Starting phenix.real_space_refine on Tue Feb 20 02:14:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8w_22733/02_2024/7k8w_22733_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8w_22733/02_2024/7k8w_22733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8w_22733/02_2024/7k8w_22733.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8w_22733/02_2024/7k8w_22733.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8w_22733/02_2024/7k8w_22733_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8w_22733/02_2024/7k8w_22733_neut.pdb" } resolution = 3.6 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= 0.002 sd= 0.019 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 122 5.16 5 C 16817 2.51 5 N 4356 2.21 5 O 5204 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 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 663": "OD1" <-> "OD2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 773": "OE1" <-> "OE2" 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 TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "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 ARG 1107": "NH1" <-> "NH2" Residue "A PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 287": "OD1" <-> "OD2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 756": "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 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 819": "OE1" <-> "OE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 918": "OE1" <-> "OE2" Residue "B ASP 950": "OD1" <-> "OD2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 994": "OD1" <-> "OD2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 53": "OD1" <-> "OD2" Residue "G PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 364": "OD1" <-> "OD2" Residue "G TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 405": "OD1" <-> "OD2" Residue "G PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 466": "NH1" <-> "NH2" Residue "G PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 516": "OE1" <-> "OE2" Residue "G PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 583": "OE1" <-> "OE2" Residue "G PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 663": "OD1" <-> "OD2" Residue "G TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 775": "OD1" <-> "OD2" Residue "G PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 820": "OD1" <-> "OD2" Residue "G PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 990": "OE1" <-> "OE2" Residue "G ARG 1019": "NH1" <-> "NH2" Residue "G GLU 1031": "OE1" <-> "OE2" Residue "G PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 38": "NH1" <-> "NH2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 66": "NH1" <-> "NH2" Residue "H ARG 71": "NH1" <-> "NH2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 94": "NH1" <-> "NH2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 53": "NH1" <-> "NH2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "N TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 38": "NH1" <-> "NH2" Residue "N TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "N TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 94": "NH1" <-> "NH2" Residue "N TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 53": "NH1" <-> "NH2" Residue "S ARG 60": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26499 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 7612 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 990, 7606 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'CIS': 1, 'PTRANS': 48, 'TRANS': 940} Chain breaks: 10 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 88 Conformer: "B" Number of residues, atoms: 990, 7606 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'CIS': 1, 'PTRANS': 48, 'TRANS': 940} Chain breaks: 10 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 88 bond proxies already assigned to first conformer: 7766 Chain: "B" Number of atoms: 6865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 6865 Classifications: {'peptide': 949} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 46, 'TRANS': 902} Chain breaks: 13 Unresolved non-hydrogen bonds: 576 Unresolved non-hydrogen angles: 742 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 13, 'ASN:plan1': 17, 'TRP:plan': 2, 'ASP:plan': 13, 'PHE:plan': 9, 'GLU:plan': 12, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 382 Chain: "G" Number of atoms: 7604 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 990, 7598 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 48, 'TRANS': 941} Chain breaks: 8 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 10, 'ASN:plan1': 4, 'TYR:plan': 1, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 94 Conformer: "B" Number of residues, atoms: 990, 7598 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 48, 'TRANS': 941} Chain breaks: 8 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 10, 'ASN:plan1': 4, 'TYR:plan': 1, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 94 bond proxies already assigned to first conformer: 7761 Chain: "H" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 988 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "L" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 801 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 105} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "N" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 988 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "S" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 801 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 105} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "G" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ASER A 459 " occ=0.60 ... (10 atoms not shown) pdb=" OG BSER A 459 " occ=0.40 residue: pdb=" N ASER G 459 " occ=0.60 ... (10 atoms not shown) pdb=" OG BSER G 459 " occ=0.40 Time building chain proxies: 21.55, per 1000 atoms: 0.81 Number of scatterers: 26499 At special positions: 0 Unit cell: (134.596, 134.596, 203.984, 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 122 16.00 O 5204 8.00 N 4356 7.00 C 16817 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.01 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 166 " distance=2.02 Simple disulfide: pdb=" SG CYS G 291 " - pdb=" SG CYS G 301 " distance=2.03 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=2.01 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 391 " - pdb=" SG CYS G 525 " distance=2.04 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 488 " distance=2.03 Simple disulfide: pdb=" SG CYS G 538 " - pdb=" SG CYS G 590 " distance=2.03 Simple disulfide: pdb=" SG CYS G 617 " - pdb=" SG CYS G 649 " distance=2.03 Simple disulfide: pdb=" SG CYS G 662 " - pdb=" SG CYS G 671 " distance=2.03 Simple disulfide: pdb=" SG CYS G 738 " - pdb=" SG CYS G 760 " distance=2.03 Simple disulfide: pdb=" SG CYS G 743 " - pdb=" SG CYS G 749 " distance=2.02 Simple disulfide: pdb=" SG CYS G1032 " - pdb=" SG CYS G1043 " distance=2.03 Simple disulfide: pdb=" SG CYS G1082 " - pdb=" SG CYS G1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 87 " 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 C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " 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 O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A 343 " " NAG A1310 " - " ASN A 331 " " 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 343 " " NAG B1307 " - " ASN B 603 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B 717 " " NAG B1312 " - " ASN B1074 " " NAG B1313 " - " ASN B 165 " " NAG C 1 " - " ASN A 234 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1098 " " NAG G1301 " - " ASN G 61 " " NAG G1302 " - " ASN G 122 " " NAG G1303 " - " ASN G 234 " " NAG G1304 " - " ASN G 282 " " NAG G1305 " - " ASN G 603 " " NAG G1306 " - " ASN G 616 " " NAG G1307 " - " ASN G 657 " " NAG G1308 " - " ASN G 709 " " NAG G1309 " - " ASN G1074 " " NAG G1310 " - " ASN G 165 " " NAG G1311 " - " ASN G 331 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG O 1 " - " ASN G 717 " " NAG P 1 " - " ASN G 801 " " NAG Q 1 " - " ASN G1098 " " NAG R 1 " - " ASN G1134 " " NAG T 1 " - " ASN G 343 " Time building additional restraints: 11.77 Conformation dependent library (CDL) restraints added in 7.2 seconds 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6346 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 55 sheets defined 23.4% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.69 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 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 403 through 410 removed outlier: 4.086A 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 737 through 744 removed outlier: 3.615A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 4.086A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.977A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.783A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.845A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.754A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.608A pdb=" N GLN A 965 " --> pdb=" O THR A 961 " (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 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.551A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.030A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.901A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.649A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.645A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.780A pdb=" N THR B 881 " --> pdb=" O LEU B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.031A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 907 removed outlier: 3.512A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 910 No H-bonds generated for 'chain 'B' and resid 908 through 910' Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.791A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.585A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.314A 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 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.823A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.970A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 304 removed outlier: 3.573A pdb=" N THR G 302 " --> pdb=" O GLU G 298 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 343 Processing helix chain 'G' and resid 365 through 370 Processing helix chain 'G' and resid 386 through 390 removed outlier: 3.882A pdb=" N LEU G 390 " --> pdb=" O LEU G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 410 Processing helix chain 'G' and resid 416 through 422 Processing helix chain 'G' and resid 616 through 620 Processing helix chain 'G' and resid 737 through 744 Processing helix chain 'G' and resid 746 through 755 removed outlier: 4.038A pdb=" N LEU G 752 " --> pdb=" O GLU G 748 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN G 755 " --> pdb=" O ASN G 751 " (cutoff:3.500A) Processing helix chain 'G' and resid 758 through 783 Processing helix chain 'G' and resid 816 through 825 removed outlier: 3.518A pdb=" N LEU G 822 " --> pdb=" O ILE G 818 " (cutoff:3.500A) Processing helix chain 'G' and resid 866 through 885 removed outlier: 3.511A pdb=" N THR G 881 " --> pdb=" O LEU G 877 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY G 885 " --> pdb=" O THR G 881 " (cutoff:3.500A) Processing helix chain 'G' and resid 886 through 891 removed outlier: 4.140A pdb=" N ALA G 890 " --> pdb=" O TRP G 886 " (cutoff:3.500A) Processing helix chain 'G' and resid 897 through 908 removed outlier: 3.614A pdb=" N ALA G 903 " --> pdb=" O ALA G 899 " (cutoff:3.500A) Processing helix chain 'G' and resid 913 through 918 removed outlier: 3.609A pdb=" N TYR G 917 " --> pdb=" O GLN G 913 " (cutoff:3.500A) Processing helix chain 'G' and resid 919 through 941 removed outlier: 3.679A pdb=" N ILE G 934 " --> pdb=" O ALA G 930 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN G 935 " --> pdb=" O ILE G 931 " (cutoff:3.500A) Processing helix chain 'G' and resid 942 through 944 No H-bonds generated for 'chain 'G' and resid 942 through 944' Processing helix chain 'G' and resid 945 through 965 removed outlier: 3.610A pdb=" N ASN G 955 " --> pdb=" O VAL G 951 " (cutoff:3.500A) Processing helix chain 'G' and resid 966 through 968 No H-bonds generated for 'chain 'G' and resid 966 through 968' Processing helix chain 'G' and resid 976 through 984 removed outlier: 3.549A pdb=" N ILE G 980 " --> pdb=" O VAL G 976 " (cutoff:3.500A) Processing helix chain 'G' and resid 985 through 1033 removed outlier: 4.476A pdb=" N VAL G 991 " --> pdb=" O PRO G 987 " (cutoff:3.500A) Processing helix chain 'G' and resid 1140 through 1147 removed outlier: 3.949A pdb=" N GLU G1144 " --> pdb=" O PRO G1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 78 through 82 Processing helix chain 'N' and resid 61 through 64 Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'S' and resid 78 through 82 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.633A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.440A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.513A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.060A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.354A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 448 through 454 removed outlier: 3.559A pdb=" N GLY A 496 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ASN A 450 " --> pdb=" O SER A 494 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N SER A 494 " --> pdb=" O ASN A 450 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N LEU A 452 " --> pdb=" O LEU A 492 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N LEU A 492 " --> pdb=" O LEU A 452 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 538 through 543 removed outlier: 5.787A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.921A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.504A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.504A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 789 through 790 removed outlier: 3.596A pdb=" N LYS A 790 " --> pdb=" O ASN G 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 3.950A pdb=" N SER A1123 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 31 removed outlier: 4.084A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.645A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.174A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.642A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.545A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.725A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL B 595 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.562A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.307A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC6, first strand: chain 'B' and resid 538 through 541 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 656 removed outlier: 6.076A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.138A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.138A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 5.748A pdb=" N VAL B1122 " --> pdb=" O PHE B1089 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N PHE B1089 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD4, first strand: chain 'G' and resid 28 through 31 removed outlier: 4.094A pdb=" N SER G 60 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ASN G 61 " --> pdb=" O TYR G 269 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N TYR G 269 " --> pdb=" O ASN G 61 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR G 265 " --> pdb=" O PHE G 65 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN G 188 " --> pdb=" O GLU G 96 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL G 227 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N SER G 205 " --> pdb=" O PRO G 225 " (cutoff:3.500A) removed outlier: 9.395A pdb=" N HIS G 207 " --> pdb=" O LEU G 223 " (cutoff:3.500A) removed outlier: 9.640A pdb=" N LEU G 223 " --> pdb=" O HIS G 207 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N VAL G 36 " --> pdb=" O LEU G 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 48 through 55 removed outlier: 4.167A pdb=" N ASP G 287 " --> pdb=" O LYS G 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 83 through 85 Processing sheet with id=AD7, first strand: chain 'G' and resid 311 through 319 removed outlier: 6.079A pdb=" N ILE G 312 " --> pdb=" O THR G 599 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N THR G 599 " --> pdb=" O ILE G 312 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N GLN G 314 " --> pdb=" O VAL G 597 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL G 597 " --> pdb=" O GLN G 314 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER G 316 " --> pdb=" O VAL G 595 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLY G 594 " --> pdb=" O GLN G 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 324 through 325 removed outlier: 7.225A pdb=" N GLU G 324 " --> pdb=" O ASN G 540 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N ASN G 542 " --> pdb=" O GLU G 324 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ASP G 574 " --> pdb=" O ILE G 587 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA G 575 " --> pdb=" O GLY G 566 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 354 through 358 removed outlier: 4.391A pdb=" N ASN G 354 " --> pdb=" O SER G 399 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER G 399 " --> pdb=" O ASN G 354 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY G 431 " --> pdb=" O TYR G 380 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 448 through 454 removed outlier: 7.837A pdb=" N TYR G 451 " --> pdb=" O TYR G 495 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 473 through 474 Processing sheet with id=AE3, first strand: chain 'G' and resid 654 through 660 removed outlier: 4.277A pdb=" N THR G 696 " --> pdb=" O VAL G 656 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASN G 658 " --> pdb=" O THR G 696 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE G 670 " --> pdb=" O ILE G 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 711 through 728 removed outlier: 3.546A pdb=" N LYS G1073 " --> pdb=" O ILE G 714 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLN G1071 " --> pdb=" O THR G 716 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N PHE G 718 " --> pdb=" O PRO G1069 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ILE G 720 " --> pdb=" O TYR G1067 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N TYR G1067 " --> pdb=" O ILE G 720 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL G 722 " --> pdb=" O VAL G1065 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL G1065 " --> pdb=" O VAL G 722 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR G 724 " --> pdb=" O LEU G1063 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU G1063 " --> pdb=" O THR G 724 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE G 726 " --> pdb=" O VAL G1061 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL G1061 " --> pdb=" O ILE G 726 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N GLY G1059 " --> pdb=" O PRO G 728 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE G1052 " --> pdb=" O LEU G1063 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N TYR G1067 " --> pdb=" O HIS G1048 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N HIS G1048 " --> pdb=" O TYR G1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 711 through 728 removed outlier: 3.546A pdb=" N LYS G1073 " --> pdb=" O ILE G 714 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLN G1071 " --> pdb=" O THR G 716 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N PHE G 718 " --> pdb=" O PRO G1069 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ILE G 720 " --> pdb=" O TYR G1067 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N TYR G1067 " --> pdb=" O ILE G 720 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL G 722 " --> pdb=" O VAL G1065 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL G1065 " --> pdb=" O VAL G 722 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR G 724 " --> pdb=" O LEU G1063 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU G1063 " --> pdb=" O THR G 724 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE G 726 " --> pdb=" O VAL G1061 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL G1061 " --> pdb=" O ILE G 726 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N GLY G1059 " --> pdb=" O PRO G 728 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR G1076 " --> pdb=" O SER G1097 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 734 through 736 Processing sheet with id=AE7, first strand: chain 'G' and resid 1120 through 1125 removed outlier: 5.696A pdb=" N VAL G1122 " --> pdb=" O PHE G1089 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N PHE G1089 " --> pdb=" O VAL G1122 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLY G1124 " --> pdb=" O ALA G1087 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.573A pdb=" N LEU H 82 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU H 81 " --> pdb=" O THR H 68 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR H 68 " --> pdb=" O GLU H 81 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AF1, first strand: chain 'H' and resid 57 through 59 removed outlier: 3.501A pdb=" N SER H 58 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ILE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N MET H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.644A pdb=" N GLY L 12 " --> pdb=" O THR L 104 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N GLN L 36 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU L 45 " --> pdb=" O GLN L 36 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.644A pdb=" N GLY L 12 " --> pdb=" O THR L 104 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AF5, first strand: chain 'N' and resid 10 through 12 Processing sheet with id=AF6, first strand: chain 'N' and resid 17 through 23 removed outlier: 3.573A pdb=" N LEU N 82 " --> pdb=" O VAL N 18 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU N 81 " --> pdb=" O THR N 68 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR N 68 " --> pdb=" O GLU N 81 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 57 through 59 removed outlier: 3.501A pdb=" N SER N 58 " --> pdb=" O ILE N 50 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N TRP N 36 " --> pdb=" O MET N 48 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ILE N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N MET N 34 " --> pdb=" O ILE N 50 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL N 102 " --> pdb=" O ARG N 94 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'S' and resid 9 through 12 removed outlier: 3.643A pdb=" N GLY S 12 " --> pdb=" O THR S 104 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'S' and resid 9 through 12 removed outlier: 3.643A pdb=" N GLY S 12 " --> pdb=" O THR S 104 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'S' and resid 18 through 23 1036 hydrogen bonds defined for protein. 2796 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.38 Time building geometry restraints manager: 12.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.08 - 1.23: 782 1.23 - 1.38: 9848 1.38 - 1.54: 15867 1.54 - 1.69: 393 1.69 - 1.84: 161 Bond restraints: 27051 Sorted by residual: bond pdb=" N PRO A 330 " pdb=" CA PRO A 330 " ideal model delta sigma weight residual 1.466 1.689 -0.223 1.24e-02 6.50e+03 3.23e+02 bond pdb=" CG PRO G1079 " pdb=" CD PRO G1079 " ideal model delta sigma weight residual 1.503 1.167 0.336 3.40e-02 8.65e+02 9.76e+01 bond pdb=" C PHE A 329 " pdb=" N PRO A 330 " ideal model delta sigma weight residual 1.332 1.448 -0.117 1.34e-02 5.57e+03 7.57e+01 bond pdb=" CB PRO G1079 " pdb=" CG PRO G1079 " ideal model delta sigma weight residual 1.492 1.079 0.413 5.00e-02 4.00e+02 6.82e+01 bond pdb=" CG PRO A 479 " pdb=" CD PRO A 479 " ideal model delta sigma weight residual 1.503 1.243 0.260 3.40e-02 8.65e+02 5.83e+01 ... (remaining 27046 not shown) Histogram of bond angle deviations from ideal: 76.11 - 93.08: 4 93.08 - 110.06: 5650 110.06 - 127.03: 30949 127.03 - 144.01: 250 144.01 - 160.98: 1 Bond angle restraints: 36854 Sorted by residual: angle pdb=" C PHE A 329 " pdb=" N PRO A 330 " pdb=" CA PRO A 330 " ideal model delta sigma weight residual 119.78 139.63 -19.85 1.03e+00 9.43e-01 3.72e+02 angle pdb=" N PRO G1079 " pdb=" CD PRO G1079 " pdb=" CG PRO G1079 " ideal model delta sigma weight residual 103.20 76.11 27.09 1.50e+00 4.44e-01 3.26e+02 angle pdb=" CB PRO G1079 " pdb=" CG PRO G1079 " pdb=" CD PRO G1079 " ideal model delta sigma weight residual 106.10 160.98 -54.88 3.20e+00 9.77e-02 2.94e+02 angle pdb=" CA PRO A 479 " pdb=" N PRO A 479 " pdb=" CD PRO A 479 " ideal model delta sigma weight residual 112.00 93.36 18.64 1.40e+00 5.10e-01 1.77e+02 angle pdb=" C VAL A 382 " pdb=" N SER A 383 " pdb=" CA SER A 383 " ideal model delta sigma weight residual 120.68 100.82 19.86 1.52e+00 4.33e-01 1.71e+02 ... (remaining 36849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.11: 15631 18.11 - 36.23: 920 36.23 - 54.34: 184 54.34 - 72.46: 51 72.46 - 90.57: 34 Dihedral angle restraints: 16820 sinusoidal: 6953 harmonic: 9867 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -3.64 -82.36 1 1.00e+01 1.00e-02 8.32e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 170.49 -77.49 1 1.00e+01 1.00e-02 7.52e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 169.44 -76.44 1 1.00e+01 1.00e-02 7.35e+01 ... (remaining 16817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.276: 4434 0.276 - 0.552: 5 0.552 - 0.827: 2 0.827 - 1.103: 1 1.103 - 1.379: 1 Chirality restraints: 4443 Sorted by residual: chirality pdb=" C1 NAG A1310 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1310 " pdb=" O5 NAG A1310 " both_signs ideal model delta sigma weight residual False -2.40 -1.02 -1.38 2.00e-01 2.50e+01 4.76e+01 chirality pdb=" C1 NAG G1308 " pdb=" ND2 ASN G 709 " pdb=" C2 NAG G1308 " pdb=" O5 NAG G1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.37 -1.03 2.00e-01 2.50e+01 2.64e+01 chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 282 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.64 -0.76 2.00e-01 2.50e+01 1.43e+01 ... (remaining 4440 not shown) Planarity restraints: 4715 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 478 " 0.091 5.00e-02 4.00e+02 1.22e-01 2.36e+01 pdb=" N PRO A 479 " -0.209 5.00e-02 4.00e+02 pdb=" CA PRO A 479 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 479 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 449 " 0.031 2.00e-02 2.50e+03 3.18e-02 2.02e+01 pdb=" CG TYR G 449 " -0.077 2.00e-02 2.50e+03 pdb=" CD1 TYR G 449 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR G 449 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR G 449 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR G 449 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR G 449 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR G 449 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 329 " 0.068 5.00e-02 4.00e+02 1.02e-01 1.65e+01 pdb=" N PRO B 330 " -0.176 5.00e-02 4.00e+02 pdb=" CA PRO B 330 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO B 330 " 0.056 5.00e-02 4.00e+02 ... (remaining 4712 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.17: 18 2.17 - 2.85: 9592 2.85 - 3.53: 36977 3.53 - 4.22: 61511 4.22 - 4.90: 103228 Nonbonded interactions: 211326 Sorted by model distance: nonbonded pdb=" NH2 ARG G 403 " pdb=" OD1 ASP N 100B" model vdw 1.483 2.520 nonbonded pdb=" OH TYR N 100I" pdb=" OD1 ASP S 49 " model vdw 1.566 2.440 nonbonded pdb=" OD1 ASN A 331 " pdb=" OE1 GLN A 580 " model vdw 1.891 3.040 nonbonded pdb=" OG SER A 816 " pdb=" OE1 GLU A 819 " model vdw 2.017 2.440 nonbonded pdb=" OD1 ASN G 450 " pdb=" OG SER S 92 " model vdw 2.043 2.440 ... (remaining 211321 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 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 66 or resid 82 throug \ h 87 or (resid 88 and (name N or name CA or name C or name O or name CB )) or re \ sid 89 through 95 or (resid 96 through 97 and (name N or name CA or name C or na \ me O or name CB )) or resid 98 through 109 or (resid 110 through 113 and (name N \ or name CA or name C or name O or name CB )) or resid 116 through 124 or (resid \ 125 and (name N or name CA or name C or name O or name CB )) or resid 126 throu \ gh 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) or \ resid 133 or (resid 134 through 138 and (name N or name CA or name C or name O \ or name CB )) or resid 139 through 140 or resid 166 through 168 or (resid 169 an \ d (name N or name CA or name C or name O or name CB )) or resid 170 through 171 \ or (resid 172 and (name N or name CA or name C or name O or name CB )) or resid \ 186 through 190 or (resid 191 and (name N or name CA or name C or name O or name \ CB )) or resid 192 through 196 or resid 200 through 210 or (resid 211 and (name \ N or name CA or name C or name O or name CB )) or (resid 215 and (name N or nam \ e CA or name C or name O or name CB )) or resid 216 through 217 or (resid 218 an \ d (name N or name CA or name C or name O or name CB )) or resid 219 through 223 \ or (resid 224 and (name N or name CA or name C or name O or name CB )) or resid \ 225 through 238 or (resid 239 and (name N or name CA or name C or name O or name \ CB )) or resid 240 through 263 or resid 265 through 308 or (resid 309 and (name \ N or name CA or name C or name O or name CB )) or resid 310 through 323 or (res \ id 324 and (name N or name CA or name C or name O or name CB )) or resid 325 thr \ ough 332 or (resid 333 through 334 and (name N or name CA or name C or name O or \ name CB )) or resid 335 through 339 or (resid 340 and (name N or name CA or nam \ e C or name O or name CB )) or resid 341 through 344 or (resid 345 through 360 a \ nd (name N or name CA or name C or name O or name CB )) or resid 361 or (resid 3 \ 62 through 378 and (name N or name CA or name C or name O or name CB )) or resid \ 379 or (resid 380 and (name N or name CA or name C or name O or name CB )) or r \ esid 381 or (resid 382 through 383 and (name N or name CA or name C or name O or \ name CB )) or resid 384 or (resid 385 through 390 and (name N or name CA or nam \ e C or name O or name CB )) or resid 391 or (resid 392 through 403 and (name N o \ r name CA or name C or name O or name CB )) or resid 404 or (resid 405 through 4 \ 11 and (name N or name CA or name C or name O or name CB )) or resid 412 through \ 413 or (resid 414 through 415 and (name N or name CA or name C or name O or nam \ e CB )) or resid 416 or (resid 417 through 425 and (name N or name CA or name C \ or name O or name CB )) or resid 426 or (resid 427 through 430 and (name N or na \ me CA or name C or name O or name CB )) or resid 431 through 432 or (resid 433 t \ hrough 445 and (name N or name CA or name C or name O or name CB )) or resid 446 \ through 447 or (resid 448 through 454 and (name N or name CA or name C or name \ O or name CB )) or (resid 462 and (name N or name CA or name C or name O or name \ CB )) or resid 463 or (resid 464 through 466 and (name N or name CA or name C o \ r name O or name CB )) or resid 491 or (resid 492 through 495 and (name N or nam \ e CA or name C or name O or name CB )) or resid 496 or (resid 497 through 498 an \ d (name N or name CA or name C or name O or name CB )) or resid 499 or (resid 50 \ 0 through 501 and (name N or name CA or name C or name O or name CB )) or resid \ 502 or (resid 503 and (name N or name CA or name C or name O or name CB )) or (r \ esid 504 through 506 and (name N or name CA or name C or name O or name CB )) or \ resid 507 or (resid 508 through 515 and (name N or name CA or name C or name O \ or name CB )) or (resid 522 through 524 and (name N or name CA or name C or name \ O or name CB )) or resid 525 through 527 or (resid 528 through 529 and (name N \ or name CA or name C or name O or name CB )) or resid 530 through 553 or (resid \ 554 and (name N or name CA or name C or name O or name CB )) or resid 555 throug \ h 793 or (resid 794 and (name N or name CA or name C or name O or name CB )) or \ resid 795 or (resid 796 and (name N or name CA or name C or name O or name CB )) \ or resid 797 through 810 or (resid 811 and (name N or name CA or name C or name \ O or name CB )) or resid 813 through 827 or resid 856 through 866 or (resid 867 \ through 868 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 69 through 939 or (resid 940 and (name N or name CA or name C or name O or name \ CB )) or resid 941 through 984 or (resid 985 and (name N or name CA or name C or \ name O or name CB )) or resid 986 through 987 or (resid 988 through 989 and (na \ me N or name CA or name C or name O or name CB )) or resid 990 through 1141 or ( \ resid 1142 and (name N or name CA or name C or name O or name CB )) or resid 114 \ 3 through 1144 or (resid 1145 through 1146 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1147 or resid 1301 through 1310)) selection = (chain 'B' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or re \ sid 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or \ resid 100 through 109 or (resid 110 through 113 and (name N or name CA or name C \ or name O or name CB )) or resid 116 through 128 or (resid 129 and (name N or n \ ame CA or name C or name O or name CB )) or resid 130 through 134 or (resid 135 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 140 or resid 166 through 168 or (resid 169 and (name N or name CA or n \ ame C or name O or name CB )) or resid 170 through 187 or (resid 188 and (name N \ or name CA or name C or name O or name CB )) or resid 189 through 190 or (resid \ 191 and (name N or name CA or name C or name O or name CB )) or resid 192 throu \ gh 195 or (resid 196 and (name N or name CA or name C or name O or name CB )) or \ resid 200 through 210 or (resid 211 through 215 and (name N or name CA or name \ C or name O or name CB )) or resid 216 through 241 or (resid 242 through 263 and \ (name N or name CA or name C or name O or name CB )) or resid 265 through 280 o \ r (resid 281 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 82 through 323 or (resid 324 and (name N or name CA or name C or name O or name \ CB )) or resid 325 through 567 or (resid 568 and (name N or name CA or name C or \ name O or name CB )) or resid 569 through 570 or (resid 571 and (name N or name \ CA or name C or name O or name CB )) or resid 572 through 581 or (resid 582 thr \ ough 583 and (name N or name CA or name C or name O or name CB )) or resid 584 t \ hrough 585 or (resid 586 and (name N or name CA or name C or name O or name CB ) \ ) or resid 587 through 613 or (resid 614 and (name N or name CA or name C or nam \ e O or name CB )) or resid 615 through 618 or (resid 619 and (name N or name CA \ or name C or name O or name CB )) or resid 620 through 676 or resid 690 through \ 744 or (resid 745 and (name N or name CA or name C or name O or name CB )) or re \ sid 746 through 810 or (resid 811 and (name N or name CA or name C or name O or \ name CB )) or resid 813 through 827 or resid 856 through 866 or (resid 867 throu \ gh 868 and (name N or name CA or name C or name O or name CB )) or resid 869 thr \ ough 920 or (resid 921 and (name N or name CA or name C or name O or name CB )) \ or resid 922 through 939 or (resid 940 and (name N or name CA or name C or name \ O or name CB )) or resid 941 through 984 or (resid 985 and (name N or name CA or \ name C or name O or name CB )) or resid 986 through 987 or (resid 988 through 9 \ 89 and (name N or name CA or name C or name O or name CB )) or resid 990 through \ 1072 or (resid 1073 and (name N or name CA or name C or name O or name CB )) or \ resid 1074 through 1117 or (resid 1118 and (name N or name CA or name C or name \ O or name CB )) or resid 1119 through 1143 or (resid 1144 through 1146 and (nam \ e N or name CA or name C or name O or name CB )) or resid 1147 or resid 1301 thr \ ough 1310)) selection = (chain 'G' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 110 or (resid 111 through 113 and (name N or name CA or name C o \ r name O or name CB )) or resid 116 through 134 or (resid 135 through 138 and (n \ ame N or name CA or name C or name O or name CB )) or resid 139 through 140 or r \ esid 166 through 187 or (resid 188 and (name N or name CA or name C or name O or \ name CB )) or resid 189 through 195 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB )) or resid 200 through 211 or resid 215 through 217 or \ (resid 218 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 9 through 223 or (resid 224 and (name N or name CA or name C or name O or name C \ B )) or resid 225 through 238 or (resid 239 and (name N or name CA or name C or \ name O or name CB )) or resid 240 through 308 or (resid 309 and (name N or name \ CA or name C or name O or name CB )) or resid 310 through 332 or (resid 333 thro \ ugh 334 and (name N or name CA or name C or name O or name CB )) or resid 335 th \ rough 339 or (resid 340 and (name N or name CA or name C or name O or name CB )) \ or resid 341 through 344 or (resid 345 through 360 and (name N or name CA or na \ me C or name O or name CB )) or resid 361 or (resid 362 through 378 and (name N \ or name CA or name C or name O or name CB )) or resid 379 or (resid 380 and (nam \ e N or name CA or name C or name O or name CB )) or resid 381 or (resid 382 thro \ ugh 383 and (name N or name CA or name C or name O or name CB )) or resid 384 or \ (resid 385 through 390 and (name N or name CA or name C or name O or name CB )) \ or resid 391 or (resid 392 through 403 and (name N or name CA or name C or name \ O or name CB )) or resid 404 or (resid 405 through 411 and (name N or name CA o \ r name C or name O or name CB )) or resid 412 through 413 or (resid 414 through \ 415 and (name N or name CA or name C or name O or name CB )) or resid 416 or (re \ sid 417 through 425 and (name N or name CA or name C or name O or name CB )) or \ resid 426 or (resid 427 through 430 and (name N or name CA or name C or name O o \ r name CB )) or resid 431 through 432 or (resid 433 through 445 and (name N or n \ ame CA or name C or name O or name CB )) or resid 446 through 447 or (resid 448 \ through 454 and (name N or name CA or name C or name O or name CB )) or (resid 4 \ 62 and (name N or name CA or name C or name O or name CB )) or resid 463 or (res \ id 464 through 466 and (name N or name CA or name C or name O or name CB )) or r \ esid 491 or (resid 492 through 495 and (name N or name CA or name C or name O or \ name CB )) or resid 496 or (resid 497 through 498 and (name N or name CA or nam \ e C or name O or name CB )) or resid 499 or (resid 500 through 501 and (name N o \ r name CA or name C or name O or name CB )) or resid 502 or (resid 503 and (name \ N or name CA or name C or name O or name CB )) or (resid 504 through 506 and (n \ ame N or name CA or name C or name O or name CB )) or resid 507 or (resid 508 th \ rough 515 and (name N or name CA or name C or name O or name CB )) or (resid 522 \ through 524 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 25 through 527 or (resid 528 through 529 and (name N or name CA or name C or nam \ e O or name CB )) or resid 530 through 553 or (resid 554 and (name N or name CA \ or name C or name O or name CB )) or resid 555 through 567 or (resid 568 and (na \ me N or name CA or name C or name O or name CB )) or resid 569 through 570 or (r \ esid 571 and (name N or name CA or name C or name O or name CB )) or resid 572 t \ hrough 581 or (resid 582 through 583 and (name N or name CA or name C or name O \ or name CB )) or resid 584 through 585 or (resid 586 and (name N or name CA or n \ ame C or name O or name CB )) or resid 587 through 618 or (resid 619 and (name N \ or name CA or name C or name O or name CB )) or resid 620 through 645 or (resid \ 646 through 647 and (name N or name CA or name C or name O or name CB )) or res \ id 648 through 793 or (resid 794 and (name N or name CA or name C or name O or n \ ame CB )) or resid 795 or (resid 796 and (name N or name CA or name C or name O \ or name CB )) or resid 797 through 920 or (resid 921 and (name N or name CA or n \ ame C or name O or name CB )) or resid 922 through 1072 or (resid 1073 and (name \ N or name CA or name C or name O or name CB )) or resid 1074 through 1117 or (r \ esid 1118 and (name N or name CA or name C or name O or name CB )) or resid 1119 \ through 1141 or (resid 1142 and (name N or name CA or name C or name O or name \ CB )) or resid 1143 or (resid 1144 through 1146 and (name N or name CA or name C \ or name O or name CB )) or resid 1147 or resid 1301 through 1310)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' } ncs_group { reference = chain 'H' selection = chain 'N' } ncs_group { reference = chain 'L' selection = chain 'S' } 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=0.40 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: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 10.780 Check model and map are aligned: 0.360 Set scattering table: 0.220 Process input model: 85.670 Find NCS groups from input model: 2.240 Set up NCS constraints: 0.390 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 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 : 0.008 0.413 27051 Z= 0.518 Angle : 1.051 54.885 36854 Z= 0.584 Chirality : 0.061 1.379 4443 Planarity : 0.006 0.122 4668 Dihedral : 12.579 90.574 10348 Min Nonbonded Distance : 1.483 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.13 % Favored : 93.81 % Rotamer: Outliers : 0.26 % Allowed : 0.95 % Favored : 98.79 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -1.54 (0.14), residues: 3333 helix: -0.51 (0.19), residues: 647 sheet: -0.68 (0.18), residues: 798 loop : -1.36 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP H 103 HIS 0.015 0.002 HIS S 38 PHE 0.043 0.003 PHE A1121 TYR 0.077 0.003 TYR G 449 ARG 0.012 0.001 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 384 time to evaluate : 2.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 698 SER cc_start: 0.8764 (t) cc_final: 0.8239 (p) REVERT: A 739 THR cc_start: 0.7581 (m) cc_final: 0.7353 (m) REVERT: A 1107 ARG cc_start: 0.7237 (mtt90) cc_final: 0.7031 (mpt180) REVERT: B 64 TRP cc_start: 0.8065 (t60) cc_final: 0.7568 (t60) REVERT: B 773 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8104 (mt-10) REVERT: B 1111 GLU cc_start: 0.7630 (mp0) cc_final: 0.7399 (mp0) REVERT: G 287 ASP cc_start: 0.8274 (m-30) cc_final: 0.7828 (m-30) REVERT: G 290 ASP cc_start: 0.6999 (t0) cc_final: 0.6417 (t0) REVERT: H 34 MET cc_start: 0.8861 (mmp) cc_final: 0.8273 (mmm) REVERT: H 82 LEU cc_start: 0.7145 (mt) cc_final: 0.6816 (tp) REVERT: L 20 ILE cc_start: 0.8251 (mt) cc_final: 0.8007 (tt) REVERT: L 34 TRP cc_start: 0.4188 (m100) cc_final: 0.3841 (m100) REVERT: L 85 TYR cc_start: 0.5541 (m-80) cc_final: 0.5106 (m-80) REVERT: L 86 TYR cc_start: 0.7144 (m-80) cc_final: 0.6876 (m-80) REVERT: N 36 TRP cc_start: 0.7206 (m100) cc_final: 0.6793 (m100) REVERT: N 48 MET cc_start: 0.8375 (mmt) cc_final: 0.7953 (mmt) REVERT: S 46 MET cc_start: 0.6997 (mtp) cc_final: 0.6514 (ptp) REVERT: S 103 LEU cc_start: 0.8021 (tp) cc_final: 0.7803 (mt) outliers start: 7 outliers final: 2 residues processed: 389 average time/residue: 0.3490 time to fit residues: 223.5251 Evaluate side-chains 257 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 255 time to evaluate : 3.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain G residue 517 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 285 optimal weight: 3.9990 chunk 256 optimal weight: 4.9990 chunk 142 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 172 optimal weight: 4.9990 chunk 136 optimal weight: 50.0000 chunk 264 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 197 optimal weight: 20.0000 chunk 306 optimal weight: 20.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN A 935 GLN ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 207 HIS B 935 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1005 GLN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS G 370 ASN ** G 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 804 GLN ** G 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 901 GLN G1023 ASN ** G1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1119 ASN N 97 HIS ** S 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 27051 Z= 0.336 Angle : 0.768 12.762 36854 Z= 0.399 Chirality : 0.051 0.779 4443 Planarity : 0.005 0.063 4668 Dihedral : 7.635 59.936 4885 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.58 % Favored : 93.36 % Rotamer: Outliers : 1.43 % Allowed : 8.26 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.14), residues: 3333 helix: 0.18 (0.20), residues: 663 sheet: -0.60 (0.17), residues: 797 loop : -1.37 (0.14), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP H 103 HIS 0.008 0.002 HIS G1101 PHE 0.037 0.003 PHE A1121 TYR 0.033 0.002 TYR G 449 ARG 0.013 0.001 ARG G1107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 313 time to evaluate : 3.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 290 ASP cc_start: 0.7528 (t70) cc_final: 0.7240 (p0) REVERT: A 297 SER cc_start: 0.8363 (m) cc_final: 0.7816 (t) REVERT: A 698 SER cc_start: 0.8664 (t) cc_final: 0.8311 (p) REVERT: A 759 PHE cc_start: 0.8875 (m-80) cc_final: 0.8462 (m-80) REVERT: A 873 TYR cc_start: 0.7787 (m-80) cc_final: 0.7339 (m-80) REVERT: A 915 VAL cc_start: 0.6893 (p) cc_final: 0.6555 (t) REVERT: B 317 ASN cc_start: 0.8175 (t0) cc_final: 0.7762 (p0) REVERT: B 731 MET cc_start: 0.8473 (ttp) cc_final: 0.8260 (mtp) REVERT: B 878 LEU cc_start: 0.8420 (tp) cc_final: 0.8196 (tp) REVERT: B 1050 MET cc_start: 0.7293 (ptt) cc_final: 0.7073 (ptp) REVERT: B 1107 ARG cc_start: 0.6783 (mpt180) cc_final: 0.6367 (mpt180) REVERT: G 135 PHE cc_start: 0.5129 (m-80) cc_final: 0.4840 (m-80) REVERT: G 265 TYR cc_start: 0.5912 (p90) cc_final: 0.5643 (p90) REVERT: G 287 ASP cc_start: 0.8294 (m-30) cc_final: 0.7605 (m-30) REVERT: G 1002 GLN cc_start: 0.8677 (tm-30) cc_final: 0.8381 (tm-30) REVERT: H 34 MET cc_start: 0.8719 (mmp) cc_final: 0.8198 (mmm) REVERT: H 63 LEU cc_start: 0.8341 (tp) cc_final: 0.7336 (mt) REVERT: H 69 MET cc_start: 0.4613 (pmm) cc_final: 0.4096 (pmm) REVERT: H 80 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8135 (mmm) REVERT: H 81 GLU cc_start: 0.7020 (mp0) cc_final: 0.6521 (mp0) REVERT: L 85 TYR cc_start: 0.5471 (m-80) cc_final: 0.5038 (m-80) REVERT: N 36 TRP cc_start: 0.6064 (m100) cc_final: 0.5536 (m100) REVERT: N 48 MET cc_start: 0.8364 (mmt) cc_final: 0.7875 (mmt) REVERT: S 30 LYS cc_start: 0.5967 (pttt) cc_final: 0.5406 (ptpp) REVERT: S 46 MET cc_start: 0.7378 (mtp) cc_final: 0.6703 (ptt) outliers start: 39 outliers final: 24 residues processed: 338 average time/residue: 0.3496 time to fit residues: 195.4053 Evaluate side-chains 278 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 253 time to evaluate : 2.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 315 THR Chi-restraints excluded: chain G residue 574 ASP Chi-restraints excluded: chain G residue 716 THR Chi-restraints excluded: chain G residue 721 SER Chi-restraints excluded: chain G residue 969 ASN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 103 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 170 optimal weight: 0.9990 chunk 95 optimal weight: 0.2980 chunk 255 optimal weight: 0.8980 chunk 209 optimal weight: 20.0000 chunk 84 optimal weight: 0.9980 chunk 307 optimal weight: 6.9990 chunk 332 optimal weight: 20.0000 chunk 273 optimal weight: 0.9980 chunk 304 optimal weight: 0.2980 chunk 104 optimal weight: 8.9990 chunk 246 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN B 207 HIS ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B 949 GLN B1010 GLN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS G 388 ASN G 895 GLN G1088 HIS ** G1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 97 HIS ** S 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27051 Z= 0.198 Angle : 0.655 11.871 36854 Z= 0.337 Chirality : 0.047 0.630 4443 Planarity : 0.004 0.059 4668 Dihedral : 6.777 55.002 4881 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.87 % Favored : 95.07 % Rotamer: Outliers : 1.50 % Allowed : 10.56 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.14), residues: 3333 helix: 0.76 (0.20), residues: 650 sheet: -0.44 (0.17), residues: 815 loop : -1.21 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP S 34 HIS 0.006 0.001 HIS A1064 PHE 0.025 0.002 PHE B 888 TYR 0.024 0.002 TYR G 707 ARG 0.013 0.001 ARG G1107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 296 time to evaluate : 3.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 GLN cc_start: 0.8239 (tp-100) cc_final: 0.8003 (mm-40) REVERT: A 698 SER cc_start: 0.8689 (t) cc_final: 0.8263 (p) REVERT: A 759 PHE cc_start: 0.8706 (m-80) cc_final: 0.8395 (m-80) REVERT: A 1042 PHE cc_start: 0.7472 (t80) cc_final: 0.7163 (t80) REVERT: B 317 ASN cc_start: 0.8443 (t0) cc_final: 0.7559 (p0) REVERT: B 787 GLN cc_start: 0.7078 (mm-40) cc_final: 0.6840 (mm-40) REVERT: B 1107 ARG cc_start: 0.6920 (mpt180) cc_final: 0.6465 (mpt180) REVERT: G 265 TYR cc_start: 0.5889 (p90) cc_final: 0.5592 (p90) REVERT: G 287 ASP cc_start: 0.8222 (m-30) cc_final: 0.7497 (m-30) REVERT: G 378 LYS cc_start: 0.7776 (ttpt) cc_final: 0.7540 (tmmt) REVERT: G 584 ILE cc_start: 0.9374 (mm) cc_final: 0.8888 (mm) REVERT: G 1002 GLN cc_start: 0.8643 (tm-30) cc_final: 0.8394 (tm-30) REVERT: G 1107 ARG cc_start: 0.6698 (mmt180) cc_final: 0.5598 (ttt180) REVERT: H 34 MET cc_start: 0.8675 (mmp) cc_final: 0.8288 (mmm) REVERT: H 48 MET cc_start: 0.7314 (mmt) cc_final: 0.7107 (mpp) REVERT: H 63 LEU cc_start: 0.8272 (tp) cc_final: 0.7481 (mt) REVERT: H 69 MET cc_start: 0.4661 (pmm) cc_final: 0.4232 (pmm) REVERT: H 81 GLU cc_start: 0.7311 (mp0) cc_final: 0.7063 (mp0) REVERT: L 34 TRP cc_start: 0.6647 (m100) cc_final: 0.5931 (m100) REVERT: L 85 TYR cc_start: 0.5669 (m-80) cc_final: 0.5117 (m-80) REVERT: N 35 HIS cc_start: 0.8688 (m90) cc_final: 0.7947 (m90) REVERT: N 36 TRP cc_start: 0.5567 (m100) cc_final: 0.5224 (m100) REVERT: N 80 MET cc_start: 0.7674 (tmm) cc_final: 0.6870 (tmm) REVERT: N 100 TYR cc_start: 0.5217 (m-10) cc_final: 0.4861 (m-10) REVERT: S 30 LYS cc_start: 0.5609 (pttt) cc_final: 0.5137 (ptpp) REVERT: S 46 MET cc_start: 0.7376 (mtp) cc_final: 0.6656 (ptt) outliers start: 41 outliers final: 24 residues processed: 323 average time/residue: 0.3589 time to fit residues: 190.0615 Evaluate side-chains 278 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 254 time to evaluate : 3.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1065 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 772 VAL Chi-restraints excluded: chain G residue 969 ASN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain N residue 92 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 303 optimal weight: 9.9990 chunk 231 optimal weight: 20.0000 chunk 159 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 146 optimal weight: 8.9990 chunk 206 optimal weight: 4.9990 chunk 308 optimal weight: 0.0970 chunk 326 optimal weight: 9.9990 chunk 161 optimal weight: 1.9990 chunk 292 optimal weight: 20.0000 chunk 88 optimal weight: 2.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 895 GLN B1054 GLN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS B1108 ASN G 895 GLN G 969 ASN ** G1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 27051 Z= 0.334 Angle : 0.708 11.226 36854 Z= 0.365 Chirality : 0.048 0.579 4443 Planarity : 0.005 0.059 4668 Dihedral : 6.667 59.240 4881 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.73 % Favored : 93.24 % Rotamer: Outliers : 2.41 % Allowed : 11.99 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.14), residues: 3333 helix: 0.55 (0.20), residues: 654 sheet: -0.57 (0.17), residues: 822 loop : -1.24 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP S 34 HIS 0.006 0.001 HIS B 207 PHE 0.038 0.002 PHE G1089 TYR 0.025 0.002 TYR B1047 ARG 0.015 0.001 ARG G1107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 271 time to evaluate : 3.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7276 (t80) cc_final: 0.6995 (t80) REVERT: A 698 SER cc_start: 0.8740 (t) cc_final: 0.8403 (p) REVERT: B 317 ASN cc_start: 0.8381 (t0) cc_final: 0.7735 (p0) REVERT: B 773 GLU cc_start: 0.7895 (tt0) cc_final: 0.7194 (tm-30) REVERT: B 787 GLN cc_start: 0.7019 (mm-40) cc_final: 0.6783 (mm-40) REVERT: B 1107 ARG cc_start: 0.7074 (mpt180) cc_final: 0.6647 (mpt180) REVERT: B 1111 GLU cc_start: 0.8080 (mp0) cc_final: 0.7398 (mp0) REVERT: G 192 PHE cc_start: 0.8132 (m-80) cc_final: 0.7649 (m-10) REVERT: G 287 ASP cc_start: 0.8284 (m-30) cc_final: 0.7657 (m-30) REVERT: G 378 LYS cc_start: 0.7933 (ttpt) cc_final: 0.7706 (tmmt) REVERT: G 517 LEU cc_start: 0.5018 (OUTLIER) cc_final: 0.4587 (pt) REVERT: G 584 ILE cc_start: 0.9363 (mm) cc_final: 0.8827 (mm) REVERT: G 1002 GLN cc_start: 0.8737 (tm-30) cc_final: 0.8520 (tp-100) REVERT: G 1006 THR cc_start: 0.8613 (m) cc_final: 0.8347 (m) REVERT: G 1107 ARG cc_start: 0.6787 (mmt180) cc_final: 0.5771 (ttt180) REVERT: H 34 MET cc_start: 0.8753 (mmp) cc_final: 0.8315 (mmm) REVERT: H 48 MET cc_start: 0.7322 (OUTLIER) cc_final: 0.7089 (mpp) REVERT: H 63 LEU cc_start: 0.8437 (tp) cc_final: 0.7697 (mt) REVERT: H 69 MET cc_start: 0.4747 (pmm) cc_final: 0.4287 (pmm) REVERT: H 80 MET cc_start: 0.8391 (tpp) cc_final: 0.8112 (mmm) REVERT: H 81 GLU cc_start: 0.7283 (mp0) cc_final: 0.6056 (mp0) REVERT: H 82 LEU cc_start: 0.6985 (mt) cc_final: 0.6544 (tt) REVERT: H 100 TYR cc_start: 0.5485 (p90) cc_final: 0.5005 (p90) REVERT: L 34 TRP cc_start: 0.6525 (m100) cc_final: 0.5894 (m100) REVERT: L 60 ARG cc_start: 0.6203 (mtm110) cc_final: 0.5952 (ttp-110) REVERT: N 34 MET cc_start: 0.7931 (mmm) cc_final: 0.7440 (mmm) REVERT: N 35 HIS cc_start: 0.8719 (m90) cc_final: 0.7950 (m90) REVERT: S 30 LYS cc_start: 0.5542 (pttt) cc_final: 0.5288 (ptpp) REVERT: S 32 VAL cc_start: 0.7568 (t) cc_final: 0.7315 (m) REVERT: S 34 TRP cc_start: 0.4329 (m-10) cc_final: 0.3656 (m-10) REVERT: S 46 MET cc_start: 0.7423 (mtp) cc_final: 0.6742 (ptt) outliers start: 66 outliers final: 48 residues processed: 317 average time/residue: 0.3500 time to fit residues: 183.5609 Evaluate side-chains 289 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 239 time to evaluate : 3.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 312 ILE Chi-restraints excluded: chain G residue 326 ILE Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 716 THR Chi-restraints excluded: chain G residue 738 CYS Chi-restraints excluded: chain G residue 772 VAL Chi-restraints excluded: chain G residue 915 VAL Chi-restraints excluded: chain G residue 969 ASN Chi-restraints excluded: chain G residue 1117 THR Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 38 HIS Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain N residue 92 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 272 optimal weight: 4.9990 chunk 185 optimal weight: 2.9990 chunk 4 optimal weight: 0.1980 chunk 243 optimal weight: 0.8980 chunk 134 optimal weight: 40.0000 chunk 278 optimal weight: 2.9990 chunk 225 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 166 optimal weight: 3.9990 chunk 293 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 787 GLN B 895 GLN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS G 895 GLN G1005 GLN ** G1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 ASN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 27051 Z= 0.247 Angle : 0.636 9.840 36854 Z= 0.329 Chirality : 0.046 0.550 4443 Planarity : 0.004 0.055 4668 Dihedral : 6.363 55.123 4881 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.41 % Favored : 94.56 % Rotamer: Outliers : 2.49 % Allowed : 13.19 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.90 (0.14), residues: 3333 helix: 0.81 (0.20), residues: 642 sheet: -0.52 (0.17), residues: 816 loop : -1.12 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B1102 HIS 0.005 0.001 HIS B1064 PHE 0.027 0.002 PHE B 888 TYR 0.026 0.002 TYR A 904 ARG 0.012 0.001 ARG G1107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 257 time to evaluate : 2.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7236 (t80) cc_final: 0.6976 (t80) REVERT: A 698 SER cc_start: 0.8711 (t) cc_final: 0.8335 (p) REVERT: B 317 ASN cc_start: 0.8337 (t0) cc_final: 0.7781 (p0) REVERT: B 878 LEU cc_start: 0.8396 (tp) cc_final: 0.7871 (mp) REVERT: B 1107 ARG cc_start: 0.7034 (mpt180) cc_final: 0.6616 (mpt180) REVERT: G 287 ASP cc_start: 0.8238 (m-30) cc_final: 0.7516 (m-30) REVERT: G 378 LYS cc_start: 0.7921 (ttpt) cc_final: 0.7717 (ttmt) REVERT: G 584 ILE cc_start: 0.9350 (mm) cc_final: 0.8798 (mm) REVERT: G 1002 GLN cc_start: 0.8693 (tm-30) cc_final: 0.8445 (tp-100) REVERT: G 1006 THR cc_start: 0.8613 (m) cc_final: 0.8362 (m) REVERT: G 1107 ARG cc_start: 0.6729 (mmt180) cc_final: 0.5778 (ttt180) REVERT: H 34 MET cc_start: 0.8699 (mmp) cc_final: 0.8339 (mmm) REVERT: H 48 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.7058 (mpp) REVERT: H 63 LEU cc_start: 0.8428 (tp) cc_final: 0.7690 (mt) REVERT: H 69 MET cc_start: 0.4779 (pmm) cc_final: 0.4412 (pmm) REVERT: H 80 MET cc_start: 0.8276 (tpp) cc_final: 0.7681 (mmm) REVERT: H 81 GLU cc_start: 0.7403 (mp0) cc_final: 0.6520 (mm-30) REVERT: H 82 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6541 (tt) REVERT: H 100 TYR cc_start: 0.5439 (p90) cc_final: 0.4974 (p90) REVERT: L 34 TRP cc_start: 0.6266 (m100) cc_final: 0.5493 (m100) REVERT: N 35 HIS cc_start: 0.8515 (m90) cc_final: 0.8026 (m90) REVERT: N 48 MET cc_start: 0.7839 (mmt) cc_final: 0.6936 (mmt) REVERT: S 30 LYS cc_start: 0.5896 (pttt) cc_final: 0.5306 (ptpp) REVERT: S 32 VAL cc_start: 0.7548 (t) cc_final: 0.7317 (m) REVERT: S 34 TRP cc_start: 0.4466 (m-10) cc_final: 0.3584 (m100) REVERT: S 46 MET cc_start: 0.7360 (mtp) cc_final: 0.6638 (ptt) outliers start: 68 outliers final: 52 residues processed: 307 average time/residue: 0.3387 time to fit residues: 173.4981 Evaluate side-chains 289 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 235 time to evaluate : 3.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 326 ILE Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 525 CYS Chi-restraints excluded: chain G residue 738 CYS Chi-restraints excluded: chain G residue 969 ASN Chi-restraints excluded: chain G residue 1117 THR Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 38 HIS Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain N residue 5 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 109 optimal weight: 10.0000 chunk 294 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 191 optimal weight: 8.9990 chunk 80 optimal weight: 0.7980 chunk 327 optimal weight: 20.0000 chunk 271 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 chunk 171 optimal weight: 6.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 644 GLN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1108 ASN ** G 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1071 GLN ** G1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 ASN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.124 27051 Z= 0.485 Angle : 0.804 13.134 36854 Z= 0.416 Chirality : 0.051 0.595 4443 Planarity : 0.006 0.084 4668 Dihedral : 7.055 59.960 4881 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 19.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.42 % Favored : 91.55 % Rotamer: Outliers : 3.44 % Allowed : 13.71 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.14), residues: 3333 helix: 0.25 (0.20), residues: 655 sheet: -0.75 (0.17), residues: 813 loop : -1.41 (0.14), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1102 HIS 0.005 0.001 HIS A 655 PHE 0.042 0.003 PHE G1089 TYR 0.037 0.002 TYR A 904 ARG 0.014 0.001 ARG G1107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 244 time to evaluate : 2.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 698 SER cc_start: 0.8842 (t) cc_final: 0.8496 (p) REVERT: A 856 ASN cc_start: 0.7707 (OUTLIER) cc_final: 0.7391 (t0) REVERT: A 1109 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.7376 (m-80) REVERT: B 317 ASN cc_start: 0.8382 (t0) cc_final: 0.8015 (p0) REVERT: B 1108 ASN cc_start: 0.7286 (OUTLIER) cc_final: 0.7066 (m-40) REVERT: G 287 ASP cc_start: 0.8426 (m-30) cc_final: 0.7632 (m-30) REVERT: G 584 ILE cc_start: 0.9344 (mm) cc_final: 0.8754 (mm) REVERT: G 869 MET cc_start: 0.7330 (mtp) cc_final: 0.7103 (mtp) REVERT: G 1002 GLN cc_start: 0.8778 (tm-30) cc_final: 0.8521 (tp-100) REVERT: G 1006 THR cc_start: 0.8931 (m) cc_final: 0.8702 (m) REVERT: G 1107 ARG cc_start: 0.6998 (mmt180) cc_final: 0.6071 (ttt180) REVERT: G 1109 PHE cc_start: 0.8108 (t80) cc_final: 0.7718 (t80) REVERT: H 34 MET cc_start: 0.8663 (mmp) cc_final: 0.8331 (mmm) REVERT: H 47 TRP cc_start: 0.6968 (t60) cc_final: 0.6168 (t60) REVERT: H 48 MET cc_start: 0.7344 (OUTLIER) cc_final: 0.6900 (mpp) REVERT: H 63 LEU cc_start: 0.8457 (tp) cc_final: 0.7759 (mt) REVERT: H 69 MET cc_start: 0.4655 (pmm) cc_final: 0.4264 (pmm) REVERT: H 80 MET cc_start: 0.8306 (tpp) cc_final: 0.7898 (mmm) REVERT: H 81 GLU cc_start: 0.7538 (mp0) cc_final: 0.6468 (mp0) REVERT: H 82 LEU cc_start: 0.6822 (OUTLIER) cc_final: 0.6223 (tt) REVERT: L 34 TRP cc_start: 0.6666 (m100) cc_final: 0.5845 (m100) REVERT: N 35 HIS cc_start: 0.8501 (m90) cc_final: 0.7921 (m90) REVERT: S 4 LEU cc_start: 0.7227 (mm) cc_final: 0.6515 (mt) REVERT: S 46 MET cc_start: 0.7485 (mtp) cc_final: 0.6819 (ptt) outliers start: 94 outliers final: 70 residues processed: 315 average time/residue: 0.3263 time to fit residues: 172.0163 Evaluate side-chains 295 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 220 time to evaluate : 3.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1109 PHE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 881 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1108 ASN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 312 ILE Chi-restraints excluded: chain G residue 326 ILE Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 461 LEU Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 525 CYS Chi-restraints excluded: chain G residue 534 VAL Chi-restraints excluded: chain G residue 716 THR Chi-restraints excluded: chain G residue 723 THR Chi-restraints excluded: chain G residue 738 CYS Chi-restraints excluded: chain G residue 772 VAL Chi-restraints excluded: chain G residue 915 VAL Chi-restraints excluded: chain G residue 1029 MET Chi-restraints excluded: chain G residue 1077 THR Chi-restraints excluded: chain G residue 1117 THR Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 38 HIS Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain N residue 5 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 315 optimal weight: 30.0000 chunk 36 optimal weight: 4.9990 chunk 186 optimal weight: 1.9990 chunk 238 optimal weight: 0.9990 chunk 185 optimal weight: 0.8980 chunk 275 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 chunk 325 optimal weight: 7.9990 chunk 203 optimal weight: 8.9990 chunk 198 optimal weight: 9.9990 chunk 150 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 644 GLN B 895 GLN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS B1108 ASN G 360 ASN G 501 ASN ** G 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 913 GLN ** G1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 ASN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 27051 Z= 0.222 Angle : 0.654 10.344 36854 Z= 0.334 Chirality : 0.046 0.539 4443 Planarity : 0.004 0.055 4668 Dihedral : 6.359 57.014 4881 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.41 % Allowed : 15.61 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.14), residues: 3333 helix: 0.69 (0.20), residues: 651 sheet: -0.60 (0.18), residues: 824 loop : -1.20 (0.14), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP S 34 HIS 0.006 0.001 HIS H 97 PHE 0.028 0.002 PHE B 888 TYR 0.029 0.002 TYR A 904 ARG 0.012 0.001 ARG L 60 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 254 time to evaluate : 3.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ASN cc_start: 0.8331 (t0) cc_final: 0.7444 (p0) REVERT: A 698 SER cc_start: 0.8766 (t) cc_final: 0.8322 (p) REVERT: A 699 LEU cc_start: 0.8072 (tt) cc_final: 0.7773 (tp) REVERT: A 1109 PHE cc_start: 0.7293 (OUTLIER) cc_final: 0.6580 (m-80) REVERT: B 317 ASN cc_start: 0.8263 (t0) cc_final: 0.7965 (p0) REVERT: G 287 ASP cc_start: 0.8403 (m-30) cc_final: 0.7614 (m-30) REVERT: G 584 ILE cc_start: 0.9326 (mm) cc_final: 0.8752 (mm) REVERT: G 1002 GLN cc_start: 0.8700 (tm-30) cc_final: 0.8416 (tp-100) REVERT: G 1006 THR cc_start: 0.8851 (m) cc_final: 0.8600 (m) REVERT: G 1107 ARG cc_start: 0.6696 (mmt180) cc_final: 0.5961 (ttt180) REVERT: G 1109 PHE cc_start: 0.8068 (t80) cc_final: 0.7619 (t80) REVERT: H 34 MET cc_start: 0.8587 (mmp) cc_final: 0.8301 (mmm) REVERT: H 47 TRP cc_start: 0.6875 (t60) cc_final: 0.6374 (t60) REVERT: H 63 LEU cc_start: 0.8408 (tp) cc_final: 0.7663 (mt) REVERT: H 69 MET cc_start: 0.4906 (pmm) cc_final: 0.4545 (pmm) REVERT: H 80 MET cc_start: 0.8244 (tpp) cc_final: 0.7887 (mmm) REVERT: H 81 GLU cc_start: 0.7680 (mp0) cc_final: 0.6671 (mp0) REVERT: H 82 LEU cc_start: 0.6751 (OUTLIER) cc_final: 0.6063 (tt) REVERT: H 83 ARG cc_start: 0.7337 (mtm-85) cc_final: 0.7046 (mtm-85) REVERT: L 34 TRP cc_start: 0.6256 (m100) cc_final: 0.5694 (m100) REVERT: L 59 ASN cc_start: 0.8137 (OUTLIER) cc_final: 0.6976 (t0) REVERT: L 60 ARG cc_start: 0.6741 (mtm110) cc_final: 0.6537 (mtm110) REVERT: N 35 HIS cc_start: 0.8540 (m90) cc_final: 0.8030 (m90) REVERT: S 4 LEU cc_start: 0.7118 (mm) cc_final: 0.6448 (mt) REVERT: S 30 LYS cc_start: 0.5670 (pptt) cc_final: 0.5026 (pptt) REVERT: S 34 TRP cc_start: 0.4815 (m-10) cc_final: 0.4039 (m-10) REVERT: S 46 MET cc_start: 0.7318 (mtp) cc_final: 0.6668 (ptt) outliers start: 66 outliers final: 53 residues processed: 301 average time/residue: 0.3437 time to fit residues: 173.2692 Evaluate side-chains 293 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 237 time to evaluate : 2.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1109 PHE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 312 ILE Chi-restraints excluded: chain G residue 326 ILE Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 461 LEU Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 525 CYS Chi-restraints excluded: chain G residue 716 THR Chi-restraints excluded: chain G residue 738 CYS Chi-restraints excluded: chain G residue 772 VAL Chi-restraints excluded: chain G residue 915 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 38 HIS Chi-restraints excluded: chain L residue 59 ASN Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain N residue 5 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 201 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 194 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 207 optimal weight: 6.9990 chunk 221 optimal weight: 0.0060 chunk 161 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 256 optimal weight: 0.9980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 895 GLN B1010 GLN ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 895 GLN ** G 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 ASN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 27051 Z= 0.185 Angle : 0.618 10.223 36854 Z= 0.314 Chirality : 0.045 0.422 4443 Planarity : 0.004 0.056 4668 Dihedral : 5.839 54.808 4881 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.45 % Allowed : 16.23 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.14), residues: 3333 helix: 0.94 (0.21), residues: 642 sheet: -0.48 (0.18), residues: 836 loop : -1.05 (0.14), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP S 34 HIS 0.007 0.001 HIS B 207 PHE 0.026 0.002 PHE G 497 TYR 0.022 0.002 TYR A 423 ARG 0.010 0.001 ARG L 60 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 257 time to evaluate : 2.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ASN cc_start: 0.8333 (t0) cc_final: 0.7426 (p0) REVERT: A 698 SER cc_start: 0.8753 (t) cc_final: 0.8357 (p) REVERT: A 1109 PHE cc_start: 0.7027 (OUTLIER) cc_final: 0.5906 (m-80) REVERT: B 317 ASN cc_start: 0.8248 (t0) cc_final: 0.7948 (p0) REVERT: B 697 MET cc_start: 0.7472 (ptm) cc_final: 0.7180 (ptp) REVERT: B 878 LEU cc_start: 0.8345 (tp) cc_final: 0.7785 (mp) REVERT: B 1102 TRP cc_start: 0.3341 (t-100) cc_final: 0.2002 (m-90) REVERT: G 287 ASP cc_start: 0.8379 (m-30) cc_final: 0.7590 (m-30) REVERT: G 374 PHE cc_start: 0.8203 (m-80) cc_final: 0.7939 (m-80) REVERT: G 584 ILE cc_start: 0.9286 (mm) cc_final: 0.9016 (mm) REVERT: G 1002 GLN cc_start: 0.8637 (tm-30) cc_final: 0.8332 (tp-100) REVERT: G 1006 THR cc_start: 0.8845 (m) cc_final: 0.8609 (m) REVERT: G 1107 ARG cc_start: 0.6540 (mmt180) cc_final: 0.5849 (ttt180) REVERT: H 34 MET cc_start: 0.8550 (mmp) cc_final: 0.8329 (mmm) REVERT: H 47 TRP cc_start: 0.6893 (t60) cc_final: 0.6293 (t60) REVERT: H 63 LEU cc_start: 0.8408 (tp) cc_final: 0.7737 (mt) REVERT: H 69 MET cc_start: 0.4888 (pmm) cc_final: 0.4592 (pmm) REVERT: H 80 MET cc_start: 0.8188 (tpp) cc_final: 0.7943 (mmm) REVERT: H 81 GLU cc_start: 0.7674 (mp0) cc_final: 0.7268 (mp0) REVERT: H 83 ARG cc_start: 0.7458 (mtm-85) cc_final: 0.7173 (mtm-85) REVERT: H 100 TYR cc_start: 0.4993 (p90) cc_final: 0.4677 (p90) REVERT: L 34 TRP cc_start: 0.6257 (m100) cc_final: 0.5434 (m100) REVERT: L 36 GLN cc_start: 0.6169 (OUTLIER) cc_final: 0.5772 (pm20) REVERT: L 59 ASN cc_start: 0.8107 (OUTLIER) cc_final: 0.6920 (t0) REVERT: L 60 ARG cc_start: 0.6704 (mtm110) cc_final: 0.6195 (ttp-110) REVERT: L 85 TYR cc_start: 0.5938 (m-80) cc_final: 0.5116 (m-80) REVERT: N 23 LYS cc_start: 0.8095 (mppt) cc_final: 0.6996 (tptp) REVERT: N 35 HIS cc_start: 0.8548 (m90) cc_final: 0.8107 (m90) REVERT: S 4 LEU cc_start: 0.7140 (mm) cc_final: 0.6463 (mt) REVERT: S 30 LYS cc_start: 0.5436 (OUTLIER) cc_final: 0.4963 (pptt) REVERT: S 46 MET cc_start: 0.7265 (mtp) cc_final: 0.6599 (ptt) outliers start: 67 outliers final: 49 residues processed: 306 average time/residue: 0.3371 time to fit residues: 172.2181 Evaluate side-chains 279 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 226 time to evaluate : 3.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1109 PHE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 312 ILE Chi-restraints excluded: chain G residue 326 ILE Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 461 LEU Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 525 CYS Chi-restraints excluded: chain G residue 738 CYS Chi-restraints excluded: chain G residue 772 VAL Chi-restraints excluded: chain G residue 915 VAL Chi-restraints excluded: chain G residue 1117 THR Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 36 GLN Chi-restraints excluded: chain L residue 38 HIS Chi-restraints excluded: chain L residue 59 ASN Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 92 CYS Chi-restraints excluded: chain S residue 30 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 296 optimal weight: 4.9990 chunk 312 optimal weight: 7.9990 chunk 284 optimal weight: 5.9990 chunk 303 optimal weight: 10.0000 chunk 182 optimal weight: 6.9990 chunk 132 optimal weight: 30.0000 chunk 238 optimal weight: 10.0000 chunk 93 optimal weight: 0.6980 chunk 274 optimal weight: 4.9990 chunk 287 optimal weight: 0.9990 chunk 302 optimal weight: 8.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 644 GLN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 895 GLN ** G 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 27051 Z= 0.363 Angle : 0.714 11.676 36854 Z= 0.366 Chirality : 0.048 0.452 4443 Planarity : 0.005 0.058 4668 Dihedral : 6.178 57.825 4881 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 2.49 % Allowed : 16.74 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.14), residues: 3333 helix: 0.71 (0.20), residues: 644 sheet: -0.58 (0.18), residues: 832 loop : -1.22 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.003 TRP S 34 HIS 0.005 0.001 HIS B1064 PHE 0.032 0.003 PHE G1089 TYR 0.029 0.002 TYR A 423 ARG 0.009 0.001 ARG L 60 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 224 time to evaluate : 3.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ASN cc_start: 0.8393 (t0) cc_final: 0.7502 (p0) REVERT: A 698 SER cc_start: 0.8908 (t) cc_final: 0.8579 (p) REVERT: A 1109 PHE cc_start: 0.7482 (OUTLIER) cc_final: 0.7065 (m-80) REVERT: B 317 ASN cc_start: 0.8364 (t0) cc_final: 0.8119 (p0) REVERT: G 287 ASP cc_start: 0.8446 (m-30) cc_final: 0.7624 (m-30) REVERT: G 374 PHE cc_start: 0.8189 (m-80) cc_final: 0.7902 (m-80) REVERT: G 584 ILE cc_start: 0.9295 (mm) cc_final: 0.8687 (mm) REVERT: G 1002 GLN cc_start: 0.8698 (tm-30) cc_final: 0.8408 (tp-100) REVERT: G 1006 THR cc_start: 0.8938 (m) cc_final: 0.8721 (m) REVERT: G 1107 ARG cc_start: 0.6604 (mmt180) cc_final: 0.5948 (ttt180) REVERT: H 34 MET cc_start: 0.8634 (mmp) cc_final: 0.8407 (mmm) REVERT: H 69 MET cc_start: 0.4993 (pmm) cc_final: 0.4713 (pmm) REVERT: H 80 MET cc_start: 0.8235 (tpp) cc_final: 0.7926 (mmm) REVERT: H 81 GLU cc_start: 0.7763 (mp0) cc_final: 0.6779 (mp0) REVERT: H 82 LEU cc_start: 0.6908 (mt) cc_final: 0.6075 (tt) REVERT: H 83 ARG cc_start: 0.7445 (mtm-85) cc_final: 0.6959 (mtm-85) REVERT: H 100 TYR cc_start: 0.4958 (p90) cc_final: 0.4645 (p90) REVERT: L 34 TRP cc_start: 0.6284 (m100) cc_final: 0.5503 (m100) REVERT: L 35 TYR cc_start: 0.6769 (m-80) cc_final: 0.6401 (m-80) REVERT: L 36 GLN cc_start: 0.6055 (OUTLIER) cc_final: 0.5764 (pm20) REVERT: L 60 ARG cc_start: 0.6884 (mtm110) cc_final: 0.6306 (ttp-110) REVERT: N 35 HIS cc_start: 0.8450 (m90) cc_final: 0.8050 (m90) REVERT: S 4 LEU cc_start: 0.7032 (mm) cc_final: 0.6444 (mt) REVERT: S 30 LYS cc_start: 0.5724 (OUTLIER) cc_final: 0.5123 (pptt) REVERT: S 46 MET cc_start: 0.7304 (mtp) cc_final: 0.6699 (ptt) REVERT: S 103 LEU cc_start: 0.7508 (mt) cc_final: 0.7297 (tt) outliers start: 68 outliers final: 60 residues processed: 278 average time/residue: 0.3473 time to fit residues: 160.9709 Evaluate side-chains 283 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 220 time to evaluate : 3.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1109 PHE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 312 ILE Chi-restraints excluded: chain G residue 326 ILE Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 461 LEU Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 525 CYS Chi-restraints excluded: chain G residue 738 CYS Chi-restraints excluded: chain G residue 772 VAL Chi-restraints excluded: chain G residue 895 GLN Chi-restraints excluded: chain G residue 915 VAL Chi-restraints excluded: chain G residue 1029 MET Chi-restraints excluded: chain G residue 1117 THR Chi-restraints excluded: chain G residue 1125 ASN Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 36 GLN Chi-restraints excluded: chain L residue 38 HIS Chi-restraints excluded: chain L residue 59 ASN Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 92 CYS Chi-restraints excluded: chain S residue 30 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 199 optimal weight: 6.9990 chunk 321 optimal weight: 20.0000 chunk 195 optimal weight: 7.9990 chunk 152 optimal weight: 1.9990 chunk 223 optimal weight: 0.8980 chunk 336 optimal weight: 5.9990 chunk 309 optimal weight: 5.9990 chunk 268 optimal weight: 0.0770 chunk 27 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 chunk 164 optimal weight: 0.4980 overall best weight: 1.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.178 27051 Z= 0.395 Angle : 0.839 59.191 36854 Z= 0.451 Chirality : 0.048 0.584 4443 Planarity : 0.005 0.059 4668 Dihedral : 6.176 57.841 4881 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 2.63 % Allowed : 16.81 % Favored : 80.56 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.14), residues: 3333 helix: 0.70 (0.20), residues: 645 sheet: -0.58 (0.18), residues: 832 loop : -1.23 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP S 34 HIS 0.004 0.001 HIS B1064 PHE 0.029 0.002 PHE G1089 TYR 0.032 0.002 TYR A 451 ARG 0.008 0.001 ARG G1107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6666 Ramachandran restraints generated. 3333 Oldfield, 0 Emsley, 3333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 220 time to evaluate : 3.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 ASN cc_start: 0.8396 (t0) cc_final: 0.7498 (p0) REVERT: A 698 SER cc_start: 0.8895 (t) cc_final: 0.8563 (p) REVERT: A 1109 PHE cc_start: 0.7473 (OUTLIER) cc_final: 0.7058 (m-80) REVERT: B 317 ASN cc_start: 0.8364 (t0) cc_final: 0.8124 (p0) REVERT: G 287 ASP cc_start: 0.8445 (m-30) cc_final: 0.7621 (m-30) REVERT: G 374 PHE cc_start: 0.8188 (m-80) cc_final: 0.7901 (m-80) REVERT: G 584 ILE cc_start: 0.9294 (mm) cc_final: 0.8686 (mm) REVERT: G 1002 GLN cc_start: 0.8695 (tm-30) cc_final: 0.8403 (tp-100) REVERT: G 1006 THR cc_start: 0.8939 (m) cc_final: 0.8724 (m) REVERT: G 1107 ARG cc_start: 0.6593 (mmt180) cc_final: 0.5941 (ttt180) REVERT: H 34 MET cc_start: 0.8608 (mmp) cc_final: 0.8391 (mmm) REVERT: H 69 MET cc_start: 0.5001 (pmm) cc_final: 0.4716 (pmm) REVERT: H 80 MET cc_start: 0.8235 (tpp) cc_final: 0.7931 (mmm) REVERT: H 81 GLU cc_start: 0.7767 (mp0) cc_final: 0.6780 (mp0) REVERT: H 82 LEU cc_start: 0.6916 (mt) cc_final: 0.6073 (tt) REVERT: H 83 ARG cc_start: 0.7460 (mtm-85) cc_final: 0.6968 (mtm-85) REVERT: H 100 TYR cc_start: 0.4955 (p90) cc_final: 0.4647 (p90) REVERT: L 34 TRP cc_start: 0.6267 (m100) cc_final: 0.5500 (m100) REVERT: L 35 TYR cc_start: 0.6835 (m-80) cc_final: 0.6400 (m-80) REVERT: L 36 GLN cc_start: 0.6089 (OUTLIER) cc_final: 0.5754 (pm20) REVERT: L 60 ARG cc_start: 0.6882 (mtm110) cc_final: 0.6314 (ttp-110) REVERT: N 35 HIS cc_start: 0.8469 (m90) cc_final: 0.8047 (m90) REVERT: S 4 LEU cc_start: 0.7034 (mm) cc_final: 0.6442 (mt) REVERT: S 30 LYS cc_start: 0.5751 (OUTLIER) cc_final: 0.5131 (pptt) REVERT: S 46 MET cc_start: 0.7304 (mtp) cc_final: 0.6691 (ptt) outliers start: 72 outliers final: 67 residues processed: 273 average time/residue: 0.3570 time to fit residues: 163.0940 Evaluate side-chains 288 residues out of total 2960 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 218 time to evaluate : 3.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1109 PHE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 779 GLN Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 312 ILE Chi-restraints excluded: chain G residue 326 ILE Chi-restraints excluded: chain G residue 390 LEU Chi-restraints excluded: chain G residue 461 LEU Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain G residue 525 CYS Chi-restraints excluded: chain G residue 723 THR Chi-restraints excluded: chain G residue 738 CYS Chi-restraints excluded: chain G residue 772 VAL Chi-restraints excluded: chain G residue 911 VAL Chi-restraints excluded: chain G residue 915 VAL Chi-restraints excluded: chain G residue 1029 MET Chi-restraints excluded: chain G residue 1077 THR Chi-restraints excluded: chain G residue 1117 THR Chi-restraints excluded: chain G residue 1125 ASN Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 36 GLN Chi-restraints excluded: chain L residue 38 HIS Chi-restraints excluded: chain L residue 59 ASN Chi-restraints excluded: chain L residue 86 TYR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 92 CYS Chi-restraints excluded: chain S residue 30 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 212 optimal weight: 0.9980 chunk 285 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 247 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 74 optimal weight: 0.7980 chunk 268 optimal weight: 0.0970 chunk 112 optimal weight: 0.9980 chunk 275 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.139008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.096668 restraints weight = 100773.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.100418 restraints weight = 43287.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.102924 restraints weight = 25448.401| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3589 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3589 r_free = 0.3589 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3589 r_free = 0.3589 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.178 27051 Z= 0.395 Angle : 0.839 59.191 36854 Z= 0.451 Chirality : 0.048 0.584 4443 Planarity : 0.005 0.059 4668 Dihedral : 6.176 57.841 4881 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 2.60 % Allowed : 16.92 % Favored : 80.48 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.14), residues: 3333 helix: 0.70 (0.20), residues: 645 sheet: -0.58 (0.18), residues: 832 loop : -1.23 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP S 34 HIS 0.004 0.001 HIS B1064 PHE 0.029 0.002 PHE G1089 TYR 0.032 0.002 TYR A 451 ARG 0.008 0.001 ARG G1107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5324.85 seconds wall clock time: 99 minutes 8.02 seconds (5948.02 seconds total)