Starting phenix.real_space_refine on Wed Apr 17 12:16:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lua_23519/04_2024/7lua_23519_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lua_23519/04_2024/7lua_23519.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lua_23519/04_2024/7lua_23519.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lua_23519/04_2024/7lua_23519.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lua_23519/04_2024/7lua_23519_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lua_23519/04_2024/7lua_23519_trim.pdb" } resolution = 4.7 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= 0.027 sd= 0.115 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: 5 Type Number sf(0) Gaussians S 129 5.16 5 C 13955 2.51 5 N 3627 2.21 5 O 4679 1.98 5 H 20105 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a GLU 32": "OE1" <-> "OE2" Residue "a PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 64": "OE1" <-> "OE2" Residue "a GLU 83": "OE1" <-> "OE2" Residue "a GLU 91": "OE1" <-> "OE2" Residue "a GLU 150": "OE1" <-> "OE2" Residue "a PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 169": "OE1" <-> "OE2" Residue "a TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 211": "OE1" <-> "OE2" Residue "a GLU 269": "OE1" <-> "OE2" Residue "a GLU 293": "OE1" <-> "OE2" Residue "a ASP 325": "OD1" <-> "OD2" Residue "a GLU 335": "OE1" <-> "OE2" Residue "a TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 464": "OE1" <-> "OE2" Residue "a TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ARG 530": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ASP 612": "OD1" <-> "OD2" Residue "b GLU 636": "OE1" <-> "OE2" Residue "b ASP 652": "OD1" <-> "OD2" Residue "c GLU 32": "OE1" <-> "OE2" Residue "c GLU 64": "OE1" <-> "OE2" Residue "c GLU 83": "OE1" <-> "OE2" Residue "c GLU 150": "OE1" <-> "OE2" Residue "c PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c GLU 169": "OE1" <-> "OE2" Residue "c TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c GLU 211": "OE1" <-> "OE2" Residue "c TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c GLU 269": "OE1" <-> "OE2" Residue "c GLU 293": "OE1" <-> "OE2" Residue "c ASP 325": "OD1" <-> "OD2" Residue "c GLU 335": "OE1" <-> "OE2" Residue "c PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c GLU 464": "OE1" <-> "OE2" Residue "d PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "d ARG 530": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "d ASP 612": "OD1" <-> "OD2" Residue "d GLU 636": "OE1" <-> "OE2" Residue "e PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e GLU 64": "OE1" <-> "OE2" Residue "e GLU 83": "OE1" <-> "OE2" Residue "e GLU 91": "OE1" <-> "OE2" Residue "e PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e GLU 169": "OE1" <-> "OE2" Residue "e TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e GLU 267": "OE1" <-> "OE2" Residue "e GLU 293": "OE1" <-> "OE2" Residue "e GLU 335": "OE1" <-> "OE2" Residue "e PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e GLU 464": "OE1" <-> "OE2" Residue "e TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f ARG 530": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "f GLU 609": "OE1" <-> "OE2" Residue "f ASP 612": "OD1" <-> "OD2" Residue "f GLU 636": "OE1" <-> "OE2" Residue "g GLU 17": "OE1" <-> "OE2" Residue "g TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g GLU 79": "OE1" <-> "OE2" Residue "g ASP 81": "OD1" <-> "OD2" Residue "g PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g GLU 143": "OE1" <-> "OE2" Residue "g GLU 161": "OE1" <-> "OE2" Residue "g TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "g GLU 195": "OE1" <-> "OE2" Residue "h ASP 65": "OD1" <-> "OD2" Residue "h ASP 76": "OD1" <-> "OD2" Residue "h TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "h TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "i ASP 2": "OD1" <-> "OD2" Residue "i GLU 13": "OE1" <-> "OE2" Residue "i PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "i ASP 31": "OD1" <-> "OD2" Residue "i TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "i GLU 50": "OE1" <-> "OE2" Residue "i ASP 65": "OD1" <-> "OD2" Residue "i GLU 96": "OE1" <-> "OE2" Residue "i PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "i GLU 133": "OE1" <-> "OE2" Residue "i PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "i TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "i TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j GLU 1": "OE1" <-> "OE2" Residue "j TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j ASP 60": "OD1" <-> "OD2" Residue "j PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j ASP 81": "OD1" <-> "OD2" Residue "j PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j ASP 123": "OD1" <-> "OD2" Residue "j PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "j GLU 143": "OE1" <-> "OE2" Residue "j GLU 165": "OE1" <-> "OE2" Residue "j ASP 167": "OD1" <-> "OD2" Residue "j GLU 195": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 42495 Number of models: 1 Model: "" Number of chains: 56 Chain: "a" Number of atoms: 7192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 7192 Classifications: {'peptide': 466} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 23, 'TRANS': 442} Chain: "b" Number of atoms: 1985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1985 Classifications: {'peptide': 126} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "c" Number of atoms: 7192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 7192 Classifications: {'peptide': 466} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 23, 'TRANS': 442} Chain: "d" Number of atoms: 1985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1985 Classifications: {'peptide': 126} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "e" Number of atoms: 7195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 7195 Classifications: {'peptide': 466} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 23, 'TRANS': 442} Chain: "f" Number of atoms: 1985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1985 Classifications: {'peptide': 126} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "g" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3275 Classifications: {'peptide': 218} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 206} Chain: "h" Number of atoms: 3295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 3295 Classifications: {'peptide': 219} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 203} Chain: "i" Number of atoms: 3296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 3296 Classifications: {'peptide': 219} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 4, 'PTRANS': 11, 'TRANS': 203} Chain: "j" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3275 Classifications: {'peptide': 218} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" 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: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" 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: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "p" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "u" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "v" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "x" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "b" 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: "c" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 Time building chain proxies: 17.88, per 1000 atoms: 0.42 Number of scatterers: 42495 At special positions: 0 Unit cell: (123.714, 123.714, 203.701, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 129 16.00 O 4679 8.00 N 3627 7.00 C 13955 6.00 H 20105 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS a 54 " - pdb=" SG CYS a 74 " distance=2.05 Simple disulfide: pdb=" SG CYS a 119 " - pdb=" SG CYS a 205 " distance=2.04 Simple disulfide: pdb=" SG CYS a 126 " - pdb=" SG CYS a 196 " distance=2.02 Simple disulfide: pdb=" SG CYS a 131 " - pdb=" SG CYS a 157 " distance=2.02 Simple disulfide: pdb=" SG CYS a 201 " - pdb=" SG CYS a 433 " distance=2.01 Simple disulfide: pdb=" SG CYS a 218 " - pdb=" SG CYS a 247 " distance=2.03 Simple disulfide: pdb=" SG CYS a 228 " - pdb=" SG CYS a 239 " distance=2.04 Simple disulfide: pdb=" SG CYS a 296 " - pdb=" SG CYS a 331 " distance=2.03 Simple disulfide: pdb=" SG CYS a 378 " - pdb=" SG CYS a 445 " distance=2.02 Simple disulfide: pdb=" SG CYS a 385 " - pdb=" SG CYS a 418 " distance=2.01 Simple disulfide: pdb=" SG CYS a 501 " - pdb=" SG CYS b 593 " distance=2.01 Simple disulfide: pdb=" SG CYS b 586 " - pdb=" SG CYS b 592 " distance=2.02 Simple disulfide: pdb=" SG CYS c 54 " - pdb=" SG CYS c 74 " distance=2.02 Simple disulfide: pdb=" SG CYS c 119 " - pdb=" SG CYS c 205 " distance=2.03 Simple disulfide: pdb=" SG CYS c 126 " - pdb=" SG CYS c 196 " distance=2.03 Simple disulfide: pdb=" SG CYS c 131 " - pdb=" SG CYS c 157 " distance=2.02 Simple disulfide: pdb=" SG CYS c 201 " - pdb=" SG CYS c 433 " distance=2.03 Simple disulfide: pdb=" SG CYS c 218 " - pdb=" SG CYS c 247 " distance=2.03 Simple disulfide: pdb=" SG CYS c 228 " - pdb=" SG CYS c 239 " distance=2.03 Simple disulfide: pdb=" SG CYS c 296 " - pdb=" SG CYS c 331 " distance=2.02 Simple disulfide: pdb=" SG CYS c 378 " - pdb=" SG CYS c 445 " distance=2.02 Simple disulfide: pdb=" SG CYS c 385 " - pdb=" SG CYS c 418 " distance=2.03 Simple disulfide: pdb=" SG CYS c 501 " - pdb=" SG CYS d 593 " distance=2.01 Simple disulfide: pdb=" SG CYS d 586 " - pdb=" SG CYS d 592 " distance=2.03 Simple disulfide: pdb=" SG CYS e 54 " - pdb=" SG CYS e 74 " distance=2.03 Simple disulfide: pdb=" SG CYS e 119 " - pdb=" SG CYS e 205 " distance=2.03 Simple disulfide: pdb=" SG CYS e 126 " - pdb=" SG CYS e 196 " distance=2.02 Simple disulfide: pdb=" SG CYS e 131 " - pdb=" SG CYS e 157 " distance=2.03 Simple disulfide: pdb=" SG CYS e 201 " - pdb=" SG CYS e 433 " distance=2.01 Simple disulfide: pdb=" SG CYS e 218 " - pdb=" SG CYS e 247 " distance=2.02 Simple disulfide: pdb=" SG CYS e 228 " - pdb=" SG CYS e 239 " distance=2.04 Simple disulfide: pdb=" SG CYS e 296 " - pdb=" SG CYS e 331 " distance=2.01 Simple disulfide: pdb=" SG CYS e 378 " - pdb=" SG CYS e 445 " distance=2.03 Simple disulfide: pdb=" SG CYS e 385 " - pdb=" SG CYS e 418 " distance=2.01 Simple disulfide: pdb=" SG CYS e 501 " - pdb=" SG CYS f 593 " distance=2.03 Simple disulfide: pdb=" SG CYS f 586 " - pdb=" SG CYS f 592 " distance=2.02 Simple disulfide: pdb=" SG CYS g 23 " - pdb=" SG CYS g 88 " distance=2.03 Simple disulfide: pdb=" SG CYS g 134 " - pdb=" SG CYS g 194 " distance=2.01 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 92 " distance=2.01 Simple disulfide: pdb=" SG CYS h 140 " - pdb=" SG CYS h 196 " distance=2.02 Simple disulfide: pdb=" SG CYS i 22 " - pdb=" SG CYS i 92 " distance=2.02 Simple disulfide: pdb=" SG CYS i 140 " - pdb=" SG CYS i 196 " distance=2.04 Simple disulfide: pdb=" SG CYS j 23 " - pdb=" SG CYS j 88 " distance=2.01 Simple disulfide: pdb=" SG CYS j 134 " - pdb=" SG CYS j 194 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA M 3 " - " MAN M 6 " " BMA N 3 " - " MAN N 4 " " BMA S 3 " - " MAN S 4 " " BMA p 3 " - " MAN p 4 " ALPHA1-6 " BMA D 3 " - " MAN D 5 " " BMA M 3 " - " MAN M 4 " " MAN M 4 " - " MAN M 5 " " BMA N 3 " - " MAN N 5 " " BMA S 3 " - " MAN S 5 " " BMA p 3 " - " MAN p 5 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " NAG-ASN " NAG B 1 " - " ASN e 234 " " NAG D 1 " - " ASN e 262 " " NAG E 1 " - " ASN e 156 " " NAG G 1 " - " ASN e 301 " " NAG H 1 " - " ASN e 332 " " NAG I 1 " - " ASN e 339 " " NAG J 1 " - " ASN e 136 " " NAG K 1 " - " ASN e 160 " " NAG L 1 " - " ASN e 197 " " NAG N 1 " - " ASN e 276 " " NAG O 1 " - " ASN a 362 " " NAG P 1 " - " ASN a 392 " " NAG Q 1 " - " ASN a 234 " " NAG R 1 " - " ASN a 241 " " NAG S 1 " - " ASN a 262 " " NAG T 1 " - " ASN a 156 " " NAG V 1 " - " ASN a 301 " " NAG W 1 " - " ASN a 332 " " NAG X 1 " - " ASN a 339 " " NAG Y 1 " - " ASN a 136 " " NAG Z 1 " - " ASN a 160 " " NAG a 601 " - " ASN a 88 " " NAG a 602 " - " ASN a 276 " " NAG a 603 " - " ASN a 448 " " NAG a 604 " - " ASN a 442 " " NAG b 701 " - " ASN b 599 " " NAG b 702 " - " ASN b 625 " " NAG c 601 " - " ASN c 88 " " NAG c 602 " - " ASN c 276 " " NAG c 603 " - " ASN c 448 " " NAG c 604 " - " ASN c 442 " " NAG d 701 " - " ASN d 599 " " NAG d 702 " - " ASN d 625 " " NAG e 601 " - " ASN e 88 " " NAG e 602 " - " ASN e 448 " " NAG f 701 " - " ASN f 599 " " NAG f 702 " - " ASN f 625 " " NAG k 1 " - " ASN a 197 " " NAG l 1 " - " ASN c 362 " " NAG m 1 " - " ASN c 392 " " NAG n 1 " - " ASN c 234 " " NAG o 1 " - " ASN c 241 " " NAG p 1 " - " ASN c 262 " " NAG q 1 " - " ASN c 156 " " NAG s 1 " - " ASN c 301 " " NAG t 1 " - " ASN c 332 " " NAG u 1 " - " ASN c 339 " " NAG v 1 " - " ASN c 136 " " NAG w 1 " - " ASN c 160 " " NAG x 1 " - " ASN c 197 " NAG-SER " NAG F 1 " - " SER e 388 " " NAG U 1 " - " SER a 388 " " NAG r 1 " - " SER c 388 " Time building additional restraints: 36.39 Conformation dependent library (CDL) restraints added in 4.2 seconds 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4926 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 46 sheets defined 21.2% alpha, 31.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.63 Creating SS restraints... Processing helix chain 'a' and resid 58 through 63 Processing helix chain 'a' and resid 99 through 117 Processing helix chain 'a' and resid 123 through 126 Processing helix chain 'a' and resid 138 through 142 Processing helix chain 'a' and resid 335 through 353 Processing helix chain 'a' and resid 368 through 373 Processing helix chain 'a' and resid 377 through 381 Processing helix chain 'a' and resid 386 through 391 removed outlier: 4.026A pdb=" N LEU a 390 " --> pdb=" O ASN a 386 " (cutoff:3.500A) Processing helix chain 'a' and resid 399 through 403 Processing helix chain 'a' and resid 474 through 484 removed outlier: 3.802A pdb=" N ASN a 478 " --> pdb=" O ASP a 474 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU a 482 " --> pdb=" O ASN a 478 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR a 484 " --> pdb=" O ARG a 480 " (cutoff:3.500A) Processing helix chain 'b' and resid 517 through 523 removed outlier: 4.155A pdb=" N MET b 523 " --> pdb=" O GLY b 519 " (cutoff:3.500A) Processing helix chain 'b' and resid 524 through 531 removed outlier: 3.770A pdb=" N GLN b 528 " --> pdb=" O THR b 524 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN b 531 " --> pdb=" O VAL b 527 " (cutoff:3.500A) Processing helix chain 'b' and resid 559 through 584 removed outlier: 3.801A pdb=" N LEU b 569 " --> pdb=" O GLN b 565 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLU b 572 " --> pdb=" O VAL b 568 " (cutoff:3.500A) Processing helix chain 'b' and resid 606 through 612 removed outlier: 3.680A pdb=" N ILE b 610 " --> pdb=" O ASN b 606 " (cutoff:3.500A) Processing helix chain 'b' and resid 615 through 624 removed outlier: 4.092A pdb=" N LYS b 621 " --> pdb=" O LEU b 617 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU b 622 " --> pdb=" O GLN b 618 " (cutoff:3.500A) Processing helix chain 'b' and resid 625 through 627 No H-bonds generated for 'chain 'b' and resid 625 through 627' Processing helix chain 'b' and resid 628 through 636 Processing helix chain 'b' and resid 638 through 652 Processing helix chain 'c' and resid 96 through 98 No H-bonds generated for 'chain 'c' and resid 96 through 98' Processing helix chain 'c' and resid 99 through 117 Processing helix chain 'c' and resid 123 through 126 Processing helix chain 'c' and resid 335 through 353 Processing helix chain 'c' and resid 368 through 373 Processing helix chain 'c' and resid 386 through 391 Processing helix chain 'c' and resid 399 through 403 Processing helix chain 'c' and resid 474 through 484 removed outlier: 3.754A pdb=" N ASN c 478 " --> pdb=" O ASP c 474 " (cutoff:3.500A) Processing helix chain 'd' and resid 517 through 522 Processing helix chain 'd' and resid 524 through 531 removed outlier: 3.620A pdb=" N GLN d 528 " --> pdb=" O THR d 524 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN d 531 " --> pdb=" O VAL d 527 " (cutoff:3.500A) Processing helix chain 'd' and resid 558 through 584 removed outlier: 4.132A pdb=" N LYS d 562 " --> pdb=" O VAL d 558 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG d 567 " --> pdb=" O GLN d 563 " (cutoff:3.500A) Processing helix chain 'd' and resid 606 through 612 removed outlier: 3.681A pdb=" N ILE d 610 " --> pdb=" O ASN d 606 " (cutoff:3.500A) Processing helix chain 'd' and resid 615 through 624 removed outlier: 4.807A pdb=" N LYS d 621 " --> pdb=" O LEU d 617 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU d 622 " --> pdb=" O GLN d 618 " (cutoff:3.500A) Processing helix chain 'd' and resid 625 through 627 No H-bonds generated for 'chain 'd' and resid 625 through 627' Processing helix chain 'd' and resid 628 through 636 removed outlier: 3.855A pdb=" N LEU d 633 " --> pdb=" O ILE d 629 " (cutoff:3.500A) Processing helix chain 'd' and resid 638 through 652 Processing helix chain 'e' and resid 58 through 63 removed outlier: 3.503A pdb=" N TYR e 61 " --> pdb=" O ALA e 58 " (cutoff:3.500A) Processing helix chain 'e' and resid 99 through 117 removed outlier: 3.721A pdb=" N GLN e 114 " --> pdb=" O SER e 110 " (cutoff:3.500A) Processing helix chain 'e' and resid 122 through 126 Processing helix chain 'e' and resid 335 through 351 removed outlier: 3.849A pdb=" N LYS e 344 " --> pdb=" O ASP e 340 " (cutoff:3.500A) Processing helix chain 'e' and resid 368 through 372 Processing helix chain 'e' and resid 397 through 401 removed outlier: 3.671A pdb=" N SER e 401 " --> pdb=" O GLY e 398 " (cutoff:3.500A) Processing helix chain 'e' and resid 474 through 484 removed outlier: 3.649A pdb=" N GLU e 482 " --> pdb=" O ASN e 478 " (cutoff:3.500A) Processing helix chain 'f' and resid 517 through 523 removed outlier: 3.805A pdb=" N MET f 523 " --> pdb=" O GLY f 519 " (cutoff:3.500A) Processing helix chain 'f' and resid 524 through 532 removed outlier: 3.617A pdb=" N GLN f 528 " --> pdb=" O THR f 524 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN f 531 " --> pdb=" O VAL f 527 " (cutoff:3.500A) Processing helix chain 'f' and resid 558 through 584 removed outlier: 4.015A pdb=" N LYS f 562 " --> pdb=" O VAL f 558 " (cutoff:3.500A) Processing helix chain 'f' and resid 606 through 612 Processing helix chain 'f' and resid 615 through 624 removed outlier: 4.415A pdb=" N LYS f 621 " --> pdb=" O LEU f 617 " (cutoff:3.500A) Processing helix chain 'f' and resid 625 through 627 No H-bonds generated for 'chain 'f' and resid 625 through 627' Processing helix chain 'f' and resid 628 through 636 Processing helix chain 'f' and resid 638 through 651 Processing helix chain 'g' and resid 79 through 83 Processing helix chain 'g' and resid 121 through 127 removed outlier: 4.157A pdb=" N VAL g 125 " --> pdb=" O SER g 121 " (cutoff:3.500A) Processing helix chain 'g' and resid 183 through 189 Processing helix chain 'h' and resid 28 through 32 removed outlier: 3.537A pdb=" N TYR h 32 " --> pdb=" O PHE h 29 " (cutoff:3.500A) Processing helix chain 'h' and resid 60 through 65 removed outlier: 4.655A pdb=" N ASP h 65 " --> pdb=" O LYS h 61 " (cutoff:3.500A) Processing helix chain 'h' and resid 189 through 193 removed outlier: 3.686A pdb=" N GLN h 192 " --> pdb=" O LEU h 189 " (cutoff:3.500A) Processing helix chain 'h' and resid 201 through 204 Processing helix chain 'i' and resid 83 through 87 Processing helix chain 'i' and resid 98 through 100B Processing helix chain 'i' and resid 156 through 158 No H-bonds generated for 'chain 'i' and resid 156 through 158' Processing helix chain 'i' and resid 186 through 192 Processing helix chain 'j' and resid 79 through 83 removed outlier: 4.481A pdb=" N VAL j 83 " --> pdb=" O ALA j 80 " (cutoff:3.500A) Processing helix chain 'j' and resid 121 through 127 Processing helix chain 'j' and resid 183 through 188 Processing sheet with id=AA1, first strand: chain 'a' and resid 494 through 499 removed outlier: 6.440A pdb=" N VAL a 36 " --> pdb=" O THR b 594 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 45 through 47 removed outlier: 3.864A pdb=" N ILE a 225 " --> pdb=" O VAL a 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 55 through 56 Processing sheet with id=AA4, first strand: chain 'a' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'a' and resid 120 through 121 removed outlier: 6.117A pdb=" N THR a 202 " --> pdb=" O TYR a 435 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N ARG a 432 " --> pdb=" O MET a 426 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N MET a 426 " --> pdb=" O ARG a 432 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'a' and resid 169 through 177 Processing sheet with id=AA7, first strand: chain 'a' and resid 259 through 261 removed outlier: 6.305A pdb=" N LEU a 260 " --> pdb=" O THR a 450 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLY a 451 " --> pdb=" O THR a 290 " (cutoff:3.500A) removed outlier: 10.934A pdb=" N THR a 290 " --> pdb=" O GLY a 451 " (cutoff:3.500A) removed outlier: 12.028A pdb=" N LEU a 453 " --> pdb=" O LEU a 288 " (cutoff:3.500A) removed outlier: 11.979A pdb=" N LEU a 288 " --> pdb=" O LEU a 453 " (cutoff:3.500A) removed outlier: 11.015A pdb=" N THR a 455 " --> pdb=" O VAL a 286 " (cutoff:3.500A) removed outlier: 10.257A pdb=" N VAL a 286 " --> pdb=" O THR a 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 284 through 297 current: chain 'a' and resid 358 through 361 Processing sheet with id=AA8, first strand: chain 'a' and resid 272 through 273 removed outlier: 10.257A pdb=" N VAL a 286 " --> pdb=" O THR a 455 " (cutoff:3.500A) removed outlier: 11.015A pdb=" N THR a 455 " --> pdb=" O VAL a 286 " (cutoff:3.500A) removed outlier: 11.979A pdb=" N LEU a 288 " --> pdb=" O LEU a 453 " (cutoff:3.500A) removed outlier: 12.028A pdb=" N LEU a 453 " --> pdb=" O LEU a 288 " (cutoff:3.500A) removed outlier: 10.934A pdb=" N THR a 290 " --> pdb=" O GLY a 451 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLY a 451 " --> pdb=" O THR a 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 444 through 456 current: chain 'a' and resid 413 through 420 removed outlier: 3.848A pdb=" N PHE a 383 " --> pdb=" O PHE a 376 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE a 376 " --> pdb=" O PHE a 383 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'a' and resid 301 through 308 removed outlier: 6.225A pdb=" N ASN a 301 " --> pdb=" O ILE a 323 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE a 323 " --> pdb=" O ASN a 301 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N THR a 303 " --> pdb=" O GLY a 321 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'c' and resid 495 through 499 removed outlier: 5.046A pdb=" N VAL d 596 " --> pdb=" O VAL c 36 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N VAL c 38 " --> pdb=" O THR d 594 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N THR d 594 " --> pdb=" O VAL c 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'c' and resid 45 through 47 Processing sheet with id=AB3, first strand: chain 'c' and resid 75 through 76 removed outlier: 3.529A pdb=" N CYS c 218 " --> pdb=" O PHE c 53 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'c' and resid 91 through 94 removed outlier: 3.967A pdb=" N GLU c 91 " --> pdb=" O CYS c 239 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'c' and resid 120 through 121 removed outlier: 3.933A pdb=" N VAL c 120 " --> pdb=" O GLN c 203 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N THR c 202 " --> pdb=" O TYR c 435 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'c' and resid 169 through 177 removed outlier: 3.794A pdb=" N THR c 161 " --> pdb=" O LYS c 170 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'c' and resid 259 through 261 removed outlier: 6.505A pdb=" N LEU c 260 " --> pdb=" O THR c 450 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLY c 451 " --> pdb=" O THR c 290 " (cutoff:3.500A) removed outlier: 10.010A pdb=" N THR c 290 " --> pdb=" O GLY c 451 " (cutoff:3.500A) removed outlier: 11.637A pdb=" N LEU c 453 " --> pdb=" O LEU c 288 " (cutoff:3.500A) removed outlier: 11.474A pdb=" N LEU c 288 " --> pdb=" O LEU c 453 " (cutoff:3.500A) removed outlier: 11.034A pdb=" N THR c 455 " --> pdb=" O VAL c 286 " (cutoff:3.500A) removed outlier: 10.105A pdb=" N VAL c 286 " --> pdb=" O THR c 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 284 through 297 current: chain 'c' and resid 358 through 361 Processing sheet with id=AB8, first strand: chain 'c' and resid 272 through 273 removed outlier: 10.105A pdb=" N VAL c 286 " --> pdb=" O THR c 455 " (cutoff:3.500A) removed outlier: 11.034A pdb=" N THR c 455 " --> pdb=" O VAL c 286 " (cutoff:3.500A) removed outlier: 11.474A pdb=" N LEU c 288 " --> pdb=" O LEU c 453 " (cutoff:3.500A) removed outlier: 11.637A pdb=" N LEU c 453 " --> pdb=" O LEU c 288 " (cutoff:3.500A) removed outlier: 10.010A pdb=" N THR c 290 " --> pdb=" O GLY c 451 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLY c 451 " --> pdb=" O THR c 290 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 444 through 456 current: chain 'c' and resid 413 through 421 removed outlier: 3.814A pdb=" N LYS c 421 " --> pdb=" O PHE c 382 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N PHE c 382 " --> pdb=" O LYS c 421 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'c' and resid 300 through 309 removed outlier: 6.416A pdb=" N ASN c 301 " --> pdb=" O ILE c 323 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ILE c 323 " --> pdb=" O ASN c 301 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N THR c 303 " --> pdb=" O GLY c 321 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'e' and resid 495 through 499 removed outlier: 5.140A pdb=" N VAL f 596 " --> pdb=" O VAL e 36 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N VAL e 38 " --> pdb=" O THR f 594 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N THR f 594 " --> pdb=" O VAL e 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'e' and resid 45 through 47 removed outlier: 3.641A pdb=" N ILE e 225 " --> pdb=" O VAL e 245 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'e' and resid 53 through 56 Processing sheet with id=AC4, first strand: chain 'e' and resid 91 through 92 removed outlier: 3.920A pdb=" N GLU e 91 " --> pdb=" O CYS e 239 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'e' and resid 169 through 177 removed outlier: 3.842A pdb=" N LYS e 170 " --> pdb=" O THR e 161 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR e 161 " --> pdb=" O LYS e 170 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'e' and resid 201 through 203 removed outlier: 6.365A pdb=" N THR e 202 " --> pdb=" O TYR e 435 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ARG e 432 " --> pdb=" O ASN e 425 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ASN e 425 " --> pdb=" O ARG e 432 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N MET e 434 " --> pdb=" O ILE e 423 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE e 423 " --> pdb=" O MET e 434 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'e' and resid 259 through 261 removed outlier: 3.898A pdb=" N GLY e 451 " --> pdb=" O LEU e 260 " (cutoff:3.500A) removed outlier: 10.632A pdb=" N THR e 444 " --> pdb=" O ILE e 294 " (cutoff:3.500A) removed outlier: 11.943A pdb=" N ILE e 294 " --> pdb=" O THR e 444 " (cutoff:3.500A) removed outlier: 10.253A pdb=" N ARG e 446 " --> pdb=" O VAL e 292 " (cutoff:3.500A) removed outlier: 11.261A pdb=" N VAL e 292 " --> pdb=" O ARG e 446 " (cutoff:3.500A) removed outlier: 9.832A pdb=" N ASN e 448 " --> pdb=" O THR e 290 " (cutoff:3.500A) removed outlier: 10.739A pdb=" N THR e 290 " --> pdb=" O ASN e 448 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N THR e 450 " --> pdb=" O LEU e 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 284 through 298 current: chain 'e' and resid 358 through 361 Processing sheet with id=AC8, first strand: chain 'e' and resid 271 through 273 removed outlier: 4.302A pdb=" N VAL e 271 " --> pdb=" O HIS e 287 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS e 287 " --> pdb=" O VAL e 271 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N THR e 450 " --> pdb=" O LEU e 288 " (cutoff:3.500A) removed outlier: 10.739A pdb=" N THR e 290 " --> pdb=" O ASN e 448 " (cutoff:3.500A) removed outlier: 9.832A pdb=" N ASN e 448 " --> pdb=" O THR e 290 " (cutoff:3.500A) removed outlier: 11.261A pdb=" N VAL e 292 " --> pdb=" O ARG e 446 " (cutoff:3.500A) removed outlier: 10.253A pdb=" N ARG e 446 " --> pdb=" O VAL e 292 " (cutoff:3.500A) removed outlier: 11.943A pdb=" N ILE e 294 " --> pdb=" O THR e 444 " (cutoff:3.500A) removed outlier: 10.632A pdb=" N THR e 444 " --> pdb=" O ILE e 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 443 through 456 current: chain 'e' and resid 413 through 419 removed outlier: 4.338A pdb=" N GLN e 417 " --> pdb=" O ASN e 386 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'e' and resid 301 through 305 removed outlier: 6.993A pdb=" N ASN e 301 " --> pdb=" O ILE e 323 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE e 323 " --> pdb=" O ASN e 301 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N THR e 303 " --> pdb=" O GLY e 321 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'g' and resid 4 through 7 Processing sheet with id=AD2, first strand: chain 'g' and resid 10 through 13 removed outlier: 5.994A pdb=" N LEU g 33 " --> pdb=" O PHE g 49 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE g 49 " --> pdb=" O LEU g 33 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TRP g 35 " --> pdb=" O LEU g 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'g' and resid 114 through 118 removed outlier: 3.656A pdb=" N PHE g 116 " --> pdb=" O LEU g 135 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'g' and resid 144 through 150 Processing sheet with id=AD5, first strand: chain 'h' and resid 4 through 6 Processing sheet with id=AD6, first strand: chain 'h' and resid 10 through 12 removed outlier: 4.090A pdb=" N HIS h 35 " --> pdb=" O THR h 93 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ARG h 38 " --> pdb=" O TRP h 47 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N TRP h 47 " --> pdb=" O ARG h 38 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N LYS h 52 " --> pdb=" O VAL h 56 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N VAL h 56 " --> pdb=" O LYS h 52 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'h' and resid 10 through 12 Processing sheet with id=AD8, first strand: chain 'h' and resid 122 through 124 removed outlier: 5.480A pdb=" N ALA h 137 " --> pdb=" O VAL h 184 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL h 184 " --> pdb=" O ALA h 137 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLY h 139 " --> pdb=" O VAL h 182 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL h 182 " --> pdb=" O GLY h 139 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N LEU h 141 " --> pdb=" O SER h 180 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N SER h 180 " --> pdb=" O LEU h 141 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N LYS h 143 " --> pdb=" O LEU h 178 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU h 178 " --> pdb=" O LYS h 143 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'h' and resid 122 through 124 removed outlier: 5.480A pdb=" N ALA h 137 " --> pdb=" O VAL h 184 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL h 184 " --> pdb=" O ALA h 137 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLY h 139 " --> pdb=" O VAL h 182 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL h 182 " --> pdb=" O GLY h 139 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N LEU h 141 " --> pdb=" O SER h 180 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N SER h 180 " --> pdb=" O LEU h 141 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N LYS h 143 " --> pdb=" O LEU h 178 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU h 178 " --> pdb=" O LYS h 143 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU h 175 " --> pdb=" O GLN h 171 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'h' and resid 151 through 153 Processing sheet with id=AE2, first strand: chain 'i' and resid 5 through 6 Processing sheet with id=AE3, first strand: chain 'i' and resid 10 through 12 removed outlier: 3.836A pdb=" N GLU i 10 " --> pdb=" O LEU i 108 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE i 34 " --> pdb=" O GLU i 50 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLU i 50 " --> pdb=" O ILE i 34 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TRP i 36 " --> pdb=" O LEU i 48 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'i' and resid 120 through 122 removed outlier: 5.476A pdb=" N TYR i 176 " --> pdb=" O ASP i 144 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N SER i 179 " --> pdb=" O PRO i 167 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N VAL i 181 " --> pdb=" O THR i 165 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N THR i 165 " --> pdb=" O VAL i 181 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'i' and resid 151 through 154 Processing sheet with id=AE6, first strand: chain 'j' and resid 5 through 7 removed outlier: 3.507A pdb=" N ASN j 70 " --> pdb=" O ALA j 67 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'j' and resid 10 through 13 removed outlier: 6.319A pdb=" N TRP j 35 " --> pdb=" O LEU j 47 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY j 50 " --> pdb=" O LYS j 53 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'j' and resid 114 through 117 removed outlier: 5.093A pdb=" N TYR j 173 " --> pdb=" O ASN j 138 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'j' and resid 145 through 146 Processing sheet with id=AF1, first strand: chain 'j' and resid 145 through 146 749 hydrogen bonds defined for protein. 1953 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: 19.71 Time building geometry restraints manager: 37.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.70 - 0.92: 36 0.92 - 1.15: 20069 1.15 - 1.37: 7178 1.37 - 1.60: 15489 1.60 - 1.82: 170 Bond restraints: 42942 Sorted by residual: bond pdb=" N LEU f 556 " pdb=" H LEU f 556 " ideal model delta sigma weight residual 0.860 0.696 0.164 2.00e-02 2.50e+03 6.72e+01 bond pdb=" N GLN c 82 " pdb=" H GLN c 82 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.60e+01 bond pdb=" N ARG c 476 " pdb=" H ARG c 476 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.60e+01 bond pdb=" N ILE a 333 " pdb=" H ILE a 333 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.60e+01 bond pdb=" CD1 TYR e 486 " pdb=" HD1 TYR e 486 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.60e+01 ... (remaining 42937 not shown) Histogram of bond angle deviations from ideal: 97.94 - 105.50: 931 105.50 - 113.06: 48135 113.06 - 120.63: 18412 120.63 - 128.19: 9023 128.19 - 135.76: 220 Bond angle restraints: 76721 Sorted by residual: angle pdb=" CA HIS a 374 " pdb=" CB HIS a 374 " pdb=" CG HIS a 374 " ideal model delta sigma weight residual 113.80 105.93 7.87 1.00e+00 1.00e+00 6.19e+01 angle pdb=" CB HIS c 374 " pdb=" CG HIS c 374 " pdb=" CD2 HIS c 374 " ideal model delta sigma weight residual 131.20 122.25 8.95 1.30e+00 5.92e-01 4.74e+01 angle pdb=" CA HIS c 374 " pdb=" CB HIS c 374 " pdb=" CG HIS c 374 " ideal model delta sigma weight residual 113.80 107.08 6.72 1.00e+00 1.00e+00 4.51e+01 angle pdb=" N ALA e 497 " pdb=" CA ALA e 497 " pdb=" C ALA e 497 " ideal model delta sigma weight residual 108.22 114.25 -6.03 9.00e-01 1.23e+00 4.49e+01 angle pdb=" CA ASP a 325 " pdb=" CB ASP a 325 " pdb=" CG ASP a 325 " ideal model delta sigma weight residual 112.60 119.20 -6.60 1.00e+00 1.00e+00 4.36e+01 ... (remaining 76716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.63: 19995 21.63 - 43.25: 1384 43.25 - 64.88: 611 64.88 - 86.51: 278 86.51 - 108.14: 132 Dihedral angle restraints: 22400 sinusoidal: 13488 harmonic: 8912 Sorted by residual: dihedral pdb=" CB CYS a 126 " pdb=" SG CYS a 126 " pdb=" SG CYS a 196 " pdb=" CB CYS a 196 " ideal model delta sinusoidal sigma weight residual 93.00 146.62 -53.62 1 1.00e+01 1.00e-02 3.91e+01 dihedral pdb=" CA VAL e 65 " pdb=" C VAL e 65 " pdb=" N HIS e 66 " pdb=" CA HIS e 66 " ideal model delta harmonic sigma weight residual 180.00 150.58 29.42 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA ALA i 137 " pdb=" C ALA i 137 " pdb=" N LEU i 138 " pdb=" CA LEU i 138 " ideal model delta harmonic sigma weight residual 180.00 150.62 29.38 0 5.00e+00 4.00e-02 3.45e+01 ... (remaining 22397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 2176 0.090 - 0.181: 1363 0.181 - 0.271: 332 0.271 - 0.362: 55 0.362 - 0.452: 19 Chirality restraints: 3945 Sorted by residual: chirality pdb=" C1 BMA R 3 " pdb=" O4 NAG R 2 " pdb=" C2 BMA R 3 " pdb=" O5 BMA R 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.45e+02 chirality pdb=" C1 BMA Z 3 " pdb=" O4 NAG Z 2 " pdb=" C2 BMA Z 3 " pdb=" O5 BMA Z 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.19e+02 chirality pdb=" C1 BMA w 3 " pdb=" O4 NAG w 2 " pdb=" C2 BMA w 3 " pdb=" O5 BMA w 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.18e+02 ... (remaining 3942 not shown) Planarity restraints: 6333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP g 35 " -0.375 2.00e-02 2.50e+03 1.39e-01 7.76e+02 pdb=" CG TRP g 35 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP g 35 " 0.072 2.00e-02 2.50e+03 pdb=" CD2 TRP g 35 " 0.062 2.00e-02 2.50e+03 pdb=" NE1 TRP g 35 " 0.146 2.00e-02 2.50e+03 pdb=" CE2 TRP g 35 " 0.040 2.00e-02 2.50e+03 pdb=" CE3 TRP g 35 " 0.105 2.00e-02 2.50e+03 pdb=" CZ2 TRP g 35 " -0.090 2.00e-02 2.50e+03 pdb=" CZ3 TRP g 35 " 0.067 2.00e-02 2.50e+03 pdb=" CH2 TRP g 35 " -0.074 2.00e-02 2.50e+03 pdb=" HD1 TRP g 35 " -0.008 2.00e-02 2.50e+03 pdb=" HE1 TRP g 35 " 0.161 2.00e-02 2.50e+03 pdb=" HE3 TRP g 35 " 0.148 2.00e-02 2.50e+03 pdb=" HZ2 TRP g 35 " -0.166 2.00e-02 2.50e+03 pdb=" HZ3 TRP g 35 " 0.101 2.00e-02 2.50e+03 pdb=" HH2 TRP g 35 " -0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP i 47 " -0.220 2.00e-02 2.50e+03 1.32e-01 6.95e+02 pdb=" CG TRP i 47 " -0.105 2.00e-02 2.50e+03 pdb=" CD1 TRP i 47 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP i 47 " 0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP i 47 " 0.076 2.00e-02 2.50e+03 pdb=" CE2 TRP i 47 " -0.039 2.00e-02 2.50e+03 pdb=" CE3 TRP i 47 " 0.078 2.00e-02 2.50e+03 pdb=" CZ2 TRP i 47 " -0.119 2.00e-02 2.50e+03 pdb=" CZ3 TRP i 47 " 0.070 2.00e-02 2.50e+03 pdb=" CH2 TRP i 47 " -0.035 2.00e-02 2.50e+03 pdb=" HD1 TRP i 47 " 0.016 2.00e-02 2.50e+03 pdb=" HE1 TRP i 47 " 0.332 2.00e-02 2.50e+03 pdb=" HE3 TRP i 47 " 0.116 2.00e-02 2.50e+03 pdb=" HZ2 TRP i 47 " -0.212 2.00e-02 2.50e+03 pdb=" HZ3 TRP i 47 " 0.108 2.00e-02 2.50e+03 pdb=" HH2 TRP i 47 " -0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP f 598 " -0.331 2.00e-02 2.50e+03 1.26e-01 6.32e+02 pdb=" CG TRP f 598 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP f 598 " 0.071 2.00e-02 2.50e+03 pdb=" CD2 TRP f 598 " 0.113 2.00e-02 2.50e+03 pdb=" NE1 TRP f 598 " 0.123 2.00e-02 2.50e+03 pdb=" CE2 TRP f 598 " 0.071 2.00e-02 2.50e+03 pdb=" CE3 TRP f 598 " 0.099 2.00e-02 2.50e+03 pdb=" CZ2 TRP f 598 " -0.043 2.00e-02 2.50e+03 pdb=" CZ3 TRP f 598 " 0.033 2.00e-02 2.50e+03 pdb=" CH2 TRP f 598 " -0.057 2.00e-02 2.50e+03 pdb=" HD1 TRP f 598 " -0.118 2.00e-02 2.50e+03 pdb=" HE1 TRP f 598 " 0.128 2.00e-02 2.50e+03 pdb=" HE3 TRP f 598 " 0.122 2.00e-02 2.50e+03 pdb=" HZ2 TRP f 598 " -0.137 2.00e-02 2.50e+03 pdb=" HZ3 TRP f 598 " 0.021 2.00e-02 2.50e+03 pdb=" HH2 TRP f 598 " -0.148 2.00e-02 2.50e+03 ... (remaining 6330 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 3546 2.19 - 2.79: 75063 2.79 - 3.40: 120887 3.40 - 4.00: 160150 4.00 - 4.60: 231296 Nonbonded interactions: 590942 Sorted by model distance: nonbonded pdb=" OE1 GLU i 133 " pdb=" HG SER i 186 " model vdw 1.588 1.850 nonbonded pdb=" HG SER i 127 " pdb=" O GLU i 212 " model vdw 1.595 1.850 nonbonded pdb=" OE2 GLU g 161 " pdb=" HG SER g 177 " model vdw 1.599 1.850 nonbonded pdb=" OD2 ASP g 167 " pdb=" HG1 THR g 172 " model vdw 1.605 1.850 nonbonded pdb=" OD1 ASP i 72 " pdb=" HG SER i 74 " model vdw 1.607 1.850 ... (remaining 590937 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' selection = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'o' selection = chain 'q' selection = chain 'r' selection = chain 't' selection = chain 'u' selection = chain 'w' selection = chain 'x' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'J' selection = chain 'Q' selection = chain 'V' selection = chain 'Y' selection = chain 'n' selection = chain 's' selection = chain 'v' } ncs_group { reference = chain 'D' selection = chain 'N' selection = chain 'S' selection = chain 'p' } ncs_group { reference = (chain 'a' and (resid 31 through 248 or (resid 249 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 250 through 506F or resid 601 through 603)) selection = (chain 'c' and (resid 31 through 248 or (resid 249 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 250 through 506F or resid 601 through 603)) selection = (chain 'e' and (resid 31 through 240 or (resid 241 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA \ or name HB2 or name HB3 or name HD21)) or resid 242 through 361 or (resid 362 a \ nd (name N or name CA or name C or name O or name CB or name CG or name OD1 or n \ ame ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 363 \ through 391 or (resid 392 and (name N or name CA or name C or name O or name CB \ or name CG or name OD1 or name ND2 or name H or name HA or name HB2 or name HB3 \ or name HD21)) or resid 393 through 441 or (resid 442 and (name N or name CA or \ name C or name O or name CB or name CG or name OD1 or name ND2 or name H or nam \ e HA or name HB2 or name HB3 or name HD21)) or resid 443 through 506F or resid 6 \ 01 through 603)) } ncs_group { reference = chain 'b' selection = chain 'd' selection = chain 'f' } ncs_group { reference = chain 'g' selection = chain 'j' } ncs_group { reference = chain 'h' selection = (chain 'i' and (resid 1 through 34 or (resid 35 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE \ 2)) or resid 36 through 212)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 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: 0.590 Extract box with map and model: 5.870 Check model and map are aligned: 0.620 Set scattering table: 0.390 Process input model: 135.630 Find NCS groups from input model: 2.280 Set up NCS constraints: 0.850 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 150.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 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 : 0.015 0.083 22837 Z= 0.949 Angle : 1.966 9.743 31080 Z= 1.240 Chirality : 0.115 0.452 3945 Planarity : 0.018 0.169 3770 Dihedral : 20.573 108.135 10442 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 1.11 % Allowed : 9.11 % Favored : 89.79 % Rotamer: Outliers : 2.85 % Allowed : 6.91 % Favored : 90.25 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 8.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.14), residues: 2624 helix: -1.85 (0.21), residues: 385 sheet: -1.22 (0.23), residues: 488 loop : -1.87 (0.13), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.241 0.037 TRP f 598 HIS 0.029 0.006 HIS h 200 PHE 0.149 0.020 PHE h 122 TYR 0.195 0.029 TYR g 140 ARG 0.014 0.002 ARG g 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 125 residues out of total 2317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 59 time to evaluate : 3.700 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: 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: 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 104 MET cc_start: 0.8749 (ttm) cc_final: 0.8072 (ttm) REVERT: a 479 TRP cc_start: 0.8713 (OUTLIER) cc_final: 0.7304 (m100) REVERT: b 518 MET cc_start: 0.8686 (mtm) cc_final: 0.8350 (mtm) REVERT: b 583 ILE cc_start: 0.9626 (mt) cc_final: 0.9418 (tt) REVERT: c 158 SER cc_start: 0.9030 (OUTLIER) cc_final: 0.8778 (p) REVERT: c 475 MET cc_start: 0.8117 (ptp) cc_final: 0.7885 (ptt) REVERT: d 518 MET cc_start: 0.8693 (mtm) cc_final: 0.8191 (mtm) REVERT: g 13 VAL cc_start: 0.8136 (OUTLIER) cc_final: 0.7675 (p) REVERT: g 92 VAL cc_start: 0.4545 (OUTLIER) cc_final: 0.4282 (t) REVERT: h 74 SER cc_start: 0.9081 (OUTLIER) cc_final: 0.8725 (p) REVERT: h 75 THR cc_start: 0.7190 (OUTLIER) cc_final: 0.6658 (m) REVERT: i 150 VAL cc_start: 0.5110 (OUTLIER) cc_final: 0.4786 (p) REVERT: j 14 THR cc_start: 0.6877 (OUTLIER) cc_final: 0.6620 (m) outliers start: 66 outliers final: 36 residues processed: 123 average time/residue: 0.8315 time to fit residues: 157.4812 Evaluate side-chains 95 residues out of total 2317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 51 time to evaluate : 3.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 217 optimal weight: 5.9990 chunk 195 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 131 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 202 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 234 optimal weight: 30.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 328 GLN c 422 GLN d 528 GLN d 578 GLN ** f 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 6 GLN j 124 GLN j 138 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.130 22837 Z= 0.592 Angle : 0.941 28.782 31080 Z= 0.479 Chirality : 0.051 0.367 3945 Planarity : 0.006 0.122 3770 Dihedral : 17.076 89.787 5670 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.93 % Favored : 91.92 % Rotamer: Outliers : 0.17 % Allowed : 2.11 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.66 (0.15), residues: 2624 helix: -1.46 (0.22), residues: 405 sheet: -1.61 (0.19), residues: 628 loop : -1.96 (0.14), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP c 479 HIS 0.017 0.002 HIS a 374 PHE 0.021 0.002 PHE j 49 TYR 0.048 0.003 TYR e 396 ARG 0.010 0.001 ARG i 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 61 residues out of total 2317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 3.602 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: 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: symmetry clash REVERT: b 518 MET cc_start: 0.8583 (mtm) cc_final: 0.8126 (mtm) REVERT: b 577 ASP cc_start: 0.9393 (m-30) cc_final: 0.9147 (m-30) REVERT: d 518 MET cc_start: 0.8565 (mtm) cc_final: 0.8171 (mtm) outliers start: 4 outliers final: 4 residues processed: 61 average time/residue: 0.9211 time to fit residues: 88.5616 Evaluate side-chains 56 residues out of total 2317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 3.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 130 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 194 optimal weight: 0.9990 chunk 159 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 234 optimal weight: 20.0000 chunk 253 optimal weight: 0.0470 chunk 209 optimal weight: 50.0000 chunk 232 optimal weight: 7.9990 chunk 80 optimal weight: 20.0000 chunk 188 optimal weight: 30.0000 overall best weight: 3.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 22837 Z= 0.205 Angle : 0.787 12.224 31080 Z= 0.393 Chirality : 0.050 0.311 3945 Planarity : 0.005 0.070 3770 Dihedral : 13.632 87.649 5670 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.31 % Favored : 91.54 % Rotamer: Outliers : 0.17 % Allowed : 1.64 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.87 % Cis-general : 0.00 % Twisted Proline : 0.81 % Twisted General : 0.04 % 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: -2.50 (0.15), residues: 2624 helix: -1.08 (0.23), residues: 423 sheet: -1.63 (0.19), residues: 683 loop : -1.86 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP c 479 HIS 0.015 0.002 HIS g 34 PHE 0.018 0.002 PHE j 62 TYR 0.033 0.002 TYR g 36 ARG 0.005 0.000 ARG f 573 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 59 residues out of total 2317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 4.251 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: 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: b 518 MET cc_start: 0.8507 (mtm) cc_final: 0.8284 (mtm) REVERT: b 577 ASP cc_start: 0.9361 (m-30) cc_final: 0.9144 (m-30) REVERT: d 518 MET cc_start: 0.8527 (mtm) cc_final: 0.8237 (mtm) REVERT: e 369 MET cc_start: 0.8111 (ptm) cc_final: 0.7687 (ptm) outliers start: 4 outliers final: 4 residues processed: 59 average time/residue: 0.8022 time to fit residues: 74.6283 Evaluate side-chains 54 residues out of total 2317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 3.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 231 optimal weight: 6.9990 chunk 176 optimal weight: 7.9990 chunk 121 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 112 optimal weight: 8.9990 chunk 157 optimal weight: 10.0000 chunk 235 optimal weight: 20.0000 chunk 249 optimal weight: 50.0000 chunk 123 optimal weight: 10.0000 chunk 223 optimal weight: 20.0000 chunk 67 optimal weight: 6.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 82 GLN ** a 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 389 ASN ** f 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 27DHIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 22837 Z= 0.321 Angle : 0.773 11.444 31080 Z= 0.389 Chirality : 0.047 0.353 3945 Planarity : 0.005 0.068 3770 Dihedral : 10.339 80.795 5670 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.14 % Favored : 89.79 % Rotamer: Outliers : 0.17 % Allowed : 1.90 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.87 % Cis-general : 0.00 % Twisted Proline : 0.81 % Twisted General : 0.04 % 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: -2.71 (0.15), residues: 2624 helix: -1.09 (0.23), residues: 423 sheet: -1.75 (0.19), residues: 690 loop : -2.06 (0.15), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP j 96 HIS 0.013 0.002 HIS g 27D PHE 0.018 0.002 PHE h 68 TYR 0.030 0.003 TYR e 396 ARG 0.006 0.001 ARG f 573 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 57 residues out of total 2317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 3.555 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 518 MET cc_start: 0.8628 (mtm) cc_final: 0.8405 (mtm) REVERT: c 104 MET cc_start: 0.8932 (mtp) cc_final: 0.8682 (mtp) REVERT: d 518 MET cc_start: 0.8591 (mtm) cc_final: 0.8329 (mtm) REVERT: e 369 MET cc_start: 0.8216 (ptm) cc_final: 0.7826 (ptm) outliers start: 4 outliers final: 4 residues processed: 57 average time/residue: 0.8311 time to fit residues: 76.2395 Evaluate side-chains 52 residues out of total 2317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 3.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 207 optimal weight: 7.9990 chunk 141 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 185 optimal weight: 4.9990 chunk 102 optimal weight: 9.9990 chunk 212 optimal weight: 30.0000 chunk 172 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 223 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 22837 Z= 0.268 Angle : 0.712 11.522 31080 Z= 0.361 Chirality : 0.046 0.347 3945 Planarity : 0.004 0.050 3770 Dihedral : 9.680 78.077 5670 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.79 % Favored : 90.13 % Rotamer: Outliers : 0.17 % Allowed : 1.08 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.87 % Cis-general : 0.00 % Twisted Proline : 0.81 % 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: -2.73 (0.15), residues: 2624 helix: -0.97 (0.23), residues: 425 sheet: -1.80 (0.19), residues: 668 loop : -2.11 (0.15), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP j 96 HIS 0.010 0.002 HIS a 374 PHE 0.020 0.002 PHE j 85 TYR 0.026 0.002 TYR a 384 ARG 0.005 0.000 ARG f 573 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 57 residues out of total 2317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 3.570 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: 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: b 518 MET cc_start: 0.8650 (mtm) cc_final: 0.8385 (mtm) REVERT: c 104 MET cc_start: 0.9032 (mtp) cc_final: 0.8689 (mtp) REVERT: c 426 MET cc_start: 0.9044 (tpt) cc_final: 0.8801 (tpt) REVERT: c 434 MET cc_start: 0.8830 (tmm) cc_final: 0.8591 (tmm) REVERT: d 518 MET cc_start: 0.8623 (mtm) cc_final: 0.8334 (mtm) REVERT: e 369 MET cc_start: 0.8221 (ptm) cc_final: 0.7806 (ptm) outliers start: 4 outliers final: 4 residues processed: 57 average time/residue: 0.8011 time to fit residues: 73.7142 Evaluate side-chains 54 residues out of total 2317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 4.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 83 optimal weight: 10.0000 chunk 224 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 61 optimal weight: 20.0000 chunk 249 optimal weight: 8.9990 chunk 207 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 82 optimal weight: 30.0000 chunk 131 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 300 ASN c 82 GLN e 328 GLN e 417 GLN ** f 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 22837 Z= 0.273 Angle : 0.693 8.372 31080 Z= 0.352 Chirality : 0.045 0.356 3945 Planarity : 0.005 0.057 3770 Dihedral : 8.974 76.036 5670 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.86 % Favored : 89.06 % Rotamer: Outliers : 0.17 % Allowed : 1.25 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.87 % Cis-general : 0.00 % Twisted Proline : 0.81 % 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: -2.73 (0.15), residues: 2624 helix: -0.84 (0.24), residues: 415 sheet: -1.82 (0.19), residues: 657 loop : -2.14 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP e 479 HIS 0.019 0.002 HIS g 189 PHE 0.014 0.002 PHE h 68 TYR 0.025 0.002 TYR a 384 ARG 0.005 0.000 ARG f 573 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 55 residues out of total 2317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 3.699 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: 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: b 518 MET cc_start: 0.8678 (mtm) cc_final: 0.8350 (mtm) REVERT: c 426 MET cc_start: 0.8989 (tpt) cc_final: 0.8765 (tpt) REVERT: c 434 MET cc_start: 0.8868 (tmm) cc_final: 0.8611 (tmm) REVERT: e 369 MET cc_start: 0.8282 (ptm) cc_final: 0.7861 (ptm) outliers start: 4 outliers final: 4 residues processed: 55 average time/residue: 0.8651 time to fit residues: 76.6926 Evaluate side-chains 52 residues out of total 2317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 3.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 240 optimal weight: 9.9990 chunk 28 optimal weight: 20.0000 chunk 142 optimal weight: 10.0000 chunk 182 optimal weight: 40.0000 chunk 141 optimal weight: 0.0770 chunk 210 optimal weight: 6.9990 chunk 139 optimal weight: 10.0000 chunk 248 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 151 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 overall best weight: 5.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 422 GLN ** f 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 138 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 22837 Z= 0.213 Angle : 0.647 8.272 31080 Z= 0.327 Chirality : 0.044 0.336 3945 Planarity : 0.004 0.049 3770 Dihedral : 8.548 75.357 5670 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.57 % Favored : 90.36 % Rotamer: Outliers : 0.17 % Allowed : 0.78 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.15), residues: 2624 helix: -0.53 (0.24), residues: 416 sheet: -1.77 (0.19), residues: 655 loop : -2.06 (0.15), residues: 1553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP j 96 HIS 0.009 0.001 HIS a 374 PHE 0.013 0.002 PHE e 468 TYR 0.021 0.002 TYR d 626 ARG 0.006 0.000 ARG e 456 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 55 residues out of total 2317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 3.920 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: 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: b 518 MET cc_start: 0.8658 (mtm) cc_final: 0.8318 (mtm) REVERT: b 577 ASP cc_start: 0.9445 (m-30) cc_final: 0.9215 (m-30) REVERT: c 104 MET cc_start: 0.9049 (mtp) cc_final: 0.8744 (mtp) outliers start: 4 outliers final: 4 residues processed: 55 average time/residue: 0.8333 time to fit residues: 74.9493 Evaluate side-chains 53 residues out of total 2317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 4.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 153 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 chunk 74 optimal weight: 20.0000 chunk 48 optimal weight: 8.9990 chunk 158 optimal weight: 0.8980 chunk 169 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 195 optimal weight: 10.0000 chunk 226 optimal weight: 10.0000 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 22837 Z= 0.221 Angle : 0.642 9.816 31080 Z= 0.324 Chirality : 0.044 0.331 3945 Planarity : 0.004 0.057 3770 Dihedral : 8.271 74.956 5670 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.63 % Favored : 89.29 % Rotamer: Outliers : 0.17 % Allowed : 0.56 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.15), residues: 2624 helix: -0.23 (0.24), residues: 407 sheet: -1.72 (0.20), residues: 647 loop : -2.09 (0.15), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP j 96 HIS 0.009 0.001 HIS a 374 PHE 0.011 0.002 PHE j 118 TYR 0.049 0.002 TYR e 396 ARG 0.004 0.000 ARG f 573 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 55 residues out of total 2317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 3.787 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: 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: b 518 MET cc_start: 0.8665 (mtm) cc_final: 0.8320 (mtm) REVERT: b 577 ASP cc_start: 0.9438 (m-30) cc_final: 0.9217 (m-30) REVERT: c 104 MET cc_start: 0.9060 (mtp) cc_final: 0.8767 (mtp) REVERT: c 426 MET cc_start: 0.8966 (tpt) cc_final: 0.8719 (tpt) REVERT: c 434 MET cc_start: 0.8908 (tmm) cc_final: 0.8336 (tmm) outliers start: 4 outliers final: 4 residues processed: 55 average time/residue: 0.7872 time to fit residues: 70.0148 Evaluate side-chains 53 residues out of total 2317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 3.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 238 optimal weight: 20.0000 chunk 217 optimal weight: 2.9990 chunk 231 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 181 optimal weight: 20.0000 chunk 71 optimal weight: 10.0000 chunk 209 optimal weight: 20.0000 chunk 219 optimal weight: 20.0000 chunk 230 optimal weight: 10.0000 chunk 152 optimal weight: 8.9990 overall best weight: 7.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 22837 Z= 0.261 Angle : 0.663 8.508 31080 Z= 0.335 Chirality : 0.043 0.339 3945 Planarity : 0.005 0.104 3770 Dihedral : 8.152 74.787 5670 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.55 % Favored : 88.38 % Rotamer: Outliers : 0.17 % Allowed : 0.35 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.15), residues: 2624 helix: -0.24 (0.25), residues: 406 sheet: -1.80 (0.19), residues: 653 loop : -2.16 (0.15), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP c 45 HIS 0.010 0.002 HIS a 374 PHE 0.015 0.002 PHE h 122 TYR 0.042 0.002 TYR e 396 ARG 0.005 0.000 ARG h 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 52 residues out of total 2317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 3.803 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: 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: b 518 MET cc_start: 0.8686 (mtm) cc_final: 0.8338 (mtm) REVERT: b 577 ASP cc_start: 0.9454 (m-30) cc_final: 0.9226 (m-30) REVERT: c 434 MET cc_start: 0.8915 (tmm) cc_final: 0.8349 (tmm) REVERT: i 69 MET cc_start: 0.7373 (mtp) cc_final: 0.6890 (mtp) outliers start: 4 outliers final: 4 residues processed: 52 average time/residue: 0.7776 time to fit residues: 67.8526 Evaluate side-chains 51 residues out of total 2317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 3.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 245 optimal weight: 6.9990 chunk 149 optimal weight: 0.9990 chunk 116 optimal weight: 10.0000 chunk 170 optimal weight: 9.9990 chunk 257 optimal weight: 40.0000 chunk 236 optimal weight: 6.9990 chunk 204 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 158 optimal weight: 4.9990 chunk 125 optimal weight: 7.9990 chunk 162 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22837 Z= 0.205 Angle : 0.624 8.301 31080 Z= 0.316 Chirality : 0.044 0.325 3945 Planarity : 0.004 0.059 3770 Dihedral : 7.939 73.596 5670 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.14 % Favored : 89.79 % Rotamer: Outliers : 0.17 % Allowed : 0.26 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.16), residues: 2624 helix: 0.04 (0.25), residues: 406 sheet: -1.76 (0.20), residues: 652 loop : -2.10 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP c 45 HIS 0.008 0.002 HIS a 374 PHE 0.016 0.002 PHE h 122 TYR 0.038 0.002 TYR e 396 ARG 0.005 0.000 ARG j 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Residue SER 388 is missing expected H atoms. Skipping. Evaluate side-chains 52 residues out of total 2317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 3.671 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: 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: b 518 MET cc_start: 0.8656 (mtm) cc_final: 0.8081 (mtm) REVERT: b 577 ASP cc_start: 0.9439 (m-30) cc_final: 0.9204 (m-30) REVERT: c 426 MET cc_start: 0.8965 (tpt) cc_final: 0.8761 (tpt) REVERT: c 434 MET cc_start: 0.8925 (tmm) cc_final: 0.8363 (tmm) outliers start: 4 outliers final: 4 residues processed: 52 average time/residue: 0.7654 time to fit residues: 67.3059 Evaluate side-chains 51 residues out of total 2317 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 3.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 218 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 188 optimal weight: 40.0000 chunk 30 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 205 optimal weight: 20.0000 chunk 85 optimal weight: 4.9990 chunk 210 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 chunk 179 optimal weight: 6.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 138 ASN j 171 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.033197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.026159 restraints weight = 980756.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.027064 restraints weight = 500220.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.027647 restraints weight = 318154.746| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 22837 Z= 0.232 Angle : 0.630 7.788 31080 Z= 0.318 Chirality : 0.043 0.322 3945 Planarity : 0.004 0.058 3770 Dihedral : 7.879 73.569 5670 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.20 % Favored : 88.72 % Rotamer: Outliers : 0.17 % Allowed : 0.13 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.87 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.16), residues: 2624 helix: 0.04 (0.25), residues: 406 sheet: -1.76 (0.20), residues: 649 loop : -2.12 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP c 45 HIS 0.010 0.001 HIS e 374 PHE 0.013 0.002 PHE j 118 TYR 0.038 0.002 TYR e 396 ARG 0.007 0.001 ARG j 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5398.21 seconds wall clock time: 101 minutes 54.90 seconds (6114.90 seconds total)