 TYR cc_start: 0.8268 (t80) cc_final: 0.7782 (t80) REVERT: B 1083 HIS cc_start: 0.7872 (t-90) cc_final: 0.7642 (t-90) REVERT: E 731 MET cc_start: 0.8646 (ttp) cc_final: 0.8372 (ttm) REVERT: E 1083 HIS cc_start: 0.7974 (t-90) cc_final: 0.7763 (t-90) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.3224 time to fit residues: 73.3361 Evaluate side-chains 82 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 2.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 382 optimal weight: 7.9990 chunk 291 optimal weight: 8.9990 chunk 201 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 184 optimal weight: 9.9990 chunk 260 optimal weight: 30.0000 chunk 388 optimal weight: 9.9990 chunk 411 optimal weight: 30.0000 chunk 203 optimal weight: 0.7980 chunk 368 optimal weight: 0.0470 chunk 110 optimal weight: 50.0000 overall best weight: 4.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 26712 Z= 0.502 Angle : 0.708 11.258 36899 Z= 0.382 Chirality : 0.049 0.273 4624 Planarity : 0.006 0.079 5046 Dihedral : 5.993 49.441 5860 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.13), residues: 4242 helix: 1.01 (0.19), residues: 678 sheet: 0.68 (0.14), residues: 1314 loop : -0.20 (0.13), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 886 HIS 0.009 0.003 HIS E1064 PHE 0.046 0.003 PHE E 192 TYR 0.026 0.003 TYR A1047 ARG 0.008 0.001 ARG B1000 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 2.838 Fit side-chains REVERT: A 271 GLN cc_start: 0.8384 (mp10) cc_final: 0.8127 (mp10) REVERT: A 365 TYR cc_start: 0.8428 (m-10) cc_final: 0.8148 (m-10) REVERT: A 900 MET cc_start: 0.8340 (mmt) cc_final: 0.7172 (mmt) REVERT: A 1017 GLU cc_start: 0.8353 (tm-30) cc_final: 0.8046 (tm-30) REVERT: A 1072 GLU cc_start: 0.8955 (pm20) cc_final: 0.8450 (pm20) REVERT: A 1083 HIS cc_start: 0.8202 (t-90) cc_final: 0.7959 (t-90) REVERT: B 781 VAL cc_start: 0.9644 (t) cc_final: 0.9408 (p) REVERT: B 1017 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7931 (tm-30) REVERT: E 731 MET cc_start: 0.8543 (ttp) cc_final: 0.8314 (ttm) REVERT: E 781 VAL cc_start: 0.9456 (t) cc_final: 0.9211 (p) REVERT: E 1072 GLU cc_start: 0.8948 (pm20) cc_final: 0.8711 (pm20) REVERT: E 1083 HIS cc_start: 0.8250 (t-90) cc_final: 0.8011 (t-90) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.2893 time to fit residues: 56.4293 Evaluate side-chains 85 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 2.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 342 optimal weight: 6.9990 chunk 233 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 306 optimal weight: 1.9990 chunk 169 optimal weight: 5.9990 chunk 351 optimal weight: 1.9990 chunk 284 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 210 optimal weight: 0.0570 chunk 369 optimal weight: 9.9990 chunk 103 optimal weight: 20.0000 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1023 ASN ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26712 Z= 0.183 Angle : 0.519 7.335 36899 Z= 0.277 Chirality : 0.046 0.302 4624 Planarity : 0.004 0.049 5046 Dihedral : 5.167 48.386 5860 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.81 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.57 (0.13), residues: 4242 helix: 1.58 (0.20), residues: 684 sheet: 0.62 (0.14), residues: 1281 loop : -0.06 (0.13), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 886 HIS 0.005 0.001 HIS B1048 PHE 0.030 0.002 PHE B 275 TYR 0.019 0.001 TYR E 741 ARG 0.003 0.000 ARG B 905 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 3.147 Fit side-chains REVERT: A 271 GLN cc_start: 0.8012 (mp10) cc_final: 0.7627 (mp10) REVERT: A 365 TYR cc_start: 0.8369 (m-10) cc_final: 0.8138 (m-10) REVERT: A 900 MET cc_start: 0.8498 (mmt) cc_final: 0.8029 (mmt) REVERT: A 1017 GLU cc_start: 0.8303 (tm-30) cc_final: 0.8032 (tm-30) REVERT: A 1072 GLU cc_start: 0.8912 (pm20) cc_final: 0.8395 (pm20) REVERT: A 1083 HIS cc_start: 0.8073 (t-90) cc_final: 0.7785 (t-90) REVERT: B 781 VAL cc_start: 0.9454 (t) cc_final: 0.9238 (p) REVERT: B 1017 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7851 (tm-30) REVERT: B 1083 HIS cc_start: 0.7992 (t-90) cc_final: 0.7749 (t-90) REVERT: E 1010 GLN cc_start: 0.9090 (mm-40) cc_final: 0.8815 (mp10) REVERT: E 1072 GLU cc_start: 0.8839 (pm20) cc_final: 0.8585 (pm20) REVERT: E 1083 HIS cc_start: 0.8029 (t-90) cc_final: 0.7802 (t-90) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.3137 time to fit residues: 70.8073 Evaluate side-chains 91 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 2.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 138 optimal weight: 10.0000 chunk 370 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 241 optimal weight: 8.9990 chunk 101 optimal weight: 40.0000 chunk 412 optimal weight: 30.0000 chunk 342 optimal weight: 4.9990 chunk 190 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 136 optimal weight: 30.0000 chunk 216 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1023 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1023 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1023 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 26712 Z= 0.500 Angle : 0.698 8.630 36899 Z= 0.377 Chirality : 0.049 0.328 4624 Planarity : 0.005 0.082 5046 Dihedral : 6.038 59.688 5860 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.06 (0.13), residues: 4242 helix: 1.00 (0.20), residues: 681 sheet: 0.33 (0.14), residues: 1308 loop : -0.37 (0.13), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 886 HIS 0.009 0.003 HIS E1048 PHE 0.042 0.003 PHE E 192 TYR 0.026 0.003 TYR B 313 ARG 0.004 0.001 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 2.827 Fit side-chains REVERT: A 271 GLN cc_start: 0.8506 (mp10) cc_final: 0.8134 (mp10) REVERT: A 365 TYR cc_start: 0.8565 (m-10) cc_final: 0.8222 (m-10) REVERT: A 900 MET cc_start: 0.8600 (mmt) cc_final: 0.8151 (mpp) REVERT: A 1072 GLU cc_start: 0.8942 (pm20) cc_final: 0.8382 (pm20) REVERT: A 1083 HIS cc_start: 0.8237 (t-90) cc_final: 0.7665 (t70) REVERT: A 1139 ASP cc_start: 0.8370 (t70) cc_final: 0.8164 (t0) REVERT: B 365 TYR cc_start: 0.8493 (m-10) cc_final: 0.8127 (m-10) REVERT: B 781 VAL cc_start: 0.9563 (t) cc_final: 0.9333 (p) REVERT: B 1017 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7880 (tm-30) REVERT: B 1083 HIS cc_start: 0.8222 (t-90) cc_final: 0.7754 (t70) REVERT: E 365 TYR cc_start: 0.8460 (m-10) cc_final: 0.8204 (m-10) REVERT: E 781 VAL cc_start: 0.9466 (t) cc_final: 0.9262 (p) REVERT: E 900 MET cc_start: 0.8263 (mmt) cc_final: 0.7849 (mmt) REVERT: E 1083 HIS cc_start: 0.8261 (t-90) cc_final: 0.7965 (t-90) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.3125 time to fit residues: 59.2905 Evaluate side-chains 84 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 2.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 397 optimal weight: 50.0000 chunk 46 optimal weight: 7.9990 chunk 234 optimal weight: 0.6980 chunk 300 optimal weight: 2.9990 chunk 233 optimal weight: 0.5980 chunk 346 optimal weight: 2.9990 chunk 230 optimal weight: 0.6980 chunk 410 optimal weight: 7.9990 chunk 256 optimal weight: 4.9990 chunk 250 optimal weight: 30.0000 chunk 189 optimal weight: 30.0000 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 777 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1064 HIS ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.4995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26712 Z= 0.218 Angle : 0.525 7.459 36899 Z= 0.281 Chirality : 0.046 0.278 4624 Planarity : 0.004 0.054 5046 Dihedral : 5.428 56.756 5860 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.09 % Allowed : 1.92 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.13), residues: 4242 helix: 1.49 (0.20), residues: 669 sheet: 0.42 (0.14), residues: 1314 loop : -0.29 (0.13), residues: 2259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 886 HIS 0.011 0.002 HIS B1048 PHE 0.026 0.002 PHE E 906 TYR 0.013 0.001 TYR A1067 ARG 0.005 0.001 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 2.917 Fit side-chains REVERT: A 271 GLN cc_start: 0.8417 (mp10) cc_final: 0.8050 (mp10) REVERT: A 365 TYR cc_start: 0.8532 (m-10) cc_final: 0.8194 (m-10) REVERT: A 900 MET cc_start: 0.8607 (mmt) cc_final: 0.7155 (mmp) REVERT: A 1072 GLU cc_start: 0.8967 (pm20) cc_final: 0.8505 (pm20) REVERT: A 1083 HIS cc_start: 0.8046 (t-90) cc_final: 0.7688 (t-90) REVERT: B 365 TYR cc_start: 0.8393 (m-10) cc_final: 0.8079 (m-10) REVERT: B 900 MET cc_start: 0.7912 (mmt) cc_final: 0.7591 (mmt) REVERT: B 1083 HIS cc_start: 0.8065 (t-90) cc_final: 0.7791 (t-90) REVERT: E 365 TYR cc_start: 0.8446 (m-10) cc_final: 0.8206 (m-10) REVERT: E 731 MET cc_start: 0.8475 (ttp) cc_final: 0.8240 (ttm) REVERT: E 900 MET cc_start: 0.8414 (mmt) cc_final: 0.8155 (mmt) REVERT: E 1083 HIS cc_start: 0.8072 (t-90) cc_final: 0.7782 (t-90) outliers start: 1 outliers final: 0 residues processed: 117 average time/residue: 0.3419 time to fit residues: 68.9425 Evaluate side-chains 87 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 2.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 254 optimal weight: 50.0000 chunk 163 optimal weight: 10.0000 chunk 245 optimal weight: 10.0000 chunk 123 optimal weight: 30.0000 chunk 80 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 261 optimal weight: 50.0000 chunk 279 optimal weight: 20.0000 chunk 203 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 322 optimal weight: 10.0000 overall best weight: 5.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1023 ASN ** E1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.5636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.082 26712 Z= 0.666 Angle : 0.798 9.276 36899 Z= 0.435 Chirality : 0.050 0.326 4624 Planarity : 0.006 0.087 5046 Dihedral : 6.557 56.636 5860 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.14 % Favored : 92.81 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.13), residues: 4242 helix: 0.32 (0.19), residues: 681 sheet: 0.06 (0.14), residues: 1278 loop : -0.77 (0.13), residues: 2283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.004 TRP B 886 HIS 0.009 0.004 HIS E1064 PHE 0.036 0.004 PHE B 797 TYR 0.031 0.003 TYR E1047 ARG 0.006 0.001 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 2.703 Fit side-chains REVERT: A 271 GLN cc_start: 0.8563 (mp10) cc_final: 0.8217 (mp10) REVERT: A 365 TYR cc_start: 0.8602 (m-10) cc_final: 0.8294 (m-10) REVERT: A 900 MET cc_start: 0.8711 (mmt) cc_final: 0.7543 (mmt) REVERT: A 1072 GLU cc_start: 0.8931 (pm20) cc_final: 0.8431 (pm20) REVERT: A 1083 HIS cc_start: 0.8346 (t-90) cc_final: 0.7985 (t-90) REVERT: B 365 TYR cc_start: 0.8510 (m-10) cc_final: 0.8177 (m-10) REVERT: B 900 MET cc_start: 0.8532 (mmt) cc_final: 0.8195 (mmt) REVERT: B 1083 HIS cc_start: 0.8315 (t-90) cc_final: 0.8007 (t-90) REVERT: E 365 TYR cc_start: 0.8612 (m-10) cc_final: 0.8288 (m-10) REVERT: E 781 VAL cc_start: 0.9496 (t) cc_final: 0.9265 (p) REVERT: E 900 MET cc_start: 0.7884 (mmp) cc_final: 0.7408 (mmp) REVERT: E 1072 GLU cc_start: 0.8817 (pm20) cc_final: 0.8577 (pm20) REVERT: E 1083 HIS cc_start: 0.8363 (t-90) cc_final: 0.8047 (t-90) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.3095 time to fit residues: 56.5834 Evaluate side-chains 81 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 2.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 373 optimal weight: 0.0970 chunk 393 optimal weight: 0.0060 chunk 358 optimal weight: 0.9980 chunk 382 optimal weight: 7.9990 chunk 230 optimal weight: 0.7980 chunk 166 optimal weight: 0.9980 chunk 300 optimal weight: 0.9990 chunk 117 optimal weight: 50.0000 chunk 345 optimal weight: 2.9990 chunk 361 optimal weight: 0.6980 chunk 381 optimal weight: 1.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.5455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26712 Z= 0.177 Angle : 0.527 7.684 36899 Z= 0.282 Chirality : 0.046 0.264 4624 Planarity : 0.005 0.057 5046 Dihedral : 5.425 50.163 5860 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.06 (0.13), residues: 4242 helix: 1.43 (0.20), residues: 675 sheet: 0.26 (0.14), residues: 1281 loop : -0.47 (0.13), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 886 HIS 0.009 0.001 HIS B1048 PHE 0.023 0.002 PHE E 906 TYR 0.015 0.001 TYR E1067 ARG 0.005 0.001 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 2.702 Fit side-chains REVERT: A 271 GLN cc_start: 0.8458 (mp10) cc_final: 0.8065 (mp10) REVERT: A 365 TYR cc_start: 0.8504 (m-10) cc_final: 0.8177 (m-10) REVERT: A 1072 GLU cc_start: 0.8876 (pm20) cc_final: 0.8674 (pm20) REVERT: A 1083 HIS cc_start: 0.8079 (t-90) cc_final: 0.7705 (t-90) REVERT: B 365 TYR cc_start: 0.8505 (m-10) cc_final: 0.8168 (m-10) REVERT: B 900 MET cc_start: 0.8240 (mmt) cc_final: 0.7898 (mmt) REVERT: B 1083 HIS cc_start: 0.8073 (t-90) cc_final: 0.7765 (t-90) REVERT: E 1072 GLU cc_start: 0.8664 (pm20) cc_final: 0.8372 (pm20) REVERT: E 1083 HIS cc_start: 0.8090 (t-90) cc_final: 0.7782 (t-90) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.3551 time to fit residues: 79.1347 Evaluate side-chains 92 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 2.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 251 optimal weight: 2.9990 chunk 404 optimal weight: 7.9990 chunk 246 optimal weight: 5.9990 chunk 191 optimal weight: 8.9990 chunk 281 optimal weight: 6.9990 chunk 424 optimal weight: 40.0000 chunk 390 optimal weight: 40.0000 chunk 337 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 261 optimal weight: 50.0000 chunk 207 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1023 ASN ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1023 ASN ** E1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.5975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.079 26712 Z= 0.627 Angle : 0.766 9.369 36899 Z= 0.417 Chirality : 0.050 0.323 4624 Planarity : 0.006 0.077 5046 Dihedral : 6.494 56.642 5860 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.13), residues: 4242 helix: 0.48 (0.20), residues: 666 sheet: -0.13 (0.14), residues: 1281 loop : -0.83 (0.13), residues: 2295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.005 TRP B 886 HIS 0.009 0.003 HIS A1064 PHE 0.042 0.004 PHE E 906 TYR 0.030 0.003 TYR E1047 ARG 0.005 0.001 ARG A 355 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8484 Ramachandran restraints generated. 4242 Oldfield, 0 Emsley, 4242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 2.701 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 271 GLN cc_start: 0.8559 (mp10) cc_final: 0.8223 (mp10) REVERT: A 365 TYR cc_start: 0.8594 (m-10) cc_final: 0.8307 (m-10) REVERT: A 900 MET cc_start: 0.8607 (mmt) cc_final: 0.8035 (mmt) REVERT: A 1010 GLN cc_start: 0.9115 (mm-40) cc_final: 0.8867 (mm-40) REVERT: A 1072 GLU cc_start: 0.8906 (pm20) cc_final: 0.8393 (pm20) REVERT: A 1083 HIS cc_start: 0.8320 (t-90) cc_final: 0.7952 (t-90) REVERT: B 365 TYR cc_start: 0.8553 (m-10) cc_final: 0.8185 (m-10) REVERT: B 900 MET cc_start: 0.8502 (mmt) cc_final: 0.8122 (mmt) REVERT: B 1083 HIS cc_start: 0.8329 (t-90) cc_final: 0.7998 (t-90) REVERT: E 365 TYR cc_start: 0.8549 (m-10) cc_final: 0.8323 (m-10) REVERT: E 781 VAL cc_start: 0.9486 (t) cc_final: 0.9248 (p) REVERT: E 1072 GLU cc_start: 0.8819 (pm20) cc_final: 0.8504 (pm20) REVERT: E 1083 HIS cc_start: 0.8361 (t-90) cc_final: 0.8019 (t-90) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.2992 time to fit residues: 53.9190 Evaluate side-chains 83 residues out of total 3756 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 2.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 268 optimal weight: 0.5980 chunk 360 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 chunk 311 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 338 optimal weight: 0.4980 chunk 141 optimal weight: 7.9990 chunk 347 optimal weight: 0.2980 chunk 42 optimal weight: 0.0270 chunk 62 optimal weight: 5.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1023 ASN ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 563 GLN ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.098242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.076628 restraints weight = 116327.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.074972 restraints weight = 112849.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.075774 restraints weight = 99752.350| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.5786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 26712 Z= 0.150 Angle : 0.517 8.526 36899 Z= 0.276 Chirality : 0.046 0.258 4624 Planarity : 0.005 0.055 5046 Dihedral : 5.333 50.054 5860 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.13), residues: 4242 helix: 1.61 (0.20), residues: 672 sheet: 0.19 (0.14), residues: 1278 loop : -0.52 (0.13), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 886 HIS 0.011 0.001 HIS A1048 PHE 0.031 0.002 PHE E 906 TYR 0.024 0.001 TYR E 741 ARG 0.006 0.001 ARG A 905 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3591.51 seconds wall clock time: 65 minutes 41.99 seconds (3941.99 seconds total)