Starting phenix.real_space_refine on Mon Apr 8 20:12:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lcn_23277/04_2024/7lcn_23277_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lcn_23277/04_2024/7lcn_23277.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lcn_23277/04_2024/7lcn_23277.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lcn_23277/04_2024/7lcn_23277.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lcn_23277/04_2024/7lcn_23277_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lcn_23277/04_2024/7lcn_23277_trim.pdb" } resolution = 3.35 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= -0.001 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 144 5.16 5 C 21597 2.51 5 N 5565 2.21 5 O 6762 1.98 5 H 32245 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 88": "OD1" <-> "OD2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 586": "OD1" <-> "OD2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C ASP 867": "OD1" <-> "OD2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 918": "OE1" <-> "OE2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "C ASP 1127": "OD1" <-> "OD2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H GLU 31": "OE1" <-> "OE2" Residue "H GLU 56": "OE1" <-> "OE2" Residue "H ARG 66": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 144": "OD1" <-> "OD2" Residue "H GLU 148": "OE1" <-> "OE2" Residue "H ASP 208": "OD1" <-> "OD2" Residue "H GLU 212": "OE1" <-> "OE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 161": "OE1" <-> "OE2" Residue "L ARG 190": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 199": "OE1" <-> "OE2" Residue "L GLU 204": "OE1" <-> "OE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 228": "OD1" <-> "OD2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A ASP 867": "OD1" <-> "OD2" Residue "A GLU 918": "OE1" <-> "OE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 31": "OE1" <-> "OE2" Residue "B GLU 56": "OE1" <-> "OE2" Residue "B ARG 66": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 208": "OD1" <-> "OD2" Residue "D TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 83": "OE1" <-> "OE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 184": "OE1" <-> "OE2" Residue "D ARG 190": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 204": "OE1" <-> "OE2" Residue "K TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 156": "OE1" <-> "OE2" Residue "K TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 406": "OE1" <-> "OE2" Residue "K TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 465": "OE1" <-> "OE2" Residue "K TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 516": "OE1" <-> "OE2" Residue "K PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 554": "OE1" <-> "OE2" Residue "K GLU 619": "OE1" <-> "OE2" Residue "K GLU 654": "OE1" <-> "OE2" Residue "K GLU 773": "OE1" <-> "OE2" Residue "K PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 918": "OE1" <-> "OE2" Residue "K PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 1072": "OE1" <-> "OE2" Residue "M GLU 31": "OE1" <-> "OE2" Residue "M GLU 56": "OE1" <-> "OE2" Residue "M ARG 66": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 81": "OE1" <-> "OE2" Residue "M ARG 105": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M GLU 148": "OE1" <-> "OE2" Residue "S TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S GLU 124": "OE1" <-> "OE2" Residue "S PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S GLU 161": "OE1" <-> "OE2" Residue "S ARG 190": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S GLU 204": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 66313 Number of models: 1 Model: "" Number of chains: 27 Chain: "C" Number of atoms: 15370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 15370 Classifications: {'peptide': 993} Link IDs: {'PTRANS': 48, 'TRANS': 944} Chain breaks: 10 Chain: "H" Number of atoms: 3297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3297 Classifications: {'peptide': 223} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 207} Chain: "L" Number of atoms: 3143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 3143 Classifications: {'peptide': 216} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 198} Chain: "A" Number of atoms: 15370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 15370 Classifications: {'peptide': 993} Link IDs: {'PTRANS': 48, 'TRANS': 944} Chain breaks: 10 Chain: "B" Number of atoms: 3297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3297 Classifications: {'peptide': 223} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 207} Chain: "D" Number of atoms: 3143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 3143 Classifications: {'peptide': 216} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 198} Chain: "K" Number of atoms: 15370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 15370 Classifications: {'peptide': 993} Link IDs: {'PTRANS': 48, 'TRANS': 944} Chain breaks: 10 Chain: "M" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3298 Classifications: {'peptide': 223} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 207} Chain: "S" Number of atoms: 3143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 3143 Classifications: {'peptide': 216} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 198} Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "K" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 22.65, per 1000 atoms: 0.34 Number of scatterers: 66313 At special positions: 0 Unit cell: (232.76, 226.412, 196.788, 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 144 16.00 O 6762 8.00 N 5565 7.00 C 21597 6.00 H 32245 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.02 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.01 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.00 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 194 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.00 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.00 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.05 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 92 " distance=2.04 Simple disulfide: pdb=" SG CYS B 140 " - pdb=" SG CYS B 196 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 194 " distance=2.01 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 166 " distance=2.02 Simple disulfide: pdb=" SG CYS K 291 " - pdb=" SG CYS K 301 " distance=2.00 Simple disulfide: pdb=" SG CYS K 336 " - pdb=" SG CYS K 361 " distance=2.01 Simple disulfide: pdb=" SG CYS K 379 " - pdb=" SG CYS K 432 " distance=2.04 Simple disulfide: pdb=" SG CYS K 391 " - pdb=" SG CYS K 525 " distance=2.04 Simple disulfide: pdb=" SG CYS K 538 " - pdb=" SG CYS K 590 " distance=2.02 Simple disulfide: pdb=" SG CYS K 617 " - pdb=" SG CYS K 649 " distance=2.02 Simple disulfide: pdb=" SG CYS K 662 " - pdb=" SG CYS K 671 " distance=2.03 Simple disulfide: pdb=" SG CYS K 738 " - pdb=" SG CYS K 760 " distance=2.04 Simple disulfide: pdb=" SG CYS K 743 " - pdb=" SG CYS K 749 " distance=2.01 Simple disulfide: pdb=" SG CYS K1032 " - pdb=" SG CYS K1043 " distance=1.99 Simple disulfide: pdb=" SG CYS K1082 " - pdb=" SG CYS K1126 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS M 140 " - pdb=" SG CYS M 196 " distance=2.02 Simple disulfide: pdb=" SG CYS S 23 " - pdb=" SG CYS S 88 " distance=2.02 Simple disulfide: pdb=" SG CYS S 135 " - pdb=" SG CYS S 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG T 1 " - " NAG T 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG C1311 " - " ASN C 165 " " NAG E 1 " - " ASN A 234 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A1134 " " NAG K1301 " - " ASN K 61 " " NAG K1302 " - " ASN K 122 " " NAG K1303 " - " ASN K 282 " " NAG K1304 " - " ASN K 331 " " NAG K1305 " - " ASN K 343 " " NAG K1306 " - " ASN K 603 " " NAG K1307 " - " ASN K 616 " " NAG K1308 " - " ASN K 657 " " NAG K1309 " - " ASN K 709 " " NAG K1310 " - " ASN K1074 " " NAG K1311 " - " ASN K 165 " " NAG N 1 " - " ASN C 234 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN C 801 " " NAG Q 1 " - " ASN C1098 " " NAG R 1 " - " ASN C1134 " " NAG T 1 " - " ASN K 234 " " NAG V 1 " - " ASN K 717 " " NAG W 1 " - " ASN K 801 " " NAG X 1 " - " ASN K1098 " " NAG Y 1 " - " ASN K1134 " Time building additional restraints: 44.69 Conformation dependent library (CDL) restraints added in 5.2 seconds 8436 Ramachandran restraints generated. 4218 Oldfield, 0 Emsley, 4218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8016 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 75 sheets defined 22.2% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.58 Creating SS restraints... Processing helix chain 'C' and resid 146 through 150 removed outlier: 3.743A pdb=" N ASN C 149 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.974A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 390 removed outlier: 4.277A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.439A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 756 removed outlier: 3.865A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.562A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.381A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.768A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.958A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.743A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.853A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.391A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1125 through 1129 removed outlier: 4.058A pdb=" N VAL C1128 " --> pdb=" O ASN C1125 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'H' and resid 83 through 87 removed outlier: 4.227A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 200 through 204 Processing helix chain 'L' and resid 91 through 95 Processing helix chain 'L' and resid 124 through 128 Processing helix chain 'L' and resid 182 through 189 Processing helix chain 'A' and resid 146 through 150 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 364 through 371 Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.972A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.101A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.592A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 756 removed outlier: 3.631A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.667A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.532A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.624A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.612A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.089A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1129 removed outlier: 4.138A pdb=" N VAL A1128 " --> pdb=" O ASN A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 52A through 56 removed outlier: 3.537A pdb=" N GLU B 56 " --> pdb=" O GLU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 64 removed outlier: 3.705A pdb=" N GLN B 64 " --> pdb=" O GLN B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'D' and resid 124 through 128 Processing helix chain 'D' and resid 182 through 189 Processing helix chain 'K' and resid 146 through 150 Processing helix chain 'K' and resid 196 through 200 removed outlier: 3.597A pdb=" N GLY K 199 " --> pdb=" O ASN K 196 " (cutoff:3.500A) Processing helix chain 'K' and resid 294 through 303 Processing helix chain 'K' and resid 337 through 342 Processing helix chain 'K' and resid 351 through 353 No H-bonds generated for 'chain 'K' and resid 351 through 353' Processing helix chain 'K' and resid 364 through 371 Processing helix chain 'K' and resid 386 through 389 Processing helix chain 'K' and resid 405 through 410 removed outlier: 4.319A pdb=" N ARG K 408 " --> pdb=" O ASP K 405 " (cutoff:3.500A) Processing helix chain 'K' and resid 417 through 422 Processing helix chain 'K' and resid 438 through 443 removed outlier: 3.627A pdb=" N SER K 443 " --> pdb=" O ASN K 439 " (cutoff:3.500A) Processing helix chain 'K' and resid 616 through 620 Processing helix chain 'K' and resid 737 through 744 Processing helix chain 'K' and resid 746 through 756 removed outlier: 3.602A pdb=" N LEU K 754 " --> pdb=" O SER K 750 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN K 755 " --> pdb=" O ASN K 751 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR K 756 " --> pdb=" O LEU K 752 " (cutoff:3.500A) Processing helix chain 'K' and resid 758 through 783 removed outlier: 3.571A pdb=" N ASP K 775 " --> pdb=" O ALA K 771 " (cutoff:3.500A) Processing helix chain 'K' and resid 816 through 826 removed outlier: 3.827A pdb=" N VAL K 826 " --> pdb=" O LEU K 822 " (cutoff:3.500A) Processing helix chain 'K' and resid 866 through 885 Processing helix chain 'K' and resid 886 through 891 removed outlier: 3.953A pdb=" N ALA K 890 " --> pdb=" O TRP K 886 " (cutoff:3.500A) Processing helix chain 'K' and resid 897 through 907 Processing helix chain 'K' and resid 908 through 910 No H-bonds generated for 'chain 'K' and resid 908 through 910' Processing helix chain 'K' and resid 913 through 918 removed outlier: 3.612A pdb=" N TYR K 917 " --> pdb=" O GLN K 913 " (cutoff:3.500A) Processing helix chain 'K' and resid 919 through 941 Processing helix chain 'K' and resid 942 through 944 No H-bonds generated for 'chain 'K' and resid 942 through 944' Processing helix chain 'K' and resid 945 through 966 removed outlier: 3.708A pdb=" N LEU K 966 " --> pdb=" O LEU K 962 " (cutoff:3.500A) Processing helix chain 'K' and resid 976 through 984 removed outlier: 3.518A pdb=" N ILE K 980 " --> pdb=" O VAL K 976 " (cutoff:3.500A) Processing helix chain 'K' and resid 985 through 1033 removed outlier: 5.157A pdb=" N VAL K 991 " --> pdb=" O PRO K 987 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN K 992 " --> pdb=" O GLU K 988 " (cutoff:3.500A) Processing helix chain 'K' and resid 1125 through 1129 removed outlier: 4.060A pdb=" N VAL K1128 " --> pdb=" O ASN K1125 " (cutoff:3.500A) Processing helix chain 'K' and resid 1141 through 1147 Processing helix chain 'M' and resid 60 through 64 removed outlier: 3.714A pdb=" N GLN M 64 " --> pdb=" O GLN M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'M' and resid 185 through 190 Processing helix chain 'M' and resid 200 through 204 Processing helix chain 'S' and resid 122 through 128 Processing helix chain 'S' and resid 182 through 189 Processing sheet with id=AA1, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.286A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.634A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.348A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 5.444A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.235A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.508A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.847A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.213A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR C 572 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N PHE C 565 " --> pdb=" O PHE K 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 348 through 349 removed outlier: 6.827A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.225A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 348 through 349 removed outlier: 6.827A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.225A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.342A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AB2, first strand: chain 'C' and resid 654 through 656 removed outlier: 4.527A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AB5, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.047A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'C' and resid 788 through 790 removed outlier: 6.215A pdb=" N ILE C 788 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.574A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC1, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.767A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 121 through 123 removed outlier: 5.534A pdb=" N LYS H 143 " --> pdb=" O LEU H 178 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU H 178 " --> pdb=" O LYS H 143 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 163 through 164 Processing sheet with id=AC4, first strand: chain 'H' and resid 194 through 196 Processing sheet with id=AC5, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.589A pdb=" N SER L 63 " --> pdb=" O THR L 74 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 44 through 46 removed outlier: 3.873A pdb=" N VAL L 97 " --> pdb=" O SER L 90 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 115 through 119 removed outlier: 3.838A pdb=" N ALA L 174 " --> pdb=" O THR L 164 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 149 through 151 removed outlier: 3.999A pdb=" N TRP L 149 " --> pdb=" O VAL L 156 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 192 through 193 Processing sheet with id=AD1, first strand: chain 'L' and resid 196 through 198 removed outlier: 3.599A pdb=" N VAL L 203 " --> pdb=" O VAL L 196 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 29 through 30 removed outlier: 7.431A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE A 192 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.578A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 11.271A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.992A pdb=" N ASP K 568 " --> pdb=" O THR K 573 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N THR K 573 " --> pdb=" O ASP K 568 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ASP K 574 " --> pdb=" O ILE K 587 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.831A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.516A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AD7, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AD8, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.062A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.450A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.062A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.450A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.659A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AE3, first strand: chain 'A' and resid 654 through 656 removed outlier: 4.544A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AE5, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.738A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AE7, first strand: chain 'A' and resid 787 through 790 removed outlier: 6.147A pdb=" N ILE A 788 " --> pdb=" O ASN K 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.920A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 3 through 5 Processing sheet with id=AF1, first strand: chain 'B' and resid 9 through 12 Processing sheet with id=AF2, first strand: chain 'B' and resid 121 through 123 removed outlier: 6.106A pdb=" N TYR B 176 " --> pdb=" O ASP B 144 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL B 181 " --> pdb=" O HIS B 164 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 121 through 123 removed outlier: 6.106A pdb=" N TYR B 176 " --> pdb=" O ASP B 144 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 195 through 196 Processing sheet with id=AF5, first strand: chain 'D' and resid 4 through 5 Processing sheet with id=AF6, first strand: chain 'D' and resid 45 through 46 Processing sheet with id=AF7, first strand: chain 'D' and resid 115 through 119 removed outlier: 4.123A pdb=" N LEU D 133 " --> pdb=" O LEU D 179 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N TYR D 173 " --> pdb=" O ASP D 139 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA D 174 " --> pdb=" O THR D 164 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 154 through 156 removed outlier: 3.752A pdb=" N TRP D 149 " --> pdb=" O VAL D 156 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 28 through 30 removed outlier: 8.342A pdb=" N ASN K 61 " --> pdb=" O TYR K 269 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N TYR K 269 " --> pdb=" O ASN K 61 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ALA K 264 " --> pdb=" O THR K 95 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR K 95 " --> pdb=" O ALA K 264 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N SER K 205 " --> pdb=" O PRO K 225 " (cutoff:3.500A) removed outlier: 9.702A pdb=" N HIS K 207 " --> pdb=" O LEU K 223 " (cutoff:3.500A) removed outlier: 9.569A pdb=" N LEU K 223 " --> pdb=" O HIS K 207 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL K 36 " --> pdb=" O LEU K 223 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 47 through 55 removed outlier: 3.784A pdb=" N ASP K 287 " --> pdb=" O LYS K 278 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 84 through 85 removed outlier: 6.062A pdb=" N ARG K 102 " --> pdb=" O ASN K 121 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 311 through 319 removed outlier: 5.235A pdb=" N ILE K 312 " --> pdb=" O THR K 599 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N THR K 599 " --> pdb=" O ILE K 312 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLN K 314 " --> pdb=" O VAL K 597 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL K 597 " --> pdb=" O GLN K 314 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER K 316 " --> pdb=" O VAL K 595 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLY K 594 " --> pdb=" O GLN K 613 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 348 through 349 removed outlier: 6.644A pdb=" N ALA K 348 " --> pdb=" O VAL K 401 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N ARG K 403 " --> pdb=" O ALA K 348 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 348 through 349 removed outlier: 6.644A pdb=" N ALA K 348 " --> pdb=" O VAL K 401 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N ARG K 403 " --> pdb=" O ALA K 348 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 361 through 362 removed outlier: 6.775A pdb=" N CYS K 361 " --> pdb=" O CYS K 525 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 452 through 453 Processing sheet with id=AG8, first strand: chain 'K' and resid 654 through 656 removed outlier: 4.611A pdb=" N THR K 696 " --> pdb=" O VAL K 656 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE K 670 " --> pdb=" O ILE K 666 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 711 through 715 removed outlier: 3.739A pdb=" N ALA K1078 " --> pdb=" O PHE K1095 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE K1095 " --> pdb=" O ALA K1078 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 718 through 728 removed outlier: 7.098A pdb=" N GLY K1059 " --> pdb=" O SER K1055 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N SER K1055 " --> pdb=" O GLY K1059 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL K1061 " --> pdb=" O PRO K1053 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU K1063 " --> pdb=" O SER K1051 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N SER K1051 " --> pdb=" O LEU K1063 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL K1065 " --> pdb=" O LEU K1049 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 734 through 736 Processing sheet with id=AH3, first strand: chain 'K' and resid 1120 through 1123 removed outlier: 3.538A pdb=" N ALA K1087 " --> pdb=" O SER K1123 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AH5, first strand: chain 'M' and resid 10 through 12 Processing sheet with id=AH6, first strand: chain 'M' and resid 96 through 98 removed outlier: 5.244A pdb=" N PHE M 98 " --> pdb=" O ASP M 100C" (cutoff:3.500A) removed outlier: 6.299A pdb=" N ASP M 100C" --> pdb=" O PHE M 98 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'M' and resid 121 through 124 removed outlier: 3.969A pdb=" N GLY M 139 " --> pdb=" O LEU M 124 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N TYR M 176 " --> pdb=" O ASP M 144 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'M' and resid 194 through 196 Processing sheet with id=AH9, first strand: chain 'S' and resid 4 through 5 Processing sheet with id=AI1, first strand: chain 'S' and resid 45 through 48 removed outlier: 5.349A pdb=" N LEU S 46 " --> pdb=" O GLN S 37 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N GLN S 37 " --> pdb=" O LEU S 46 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'S' and resid 115 through 119 removed outlier: 3.906A pdb=" N VAL S 134 " --> pdb=" O PHE S 119 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU S 133 " --> pdb=" O LEU S 179 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N LYS S 172 " --> pdb=" O PRO S 165 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ALA S 174 " --> pdb=" O THR S 163 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N THR S 163 " --> pdb=" O ALA S 174 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N SER S 176 " --> pdb=" O GLU S 161 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLU S 161 " --> pdb=" O SER S 176 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N TYR S 178 " --> pdb=" O GLY S 159 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'S' and resid 154 through 156 removed outlier: 4.301A pdb=" N TRP S 149 " --> pdb=" O VAL S 156 " (cutoff:3.500A) 1338 hydrogen bonds defined for protein. 3507 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: 30.34 Time building geometry restraints manager: 47.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 32239 1.03 - 1.23: 3526 1.23 - 1.43: 11402 1.43 - 1.62: 19740 1.62 - 1.82: 186 Bond restraints: 67093 Sorted by residual: bond pdb=" CA PRO L 7 " pdb=" C PRO L 7 " ideal model delta sigma weight residual 1.517 1.565 -0.048 9.30e-03 1.16e+04 2.63e+01 bond pdb=" CA PRO S 7 " pdb=" C PRO S 7 " ideal model delta sigma weight residual 1.517 1.564 -0.047 9.30e-03 1.16e+04 2.50e+01 bond pdb=" CA PRO D 7 " pdb=" C PRO D 7 " ideal model delta sigma weight residual 1.517 1.556 -0.039 9.30e-03 1.16e+04 1.75e+01 bond pdb=" C5 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.413 1.491 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C5 NAG V 2 " pdb=" O5 NAG V 2 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.45e+01 ... (remaining 67088 not shown) Histogram of bond angle deviations from ideal: 96.44 - 104.34: 599 104.34 - 112.25: 74086 112.25 - 120.16: 26251 120.16 - 128.07: 19400 128.07 - 135.98: 233 Bond angle restraints: 120569 Sorted by residual: angle pdb=" CA VAL H 2 " pdb=" CB VAL H 2 " pdb=" CG1 VAL H 2 " ideal model delta sigma weight residual 110.40 133.12 -22.72 1.70e+00 3.46e-01 1.79e+02 angle pdb=" N PRO S 7 " pdb=" CA PRO S 7 " pdb=" C PRO S 7 " ideal model delta sigma weight residual 110.70 126.73 -16.03 1.22e+00 6.72e-01 1.73e+02 angle pdb=" CA VAL M 100A" pdb=" CB VAL M 100A" pdb=" CG1 VAL M 100A" ideal model delta sigma weight residual 110.40 132.71 -22.31 1.70e+00 3.46e-01 1.72e+02 angle pdb=" CA VAL B 100A" pdb=" CB VAL B 100A" pdb=" CG1 VAL B 100A" ideal model delta sigma weight residual 110.40 132.20 -21.80 1.70e+00 3.46e-01 1.65e+02 angle pdb=" CA VAL B 2 " pdb=" CB VAL B 2 " pdb=" CG1 VAL B 2 " ideal model delta sigma weight residual 110.40 132.01 -21.61 1.70e+00 3.46e-01 1.62e+02 ... (remaining 120564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.08: 30502 18.08 - 36.16: 1938 36.16 - 54.25: 544 54.25 - 72.33: 148 72.33 - 90.41: 58 Dihedral angle restraints: 33190 sinusoidal: 18327 harmonic: 14863 Sorted by residual: dihedral pdb=" N PRO S 7 " pdb=" C PRO S 7 " pdb=" CA PRO S 7 " pdb=" CB PRO S 7 " ideal model delta harmonic sigma weight residual 115.10 140.51 -25.41 0 2.50e+00 1.60e-01 1.03e+02 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual 93.00 -176.59 -90.41 1 1.00e+01 1.00e-02 9.67e+01 dihedral pdb=" CB CYS K1082 " pdb=" SG CYS K1082 " pdb=" SG CYS K1126 " pdb=" CB CYS K1126 " ideal model delta sinusoidal sigma weight residual -86.00 -173.43 87.43 1 1.00e+01 1.00e-02 9.17e+01 ... (remaining 33187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.227: 5390 0.227 - 0.455: 157 0.455 - 0.682: 9 0.682 - 0.910: 2 0.910 - 1.137: 10 Chirality restraints: 5568 Sorted by residual: chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.34e+01 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 6.99e+01 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.79e+01 ... (remaining 5565 not shown) Planarity restraints: 10098 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN K 331 " 0.299 2.00e-02 2.50e+03 2.65e-01 1.05e+03 pdb=" CG ASN K 331 " -0.138 2.00e-02 2.50e+03 pdb=" OD1 ASN K 331 " -0.045 2.00e-02 2.50e+03 pdb=" ND2 ASN K 331 " -0.378 2.00e-02 2.50e+03 pdb="HD21 ASN K 331 " -0.127 2.00e-02 2.50e+03 pdb=" C1 NAG K1304 " 0.389 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1074 " 0.247 2.00e-02 2.50e+03 2.07e-01 6.45e+02 pdb=" CG ASN C1074 " -0.121 2.00e-02 2.50e+03 pdb=" OD1 ASN C1074 " -0.038 2.00e-02 2.50e+03 pdb=" ND2 ASN C1074 " -0.292 2.00e-02 2.50e+03 pdb="HD21 ASN C1074 " -0.091 2.00e-02 2.50e+03 pdb=" C1 NAG C1310 " 0.296 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1074 " -0.196 2.00e-02 2.50e+03 1.64e-01 4.02e+02 pdb=" CG ASN A1074 " 0.092 2.00e-02 2.50e+03 pdb=" OD1 ASN A1074 " 0.042 2.00e-02 2.50e+03 pdb=" ND2 ASN A1074 " 0.229 2.00e-02 2.50e+03 pdb="HD21 ASN A1074 " 0.068 2.00e-02 2.50e+03 pdb=" C1 NAG A1310 " -0.235 2.00e-02 2.50e+03 ... (remaining 10095 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.27: 8283 2.27 - 2.85: 146445 2.85 - 3.43: 176709 3.43 - 4.02: 240864 4.02 - 4.60: 366572 Nonbonded interactions: 938873 Sorted by model distance: nonbonded pdb=" OD1 ASP K 364 " pdb=" HG SER K 366 " model vdw 1.683 1.850 nonbonded pdb=" HE2 HIS C1048 " pdb=" HG SER C1051 " model vdw 1.691 2.100 nonbonded pdb=" OE1 GLU S 83 " pdb=" HG1 THR S 105 " model vdw 1.694 1.850 nonbonded pdb=" OD1 ASP A 364 " pdb=" HG SER A 366 " model vdw 1.694 1.850 nonbonded pdb=" HH TYR A 396 " pdb=" OE1 GLU A 516 " model vdw 1.699 1.850 ... (remaining 938868 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 'K' } ncs_group { reference = chain 'B' selection = chain 'H' selection = (chain 'M' 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 HD1 or name HD2 or name HE \ 1)) or resid 36 through 214)) } ncs_group { reference = chain 'D' selection = chain 'L' selection = chain 'S' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.780 Extract box with map and model: 9.500 Check model and map are aligned: 0.750 Set scattering table: 0.500 Process input model: 176.040 Find NCS groups from input model: 2.490 Set up NCS constraints: 0.600 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: 0.020 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 195.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 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 : 0.014 0.078 34848 Z= 0.889 Angle : 1.951 22.716 47451 Z= 1.280 Chirality : 0.116 1.137 5568 Planarity : 0.016 0.180 6033 Dihedral : 13.947 89.551 13428 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 1.59 % Allowed : 9.36 % Favored : 89.05 % Rotamer: Outliers : 2.55 % Allowed : 5.12 % Favored : 92.33 % Cbeta Deviations : 0.65 % Peptide Plane: Cis-proline : 1.25 % 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: -2.18 (0.12), residues: 4218 helix: -1.15 (0.16), residues: 732 sheet: -0.74 (0.18), residues: 757 loop : -1.83 (0.11), residues: 2729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.195 0.031 TRP H 154 HIS 0.012 0.004 HIS L 189 PHE 0.097 0.016 PHE B 98 TYR 0.222 0.028 TYR L 91 ARG 0.014 0.002 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8436 Ramachandran restraints generated. 4218 Oldfield, 0 Emsley, 4218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8436 Ramachandran restraints generated. 4218 Oldfield, 0 Emsley, 4218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 277 time to evaluate : 4.060 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: 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: symmetry clash revert: symmetry clash REVERT: C 143 VAL cc_start: 0.6782 (OUTLIER) cc_final: 0.6538 (m) REVERT: C 159 VAL cc_start: 0.5999 (OUTLIER) cc_final: 0.5424 (t) REVERT: C 160 TYR cc_start: 0.6833 (OUTLIER) cc_final: 0.6275 (t80) REVERT: H 142 VAL cc_start: 0.3792 (OUTLIER) cc_final: 0.3526 (t) REVERT: L 95 ASN cc_start: 0.8083 (m-40) cc_final: 0.7806 (m-40) REVERT: A 160 TYR cc_start: 0.7537 (OUTLIER) cc_final: 0.7280 (t80) REVERT: A 366 SER cc_start: 0.8993 (OUTLIER) cc_final: 0.8758 (p) REVERT: B 100 TRP cc_start: 0.7157 (t-100) cc_final: 0.5381 (t-100) REVERT: B 142 VAL cc_start: 0.3822 (OUTLIER) cc_final: 0.3301 (t) REVERT: K 152 TRP cc_start: 0.8271 (p90) cc_final: 0.8070 (p90) REVERT: K 159 VAL cc_start: 0.6513 (OUTLIER) cc_final: 0.6187 (m) REVERT: K 160 TYR cc_start: 0.7637 (OUTLIER) cc_final: 0.6746 (t80) REVERT: K 168 PHE cc_start: 0.8754 (t80) cc_final: 0.8529 (t80) REVERT: M 80 MET cc_start: 0.0294 (ttp) cc_final: -0.0387 (tmm) REVERT: S 27 ASP cc_start: 0.3181 (OUTLIER) cc_final: 0.2110 (t70) REVERT: S 65 SER cc_start: 0.7353 (OUTLIER) cc_final: 0.6993 (t) outliers start: 95 outliers final: 37 residues processed: 368 average time/residue: 0.9615 time to fit residues: 544.6888 Evaluate side-chains 238 residues out of total 3729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 190 time to evaluate : 4.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 160 TYR Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain L residue 39 HIS Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 178 TYR Chi-restraints excluded: chain L residue 192 TYR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 97 PRO Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain K residue 96 GLU Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 160 TYR Chi-restraints excluded: chain K residue 214 ARG Chi-restraints excluded: chain K residue 366 SER Chi-restraints excluded: chain K residue 498 GLN Chi-restraints excluded: chain K residue 578 ASP Chi-restraints excluded: chain K residue 619 GLU Chi-restraints excluded: chain K residue 1032 CYS Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 145 TYR Chi-restraints excluded: chain M residue 198 VAL Chi-restraints excluded: chain M residue 208 ASP Chi-restraints excluded: chain S residue 27 ASP Chi-restraints excluded: chain S residue 65 SER Chi-restraints excluded: chain S residue 79 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 359 optimal weight: 0.9980 chunk 322 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 chunk 217 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 333 optimal weight: 2.9990 chunk 129 optimal weight: 30.0000 chunk 203 optimal weight: 0.9980 chunk 248 optimal weight: 7.9990 chunk 386 optimal weight: 6.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 450 ASN C 784 GLN C 804 GLN C 935 GLN C1002 GLN A 334 ASN A 422 ASN A1088 HIS K1005 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 34848 Z= 0.289 Angle : 0.771 14.343 47451 Z= 0.416 Chirality : 0.047 0.348 5568 Planarity : 0.006 0.160 6033 Dihedral : 8.800 75.930 5988 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.55 % Allowed : 7.47 % Favored : 91.99 % Rotamer: Outliers : 1.96 % Allowed : 7.64 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.12), residues: 4218 helix: 0.12 (0.18), residues: 735 sheet: -0.90 (0.16), residues: 925 loop : -1.80 (0.12), residues: 2558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 64 HIS 0.007 0.001 HIS S 189 PHE 0.027 0.002 PHE K1089 TYR 0.035 0.002 TYR A 451 ARG 0.007 0.001 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8436 Ramachandran restraints generated. 4218 Oldfield, 0 Emsley, 4218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8436 Ramachandran restraints generated. 4218 Oldfield, 0 Emsley, 4218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 204 time to evaluate : 4.127 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: 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: C 159 VAL cc_start: 0.5600 (OUTLIER) cc_final: 0.4865 (t) REVERT: C 160 TYR cc_start: 0.6858 (OUTLIER) cc_final: 0.6391 (t80) REVERT: H 142 VAL cc_start: 0.3261 (OUTLIER) cc_final: 0.3000 (t) REVERT: L 95 ASN cc_start: 0.8253 (m-40) cc_final: 0.7872 (m-40) REVERT: A 241 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6849 (mp) REVERT: A 298 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6961 (mp0) REVERT: A 427 ASP cc_start: 0.8432 (m-30) cc_final: 0.8152 (m-30) REVERT: A 508 TYR cc_start: 0.8969 (m-80) cc_final: 0.8602 (m-80) REVERT: A 858 LEU cc_start: 0.9031 (tt) cc_final: 0.8559 (mp) REVERT: K 159 VAL cc_start: 0.6256 (OUTLIER) cc_final: 0.5725 (m) REVERT: K 160 TYR cc_start: 0.7701 (OUTLIER) cc_final: 0.6888 (t80) REVERT: K 168 PHE cc_start: 0.8593 (t80) cc_final: 0.8331 (t80) REVERT: K 586 ASP cc_start: 0.7255 (m-30) cc_final: 0.6823 (t0) REVERT: K 904 TYR cc_start: 0.7371 (m-10) cc_final: 0.6653 (m-80) REVERT: M 80 MET cc_start: 0.0013 (ttp) cc_final: -0.0329 (tmm) REVERT: M 98 PHE cc_start: 0.5266 (p90) cc_final: 0.4604 (p90) REVERT: S 65 SER cc_start: 0.7005 (OUTLIER) cc_final: 0.6616 (t) outliers start: 73 outliers final: 37 residues processed: 266 average time/residue: 0.9696 time to fit residues: 407.6583 Evaluate side-chains 219 residues out of total 3729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 174 time to evaluate : 4.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 160 TYR Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 176 TYR Chi-restraints excluded: chain L residue 39 HIS Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 178 TYR Chi-restraints excluded: chain L residue 192 TYR Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 97 PRO Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain K residue 96 GLU Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 160 TYR Chi-restraints excluded: chain K residue 366 SER Chi-restraints excluded: chain K residue 666 ILE Chi-restraints excluded: chain K residue 1094 VAL Chi-restraints excluded: chain K residue 1119 ASN Chi-restraints excluded: chain K residue 1130 ILE Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 145 TYR Chi-restraints excluded: chain M residue 208 ASP Chi-restraints excluded: chain S residue 65 SER Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 214 optimal weight: 1.9990 chunk 120 optimal weight: 0.2980 chunk 321 optimal weight: 20.0000 chunk 263 optimal weight: 30.0000 chunk 106 optimal weight: 30.0000 chunk 387 optimal weight: 7.9990 chunk 418 optimal weight: 9.9990 chunk 345 optimal weight: 0.4980 chunk 384 optimal weight: 0.0970 chunk 132 optimal weight: 10.0000 chunk 310 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS C1088 HIS A 66 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 34848 Z= 0.180 Angle : 0.636 13.690 47451 Z= 0.338 Chirality : 0.044 0.236 5568 Planarity : 0.005 0.160 6033 Dihedral : 7.370 62.937 5941 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.42 % Favored : 92.20 % Rotamer: Outliers : 1.69 % Allowed : 8.39 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.12), residues: 4218 helix: 0.70 (0.19), residues: 734 sheet: -0.89 (0.15), residues: 960 loop : -1.71 (0.12), residues: 2524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 35 HIS 0.006 0.001 HIS C 245 PHE 0.023 0.001 PHE K 759 TYR 0.020 0.001 TYR A 451 ARG 0.005 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8436 Ramachandran restraints generated. 4218 Oldfield, 0 Emsley, 4218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8436 Ramachandran restraints generated. 4218 Oldfield, 0 Emsley, 4218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 190 time to evaluate : 3.992 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: 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: C 62 VAL cc_start: 0.8819 (m) cc_final: 0.8429 (p) REVERT: C 160 TYR cc_start: 0.6910 (OUTLIER) cc_final: 0.6371 (t80) REVERT: C 508 TYR cc_start: 0.8694 (m-80) cc_final: 0.8225 (t80) REVERT: H 10 GLU cc_start: 0.6674 (tp30) cc_final: 0.4929 (mp0) REVERT: H 142 VAL cc_start: 0.3232 (OUTLIER) cc_final: 0.3000 (t) REVERT: A 241 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6792 (mp) REVERT: A 298 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7001 (mp0) REVERT: A 427 ASP cc_start: 0.8407 (m-30) cc_final: 0.8125 (m-30) REVERT: A 508 TYR cc_start: 0.8912 (m-80) cc_final: 0.8599 (m-80) REVERT: A 858 LEU cc_start: 0.8957 (tt) cc_final: 0.8516 (mp) REVERT: D 47 MET cc_start: 0.8783 (mmm) cc_final: 0.8531 (mmm) REVERT: K 159 VAL cc_start: 0.6302 (OUTLIER) cc_final: 0.5745 (m) REVERT: K 160 TYR cc_start: 0.7761 (OUTLIER) cc_final: 0.6884 (t80) REVERT: K 168 PHE cc_start: 0.8591 (t80) cc_final: 0.8356 (t80) REVERT: K 586 ASP cc_start: 0.6880 (m-30) cc_final: 0.6645 (t0) REVERT: K 904 TYR cc_start: 0.7256 (m-10) cc_final: 0.6522 (m-80) REVERT: K 948 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.8019 (mt) REVERT: M 80 MET cc_start: -0.0122 (ttp) cc_final: -0.0557 (tmm) outliers start: 63 outliers final: 37 residues processed: 240 average time/residue: 0.9430 time to fit residues: 358.9410 Evaluate side-chains 212 residues out of total 3729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 168 time to evaluate : 3.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 160 TYR Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 176 TYR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 178 TYR Chi-restraints excluded: chain L residue 192 TYR Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain K residue 159 VAL Chi-restraints excluded: chain K residue 160 TYR Chi-restraints excluded: chain K residue 366 SER Chi-restraints excluded: chain K residue 392 PHE Chi-restraints excluded: chain K residue 948 LEU Chi-restraints excluded: chain K residue 1094 VAL Chi-restraints excluded: chain K residue 1119 ASN Chi-restraints excluded: chain K residue 1130 ILE Chi-restraints excluded: chain M residue 48 MET Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 145 TYR Chi-restraints excluded: chain M residue 208 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 382 optimal weight: 0.8980 chunk 291 optimal weight: 9.9990 chunk 201 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 chunk 184 optimal weight: 7.9990 chunk 260 optimal weight: 50.0000 chunk 388 optimal weight: 8.9990 chunk 411 optimal weight: 30.0000 chunk 203 optimal weight: 0.7980 chunk 368 optimal weight: 3.9990 chunk 110 optimal weight: 20.0000 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 207 HIS C 334 ASN C 414 GLN C 613 GLN L 170 ASN A 926 GLN ** K 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 34848 Z= 0.321 Angle : 0.637 13.365 47451 Z= 0.338 Chirality : 0.044 0.266 5568 Planarity : 0.005 0.158 6033 Dihedral : 6.947 59.052 5931 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.30 % Favored : 91.32 % Rotamer: Outliers : 1.77 % Allowed : 9.06 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.12), residues: 4218 helix: 0.55 (0.19), residues: 749 sheet: -1.13 (0.15), residues: 995 loop : -1.79 (0.12), residues: 2474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 154 HIS 0.006 0.001 HIS C 245 PHE 0.029 0.002 PHE K1089 TYR 0.032 0.002 TYR B 145 ARG 0.006 0.000 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8436 Ramachandran restraints generated. 4218 Oldfield, 0 Emsley, 4218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8436 Ramachandran restraints generated. 4218 Oldfield, 0 Emsley, 4218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 166 time to evaluate : 4.119 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: 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: C 160 TYR cc_start: 0.7108 (OUTLIER) cc_final: 0.6511 (t80) REVERT: C 198 ASP cc_start: 0.8265 (p0) cc_final: 0.8000 (p0) REVERT: H 10 GLU cc_start: 0.6741 (tp30) cc_final: 0.4999 (mp0) REVERT: H 142 VAL cc_start: 0.2890 (OUTLIER) cc_final: 0.2646 (t) REVERT: A 298 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: A 427 ASP cc_start: 0.8461 (m-30) cc_final: 0.8219 (m-30) REVERT: A 858 LEU cc_start: 0.9016 (tt) cc_final: 0.8640 (mp) REVERT: D 47 MET cc_start: 0.8914 (mmm) cc_final: 0.8636 (mmm) REVERT: D 51 VAL cc_start: 0.6908 (OUTLIER) cc_final: 0.6634 (t) REVERT: K 160 TYR cc_start: 0.8122 (OUTLIER) cc_final: 0.7320 (t80) REVERT: K 586 ASP cc_start: 0.7049 (m-30) cc_final: 0.6763 (t0) REVERT: K 904 TYR cc_start: 0.7381 (m-10) cc_final: 0.6567 (m-80) outliers start: 66 outliers final: 49 residues processed: 223 average time/residue: 0.9189 time to fit residues: 325.1621 Evaluate side-chains 212 residues out of total 3729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 158 time to evaluate : 3.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 160 TYR Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 204 TYR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 176 TYR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 178 TYR Chi-restraints excluded: chain L residue 192 TYR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 98 PHE Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 110 LEU Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain K residue 160 TYR Chi-restraints excluded: chain K residue 204 TYR Chi-restraints excluded: chain K residue 360 ASN Chi-restraints excluded: chain K residue 366 SER Chi-restraints excluded: chain K residue 392 PHE Chi-restraints excluded: chain K residue 578 ASP Chi-restraints excluded: chain K residue 673 SER Chi-restraints excluded: chain K residue 1089 PHE Chi-restraints excluded: chain K residue 1094 VAL Chi-restraints excluded: chain K residue 1119 ASN Chi-restraints excluded: chain K residue 1130 ILE Chi-restraints excluded: chain M residue 48 MET Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 145 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 342 optimal weight: 0.6980 chunk 233 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 chunk 306 optimal weight: 4.9990 chunk 169 optimal weight: 7.9990 chunk 351 optimal weight: 1.9990 chunk 284 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 210 optimal weight: 2.9990 chunk 369 optimal weight: 2.9990 chunk 103 optimal weight: 20.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 675 GLN ** K 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 34848 Z= 0.208 Angle : 0.581 12.529 47451 Z= 0.306 Chirality : 0.043 0.247 5568 Planarity : 0.005 0.155 6033 Dihedral : 6.618 56.154 5928 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.01 % Favored : 91.61 % Rotamer: Outliers : 1.96 % Allowed : 9.41 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.12), residues: 4218 helix: 0.85 (0.19), residues: 750 sheet: -1.03 (0.15), residues: 1030 loop : -1.73 (0.12), residues: 2438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 104 HIS 0.005 0.001 HIS C 245 PHE 0.018 0.001 PHE K1089 TYR 0.021 0.001 TYR B 145 ARG 0.004 0.000 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8436 Ramachandran restraints generated. 4218 Oldfield, 0 Emsley, 4218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8436 Ramachandran restraints generated. 4218 Oldfield, 0 Emsley, 4218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 167 time to evaluate : 4.157 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: 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: C 143 VAL cc_start: 0.6226 (OUTLIER) cc_final: 0.5976 (m) REVERT: C 160 TYR cc_start: 0.7099 (OUTLIER) cc_final: 0.6505 (t80) REVERT: C 198 ASP cc_start: 0.8258 (p0) cc_final: 0.8002 (p0) REVERT: H 10 GLU cc_start: 0.6968 (tp30) cc_final: 0.5342 (mp0) REVERT: H 142 VAL cc_start: 0.2967 (OUTLIER) cc_final: 0.2698 (t) REVERT: A 298 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7080 (mp0) REVERT: A 858 LEU cc_start: 0.8996 (tt) cc_final: 0.8641 (mp) REVERT: A 869 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7761 (ttm) REVERT: A 964 LYS cc_start: 0.9422 (mttt) cc_final: 0.9209 (mtmm) REVERT: D 47 MET cc_start: 0.8929 (mmm) cc_final: 0.8648 (mmm) REVERT: K 160 TYR cc_start: 0.8049 (OUTLIER) cc_final: 0.7273 (t80) REVERT: K 586 ASP cc_start: 0.6819 (m-30) cc_final: 0.6599 (t0) REVERT: K 904 TYR cc_start: 0.7290 (m-10) cc_final: 0.6450 (m-80) REVERT: M 198 VAL cc_start: -0.5025 (OUTLIER) cc_final: -0.5230 (t) outliers start: 73 outliers final: 53 residues processed: 227 average time/residue: 0.9086 time to fit residues: 327.6003 Evaluate side-chains 222 residues out of total 3729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 162 time to evaluate : 3.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 160 TYR Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 176 TYR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 178 TYR Chi-restraints excluded: chain L residue 192 TYR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 96 GLU Chi-restraints excluded: chain K residue 110 LEU Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain K residue 160 TYR Chi-restraints excluded: chain K residue 164 ASN Chi-restraints excluded: chain K residue 360 ASN Chi-restraints excluded: chain K residue 366 SER Chi-restraints excluded: chain K residue 392 PHE Chi-restraints excluded: chain K residue 666 ILE Chi-restraints excluded: chain K residue 673 SER Chi-restraints excluded: chain K residue 1094 VAL Chi-restraints excluded: chain K residue 1116 THR Chi-restraints excluded: chain K residue 1119 ASN Chi-restraints excluded: chain K residue 1130 ILE Chi-restraints excluded: chain M residue 48 MET Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 145 TYR Chi-restraints excluded: chain M residue 198 VAL Chi-restraints excluded: chain M residue 208 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 138 optimal weight: 30.0000 chunk 370 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 241 optimal weight: 20.0000 chunk 101 optimal weight: 6.9990 chunk 412 optimal weight: 2.9990 chunk 342 optimal weight: 0.8980 chunk 190 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 136 optimal weight: 50.0000 chunk 216 optimal weight: 0.6980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 334 ASN ** K 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 34848 Z= 0.270 Angle : 0.587 12.508 47451 Z= 0.309 Chirality : 0.044 0.261 5568 Planarity : 0.005 0.154 6033 Dihedral : 6.449 54.434 5926 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.84 % Favored : 90.78 % Rotamer: Outliers : 1.98 % Allowed : 9.87 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.13), residues: 4218 helix: 0.83 (0.19), residues: 756 sheet: -1.09 (0.15), residues: 1018 loop : -1.76 (0.12), residues: 2444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 36 HIS 0.005 0.001 HIS C 245 PHE 0.022 0.002 PHE K1089 TYR 0.020 0.002 TYR B 145 ARG 0.004 0.000 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8436 Ramachandran restraints generated. 4218 Oldfield, 0 Emsley, 4218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8436 Ramachandran restraints generated. 4218 Oldfield, 0 Emsley, 4218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 156 time to evaluate : 4.124 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: 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: C 160 TYR cc_start: 0.7238 (OUTLIER) cc_final: 0.6649 (t80) REVERT: C 198 ASP cc_start: 0.8279 (p0) cc_final: 0.7974 (p0) REVERT: C 1089 PHE cc_start: 0.7606 (OUTLIER) cc_final: 0.7320 (m-80) REVERT: H 10 GLU cc_start: 0.7107 (tp30) cc_final: 0.5497 (mp0) REVERT: H 142 VAL cc_start: 0.3237 (OUTLIER) cc_final: 0.2990 (t) REVERT: A 298 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7064 (mp0) REVERT: A 858 LEU cc_start: 0.9005 (tt) cc_final: 0.8662 (mp) REVERT: D 47 MET cc_start: 0.9004 (mmm) cc_final: 0.8730 (mmm) REVERT: K 160 TYR cc_start: 0.8086 (OUTLIER) cc_final: 0.7367 (t80) REVERT: K 586 ASP cc_start: 0.6951 (m-30) cc_final: 0.6698 (t0) REVERT: K 759 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7683 (t80) REVERT: K 904 TYR cc_start: 0.7267 (m-10) cc_final: 0.6453 (m-80) outliers start: 74 outliers final: 57 residues processed: 219 average time/residue: 0.9144 time to fit residues: 320.9837 Evaluate side-chains 212 residues out of total 3729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 149 time to evaluate : 4.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 160 TYR Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 176 TYR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 192 TYR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 96 GLU Chi-restraints excluded: chain K residue 110 LEU Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain K residue 160 TYR Chi-restraints excluded: chain K residue 164 ASN Chi-restraints excluded: chain K residue 204 TYR Chi-restraints excluded: chain K residue 335 LEU Chi-restraints excluded: chain K residue 360 ASN Chi-restraints excluded: chain K residue 366 SER Chi-restraints excluded: chain K residue 392 PHE Chi-restraints excluded: chain K residue 498 GLN Chi-restraints excluded: chain K residue 673 SER Chi-restraints excluded: chain K residue 759 PHE Chi-restraints excluded: chain K residue 1094 VAL Chi-restraints excluded: chain K residue 1116 THR Chi-restraints excluded: chain K residue 1119 ASN Chi-restraints excluded: chain K residue 1130 ILE Chi-restraints excluded: chain M residue 48 MET Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 145 TYR Chi-restraints excluded: chain M residue 208 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 397 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 234 optimal weight: 3.9990 chunk 300 optimal weight: 0.4980 chunk 233 optimal weight: 0.5980 chunk 346 optimal weight: 2.9990 chunk 230 optimal weight: 4.9990 chunk 410 optimal weight: 2.9990 chunk 256 optimal weight: 30.0000 chunk 250 optimal weight: 40.0000 chunk 189 optimal weight: 5.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 34848 Z= 0.214 Angle : 0.565 11.640 47451 Z= 0.295 Chirality : 0.043 0.253 5568 Planarity : 0.005 0.151 6033 Dihedral : 6.299 55.199 5923 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.94 % Favored : 91.70 % Rotamer: Outliers : 1.69 % Allowed : 10.11 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.13), residues: 4218 helix: 1.01 (0.19), residues: 756 sheet: -1.08 (0.15), residues: 1032 loop : -1.66 (0.12), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 104 HIS 0.004 0.001 HIS C 245 PHE 0.017 0.001 PHE A 392 TYR 0.041 0.001 TYR B 145 ARG 0.010 0.000 ARG H 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8436 Ramachandran restraints generated. 4218 Oldfield, 0 Emsley, 4218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8436 Ramachandran restraints generated. 4218 Oldfield, 0 Emsley, 4218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 153 time to evaluate : 4.123 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: 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: C 160 TYR cc_start: 0.7259 (OUTLIER) cc_final: 0.6670 (t80) REVERT: C 198 ASP cc_start: 0.8291 (p0) cc_final: 0.7963 (p0) REVERT: C 1089 PHE cc_start: 0.7514 (OUTLIER) cc_final: 0.7240 (m-80) REVERT: H 10 GLU cc_start: 0.7274 (tp30) cc_final: 0.5642 (mp0) REVERT: H 142 VAL cc_start: 0.3289 (OUTLIER) cc_final: 0.3039 (t) REVERT: A 298 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: A 858 LEU cc_start: 0.8994 (tt) cc_final: 0.8657 (mp) REVERT: A 964 LYS cc_start: 0.9418 (mttt) cc_final: 0.9213 (mtmm) REVERT: D 47 MET cc_start: 0.8999 (mmm) cc_final: 0.8702 (mmm) REVERT: K 160 TYR cc_start: 0.8083 (OUTLIER) cc_final: 0.7354 (t80) REVERT: K 904 TYR cc_start: 0.7221 (m-10) cc_final: 0.6508 (m-80) outliers start: 63 outliers final: 53 residues processed: 204 average time/residue: 0.9289 time to fit residues: 303.6368 Evaluate side-chains 207 residues out of total 3729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 149 time to evaluate : 4.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 160 TYR Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 176 TYR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 192 TYR Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 96 GLU Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain K residue 160 TYR Chi-restraints excluded: chain K residue 164 ASN Chi-restraints excluded: chain K residue 335 LEU Chi-restraints excluded: chain K residue 360 ASN Chi-restraints excluded: chain K residue 392 PHE Chi-restraints excluded: chain K residue 673 SER Chi-restraints excluded: chain K residue 1094 VAL Chi-restraints excluded: chain K residue 1116 THR Chi-restraints excluded: chain K residue 1119 ASN Chi-restraints excluded: chain K residue 1130 ILE Chi-restraints excluded: chain M residue 48 MET Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 145 TYR Chi-restraints excluded: chain M residue 208 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 254 optimal weight: 50.0000 chunk 163 optimal weight: 2.9990 chunk 245 optimal weight: 40.0000 chunk 123 optimal weight: 40.0000 chunk 80 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 261 optimal weight: 50.0000 chunk 279 optimal weight: 50.0000 chunk 203 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 322 optimal weight: 9.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1011 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 784 GLN ** K 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 34848 Z= 0.349 Angle : 0.611 11.526 47451 Z= 0.322 Chirality : 0.044 0.263 5568 Planarity : 0.005 0.150 6033 Dihedral : 6.418 57.062 5922 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.22 % Favored : 90.45 % Rotamer: Outliers : 1.88 % Allowed : 10.08 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.13), residues: 4218 helix: 0.76 (0.19), residues: 756 sheet: -1.21 (0.15), residues: 1047 loop : -1.81 (0.12), residues: 2415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 64 HIS 0.004 0.001 HIS A1058 PHE 0.024 0.002 PHE K1089 TYR 0.026 0.002 TYR B 145 ARG 0.005 0.000 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8436 Ramachandran restraints generated. 4218 Oldfield, 0 Emsley, 4218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8436 Ramachandran restraints generated. 4218 Oldfield, 0 Emsley, 4218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 146 time to evaluate : 4.111 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: 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: C 160 TYR cc_start: 0.7271 (OUTLIER) cc_final: 0.6683 (t80) REVERT: C 198 ASP cc_start: 0.8262 (p0) cc_final: 0.7890 (p0) REVERT: H 10 GLU cc_start: 0.7200 (tp30) cc_final: 0.5632 (mp0) REVERT: H 142 VAL cc_start: 0.3359 (OUTLIER) cc_final: 0.3109 (t) REVERT: A 298 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7152 (mp0) REVERT: A 858 LEU cc_start: 0.9018 (tt) cc_final: 0.8683 (mp) REVERT: D 47 MET cc_start: 0.8997 (mmm) cc_final: 0.8691 (mmm) REVERT: K 160 TYR cc_start: 0.8096 (OUTLIER) cc_final: 0.7469 (t80) REVERT: K 904 TYR cc_start: 0.7323 (m-10) cc_final: 0.6614 (m-80) outliers start: 70 outliers final: 61 residues processed: 205 average time/residue: 0.9188 time to fit residues: 301.5299 Evaluate side-chains 208 residues out of total 3729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 143 time to evaluate : 4.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 160 TYR Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 176 TYR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 192 TYR Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 96 GLU Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain K residue 160 TYR Chi-restraints excluded: chain K residue 164 ASN Chi-restraints excluded: chain K residue 204 TYR Chi-restraints excluded: chain K residue 335 LEU Chi-restraints excluded: chain K residue 360 ASN Chi-restraints excluded: chain K residue 392 PHE Chi-restraints excluded: chain K residue 498 GLN Chi-restraints excluded: chain K residue 673 SER Chi-restraints excluded: chain K residue 697 MET Chi-restraints excluded: chain K residue 1089 PHE Chi-restraints excluded: chain K residue 1094 VAL Chi-restraints excluded: chain K residue 1116 THR Chi-restraints excluded: chain K residue 1119 ASN Chi-restraints excluded: chain K residue 1130 ILE Chi-restraints excluded: chain M residue 48 MET Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 145 TYR Chi-restraints excluded: chain M residue 208 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 373 optimal weight: 1.9990 chunk 393 optimal weight: 10.0000 chunk 358 optimal weight: 0.5980 chunk 382 optimal weight: 4.9990 chunk 230 optimal weight: 0.9980 chunk 166 optimal weight: 1.9990 chunk 300 optimal weight: 6.9990 chunk 117 optimal weight: 20.0000 chunk 345 optimal weight: 0.6980 chunk 361 optimal weight: 3.9990 chunk 381 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 34848 Z= 0.176 Angle : 0.553 11.170 47451 Z= 0.288 Chirality : 0.043 0.257 5568 Planarity : 0.005 0.149 6033 Dihedral : 6.180 56.734 5922 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.54 % Favored : 92.13 % Rotamer: Outliers : 1.61 % Allowed : 10.32 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.13), residues: 4218 helix: 1.12 (0.19), residues: 756 sheet: -1.12 (0.15), residues: 1062 loop : -1.62 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 104 HIS 0.004 0.001 HIS C 245 PHE 0.017 0.001 PHE A 392 TYR 0.023 0.001 TYR B 145 ARG 0.003 0.000 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8436 Ramachandran restraints generated. 4218 Oldfield, 0 Emsley, 4218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8436 Ramachandran restraints generated. 4218 Oldfield, 0 Emsley, 4218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 149 time to evaluate : 4.078 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: 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: C 160 TYR cc_start: 0.7346 (OUTLIER) cc_final: 0.6761 (t80) REVERT: C 198 ASP cc_start: 0.8161 (p0) cc_final: 0.7799 (p0) REVERT: H 10 GLU cc_start: 0.7403 (tp30) cc_final: 0.5889 (mp0) REVERT: H 142 VAL cc_start: 0.3365 (OUTLIER) cc_final: 0.3117 (t) REVERT: A 298 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: A 858 LEU cc_start: 0.8988 (tt) cc_final: 0.8648 (mp) REVERT: A 964 LYS cc_start: 0.9410 (mttt) cc_final: 0.9205 (mtmm) REVERT: D 47 MET cc_start: 0.9007 (mmm) cc_final: 0.8700 (mmm) REVERT: K 160 TYR cc_start: 0.8048 (OUTLIER) cc_final: 0.7405 (t80) REVERT: K 904 TYR cc_start: 0.7160 (m-10) cc_final: 0.6459 (m-80) outliers start: 60 outliers final: 50 residues processed: 199 average time/residue: 0.9018 time to fit residues: 287.7562 Evaluate side-chains 198 residues out of total 3729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 144 time to evaluate : 4.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 160 TYR Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 176 TYR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 192 TYR Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 96 GLU Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain K residue 160 TYR Chi-restraints excluded: chain K residue 335 LEU Chi-restraints excluded: chain K residue 360 ASN Chi-restraints excluded: chain K residue 392 PHE Chi-restraints excluded: chain K residue 673 SER Chi-restraints excluded: chain K residue 1094 VAL Chi-restraints excluded: chain K residue 1116 THR Chi-restraints excluded: chain K residue 1119 ASN Chi-restraints excluded: chain K residue 1130 ILE Chi-restraints excluded: chain M residue 48 MET Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 145 TYR Chi-restraints excluded: chain M residue 208 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 251 optimal weight: 5.9990 chunk 404 optimal weight: 40.0000 chunk 246 optimal weight: 10.0000 chunk 191 optimal weight: 1.9990 chunk 281 optimal weight: 30.0000 chunk 424 optimal weight: 20.0000 chunk 390 optimal weight: 40.0000 chunk 337 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 34848 Z= 0.371 Angle : 0.622 10.942 47451 Z= 0.327 Chirality : 0.044 0.268 5568 Planarity : 0.005 0.147 6033 Dihedral : 6.331 57.534 5919 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.44 % Favored : 90.26 % Rotamer: Outliers : 1.50 % Allowed : 10.51 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.13), residues: 4218 helix: 0.78 (0.19), residues: 759 sheet: -1.24 (0.15), residues: 1050 loop : -1.83 (0.12), residues: 2409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 64 HIS 0.005 0.001 HIS K1048 PHE 0.026 0.002 PHE K1089 TYR 0.023 0.002 TYR A 91 ARG 0.011 0.001 ARG C 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8436 Ramachandran restraints generated. 4218 Oldfield, 0 Emsley, 4218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8436 Ramachandran restraints generated. 4218 Oldfield, 0 Emsley, 4218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 142 time to evaluate : 4.108 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: 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: C 160 TYR cc_start: 0.7277 (OUTLIER) cc_final: 0.6623 (t80) REVERT: C 198 ASP cc_start: 0.8132 (p0) cc_final: 0.7733 (p0) REVERT: H 10 GLU cc_start: 0.7462 (tp30) cc_final: 0.5904 (mp0) REVERT: H 142 VAL cc_start: 0.3443 (OUTLIER) cc_final: 0.3232 (t) REVERT: A 298 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7112 (mp0) REVERT: A 858 LEU cc_start: 0.9018 (tt) cc_final: 0.8692 (mp) REVERT: D 47 MET cc_start: 0.9034 (mmm) cc_final: 0.8727 (mmm) REVERT: K 160 TYR cc_start: 0.8093 (OUTLIER) cc_final: 0.7515 (t80) REVERT: K 904 TYR cc_start: 0.7349 (m-10) cc_final: 0.6613 (m-80) outliers start: 56 outliers final: 50 residues processed: 189 average time/residue: 0.9077 time to fit residues: 276.8060 Evaluate side-chains 192 residues out of total 3729 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 138 time to evaluate : 3.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 160 TYR Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 544 ASN Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 176 TYR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 166 SER Chi-restraints excluded: chain L residue 192 TYR Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 204 TYR Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 96 GLU Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain K residue 160 TYR Chi-restraints excluded: chain K residue 331 ASN Chi-restraints excluded: chain K residue 335 LEU Chi-restraints excluded: chain K residue 360 ASN Chi-restraints excluded: chain K residue 392 PHE Chi-restraints excluded: chain K residue 498 GLN Chi-restraints excluded: chain K residue 673 SER Chi-restraints excluded: chain K residue 1089 PHE Chi-restraints excluded: chain K residue 1094 VAL Chi-restraints excluded: chain K residue 1116 THR Chi-restraints excluded: chain K residue 1119 ASN Chi-restraints excluded: chain K residue 1130 ILE Chi-restraints excluded: chain M residue 48 MET Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 145 TYR Chi-restraints excluded: chain M residue 208 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 268 optimal weight: 7.9990 chunk 360 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 311 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 338 optimal weight: 0.9980 chunk 141 optimal weight: 7.9990 chunk 347 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 394 ASN ** K 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.109586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.072809 restraints weight = 351371.234| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 4.38 r_work: 0.3170 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 34848 Z= 0.172 Angle : 0.552 10.824 47451 Z= 0.286 Chirality : 0.043 0.260 5568 Planarity : 0.005 0.147 6033 Dihedral : 6.093 57.106 5919 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.04 % Favored : 91.65 % Rotamer: Outliers : 1.47 % Allowed : 10.65 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.13), residues: 4218 helix: 1.14 (0.19), residues: 757 sheet: -1.15 (0.15), residues: 1052 loop : -1.63 (0.12), residues: 2409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 104 HIS 0.003 0.001 HIS C 655 PHE 0.017 0.001 PHE A 392 TYR 0.021 0.001 TYR B 145 ARG 0.009 0.000 ARG C 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10908.04 seconds wall clock time: 190 minutes 37.00 seconds (11437.00 seconds total)