Starting phenix.real_space_refine on Tue Apr 16 02:48:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sht_10205/04_2024/6sht_10205_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sht_10205/04_2024/6sht_10205.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sht_10205/04_2024/6sht_10205.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sht_10205/04_2024/6sht_10205.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sht_10205/04_2024/6sht_10205_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sht_10205/04_2024/6sht_10205_neut.pdb" } resolution = 2.73 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= 0.015 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: 6 Type Number sf(0) Gaussians Fe 24 7.16 5 Mg 24 5.21 5 S 192 5.16 5 C 22296 2.51 5 N 6264 2.21 5 O 8352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 60": "NH1" <-> "NH2" Residue "A ARG 60": "NH1" <-> "NH2" Residue "A ASP 89": "OD1" <-> "OD2" Residue "B PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 60": "NH1" <-> "NH2" Residue "B ARG 60": "NH1" <-> "NH2" Residue "B ASP 89": "OD1" <-> "OD2" Residue "C PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 60": "NH1" <-> "NH2" Residue "C ARG 60": "NH1" <-> "NH2" Residue "C ASP 89": "OD1" <-> "OD2" Residue "D PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "D ASP 89": "OD1" <-> "OD2" Residue "E PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 60": "NH1" <-> "NH2" Residue "E ARG 60": "NH1" <-> "NH2" Residue "E ASP 89": "OD1" <-> "OD2" Residue "F PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 60": "NH1" <-> "NH2" Residue "F ARG 60": "NH1" <-> "NH2" Residue "F ASP 89": "OD1" <-> "OD2" Residue "G PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 60": "NH1" <-> "NH2" Residue "G ARG 60": "NH1" <-> "NH2" Residue "G ASP 89": "OD1" <-> "OD2" Residue "H PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 60": "NH1" <-> "NH2" Residue "H ARG 60": "NH1" <-> "NH2" Residue "H ASP 89": "OD1" <-> "OD2" Residue "I PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 60": "NH1" <-> "NH2" Residue "I ARG 60": "NH1" <-> "NH2" Residue "I ASP 89": "OD1" <-> "OD2" Residue "J PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 60": "NH1" <-> "NH2" Residue "J ARG 60": "NH1" <-> "NH2" Residue "J ASP 89": "OD1" <-> "OD2" Residue "K PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 60": "NH1" <-> "NH2" Residue "K ARG 60": "NH1" <-> "NH2" Residue "K ASP 89": "OD1" <-> "OD2" Residue "L PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ASP 89": "OD1" <-> "OD2" Residue "M PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 60": "NH1" <-> "NH2" Residue "M ARG 60": "NH1" <-> "NH2" Residue "M ASP 89": "OD1" <-> "OD2" Residue "N PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 60": "NH1" <-> "NH2" Residue "N ARG 60": "NH1" <-> "NH2" Residue "N ASP 89": "OD1" <-> "OD2" Residue "O PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 60": "NH1" <-> "NH2" Residue "O ARG 60": "NH1" <-> "NH2" Residue "O ASP 89": "OD1" <-> "OD2" Residue "P PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 60": "NH1" <-> "NH2" Residue "P ARG 60": "NH1" <-> "NH2" Residue "P ASP 89": "OD1" <-> "OD2" Residue "Q PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 60": "NH1" <-> "NH2" Residue "Q ARG 60": "NH1" <-> "NH2" Residue "Q ASP 89": "OD1" <-> "OD2" Residue "R PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 60": "NH1" <-> "NH2" Residue "R ARG 60": "NH1" <-> "NH2" Residue "R ASP 89": "OD1" <-> "OD2" Residue "S PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 60": "NH1" <-> "NH2" Residue "S ARG 60": "NH1" <-> "NH2" Residue "S ASP 89": "OD1" <-> "OD2" Residue "T PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 60": "NH1" <-> "NH2" Residue "T ARG 60": "NH1" <-> "NH2" Residue "T ASP 89": "OD1" <-> "OD2" Residue "U PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 60": "NH1" <-> "NH2" Residue "U ARG 60": "NH1" <-> "NH2" Residue "U ASP 89": "OD1" <-> "OD2" Residue "V PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 60": "NH1" <-> "NH2" Residue "V ARG 60": "NH1" <-> "NH2" Residue "V ASP 89": "OD1" <-> "OD2" Residue "W PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 60": "NH1" <-> "NH2" Residue "W ARG 60": "NH1" <-> "NH2" Residue "W ASP 89": "OD1" <-> "OD2" Residue "X PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 60": "NH1" <-> "NH2" Residue "X ARG 60": "NH1" <-> "NH2" Residue "X ASP 89": "OD1" <-> "OD2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 37152 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1548 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS A 174 " pdbres=" FE A 201 " Not linked: pdbres=" FE A 201 " pdbres=" MG A 202 " Not linked: pdbres=" MG A 202 " pdbres="HOH A 301 " Not linked: pdbres="HOH A 301 " pdbres="HOH A 302 " Not linked: pdbres="HOH A 302 " pdbres="HOH A 303 " ... (remaining 69 not shown) Conformer: "B" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS A 174 " pdbres=" FE A 201 " Not linked: pdbres=" FE A 201 " pdbres=" MG A 202 " Not linked: pdbres=" MG A 202 " pdbres="HOH A 301 " Not linked: pdbres="HOH A 301 " pdbres="HOH A 302 " Not linked: pdbres="HOH A 302 " pdbres="HOH A 303 " ... (remaining 69 not shown) bond proxies already assigned to first conformer: 1397 Chain: "B" Number of atoms: 1548 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS B 174 " pdbres=" FE B 201 " Not linked: pdbres=" FE B 201 " pdbres=" MG B 202 " Not linked: pdbres=" MG B 202 " pdbres="HOH B 301 " Not linked: pdbres="HOH B 301 " pdbres="HOH B 302 " Not linked: pdbres="HOH B 302 " pdbres="HOH B 303 " ... (remaining 69 not shown) Conformer: "B" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS B 174 " pdbres=" FE B 201 " Not linked: pdbres=" FE B 201 " pdbres=" MG B 202 " Not linked: pdbres=" MG B 202 " pdbres="HOH B 301 " Not linked: pdbres="HOH B 301 " pdbres="HOH B 302 " Not linked: pdbres="HOH B 302 " pdbres="HOH B 303 " ... (remaining 69 not shown) bond proxies already assigned to first conformer: 1397 Chain: "C" Number of atoms: 1548 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS C 174 " pdbres=" FE C 201 " Not linked: pdbres=" FE C 201 " pdbres=" MG C 202 " Not linked: pdbres=" MG C 202 " pdbres="HOH C 301 " Not linked: pdbres="HOH C 301 " pdbres="HOH C 302 " Not linked: pdbres="HOH C 302 " pdbres="HOH C 303 " ... (remaining 69 not shown) Conformer: "B" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS C 174 " pdbres=" FE C 201 " Not linked: pdbres=" FE C 201 " pdbres=" MG C 202 " Not linked: pdbres=" MG C 202 " pdbres="HOH C 301 " Not linked: pdbres="HOH C 301 " pdbres="HOH C 302 " Not linked: pdbres="HOH C 302 " pdbres="HOH C 303 " ... (remaining 69 not shown) bond proxies already assigned to first conformer: 1397 Chain: "D" Number of atoms: 1548 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS D 174 " pdbres=" FE D 201 " Not linked: pdbres=" FE D 201 " pdbres=" MG D 202 " Not linked: pdbres=" MG D 202 " pdbres="HOH D 301 " Not linked: pdbres="HOH D 301 " pdbres="HOH D 302 " Not linked: pdbres="HOH D 302 " pdbres="HOH D 303 " ... (remaining 69 not shown) Conformer: "B" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS D 174 " pdbres=" FE D 201 " Not linked: pdbres=" FE D 201 " pdbres=" MG D 202 " Not linked: pdbres=" MG D 202 " pdbres="HOH D 301 " Not linked: pdbres="HOH D 301 " pdbres="HOH D 302 " Not linked: pdbres="HOH D 302 " pdbres="HOH D 303 " ... (remaining 69 not shown) bond proxies already assigned to first conformer: 1397 Chain: "E" Number of atoms: 1548 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS E 174 " pdbres=" FE E 201 " Not linked: pdbres=" FE E 201 " pdbres=" MG E 202 " Not linked: pdbres=" MG E 202 " pdbres="HOH E 301 " Not linked: pdbres="HOH E 301 " pdbres="HOH E 302 " Not linked: pdbres="HOH E 302 " pdbres="HOH E 303 " ... (remaining 69 not shown) Conformer: "B" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS E 174 " pdbres=" FE E 201 " Not linked: pdbres=" FE E 201 " pdbres=" MG E 202 " Not linked: pdbres=" MG E 202 " pdbres="HOH E 301 " Not linked: pdbres="HOH E 301 " pdbres="HOH E 302 " Not linked: pdbres="HOH E 302 " pdbres="HOH E 303 " ... (remaining 69 not shown) bond proxies already assigned to first conformer: 1397 Chain: "F" Number of atoms: 1548 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS F 174 " pdbres=" FE F 201 " Not linked: pdbres=" FE F 201 " pdbres=" MG F 202 " Not linked: pdbres=" MG F 202 " pdbres="HOH F 301 " Not linked: pdbres="HOH F 301 " pdbres="HOH F 302 " Not linked: pdbres="HOH F 302 " pdbres="HOH F 303 " ... (remaining 69 not shown) Conformer: "B" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS F 174 " pdbres=" FE F 201 " Not linked: pdbres=" FE F 201 " pdbres=" MG F 202 " Not linked: pdbres=" MG F 202 " pdbres="HOH F 301 " Not linked: pdbres="HOH F 301 " pdbres="HOH F 302 " Not linked: pdbres="HOH F 302 " pdbres="HOH F 303 " ... (remaining 69 not shown) bond proxies already assigned to first conformer: 1397 Chain: "G" Number of atoms: 1548 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS G 174 " pdbres=" FE G 201 " Not linked: pdbres=" FE G 201 " pdbres=" MG G 202 " Not linked: pdbres=" MG G 202 " pdbres="HOH G 301 " Not linked: pdbres="HOH G 301 " pdbres="HOH G 302 " Not linked: pdbres="HOH G 302 " pdbres="HOH G 303 " ... (remaining 69 not shown) Conformer: "B" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS G 174 " pdbres=" FE G 201 " Not linked: pdbres=" FE G 201 " pdbres=" MG G 202 " Not linked: pdbres=" MG G 202 " pdbres="HOH G 301 " Not linked: pdbres="HOH G 301 " pdbres="HOH G 302 " Not linked: pdbres="HOH G 302 " pdbres="HOH G 303 " ... (remaining 69 not shown) bond proxies already assigned to first conformer: 1397 Chain: "H" Number of atoms: 1548 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS H 174 " pdbres=" FE H 201 " Not linked: pdbres=" FE H 201 " pdbres=" MG H 202 " Not linked: pdbres=" MG H 202 " pdbres="HOH H 301 " Not linked: pdbres="HOH H 301 " pdbres="HOH H 302 " Not linked: pdbres="HOH H 302 " pdbres="HOH H 303 " ... (remaining 69 not shown) Conformer: "B" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS H 174 " pdbres=" FE H 201 " Not linked: pdbres=" FE H 201 " pdbres=" MG H 202 " Not linked: pdbres=" MG H 202 " pdbres="HOH H 301 " Not linked: pdbres="HOH H 301 " pdbres="HOH H 302 " Not linked: pdbres="HOH H 302 " pdbres="HOH H 303 " ... (remaining 69 not shown) bond proxies already assigned to first conformer: 1397 Chain: "I" Number of atoms: 1548 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS I 174 " pdbres=" FE I 201 " Not linked: pdbres=" FE I 201 " pdbres=" MG I 202 " Not linked: pdbres=" MG I 202 " pdbres="HOH I 301 " Not linked: pdbres="HOH I 301 " pdbres="HOH I 302 " Not linked: pdbres="HOH I 302 " pdbres="HOH I 303 " ... (remaining 69 not shown) Conformer: "B" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS I 174 " pdbres=" FE I 201 " Not linked: pdbres=" FE I 201 " pdbres=" MG I 202 " Not linked: pdbres=" MG I 202 " pdbres="HOH I 301 " Not linked: pdbres="HOH I 301 " pdbres="HOH I 302 " Not linked: pdbres="HOH I 302 " pdbres="HOH I 303 " ... (remaining 69 not shown) bond proxies already assigned to first conformer: 1397 Chain: "J" Number of atoms: 1548 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS J 174 " pdbres=" FE J 201 " Not linked: pdbres=" FE J 201 " pdbres=" MG J 202 " Not linked: pdbres=" MG J 202 " pdbres="HOH J 301 " Not linked: pdbres="HOH J 301 " pdbres="HOH J 302 " Not linked: pdbres="HOH J 302 " pdbres="HOH J 303 " ... (remaining 69 not shown) Conformer: "B" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS J 174 " pdbres=" FE J 201 " Not linked: pdbres=" FE J 201 " pdbres=" MG J 202 " Not linked: pdbres=" MG J 202 " pdbres="HOH J 301 " Not linked: pdbres="HOH J 301 " pdbres="HOH J 302 " Not linked: pdbres="HOH J 302 " pdbres="HOH J 303 " ... (remaining 69 not shown) bond proxies already assigned to first conformer: 1397 Chain: "K" Number of atoms: 1548 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS K 174 " pdbres=" FE K 201 " Not linked: pdbres=" FE K 201 " pdbres=" MG K 202 " Not linked: pdbres=" MG K 202 " pdbres="HOH K 301 " Not linked: pdbres="HOH K 301 " pdbres="HOH K 302 " Not linked: pdbres="HOH K 302 " pdbres="HOH K 303 " ... (remaining 69 not shown) Conformer: "B" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS K 174 " pdbres=" FE K 201 " Not linked: pdbres=" FE K 201 " pdbres=" MG K 202 " Not linked: pdbres=" MG K 202 " pdbres="HOH K 301 " Not linked: pdbres="HOH K 301 " pdbres="HOH K 302 " Not linked: pdbres="HOH K 302 " pdbres="HOH K 303 " ... (remaining 69 not shown) bond proxies already assigned to first conformer: 1397 Chain: "L" Number of atoms: 1548 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS L 174 " pdbres=" FE L 201 " Not linked: pdbres=" FE L 201 " pdbres=" MG L 202 " Not linked: pdbres=" MG L 202 " pdbres="HOH L 301 " Not linked: pdbres="HOH L 301 " pdbres="HOH L 302 " Not linked: pdbres="HOH L 302 " pdbres="HOH L 303 " ... (remaining 69 not shown) Conformer: "B" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS L 174 " pdbres=" FE L 201 " Not linked: pdbres=" FE L 201 " pdbres=" MG L 202 " Not linked: pdbres=" MG L 202 " pdbres="HOH L 301 " Not linked: pdbres="HOH L 301 " pdbres="HOH L 302 " Not linked: pdbres="HOH L 302 " pdbres="HOH L 303 " ... (remaining 69 not shown) bond proxies already assigned to first conformer: 1397 Chain: "M" Number of atoms: 1548 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS M 174 " pdbres=" FE M 201 " Not linked: pdbres=" FE M 201 " pdbres=" MG M 202 " Not linked: pdbres=" MG M 202 " pdbres="HOH M 301 " Not linked: pdbres="HOH M 301 " pdbres="HOH M 302 " Not linked: pdbres="HOH M 302 " pdbres="HOH M 303 " ... (remaining 69 not shown) Conformer: "B" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS M 174 " pdbres=" FE M 201 " Not linked: pdbres=" FE M 201 " pdbres=" MG M 202 " Not linked: pdbres=" MG M 202 " pdbres="HOH M 301 " Not linked: pdbres="HOH M 301 " pdbres="HOH M 302 " Not linked: pdbres="HOH M 302 " pdbres="HOH M 303 " ... (remaining 69 not shown) bond proxies already assigned to first conformer: 1397 Chain: "N" Number of atoms: 1548 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS N 174 " pdbres=" FE N 201 " Not linked: pdbres=" FE N 201 " pdbres=" MG N 202 " Not linked: pdbres=" MG N 202 " pdbres="HOH N 301 " Not linked: pdbres="HOH N 301 " pdbres="HOH N 302 " Not linked: pdbres="HOH N 302 " pdbres="HOH N 303 " ... (remaining 69 not shown) Conformer: "B" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS N 174 " pdbres=" FE N 201 " Not linked: pdbres=" FE N 201 " pdbres=" MG N 202 " Not linked: pdbres=" MG N 202 " pdbres="HOH N 301 " Not linked: pdbres="HOH N 301 " pdbres="HOH N 302 " Not linked: pdbres="HOH N 302 " pdbres="HOH N 303 " ... (remaining 69 not shown) bond proxies already assigned to first conformer: 1397 Chain: "O" Number of atoms: 1548 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS O 174 " pdbres=" FE O 201 " Not linked: pdbres=" FE O 201 " pdbres=" MG O 202 " Not linked: pdbres=" MG O 202 " pdbres="HOH O 301 " Not linked: pdbres="HOH O 301 " pdbres="HOH O 302 " Not linked: pdbres="HOH O 302 " pdbres="HOH O 303 " ... (remaining 69 not shown) Conformer: "B" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS O 174 " pdbres=" FE O 201 " Not linked: pdbres=" FE O 201 " pdbres=" MG O 202 " Not linked: pdbres=" MG O 202 " pdbres="HOH O 301 " Not linked: pdbres="HOH O 301 " pdbres="HOH O 302 " Not linked: pdbres="HOH O 302 " pdbres="HOH O 303 " ... (remaining 69 not shown) bond proxies already assigned to first conformer: 1397 Chain: "P" Number of atoms: 1548 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS P 174 " pdbres=" FE P 201 " Not linked: pdbres=" FE P 201 " pdbres=" MG P 202 " Not linked: pdbres=" MG P 202 " pdbres="HOH P 301 " Not linked: pdbres="HOH P 301 " pdbres="HOH P 302 " Not linked: pdbres="HOH P 302 " pdbres="HOH P 303 " ... (remaining 69 not shown) Conformer: "B" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS P 174 " pdbres=" FE P 201 " Not linked: pdbres=" FE P 201 " pdbres=" MG P 202 " Not linked: pdbres=" MG P 202 " pdbres="HOH P 301 " Not linked: pdbres="HOH P 301 " pdbres="HOH P 302 " Not linked: pdbres="HOH P 302 " pdbres="HOH P 303 " ... (remaining 69 not shown) bond proxies already assigned to first conformer: 1397 Chain: "Q" Number of atoms: 1548 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS Q 174 " pdbres=" FE Q 201 " Not linked: pdbres=" FE Q 201 " pdbres=" MG Q 202 " Not linked: pdbres=" MG Q 202 " pdbres="HOH Q 301 " Not linked: pdbres="HOH Q 301 " pdbres="HOH Q 302 " Not linked: pdbres="HOH Q 302 " pdbres="HOH Q 303 " ... (remaining 69 not shown) Conformer: "B" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS Q 174 " pdbres=" FE Q 201 " Not linked: pdbres=" FE Q 201 " pdbres=" MG Q 202 " Not linked: pdbres=" MG Q 202 " pdbres="HOH Q 301 " Not linked: pdbres="HOH Q 301 " pdbres="HOH Q 302 " Not linked: pdbres="HOH Q 302 " pdbres="HOH Q 303 " ... (remaining 69 not shown) bond proxies already assigned to first conformer: 1397 Chain: "R" Number of atoms: 1548 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS R 174 " pdbres=" FE R 201 " Not linked: pdbres=" FE R 201 " pdbres=" MG R 202 " Not linked: pdbres=" MG R 202 " pdbres="HOH R 301 " Not linked: pdbres="HOH R 301 " pdbres="HOH R 302 " Not linked: pdbres="HOH R 302 " pdbres="HOH R 303 " ... (remaining 69 not shown) Conformer: "B" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS R 174 " pdbres=" FE R 201 " Not linked: pdbres=" FE R 201 " pdbres=" MG R 202 " Not linked: pdbres=" MG R 202 " pdbres="HOH R 301 " Not linked: pdbres="HOH R 301 " pdbres="HOH R 302 " Not linked: pdbres="HOH R 302 " pdbres="HOH R 303 " ... (remaining 69 not shown) bond proxies already assigned to first conformer: 1397 Chain: "S" Number of atoms: 1548 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS S 174 " pdbres=" FE S 201 " Not linked: pdbres=" FE S 201 " pdbres=" MG S 202 " Not linked: pdbres=" MG S 202 " pdbres="HOH S 301 " Not linked: pdbres="HOH S 301 " pdbres="HOH S 302 " Not linked: pdbres="HOH S 302 " pdbres="HOH S 303 " ... (remaining 69 not shown) Conformer: "B" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS S 174 " pdbres=" FE S 201 " Not linked: pdbres=" FE S 201 " pdbres=" MG S 202 " Not linked: pdbres=" MG S 202 " pdbres="HOH S 301 " Not linked: pdbres="HOH S 301 " pdbres="HOH S 302 " Not linked: pdbres="HOH S 302 " pdbres="HOH S 303 " ... (remaining 69 not shown) bond proxies already assigned to first conformer: 1397 Chain: "T" Number of atoms: 1548 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS T 174 " pdbres=" FE T 201 " Not linked: pdbres=" FE T 201 " pdbres=" MG T 202 " Not linked: pdbres=" MG T 202 " pdbres="HOH T 301 " Not linked: pdbres="HOH T 301 " pdbres="HOH T 302 " Not linked: pdbres="HOH T 302 " pdbres="HOH T 303 " ... (remaining 69 not shown) Conformer: "B" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS T 174 " pdbres=" FE T 201 " Not linked: pdbres=" FE T 201 " pdbres=" MG T 202 " Not linked: pdbres=" MG T 202 " pdbres="HOH T 301 " Not linked: pdbres="HOH T 301 " pdbres="HOH T 302 " Not linked: pdbres="HOH T 302 " pdbres="HOH T 303 " ... (remaining 69 not shown) bond proxies already assigned to first conformer: 1397 Chain: "U" Number of atoms: 1548 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS U 174 " pdbres=" FE U 201 " Not linked: pdbres=" FE U 201 " pdbres=" MG U 202 " Not linked: pdbres=" MG U 202 " pdbres="HOH U 301 " Not linked: pdbres="HOH U 301 " pdbres="HOH U 302 " Not linked: pdbres="HOH U 302 " pdbres="HOH U 303 " ... (remaining 69 not shown) Conformer: "B" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS U 174 " pdbres=" FE U 201 " Not linked: pdbres=" FE U 201 " pdbres=" MG U 202 " Not linked: pdbres=" MG U 202 " pdbres="HOH U 301 " Not linked: pdbres="HOH U 301 " pdbres="HOH U 302 " Not linked: pdbres="HOH U 302 " pdbres="HOH U 303 " ... (remaining 69 not shown) bond proxies already assigned to first conformer: 1397 Chain: "V" Number of atoms: 1548 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS V 174 " pdbres=" FE V 201 " Not linked: pdbres=" FE V 201 " pdbres=" MG V 202 " Not linked: pdbres=" MG V 202 " pdbres="HOH V 301 " Not linked: pdbres="HOH V 301 " pdbres="HOH V 302 " Not linked: pdbres="HOH V 302 " pdbres="HOH V 303 " ... (remaining 69 not shown) Conformer: "B" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS V 174 " pdbres=" FE V 201 " Not linked: pdbres=" FE V 201 " pdbres=" MG V 202 " Not linked: pdbres=" MG V 202 " pdbres="HOH V 301 " Not linked: pdbres="HOH V 301 " pdbres="HOH V 302 " Not linked: pdbres="HOH V 302 " pdbres="HOH V 303 " ... (remaining 69 not shown) bond proxies already assigned to first conformer: 1397 Chain: "W" Number of atoms: 1548 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS W 174 " pdbres=" FE W 201 " Not linked: pdbres=" FE W 201 " pdbres=" MG W 202 " Not linked: pdbres=" MG W 202 " pdbres="HOH W 301 " Not linked: pdbres="HOH W 301 " pdbres="HOH W 302 " Not linked: pdbres="HOH W 302 " pdbres="HOH W 303 " ... (remaining 69 not shown) Conformer: "B" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS W 174 " pdbres=" FE W 201 " Not linked: pdbres=" FE W 201 " pdbres=" MG W 202 " Not linked: pdbres=" MG W 202 " pdbres="HOH W 301 " Not linked: pdbres="HOH W 301 " pdbres="HOH W 302 " Not linked: pdbres="HOH W 302 " pdbres="HOH W 303 " ... (remaining 69 not shown) bond proxies already assigned to first conformer: 1397 Chain: "X" Number of atoms: 1548 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS X 174 " pdbres=" FE X 201 " Not linked: pdbres=" FE X 201 " pdbres=" MG X 202 " Not linked: pdbres=" MG X 202 " pdbres="HOH X 301 " Not linked: pdbres="HOH X 301 " pdbres="HOH X 302 " Not linked: pdbres="HOH X 302 " pdbres="HOH X 303 " ... (remaining 69 not shown) Conformer: "B" Number of residues, atoms: 248, 1499 Unusual residues: {' FE': 1, ' MG': 1} Classifications: {'peptide': 174, 'undetermined': 2, 'water': 72} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 169, None: 74} Not linked: pdbres="HIS X 174 " pdbres=" FE X 201 " Not linked: pdbres=" FE X 201 " pdbres=" MG X 202 " Not linked: pdbres=" MG X 202 " pdbres="HOH X 301 " Not linked: pdbres="HOH X 301 " pdbres="HOH X 302 " Not linked: pdbres="HOH X 302 " pdbres="HOH X 303 " ... (remaining 69 not shown) bond proxies already assigned to first conformer: 1397 Residues with excluded nonbonded symmetry interactions: 48 residue: pdb="FE FE A 201 " occ=0.25 residue: pdb=" O HOH A 359 " occ=0.33 residue: pdb="FE FE B 201 " occ=0.25 residue: pdb=" O HOH B 359 " occ=0.33 residue: pdb="FE FE C 201 " occ=0.25 residue: pdb=" O HOH C 359 " occ=0.33 residue: pdb="FE FE D 201 " occ=0.25 residue: pdb=" O HOH D 359 " occ=0.33 residue: pdb="FE FE E 201 " occ=0.25 residue: pdb=" O HOH E 359 " occ=0.33 residue: pdb="FE FE F 201 " occ=0.25 residue: pdb=" O HOH F 359 " occ=0.33 ... (remaining 36 not shown) Time building chain proxies: 33.97, per 1000 atoms: 0.91 Number of scatterers: 37152 At special positions: 0 Unit cell: (135.36, 135.36, 135.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 24 26.01 S 192 16.00 Mg 24 11.99 O 8352 8.00 N 6264 7.00 C 22296 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 16.00 Conformation dependent library (CDL) restraints added in 12.3 seconds 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8400 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 77.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.57 Creating SS restraints... Processing helix chain 'A' and resid 10 through 40 Processing helix chain 'A' and resid 45 through 73 Processing helix chain 'A' and resid 92 through 120 Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 134 through 156 Processing helix chain 'A' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 40 Processing helix chain 'B' and resid 45 through 73 Processing helix chain 'B' and resid 92 through 120 Processing helix chain 'B' and resid 123 through 134 Processing helix chain 'B' and resid 134 through 156 Processing helix chain 'B' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR B 165 " --> pdb=" O GLY B 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 40 Processing helix chain 'C' and resid 45 through 73 Processing helix chain 'C' and resid 92 through 120 Processing helix chain 'C' and resid 123 through 134 Processing helix chain 'C' and resid 134 through 156 Processing helix chain 'C' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR C 165 " --> pdb=" O GLY C 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 40 Processing helix chain 'D' and resid 45 through 73 Processing helix chain 'D' and resid 92 through 120 Processing helix chain 'D' and resid 123 through 134 Processing helix chain 'D' and resid 134 through 156 Processing helix chain 'D' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR D 165 " --> pdb=" O GLY D 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 40 Processing helix chain 'E' and resid 45 through 73 Processing helix chain 'E' and resid 92 through 120 Processing helix chain 'E' and resid 123 through 134 Processing helix chain 'E' and resid 134 through 156 Processing helix chain 'E' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR E 165 " --> pdb=" O GLY E 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 40 Processing helix chain 'F' and resid 45 through 73 Processing helix chain 'F' and resid 92 through 120 Processing helix chain 'F' and resid 123 through 134 Processing helix chain 'F' and resid 134 through 156 Processing helix chain 'F' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR F 165 " --> pdb=" O GLY F 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 40 Processing helix chain 'G' and resid 45 through 73 Processing helix chain 'G' and resid 92 through 120 Processing helix chain 'G' and resid 123 through 134 Processing helix chain 'G' and resid 134 through 156 Processing helix chain 'G' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR G 165 " --> pdb=" O GLY G 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 40 Processing helix chain 'H' and resid 45 through 73 Processing helix chain 'H' and resid 92 through 120 Processing helix chain 'H' and resid 123 through 134 Processing helix chain 'H' and resid 134 through 156 Processing helix chain 'H' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR H 165 " --> pdb=" O GLY H 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 40 Processing helix chain 'I' and resid 45 through 73 Processing helix chain 'I' and resid 92 through 120 Processing helix chain 'I' and resid 123 through 134 Processing helix chain 'I' and resid 134 through 156 Processing helix chain 'I' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR I 165 " --> pdb=" O GLY I 161 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 40 Processing helix chain 'J' and resid 45 through 73 Processing helix chain 'J' and resid 92 through 120 Processing helix chain 'J' and resid 123 through 134 Processing helix chain 'J' and resid 134 through 156 Processing helix chain 'J' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR J 165 " --> pdb=" O GLY J 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 40 Processing helix chain 'K' and resid 45 through 73 Processing helix chain 'K' and resid 92 through 120 Processing helix chain 'K' and resid 123 through 134 Processing helix chain 'K' and resid 134 through 156 Processing helix chain 'K' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR K 165 " --> pdb=" O GLY K 161 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 40 Processing helix chain 'L' and resid 45 through 73 Processing helix chain 'L' and resid 92 through 120 Processing helix chain 'L' and resid 123 through 134 Processing helix chain 'L' and resid 134 through 156 Processing helix chain 'L' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR L 165 " --> pdb=" O GLY L 161 " (cutoff:3.500A) Processing helix chain 'M' and resid 10 through 40 Processing helix chain 'M' and resid 45 through 73 Processing helix chain 'M' and resid 92 through 120 Processing helix chain 'M' and resid 123 through 134 Processing helix chain 'M' and resid 134 through 156 Processing helix chain 'M' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR M 165 " --> pdb=" O GLY M 161 " (cutoff:3.500A) Processing helix chain 'N' and resid 10 through 40 Processing helix chain 'N' and resid 45 through 73 Processing helix chain 'N' and resid 92 through 120 Processing helix chain 'N' and resid 123 through 134 Processing helix chain 'N' and resid 134 through 156 Processing helix chain 'N' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR N 165 " --> pdb=" O GLY N 161 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 40 Processing helix chain 'O' and resid 45 through 73 Processing helix chain 'O' and resid 92 through 120 Processing helix chain 'O' and resid 123 through 134 Processing helix chain 'O' and resid 134 through 156 Processing helix chain 'O' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR O 165 " --> pdb=" O GLY O 161 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 40 Processing helix chain 'P' and resid 45 through 73 Processing helix chain 'P' and resid 92 through 120 Processing helix chain 'P' and resid 123 through 134 Processing helix chain 'P' and resid 134 through 156 Processing helix chain 'P' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR P 165 " --> pdb=" O GLY P 161 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 40 Processing helix chain 'Q' and resid 45 through 73 Processing helix chain 'Q' and resid 92 through 120 Processing helix chain 'Q' and resid 123 through 134 Processing helix chain 'Q' and resid 134 through 156 Processing helix chain 'Q' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR Q 165 " --> pdb=" O GLY Q 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 40 Processing helix chain 'R' and resid 45 through 73 Processing helix chain 'R' and resid 92 through 120 Processing helix chain 'R' and resid 123 through 134 Processing helix chain 'R' and resid 134 through 156 Processing helix chain 'R' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR R 165 " --> pdb=" O GLY R 161 " (cutoff:3.500A) Processing helix chain 'S' and resid 10 through 40 Processing helix chain 'S' and resid 45 through 73 Processing helix chain 'S' and resid 92 through 120 Processing helix chain 'S' and resid 123 through 134 Processing helix chain 'S' and resid 134 through 156 Processing helix chain 'S' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR S 165 " --> pdb=" O GLY S 161 " (cutoff:3.500A) Processing helix chain 'T' and resid 10 through 40 Processing helix chain 'T' and resid 45 through 73 Processing helix chain 'T' and resid 92 through 120 Processing helix chain 'T' and resid 123 through 134 Processing helix chain 'T' and resid 134 through 156 Processing helix chain 'T' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR T 165 " --> pdb=" O GLY T 161 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 40 Processing helix chain 'U' and resid 45 through 73 Processing helix chain 'U' and resid 92 through 120 Processing helix chain 'U' and resid 123 through 134 Processing helix chain 'U' and resid 134 through 156 Processing helix chain 'U' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR U 165 " --> pdb=" O GLY U 161 " (cutoff:3.500A) Processing helix chain 'V' and resid 10 through 40 Processing helix chain 'V' and resid 45 through 73 Processing helix chain 'V' and resid 92 through 120 Processing helix chain 'V' and resid 123 through 134 Processing helix chain 'V' and resid 134 through 156 Processing helix chain 'V' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR V 165 " --> pdb=" O GLY V 161 " (cutoff:3.500A) Processing helix chain 'W' and resid 10 through 40 Processing helix chain 'W' and resid 45 through 73 Processing helix chain 'W' and resid 92 through 120 Processing helix chain 'W' and resid 123 through 134 Processing helix chain 'W' and resid 134 through 156 Processing helix chain 'W' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR W 165 " --> pdb=" O GLY W 161 " (cutoff:3.500A) Processing helix chain 'X' and resid 10 through 40 Processing helix chain 'X' and resid 45 through 73 Processing helix chain 'X' and resid 92 through 120 Processing helix chain 'X' and resid 123 through 134 Processing helix chain 'X' and resid 134 through 156 Processing helix chain 'X' and resid 161 through 171 removed outlier: 3.872A pdb=" N TYR X 165 " --> pdb=" O GLY X 161 " (cutoff:3.500A) 2640 hydrogen bonds defined for protein. 7776 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.40 Time building geometry restraints manager: 17.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 9888 1.33 - 1.46: 8088 1.46 - 1.58: 17976 1.58 - 1.71: 48 1.71 - 1.84: 312 Bond restraints: 36312 Sorted by residual: bond pdb=" CA ALA D 157 " pdb=" CB ALA D 157 " ideal model delta sigma weight residual 1.530 1.465 0.064 1.46e-02 4.69e+03 1.94e+01 bond pdb=" CA ALA M 157 " pdb=" CB ALA M 157 " ideal model delta sigma weight residual 1.530 1.465 0.064 1.46e-02 4.69e+03 1.94e+01 bond pdb=" CA ALA B 157 " pdb=" CB ALA B 157 " ideal model delta sigma weight residual 1.530 1.465 0.064 1.46e-02 4.69e+03 1.94e+01 bond pdb=" CA ALA E 157 " pdb=" CB ALA E 157 " ideal model delta sigma weight residual 1.530 1.465 0.064 1.46e-02 4.69e+03 1.94e+01 bond pdb=" CA ALA K 157 " pdb=" CB ALA K 157 " ideal model delta sigma weight residual 1.530 1.465 0.064 1.46e-02 4.69e+03 1.94e+01 ... (remaining 36307 not shown) Histogram of bond angle deviations from ideal: 99.84 - 106.68: 1032 106.68 - 113.53: 18624 113.53 - 120.37: 16008 120.37 - 127.21: 13080 127.21 - 134.06: 360 Bond angle restraints: 49104 Sorted by residual: angle pdb=" N HIS B 170 " pdb=" CA HIS B 170 " pdb=" C HIS B 170 " ideal model delta sigma weight residual 111.69 118.63 -6.94 1.23e+00 6.61e-01 3.18e+01 angle pdb=" N HIS D 170 " pdb=" CA HIS D 170 " pdb=" C HIS D 170 " ideal model delta sigma weight residual 111.69 118.63 -6.94 1.23e+00 6.61e-01 3.18e+01 angle pdb=" N HIS Q 170 " pdb=" CA HIS Q 170 " pdb=" C HIS Q 170 " ideal model delta sigma weight residual 111.69 118.63 -6.94 1.23e+00 6.61e-01 3.18e+01 angle pdb=" N HIS U 170 " pdb=" CA HIS U 170 " pdb=" C HIS U 170 " ideal model delta sigma weight residual 111.69 118.63 -6.94 1.23e+00 6.61e-01 3.18e+01 angle pdb=" N HIS J 170 " pdb=" CA HIS J 170 " pdb=" C HIS J 170 " ideal model delta sigma weight residual 111.69 118.63 -6.94 1.23e+00 6.61e-01 3.18e+01 ... (remaining 49099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 21504 35.95 - 71.90: 1032 71.90 - 107.85: 24 107.85 - 143.80: 0 143.80 - 179.75: 24 Dihedral angle restraints: 22584 sinusoidal: 9456 harmonic: 13128 Sorted by residual: dihedral pdb=" CD BARG A 60 " pdb=" NE BARG A 60 " pdb=" CZ BARG A 60 " pdb=" NH1BARG A 60 " ideal model delta sinusoidal sigma weight residual 0.00 179.75 -179.75 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD BARG C 60 " pdb=" NE BARG C 60 " pdb=" CZ BARG C 60 " pdb=" NH1BARG C 60 " ideal model delta sinusoidal sigma weight residual 0.00 179.75 -179.75 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD BARG D 60 " pdb=" NE BARG D 60 " pdb=" CZ BARG D 60 " pdb=" NH1BARG D 60 " ideal model delta sinusoidal sigma weight residual 0.00 179.75 -179.75 1 1.00e+01 1.00e-02 1.92e+02 ... (remaining 22581 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.054: 2664 0.054 - 0.105: 1848 0.105 - 0.157: 504 0.157 - 0.209: 72 0.209 - 0.261: 24 Chirality restraints: 5112 Sorted by residual: chirality pdb=" CA VAL I 43 " pdb=" N VAL I 43 " pdb=" C VAL I 43 " pdb=" CB VAL I 43 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA VAL C 43 " pdb=" N VAL C 43 " pdb=" C VAL C 43 " pdb=" CB VAL C 43 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA VAL K 43 " pdb=" N VAL K 43 " pdb=" C VAL K 43 " pdb=" CB VAL K 43 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 5109 not shown) Planarity restraints: 6480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 134 " -0.038 2.00e-02 2.50e+03 1.99e-02 7.93e+00 pdb=" CG TYR F 134 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR F 134 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR F 134 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR F 134 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR F 134 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR F 134 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR F 134 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 134 " -0.038 2.00e-02 2.50e+03 1.99e-02 7.93e+00 pdb=" CG TYR L 134 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR L 134 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR L 134 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR L 134 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR L 134 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR L 134 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR L 134 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 134 " -0.038 2.00e-02 2.50e+03 1.99e-02 7.93e+00 pdb=" CG TYR G 134 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR G 134 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR G 134 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR G 134 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR G 134 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR G 134 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR G 134 " -0.018 2.00e-02 2.50e+03 ... (remaining 6477 not shown) Histogram of nonbonded interaction distances: 0.00 - 0.98: 60 0.98 - 1.96: 48 1.96 - 2.94: 16140 2.94 - 3.92: 107076 3.92 - 4.90: 208788 Warning: very small nonbonded interaction distances. Nonbonded interactions: 332112 Sorted by model distance: nonbonded pdb="FE FE D 201 " pdb="FE FE J 201 " model vdw 0.000 1.480 nonbonded pdb="FE FE D 201 " pdb="FE FE M 201 " model vdw 0.000 1.480 nonbonded pdb="FE FE D 201 " pdb="FE FE V 201 " model vdw 0.000 1.480 nonbonded pdb="FE FE J 201 " pdb="FE FE M 201 " model vdw 0.000 1.480 nonbonded pdb="FE FE J 201 " pdb="FE FE V 201 " model vdw 0.000 1.480 ... (remaining 332107 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'B' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'C' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'D' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'E' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'F' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'G' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'H' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'I' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'J' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'K' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'L' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'M' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'N' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'O' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'P' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'Q' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'R' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'S' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'T' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'U' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'V' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'W' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'X' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.93 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.640 Check model and map are aligned: 0.530 Set scattering table: 0.270 Process input model: 116.980 Find NCS groups from input model: 2.740 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 141.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.083 36312 Z= 0.990 Angle : 1.547 10.740 49104 Z= 1.010 Chirality : 0.070 0.261 5112 Planarity : 0.007 0.040 6480 Dihedral : 19.276 179.750 14184 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.58 % Allowed : 0.58 % Favored : 98.84 % Rotamer: Outliers : 5.56 % Allowed : 13.58 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.11), residues: 4320 helix: -1.81 (0.07), residues: 3384 sheet: None (None), residues: 0 loop : -1.17 (0.22), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.005 TRP S 90 HIS 0.007 0.003 HIS G 125 PHE 0.034 0.009 PHE T 48 TYR 0.038 0.007 TYR D 134 ARG 0.007 0.002 ARG E 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1536 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1344 time to evaluate : 4.238 Fit side-chains REVERT: A 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9083 (ttt90) REVERT: A 76 ARG cc_start: 0.9090 (mmt-90) cc_final: 0.8606 (mmt180) REVERT: A 138 GLN cc_start: 0.9462 (tp40) cc_final: 0.9237 (tp-100) REVERT: B 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9084 (ttt90) REVERT: B 76 ARG cc_start: 0.9090 (mmt-90) cc_final: 0.8607 (mmt180) REVERT: B 138 GLN cc_start: 0.9463 (tp40) cc_final: 0.9238 (tp-100) REVERT: C 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9084 (ttt90) REVERT: C 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8605 (mmt180) REVERT: C 138 GLN cc_start: 0.9463 (tp40) cc_final: 0.9240 (tp-100) REVERT: D 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9083 (ttt90) REVERT: D 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8606 (mmt180) REVERT: D 138 GLN cc_start: 0.9463 (tp40) cc_final: 0.9238 (tp-100) REVERT: E 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9084 (ttt90) REVERT: E 76 ARG cc_start: 0.9090 (mmt-90) cc_final: 0.8607 (mmt180) REVERT: E 138 GLN cc_start: 0.9463 (tp40) cc_final: 0.9238 (tp-100) REVERT: F 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9083 (ttt90) REVERT: F 76 ARG cc_start: 0.9090 (mmt-90) cc_final: 0.8606 (mmt180) REVERT: F 138 GLN cc_start: 0.9462 (tp40) cc_final: 0.9237 (tp-100) REVERT: G 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9083 (ttt90) REVERT: G 76 ARG cc_start: 0.9090 (mmt-90) cc_final: 0.8606 (mmt180) REVERT: G 138 GLN cc_start: 0.9462 (tp40) cc_final: 0.9237 (tp-100) REVERT: H 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9084 (ttt90) REVERT: H 76 ARG cc_start: 0.9090 (mmt-90) cc_final: 0.8607 (mmt180) REVERT: H 138 GLN cc_start: 0.9463 (tp40) cc_final: 0.9238 (tp-100) REVERT: I 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9083 (ttt90) REVERT: I 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8604 (mmt180) REVERT: I 138 GLN cc_start: 0.9464 (tp40) cc_final: 0.9240 (tp-100) REVERT: J 6 ARG cc_start: 0.9361 (OUTLIER) cc_final: 0.9082 (ttt90) REVERT: J 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8604 (mmt180) REVERT: J 138 GLN cc_start: 0.9462 (tp40) cc_final: 0.9238 (tp-100) REVERT: K 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9083 (ttt90) REVERT: K 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8604 (mmt180) REVERT: K 138 GLN cc_start: 0.9464 (tp40) cc_final: 0.9240 (tp-100) REVERT: L 6 ARG cc_start: 0.9361 (OUTLIER) cc_final: 0.9082 (ttt90) REVERT: L 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8604 (mmt180) REVERT: L 138 GLN cc_start: 0.9462 (tp40) cc_final: 0.9238 (tp-100) REVERT: M 6 ARG cc_start: 0.9363 (OUTLIER) cc_final: 0.9084 (ttt90) REVERT: M 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8605 (mmt180) REVERT: M 138 GLN cc_start: 0.9464 (tp40) cc_final: 0.9238 (tp-100) REVERT: N 6 ARG cc_start: 0.9363 (OUTLIER) cc_final: 0.9083 (ttt90) REVERT: N 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8605 (mmt180) REVERT: N 138 GLN cc_start: 0.9465 (tp40) cc_final: 0.9239 (tp-100) REVERT: O 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9083 (ttt90) REVERT: O 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8606 (mmt180) REVERT: O 138 GLN cc_start: 0.9463 (tp40) cc_final: 0.9238 (tp-100) REVERT: P 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9084 (ttt90) REVERT: P 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8605 (mmt180) REVERT: P 138 GLN cc_start: 0.9463 (tp40) cc_final: 0.9240 (tp-100) REVERT: Q 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9083 (ttt90) REVERT: Q 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8606 (mmt180) REVERT: Q 138 GLN cc_start: 0.9463 (tp40) cc_final: 0.9238 (tp-100) REVERT: R 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9084 (ttt90) REVERT: R 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8605 (mmt180) REVERT: R 138 GLN cc_start: 0.9463 (tp40) cc_final: 0.9240 (tp-100) REVERT: S 6 ARG cc_start: 0.9361 (OUTLIER) cc_final: 0.9082 (ttt90) REVERT: S 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8604 (mmt180) REVERT: S 138 GLN cc_start: 0.9462 (tp40) cc_final: 0.9238 (tp-100) REVERT: T 6 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.9083 (ttt90) REVERT: T 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8604 (mmt180) REVERT: T 138 GLN cc_start: 0.9464 (tp40) cc_final: 0.9240 (tp-100) REVERT: U 6 ARG cc_start: 0.9363 (OUTLIER) cc_final: 0.9084 (ttt90) REVERT: U 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8605 (mmt180) REVERT: U 138 GLN cc_start: 0.9464 (tp40) cc_final: 0.9238 (tp-100) REVERT: V 6 ARG cc_start: 0.9363 (OUTLIER) cc_final: 0.9083 (ttt90) REVERT: V 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8605 (mmt180) REVERT: V 138 GLN cc_start: 0.9465 (tp40) cc_final: 0.9239 (tp-100) REVERT: W 6 ARG cc_start: 0.9363 (OUTLIER) cc_final: 0.9083 (ttt90) REVERT: W 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8605 (mmt180) REVERT: W 138 GLN cc_start: 0.9465 (tp40) cc_final: 0.9239 (tp-100) REVERT: X 6 ARG cc_start: 0.9363 (OUTLIER) cc_final: 0.9084 (ttt90) REVERT: X 76 ARG cc_start: 0.9089 (mmt-90) cc_final: 0.8605 (mmt180) REVERT: X 138 GLN cc_start: 0.9464 (tp40) cc_final: 0.9238 (tp-100) outliers start: 192 outliers final: 24 residues processed: 1392 average time/residue: 1.9148 time to fit residues: 3095.0603 Evaluate side-chains 1026 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 978 time to evaluate : 4.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 131 GLU Chi-restraints excluded: chain B residue 6 ARG Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 131 GLU Chi-restraints excluded: chain D residue 6 ARG Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain E residue 6 ARG Chi-restraints excluded: chain E residue 131 GLU Chi-restraints excluded: chain F residue 6 ARG Chi-restraints excluded: chain F residue 131 GLU Chi-restraints excluded: chain G residue 6 ARG Chi-restraints excluded: chain G residue 131 GLU Chi-restraints excluded: chain H residue 6 ARG Chi-restraints excluded: chain H residue 131 GLU Chi-restraints excluded: chain I residue 6 ARG Chi-restraints excluded: chain I residue 131 GLU Chi-restraints excluded: chain J residue 6 ARG Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain K residue 6 ARG Chi-restraints excluded: chain K residue 131 GLU Chi-restraints excluded: chain L residue 6 ARG Chi-restraints excluded: chain L residue 131 GLU Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 131 GLU Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain N residue 131 GLU Chi-restraints excluded: chain O residue 6 ARG Chi-restraints excluded: chain O residue 131 GLU Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain P residue 131 GLU Chi-restraints excluded: chain Q residue 6 ARG Chi-restraints excluded: chain Q residue 131 GLU Chi-restraints excluded: chain R residue 6 ARG Chi-restraints excluded: chain R residue 131 GLU Chi-restraints excluded: chain S residue 6 ARG Chi-restraints excluded: chain S residue 131 GLU Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain T residue 131 GLU Chi-restraints excluded: chain U residue 6 ARG Chi-restraints excluded: chain U residue 131 GLU Chi-restraints excluded: chain V residue 6 ARG Chi-restraints excluded: chain V residue 131 GLU Chi-restraints excluded: chain W residue 6 ARG Chi-restraints excluded: chain W residue 131 GLU Chi-restraints excluded: chain X residue 6 ARG Chi-restraints excluded: chain X residue 131 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 486 optimal weight: 7.9990 chunk 436 optimal weight: 10.0000 chunk 242 optimal weight: 2.9990 chunk 149 optimal weight: 0.0270 chunk 294 optimal weight: 3.9990 chunk 233 optimal weight: 7.9990 chunk 451 optimal weight: 50.0000 chunk 174 optimal weight: 0.8980 chunk 274 optimal weight: 4.9990 chunk 336 optimal weight: 0.8980 chunk 523 optimal weight: 50.0000 overall best weight: 1.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 57 HIS B 72 GLN B 95 ASN C 72 GLN C 95 ASN E 57 HIS E 62 HIS F 62 HIS F 72 GLN ** F 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 ASN G 57 HIS G 72 GLN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 GLN I 72 GLN J 108 ASN K 55 GLN K 72 GLN L 72 GLN ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 55 GLN M 95 ASN M 108 ASN N 8 ASN N 57 HIS N 62 HIS ** O 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 72 GLN Q 55 GLN Q 72 GLN R 72 GLN R 95 ASN ** R 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 HIS S 72 GLN T 55 GLN T 57 HIS T 72 GLN U 57 HIS U 72 GLN U 95 ASN ** U 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 151 ASN V 8 ASN V 72 GLN W 55 GLN W 57 HIS W 95 ASN X 72 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.211 36312 Z= 0.531 Angle : 1.792 41.169 49104 Z= 0.906 Chirality : 0.070 0.673 5112 Planarity : 0.016 0.181 6480 Dihedral : 14.708 179.362 5136 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.73 % Allowed : 4.55 % Favored : 94.72 % Rotamer: Outliers : 6.97 % Allowed : 18.88 % Favored : 74.15 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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 (0.11), residues: 4320 helix: -0.70 (0.08), residues: 3384 sheet: None (None), residues: 0 loop : -1.81 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.009 TRP D 90 HIS 0.072 0.008 HIS N 170 PHE 0.092 0.007 PHE N 52 TYR 0.140 0.010 TYR J 31 ARG 0.095 0.004 ARG D 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1391 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 1151 time to evaluate : 4.450 Fit side-chains REVERT: A 76 ARG cc_start: 0.9097 (mmt-90) cc_final: 0.8673 (mpt180) REVERT: A 138 GLN cc_start: 0.9281 (tp40) cc_final: 0.9026 (tp-100) REVERT: B 138 GLN cc_start: 0.9193 (tp40) cc_final: 0.8947 (tp-100) REVERT: C 76 ARG cc_start: 0.9038 (mmt-90) cc_final: 0.8644 (mpt180) REVERT: C 138 GLN cc_start: 0.9311 (tp40) cc_final: 0.9017 (mm-40) REVERT: D 8 ASN cc_start: 0.9061 (t0) cc_final: 0.8681 (t0) REVERT: E 76 ARG cc_start: 0.9138 (mmt-90) cc_final: 0.8776 (mmt180) REVERT: F 14 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8223 (tp30) REVERT: F 76 ARG cc_start: 0.9098 (mmt-90) cc_final: 0.8762 (mmt180) REVERT: G 116 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7930 (mtpp) REVERT: H 41 ASP cc_start: 0.8895 (p0) cc_final: 0.8389 (p0) REVERT: H 76 ARG cc_start: 0.9026 (mmt-90) cc_final: 0.8709 (mmt-90) REVERT: I 76 ARG cc_start: 0.9086 (mmt-90) cc_final: 0.8722 (mmt-90) REVERT: K 81 ASP cc_start: 0.8550 (m-30) cc_final: 0.8328 (m-30) REVERT: K 91 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8446 (mt-10) REVERT: K 138 GLN cc_start: 0.9361 (tp40) cc_final: 0.9087 (tp-100) REVERT: L 76 ARG cc_start: 0.9039 (mmt-90) cc_final: 0.8826 (mmt-90) REVERT: M 46 LYS cc_start: 0.8618 (ttpp) cc_final: 0.8337 (ttmt) REVERT: M 72 GLN cc_start: 0.9164 (mt0) cc_final: 0.8953 (mt0) REVERT: M 76 ARG cc_start: 0.9050 (mmt-90) cc_final: 0.8749 (mpt180) REVERT: N 6 ARG cc_start: 0.9390 (OUTLIER) cc_final: 0.9067 (ttt90) REVERT: N 19 ARG cc_start: 0.8768 (mtm-85) cc_final: 0.8558 (mtt90) REVERT: N 76 ARG cc_start: 0.9080 (mmt-90) cc_final: 0.8638 (mpt180) REVERT: N 116 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7924 (mtpp) REVERT: N 117 LEU cc_start: 0.8919 (tt) cc_final: 0.8665 (tm) REVERT: O 8 ASN cc_start: 0.8957 (t0) cc_final: 0.8736 (t0) REVERT: O 19 ARG cc_start: 0.8751 (mtm-85) cc_final: 0.8492 (mtt90) REVERT: O 76 ARG cc_start: 0.8996 (mmt-90) cc_final: 0.8718 (mmt-90) REVERT: P 76 ARG cc_start: 0.9127 (mmt-90) cc_final: 0.8905 (mmt-90) REVERT: R 42 ASP cc_start: 0.8924 (p0) cc_final: 0.8684 (p0) REVERT: R 46 LYS cc_start: 0.8481 (ttpp) cc_final: 0.8279 (ttmt) REVERT: R 76 ARG cc_start: 0.9021 (mmt-90) cc_final: 0.8776 (mmt180) REVERT: R 78 PHE cc_start: 0.9170 (m-80) cc_final: 0.8934 (m-80) REVERT: S 19 ARG cc_start: 0.8902 (mtm-85) cc_final: 0.8635 (mtm110) REVERT: S 76 ARG cc_start: 0.8872 (mmt-90) cc_final: 0.8488 (mmt-90) REVERT: T 76 ARG cc_start: 0.9004 (mmt-90) cc_final: 0.8725 (mmt-90) REVERT: T 83 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8952 (mmtm) REVERT: T 138 GLN cc_start: 0.9249 (tp40) cc_final: 0.9048 (tp-100) REVERT: U 46 LYS cc_start: 0.8739 (ttpp) cc_final: 0.8416 (ttmm) REVERT: V 6 ARG cc_start: 0.9316 (OUTLIER) cc_final: 0.9035 (ttt180) REVERT: V 76 ARG cc_start: 0.9104 (mmt-90) cc_final: 0.8753 (mmt-90) REVERT: W 19 ARG cc_start: 0.8848 (mtm-85) cc_final: 0.8525 (mtt90) REVERT: W 46 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8510 (ttmm) REVERT: X 76 ARG cc_start: 0.9107 (mmt-90) cc_final: 0.8895 (mmt180) outliers start: 240 outliers final: 58 residues processed: 1219 average time/residue: 1.5680 time to fit residues: 2243.5629 Evaluate side-chains 1069 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 1003 time to evaluate : 2.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 1 SER Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain F residue 58 GLU Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain H residue 1 SER Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 162 MET Chi-restraints excluded: chain I residue 58 GLU Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 58 GLU Chi-restraints excluded: chain J residue 159 GLU Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 58 GLU Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain L residue 86 ASP Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain M residue 39 ASP Chi-restraints excluded: chain M residue 86 ASP Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain N residue 6 ARG Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain N residue 58 GLU Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain N residue 116 LYS Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 159 GLU Chi-restraints excluded: chain Q residue 39 ASP Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 89 ASP Chi-restraints excluded: chain R residue 116 LYS Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 119 THR Chi-restraints excluded: chain T residue 39 ASP Chi-restraints excluded: chain T residue 83 LYS Chi-restraints excluded: chain T residue 89 ASP Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain T residue 159 GLU Chi-restraints excluded: chain T residue 162 MET Chi-restraints excluded: chain U residue 86 ASP Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain U residue 119 THR Chi-restraints excluded: chain U residue 159 GLU Chi-restraints excluded: chain V residue 6 ARG Chi-restraints excluded: chain W residue 39 ASP Chi-restraints excluded: chain W residue 46 LYS Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain W residue 159 GLU Chi-restraints excluded: chain X residue 39 ASP Chi-restraints excluded: chain X residue 89 ASP Chi-restraints excluded: chain X residue 119 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 290 optimal weight: 2.9990 chunk 162 optimal weight: 50.0000 chunk 435 optimal weight: 3.9990 chunk 356 optimal weight: 50.0000 chunk 144 optimal weight: 8.9990 chunk 524 optimal weight: 50.0000 chunk 566 optimal weight: 4.9990 chunk 466 optimal weight: 5.9990 chunk 519 optimal weight: 0.4980 chunk 178 optimal weight: 8.9990 chunk 420 optimal weight: 3.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 72 GLN A 108 ASN B 95 ASN C 72 GLN C 102 HIS D 10 HIS D 55 GLN D 95 ASN E 8 ASN E 55 GLN E 95 ASN F 95 ASN F 102 HIS H 22 ASN H 108 ASN I 55 GLN I 72 GLN J 55 GLN J 102 HIS J 108 ASN K 10 HIS K 72 GLN L 72 GLN L 102 HIS M 72 GLN M 108 ASN ** M 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 8 ASN N 22 ASN N 55 GLN N 102 HIS P 55 GLN P 72 GLN Q 72 GLN R 10 HIS R 72 GLN S 55 GLN S 109 GLN ** S 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 ASN V 72 GLN V 95 ASN W 22 ASN ** W 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 36312 Z= 0.314 Angle : 0.613 7.447 49104 Z= 0.336 Chirality : 0.042 0.144 5112 Planarity : 0.004 0.040 6480 Dihedral : 13.147 179.924 4976 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.44 % Allowed : 1.24 % Favored : 98.33 % Rotamer: Outliers : 4.14 % Allowed : 22.56 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.12), residues: 4320 helix: 2.47 (0.08), residues: 3432 sheet: None (None), residues: 0 loop : -0.95 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 90 HIS 0.008 0.001 HIS L 102 PHE 0.021 0.002 PHE B 38 TYR 0.020 0.002 TYR P 134 ARG 0.004 0.000 ARG O 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1172 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1039 time to evaluate : 4.270 Fit side-chains REVERT: A 42 ASP cc_start: 0.9089 (p0) cc_final: 0.8751 (p0) REVERT: A 68 LYS cc_start: 0.8792 (mtpp) cc_final: 0.8338 (ttpp) REVERT: B 41 ASP cc_start: 0.8881 (p0) cc_final: 0.8183 (p0) REVERT: B 42 ASP cc_start: 0.9015 (p0) cc_final: 0.8730 (p0) REVERT: B 68 LYS cc_start: 0.8774 (mtpp) cc_final: 0.8316 (ttpp) REVERT: C 76 ARG cc_start: 0.9215 (mmt-90) cc_final: 0.8785 (mpt180) REVERT: D 68 LYS cc_start: 0.8779 (mtpp) cc_final: 0.8379 (ttpp) REVERT: E 42 ASP cc_start: 0.9079 (p0) cc_final: 0.8785 (p0) REVERT: E 68 LYS cc_start: 0.8717 (mtpp) cc_final: 0.8301 (ttpp) REVERT: F 42 ASP cc_start: 0.9104 (p0) cc_final: 0.8807 (p0) REVERT: F 46 LYS cc_start: 0.8611 (ttpp) cc_final: 0.8357 (ttmm) REVERT: F 68 LYS cc_start: 0.8810 (mtpp) cc_final: 0.8354 (ttpp) REVERT: F 76 ARG cc_start: 0.9233 (mmt-90) cc_final: 0.8938 (mpt180) REVERT: G 41 ASP cc_start: 0.8907 (p0) cc_final: 0.8178 (p0) REVERT: G 42 ASP cc_start: 0.9047 (p0) cc_final: 0.8737 (p0) REVERT: G 68 LYS cc_start: 0.8769 (mtpp) cc_final: 0.8348 (ttpp) REVERT: H 42 ASP cc_start: 0.9062 (p0) cc_final: 0.8738 (p0) REVERT: H 68 LYS cc_start: 0.8744 (mtpp) cc_final: 0.8283 (ttpp) REVERT: H 76 ARG cc_start: 0.9160 (mmt-90) cc_final: 0.8800 (mpt180) REVERT: I 42 ASP cc_start: 0.9139 (p0) cc_final: 0.8896 (p0) REVERT: I 68 LYS cc_start: 0.8804 (mtpp) cc_final: 0.8305 (ttpp) REVERT: I 76 ARG cc_start: 0.9169 (mmt-90) cc_final: 0.8771 (mpt180) REVERT: J 68 LYS cc_start: 0.8839 (mtpp) cc_final: 0.8335 (ttpp) REVERT: K 42 ASP cc_start: 0.9152 (p0) cc_final: 0.8789 (p0) REVERT: K 61 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8219 (pt0) REVERT: K 68 LYS cc_start: 0.8803 (mtpp) cc_final: 0.8312 (ttpp) REVERT: K 76 ARG cc_start: 0.9009 (mmt-90) cc_final: 0.8582 (mpt180) REVERT: L 41 ASP cc_start: 0.8702 (p0) cc_final: 0.8029 (p0) REVERT: L 68 LYS cc_start: 0.8811 (mtpp) cc_final: 0.8360 (ttpp) REVERT: L 76 ARG cc_start: 0.9115 (mmt-90) cc_final: 0.8633 (mpt180) REVERT: M 42 ASP cc_start: 0.9101 (p0) cc_final: 0.8837 (p0) REVERT: M 46 LYS cc_start: 0.8668 (ttpp) cc_final: 0.8332 (ttmm) REVERT: M 61 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8187 (pt0) REVERT: M 68 LYS cc_start: 0.8763 (mtpp) cc_final: 0.8287 (ttpp) REVERT: M 76 ARG cc_start: 0.9209 (mmt-90) cc_final: 0.8864 (mpt180) REVERT: N 68 LYS cc_start: 0.8757 (mtpp) cc_final: 0.8300 (ttpp) REVERT: N 76 ARG cc_start: 0.9190 (mmt-90) cc_final: 0.8858 (mpt180) REVERT: N 89 ASP cc_start: 0.8633 (t70) cc_final: 0.8276 (p0) REVERT: O 68 LYS cc_start: 0.8856 (mtpp) cc_final: 0.8424 (ttpp) REVERT: P 41 ASP cc_start: 0.8875 (p0) cc_final: 0.8104 (p0) REVERT: P 42 ASP cc_start: 0.9007 (p0) cc_final: 0.8738 (p0) REVERT: P 68 LYS cc_start: 0.8642 (mtpp) cc_final: 0.8315 (ttpp) REVERT: P 76 ARG cc_start: 0.9203 (mmt-90) cc_final: 0.8983 (mmt-90) REVERT: Q 42 ASP cc_start: 0.9023 (p0) cc_final: 0.8722 (p0) REVERT: Q 68 LYS cc_start: 0.8779 (mtpp) cc_final: 0.8347 (ttpp) REVERT: R 68 LYS cc_start: 0.8765 (mtpp) cc_final: 0.8317 (ttpp) REVERT: R 76 ARG cc_start: 0.9167 (mmt-90) cc_final: 0.8919 (mmt-90) REVERT: S 42 ASP cc_start: 0.9107 (p0) cc_final: 0.8770 (p0) REVERT: S 68 LYS cc_start: 0.8775 (mtpp) cc_final: 0.8290 (ttpp) REVERT: S 76 ARG cc_start: 0.9018 (mmt-90) cc_final: 0.8657 (mmt-90) REVERT: T 41 ASP cc_start: 0.8835 (OUTLIER) cc_final: 0.8191 (p0) REVERT: T 68 LYS cc_start: 0.8746 (mtpp) cc_final: 0.8281 (ttpp) REVERT: U 42 ASP cc_start: 0.9103 (p0) cc_final: 0.8783 (p0) REVERT: U 46 LYS cc_start: 0.8750 (ttpp) cc_final: 0.8375 (ttmm) REVERT: U 68 LYS cc_start: 0.8734 (mtpp) cc_final: 0.8268 (ttpp) REVERT: U 76 ARG cc_start: 0.9177 (mmt-90) cc_final: 0.8799 (mpt180) REVERT: V 68 LYS cc_start: 0.8805 (mtpp) cc_final: 0.8348 (ttpp) REVERT: W 41 ASP cc_start: 0.8908 (p0) cc_final: 0.8156 (p0) REVERT: W 42 ASP cc_start: 0.9036 (p0) cc_final: 0.8691 (p0) REVERT: W 68 LYS cc_start: 0.8785 (mtpp) cc_final: 0.8332 (ttpp) REVERT: X 42 ASP cc_start: 0.9097 (p0) cc_final: 0.8762 (p0) REVERT: X 68 LYS cc_start: 0.8761 (mtpp) cc_final: 0.8309 (ttpp) outliers start: 133 outliers final: 53 residues processed: 1080 average time/residue: 1.2891 time to fit residues: 1648.0647 Evaluate side-chains 984 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 930 time to evaluate : 4.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 174 HIS Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 106 SER Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain J residue 81 ASP Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 159 GLU Chi-restraints excluded: chain J residue 174 HIS Chi-restraints excluded: chain K residue 174 HIS Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain M residue 81 ASP Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain O residue 81 ASP Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 81 ASP Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain S residue 61 GLU Chi-restraints excluded: chain S residue 86 ASP Chi-restraints excluded: chain S residue 119 THR Chi-restraints excluded: chain S residue 174 HIS Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 61 GLU Chi-restraints excluded: chain T residue 81 ASP Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain U residue 81 ASP Chi-restraints excluded: chain U residue 119 THR Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain V residue 81 ASP Chi-restraints excluded: chain V residue 119 THR Chi-restraints excluded: chain W residue 81 ASP Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain X residue 81 ASP Chi-restraints excluded: chain X residue 119 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 517 optimal weight: 6.9990 chunk 393 optimal weight: 9.9990 chunk 271 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 250 optimal weight: 1.9990 chunk 351 optimal weight: 1.9990 chunk 525 optimal weight: 50.0000 chunk 556 optimal weight: 7.9990 chunk 274 optimal weight: 2.9990 chunk 498 optimal weight: 50.0000 chunk 150 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 95 ASN A 102 HIS B 102 HIS C 102 HIS D 8 ASN D 102 HIS E 138 GLN F 8 ASN F 102 HIS G 8 ASN G 95 ASN G 102 HIS H 95 ASN H 102 HIS I 8 ASN I 10 HIS I 62 HIS I 102 HIS J 102 HIS ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 10 HIS K 95 ASN L 8 ASN L 55 GLN L 102 HIS M 22 ASN ** M 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 HIS N 102 HIS O 8 ASN P 8 ASN P 102 HIS Q 95 ASN Q 102 HIS S 95 ASN S 102 HIS S 138 GLN T 102 HIS V 8 ASN V 102 HIS W 102 HIS ** W 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 8 ASN X 95 ASN X 102 HIS Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 36312 Z= 0.300 Angle : 0.565 7.195 49104 Z= 0.307 Chirality : 0.041 0.128 5112 Planarity : 0.003 0.035 6480 Dihedral : 13.088 179.985 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.41 % Allowed : 1.45 % Favored : 98.13 % Rotamer: Outliers : 3.73 % Allowed : 24.20 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 4.06 (0.12), residues: 4320 helix: 3.44 (0.08), residues: 3432 sheet: None (None), residues: 0 loop : -0.66 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Q 90 HIS 0.007 0.001 HIS L 102 PHE 0.019 0.002 PHE B 38 TYR 0.018 0.002 TYR P 134 ARG 0.003 0.000 ARG K 76 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1063 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 948 time to evaluate : 3.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.9051 (p0) cc_final: 0.8730 (p0) REVERT: A 68 LYS cc_start: 0.8808 (mtpp) cc_final: 0.8407 (ttpp) REVERT: B 41 ASP cc_start: 0.8923 (p0) cc_final: 0.8198 (p0) REVERT: B 42 ASP cc_start: 0.9018 (p0) cc_final: 0.8736 (p0) REVERT: B 68 LYS cc_start: 0.8800 (mtpp) cc_final: 0.8378 (ttpp) REVERT: C 46 LYS cc_start: 0.8736 (ttpp) cc_final: 0.8435 (ttmm) REVERT: C 68 LYS cc_start: 0.8831 (mtpp) cc_final: 0.8391 (ttpp) REVERT: D 42 ASP cc_start: 0.9023 (p0) cc_final: 0.8781 (p0) REVERT: D 46 LYS cc_start: 0.8729 (ttpp) cc_final: 0.8412 (ttmm) REVERT: D 68 LYS cc_start: 0.8796 (mtpp) cc_final: 0.8388 (ttpp) REVERT: E 42 ASP cc_start: 0.9039 (p0) cc_final: 0.8799 (p0) REVERT: E 68 LYS cc_start: 0.8734 (mtpp) cc_final: 0.8349 (ttpp) REVERT: F 42 ASP cc_start: 0.9098 (p0) cc_final: 0.8813 (p0) REVERT: F 46 LYS cc_start: 0.8649 (ttpp) cc_final: 0.8406 (ttmm) REVERT: F 68 LYS cc_start: 0.8829 (mtpp) cc_final: 0.8386 (ttpp) REVERT: G 42 ASP cc_start: 0.9034 (p0) cc_final: 0.8773 (p0) REVERT: G 46 LYS cc_start: 0.8734 (ttpp) cc_final: 0.8413 (ttmm) REVERT: G 68 LYS cc_start: 0.8798 (mtpp) cc_final: 0.8375 (ttpp) REVERT: H 68 LYS cc_start: 0.8752 (mtpp) cc_final: 0.8360 (ttpp) REVERT: I 42 ASP cc_start: 0.9065 (p0) cc_final: 0.8832 (p0) REVERT: I 68 LYS cc_start: 0.8809 (mtpp) cc_final: 0.8381 (ttpp) REVERT: I 76 ARG cc_start: 0.9181 (mmt-90) cc_final: 0.8781 (mpt180) REVERT: J 68 LYS cc_start: 0.8842 (mtpp) cc_final: 0.8356 (ttpp) REVERT: K 42 ASP cc_start: 0.9067 (p0) cc_final: 0.8728 (p0) REVERT: K 46 LYS cc_start: 0.8748 (ttpp) cc_final: 0.8422 (ttmm) REVERT: K 68 LYS cc_start: 0.8799 (mtpp) cc_final: 0.8374 (ttpp) REVERT: K 76 ARG cc_start: 0.9069 (mmt-90) cc_final: 0.8650 (mpt180) REVERT: L 41 ASP cc_start: 0.8756 (p0) cc_final: 0.8116 (p0) REVERT: L 68 LYS cc_start: 0.8808 (mtpp) cc_final: 0.8381 (ttpp) REVERT: L 76 ARG cc_start: 0.9155 (mmt-90) cc_final: 0.8954 (mmt-90) REVERT: M 42 ASP cc_start: 0.9027 (p0) cc_final: 0.8670 (p0) REVERT: M 46 LYS cc_start: 0.8715 (ttpp) cc_final: 0.8330 (ttmm) REVERT: M 68 LYS cc_start: 0.8772 (mtpp) cc_final: 0.8316 (ttpp) REVERT: M 76 ARG cc_start: 0.9218 (mmt-90) cc_final: 0.8826 (mpt180) REVERT: N 68 LYS cc_start: 0.8802 (mtpp) cc_final: 0.8393 (ttpp) REVERT: N 76 ARG cc_start: 0.9156 (mmt-90) cc_final: 0.8770 (mpt180) REVERT: O 42 ASP cc_start: 0.9151 (p0) cc_final: 0.8884 (p0) REVERT: O 68 LYS cc_start: 0.8871 (mtpp) cc_final: 0.8442 (ttpp) REVERT: P 42 ASP cc_start: 0.9001 (p0) cc_final: 0.8752 (p0) REVERT: P 68 LYS cc_start: 0.8702 (mtpp) cc_final: 0.8440 (ttpp) REVERT: P 76 ARG cc_start: 0.9183 (mmt-90) cc_final: 0.8970 (mmt-90) REVERT: Q 42 ASP cc_start: 0.9013 (p0) cc_final: 0.8766 (p0) REVERT: Q 68 LYS cc_start: 0.8783 (mtpp) cc_final: 0.8372 (ttpp) REVERT: R 68 LYS cc_start: 0.8797 (mtpp) cc_final: 0.8380 (ttpp) REVERT: S 42 ASP cc_start: 0.9077 (p0) cc_final: 0.8686 (p0) REVERT: S 46 LYS cc_start: 0.8701 (ttpp) cc_final: 0.8451 (ttmm) REVERT: S 68 LYS cc_start: 0.8818 (mtpp) cc_final: 0.8330 (ttpp) REVERT: S 76 ARG cc_start: 0.9075 (mmt-90) cc_final: 0.8739 (mmt-90) REVERT: T 68 LYS cc_start: 0.8788 (mtpp) cc_final: 0.8360 (ttpp) REVERT: T 76 ARG cc_start: 0.9218 (mmt-90) cc_final: 0.8696 (mpt180) REVERT: U 42 ASP cc_start: 0.9041 (p0) cc_final: 0.8713 (p0) REVERT: U 46 LYS cc_start: 0.8803 (ttpp) cc_final: 0.8399 (ttmm) REVERT: U 68 LYS cc_start: 0.8745 (mtpp) cc_final: 0.8298 (ttpp) REVERT: U 76 ARG cc_start: 0.9178 (mmt-90) cc_final: 0.8797 (mpt180) REVERT: V 68 LYS cc_start: 0.8770 (mtpp) cc_final: 0.8320 (ttpp) REVERT: W 42 ASP cc_start: 0.9016 (p0) cc_final: 0.8701 (p0) REVERT: W 68 LYS cc_start: 0.8760 (mtpp) cc_final: 0.8320 (ttpp) REVERT: X 42 ASP cc_start: 0.9050 (p0) cc_final: 0.8728 (p0) REVERT: X 68 LYS cc_start: 0.8783 (mtpp) cc_final: 0.8376 (ttpp) outliers start: 115 outliers final: 68 residues processed: 997 average time/residue: 1.7022 time to fit residues: 2010.9104 Evaluate side-chains 978 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 910 time to evaluate : 4.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 174 HIS Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 174 HIS Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain J residue 81 ASP Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 159 GLU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain J residue 174 HIS Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 174 HIS Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 67 MET Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 81 ASP Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain N residue 41 ASP Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain O residue 41 ASP Chi-restraints excluded: chain O residue 81 ASP Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 81 ASP Chi-restraints excluded: chain Q residue 86 ASP Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain S residue 81 ASP Chi-restraints excluded: chain S residue 119 THR Chi-restraints excluded: chain S residue 174 HIS Chi-restraints excluded: chain T residue 61 GLU Chi-restraints excluded: chain T residue 81 ASP Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain T residue 174 HIS Chi-restraints excluded: chain U residue 81 ASP Chi-restraints excluded: chain U residue 119 THR Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain V residue 119 THR Chi-restraints excluded: chain W residue 81 ASP Chi-restraints excluded: chain W residue 86 ASP Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain X residue 81 ASP Chi-restraints excluded: chain X residue 119 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 463 optimal weight: 1.9990 chunk 316 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 414 optimal weight: 5.9990 chunk 229 optimal weight: 2.9990 chunk 475 optimal weight: 50.0000 chunk 384 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 284 optimal weight: 50.0000 chunk 499 optimal weight: 50.0000 chunk 140 optimal weight: 50.0000 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 102 HIS B 102 HIS C 102 HIS D 8 ASN D 102 HIS F 8 ASN F 102 HIS G 8 ASN G 102 HIS H 8 ASN H 102 HIS I 8 ASN I 62 HIS I 102 HIS J 102 HIS ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 8 ASN L 8 ASN L 102 HIS M 95 ASN M 138 GLN N 62 HIS N 102 HIS O 8 ASN O 102 HIS P 102 HIS Q 102 HIS S 102 HIS T 8 ASN T 102 HIS U 55 GLN V 8 ASN V 102 HIS W 102 HIS W 138 GLN X 102 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 36312 Z= 0.243 Angle : 0.517 6.497 49104 Z= 0.282 Chirality : 0.038 0.123 5112 Planarity : 0.003 0.034 6480 Dihedral : 13.050 180.000 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.39 % Allowed : 1.48 % Favored : 98.13 % Rotamer: Outliers : 3.91 % Allowed : 24.79 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 4.66 (0.12), residues: 4320 helix: 3.87 (0.08), residues: 3432 sheet: None (None), residues: 0 loop : -0.48 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q 90 HIS 0.006 0.001 HIS Q 102 PHE 0.016 0.002 PHE B 38 TYR 0.016 0.001 TYR P 134 ARG 0.002 0.000 ARG K 76 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1109 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 986 time to evaluate : 4.250 Fit side-chains revert: symmetry clash REVERT: A 42 ASP cc_start: 0.8961 (p0) cc_final: 0.8662 (p0) REVERT: A 46 LYS cc_start: 0.8651 (ttpp) cc_final: 0.8378 (ttmm) REVERT: A 68 LYS cc_start: 0.8732 (mtpp) cc_final: 0.8351 (ttpp) REVERT: B 41 ASP cc_start: 0.8858 (p0) cc_final: 0.8149 (p0) REVERT: B 42 ASP cc_start: 0.8952 (p0) cc_final: 0.8691 (p0) REVERT: B 68 LYS cc_start: 0.8700 (mtpp) cc_final: 0.8286 (ttpp) REVERT: C 46 LYS cc_start: 0.8639 (ttpp) cc_final: 0.8345 (ttmm) REVERT: C 68 LYS cc_start: 0.8747 (mtpp) cc_final: 0.8331 (ttpp) REVERT: D 42 ASP cc_start: 0.8958 (p0) cc_final: 0.8724 (p0) REVERT: D 46 LYS cc_start: 0.8685 (ttpp) cc_final: 0.8354 (ttmm) REVERT: D 68 LYS cc_start: 0.8702 (mtpp) cc_final: 0.8336 (ttpp) REVERT: E 42 ASP cc_start: 0.8956 (p0) cc_final: 0.8728 (p0) REVERT: E 46 LYS cc_start: 0.8649 (ttpp) cc_final: 0.8381 (ttmm) REVERT: E 68 LYS cc_start: 0.8686 (mtpp) cc_final: 0.8315 (ttpp) REVERT: F 41 ASP cc_start: 0.8872 (OUTLIER) cc_final: 0.8150 (p0) REVERT: F 42 ASP cc_start: 0.8970 (p0) cc_final: 0.8684 (p0) REVERT: F 46 LYS cc_start: 0.8583 (ttpp) cc_final: 0.8318 (ttmm) REVERT: F 68 LYS cc_start: 0.8758 (mtpp) cc_final: 0.8356 (ttpp) REVERT: G 42 ASP cc_start: 0.8914 (p0) cc_final: 0.8680 (p0) REVERT: G 46 LYS cc_start: 0.8677 (ttpp) cc_final: 0.8352 (ttmm) REVERT: G 68 LYS cc_start: 0.8697 (mtpp) cc_final: 0.8295 (ttpp) REVERT: H 42 ASP cc_start: 0.8946 (p0) cc_final: 0.8601 (p0) REVERT: H 68 LYS cc_start: 0.8644 (mtpp) cc_final: 0.8290 (ttpp) REVERT: I 41 ASP cc_start: 0.8862 (OUTLIER) cc_final: 0.8151 (p0) REVERT: I 42 ASP cc_start: 0.8970 (p0) cc_final: 0.8710 (p0) REVERT: I 46 LYS cc_start: 0.8758 (ttpp) cc_final: 0.8351 (ttmm) REVERT: I 68 LYS cc_start: 0.8717 (mtpp) cc_final: 0.8295 (ttpp) REVERT: I 76 ARG cc_start: 0.9179 (mmt-90) cc_final: 0.8703 (mmt180) REVERT: J 68 LYS cc_start: 0.8758 (mtpp) cc_final: 0.8303 (ttpp) REVERT: K 41 ASP cc_start: 0.8917 (OUTLIER) cc_final: 0.8187 (p0) REVERT: K 42 ASP cc_start: 0.8976 (p0) cc_final: 0.8657 (p0) REVERT: K 46 LYS cc_start: 0.8662 (ttpp) cc_final: 0.8345 (ttmm) REVERT: K 68 LYS cc_start: 0.8718 (mtpp) cc_final: 0.8337 (ttpp) REVERT: K 76 ARG cc_start: 0.9102 (mmt-90) cc_final: 0.8710 (mpt180) REVERT: L 41 ASP cc_start: 0.8735 (p0) cc_final: 0.8031 (p0) REVERT: L 46 LYS cc_start: 0.8649 (ttpp) cc_final: 0.8377 (ttmm) REVERT: L 68 LYS cc_start: 0.8811 (mtpp) cc_final: 0.8359 (ttpp) REVERT: L 76 ARG cc_start: 0.9161 (mmt-90) cc_final: 0.8960 (mmt-90) REVERT: M 42 ASP cc_start: 0.8937 (p0) cc_final: 0.8583 (p0) REVERT: M 46 LYS cc_start: 0.8646 (ttpp) cc_final: 0.8304 (ttmm) REVERT: M 68 LYS cc_start: 0.8727 (mtpp) cc_final: 0.8293 (ttpp) REVERT: M 76 ARG cc_start: 0.9222 (mmt-90) cc_final: 0.8758 (mmt180) REVERT: N 46 LYS cc_start: 0.8706 (ttpp) cc_final: 0.8398 (ttmm) REVERT: N 68 LYS cc_start: 0.8692 (mtpp) cc_final: 0.8289 (ttpp) REVERT: N 76 ARG cc_start: 0.9155 (mmt-90) cc_final: 0.8779 (mpt180) REVERT: O 42 ASP cc_start: 0.8997 (p0) cc_final: 0.8756 (p0) REVERT: O 68 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8406 (ttpp) REVERT: O 76 ARG cc_start: 0.9155 (mmt-90) cc_final: 0.8813 (mpt180) REVERT: P 41 ASP cc_start: 0.8901 (p0) cc_final: 0.8170 (p0) REVERT: P 46 LYS cc_start: 0.8710 (ttpp) cc_final: 0.8336 (ttmm) REVERT: P 68 LYS cc_start: 0.8606 (mtpp) cc_final: 0.8391 (ttpp) REVERT: Q 42 ASP cc_start: 0.8915 (p0) cc_final: 0.8706 (p0) REVERT: Q 46 LYS cc_start: 0.8647 (ttpp) cc_final: 0.8348 (ttmm) REVERT: Q 68 LYS cc_start: 0.8685 (mtpp) cc_final: 0.8285 (ttpp) REVERT: R 68 LYS cc_start: 0.8705 (mtpp) cc_final: 0.8324 (ttpp) REVERT: S 42 ASP cc_start: 0.8981 (p0) cc_final: 0.8596 (p0) REVERT: S 46 LYS cc_start: 0.8636 (ttpp) cc_final: 0.8387 (ttmm) REVERT: S 68 LYS cc_start: 0.8748 (mtpp) cc_final: 0.8286 (ttpp) REVERT: S 76 ARG cc_start: 0.9102 (mmt-90) cc_final: 0.8733 (mmt-90) REVERT: T 41 ASP cc_start: 0.8826 (OUTLIER) cc_final: 0.8160 (p0) REVERT: T 68 LYS cc_start: 0.8731 (mtpp) cc_final: 0.8328 (ttpp) REVERT: T 76 ARG cc_start: 0.9212 (mmt-90) cc_final: 0.8685 (mpt180) REVERT: T 83 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8865 (mmtt) REVERT: U 42 ASP cc_start: 0.8945 (p0) cc_final: 0.8649 (p0) REVERT: U 46 LYS cc_start: 0.8688 (ttpp) cc_final: 0.8290 (ttmm) REVERT: U 68 LYS cc_start: 0.8685 (mtpp) cc_final: 0.8271 (ttpp) REVERT: U 76 ARG cc_start: 0.9179 (mmt-90) cc_final: 0.8764 (mpt180) REVERT: V 41 ASP cc_start: 0.8869 (OUTLIER) cc_final: 0.8225 (p0) REVERT: V 46 LYS cc_start: 0.8696 (ttpp) cc_final: 0.8368 (ttmm) REVERT: V 68 LYS cc_start: 0.8740 (mtpp) cc_final: 0.8325 (ttpp) REVERT: W 42 ASP cc_start: 0.8931 (p0) cc_final: 0.8651 (p0) REVERT: W 46 LYS cc_start: 0.8614 (ttpp) cc_final: 0.8349 (ttmm) REVERT: W 68 LYS cc_start: 0.8727 (mtpp) cc_final: 0.8323 (ttpp) REVERT: W 141 SER cc_start: 0.9087 (m) cc_final: 0.8886 (m) REVERT: X 42 ASP cc_start: 0.8953 (p0) cc_final: 0.8665 (p0) REVERT: X 46 LYS cc_start: 0.8640 (ttpp) cc_final: 0.8375 (ttmm) REVERT: X 68 LYS cc_start: 0.8696 (mtpp) cc_final: 0.8325 (ttpp) outliers start: 123 outliers final: 68 residues processed: 1044 average time/residue: 1.3202 time to fit residues: 1628.2294 Evaluate side-chains 1003 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 928 time to evaluate : 2.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 174 HIS Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 81 ASP Chi-restraints excluded: chain J residue 86 ASP Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 159 GLU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain J residue 174 HIS Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 174 HIS Chi-restraints excluded: chain L residue 67 MET Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain M residue 81 ASP Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 159 GLU Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain O residue 86 ASP Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 81 ASP Chi-restraints excluded: chain Q residue 86 ASP Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain R residue 81 ASP Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 174 HIS Chi-restraints excluded: chain S residue 61 GLU Chi-restraints excluded: chain S residue 81 ASP Chi-restraints excluded: chain S residue 119 THR Chi-restraints excluded: chain S residue 174 HIS Chi-restraints excluded: chain T residue 41 ASP Chi-restraints excluded: chain T residue 81 ASP Chi-restraints excluded: chain T residue 83 LYS Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain T residue 174 HIS Chi-restraints excluded: chain U residue 81 ASP Chi-restraints excluded: chain U residue 119 THR Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain V residue 81 ASP Chi-restraints excluded: chain V residue 119 THR Chi-restraints excluded: chain W residue 81 ASP Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain X residue 61 GLU Chi-restraints excluded: chain X residue 81 ASP Chi-restraints excluded: chain X residue 119 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 187 optimal weight: 50.0000 chunk 501 optimal weight: 50.0000 chunk 110 optimal weight: 1.9990 chunk 326 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 chunk 557 optimal weight: 3.9990 chunk 462 optimal weight: 2.9990 chunk 258 optimal weight: 50.0000 chunk 46 optimal weight: 50.0000 chunk 184 optimal weight: 7.9990 chunk 292 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 102 HIS B 55 GLN B 102 HIS C 55 GLN C 102 HIS D 8 ASN D 102 HIS E 102 HIS F 8 ASN F 102 HIS G 8 ASN G 102 HIS H 8 ASN H 55 GLN H 102 HIS I 8 ASN I 62 HIS I 102 HIS J 95 ASN J 102 HIS J 138 GLN K 8 ASN L 8 ASN L 102 HIS M 8 ASN N 62 HIS N 102 HIS O 8 ASN O 102 HIS P 8 ASN P 95 ASN P 102 HIS Q 102 HIS R 55 GLN S 8 ASN S 102 HIS T 8 ASN T 95 ASN T 102 HIS U 8 ASN V 8 ASN V 102 HIS W 102 HIS X 8 ASN X 55 GLN X 102 HIS Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 36312 Z= 0.419 Angle : 0.603 6.758 49104 Z= 0.327 Chirality : 0.043 0.141 5112 Planarity : 0.004 0.035 6480 Dihedral : 13.006 179.556 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.39 % Allowed : 1.55 % Favored : 98.06 % Rotamer: Outliers : 4.84 % Allowed : 23.69 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 4.32 (0.12), residues: 4320 helix: 3.61 (0.08), residues: 3432 sheet: None (None), residues: 0 loop : -0.47 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 90 HIS 0.008 0.001 HIS N 170 PHE 0.021 0.003 PHE B 38 TYR 0.018 0.002 TYR P 134 ARG 0.004 0.001 ARG K 76 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1105 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 949 time to evaluate : 4.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.9155 (p0) cc_final: 0.8788 (p0) REVERT: A 68 LYS cc_start: 0.8905 (mtpp) cc_final: 0.8485 (ttpp) REVERT: B 42 ASP cc_start: 0.9104 (p0) cc_final: 0.8793 (p0) REVERT: B 68 LYS cc_start: 0.8889 (mtpp) cc_final: 0.8454 (ttpp) REVERT: B 138 GLN cc_start: 0.9220 (tp40) cc_final: 0.8907 (mm-40) REVERT: C 46 LYS cc_start: 0.8782 (ttpp) cc_final: 0.8441 (ttmm) REVERT: C 68 LYS cc_start: 0.8897 (mtpp) cc_final: 0.8474 (ttpp) REVERT: D 42 ASP cc_start: 0.9079 (p0) cc_final: 0.8797 (p0) REVERT: D 46 LYS cc_start: 0.8785 (ttpp) cc_final: 0.8497 (ttmm) REVERT: D 68 LYS cc_start: 0.8848 (mtpp) cc_final: 0.8448 (ttpp) REVERT: E 42 ASP cc_start: 0.9152 (p0) cc_final: 0.8871 (p0) REVERT: E 68 LYS cc_start: 0.8856 (mtpp) cc_final: 0.8434 (ttpp) REVERT: F 42 ASP cc_start: 0.9132 (p0) cc_final: 0.8789 (p0) REVERT: F 46 LYS cc_start: 0.8738 (ttpp) cc_final: 0.8482 (ttmm) REVERT: F 68 LYS cc_start: 0.8862 (mtpp) cc_final: 0.8412 (ttpp) REVERT: G 42 ASP cc_start: 0.9133 (p0) cc_final: 0.8836 (p0) REVERT: G 46 LYS cc_start: 0.8787 (ttpp) cc_final: 0.8467 (ttmm) REVERT: G 68 LYS cc_start: 0.8836 (mtpp) cc_final: 0.8404 (ttpp) REVERT: H 42 ASP cc_start: 0.9164 (p0) cc_final: 0.8790 (p0) REVERT: H 68 LYS cc_start: 0.8835 (mtpp) cc_final: 0.8447 (ttpp) REVERT: I 42 ASP cc_start: 0.9178 (p0) cc_final: 0.8883 (p0) REVERT: I 68 LYS cc_start: 0.8880 (mtpp) cc_final: 0.8442 (ttpp) REVERT: I 76 ARG cc_start: 0.9196 (mmt-90) cc_final: 0.8703 (mmt180) REVERT: J 42 ASP cc_start: 0.9143 (p0) cc_final: 0.8828 (p0) REVERT: J 68 LYS cc_start: 0.8869 (mtpp) cc_final: 0.8413 (ttpp) REVERT: K 42 ASP cc_start: 0.9158 (p0) cc_final: 0.8801 (p0) REVERT: K 46 LYS cc_start: 0.8794 (ttpp) cc_final: 0.8456 (ttmm) REVERT: K 68 LYS cc_start: 0.8888 (mtpp) cc_final: 0.8447 (ttpp) REVERT: K 76 ARG cc_start: 0.9113 (mmt-90) cc_final: 0.8748 (mpt180) REVERT: L 68 LYS cc_start: 0.8905 (mtpp) cc_final: 0.8465 (ttpp) REVERT: M 42 ASP cc_start: 0.9107 (p0) cc_final: 0.8720 (p0) REVERT: M 46 LYS cc_start: 0.8748 (ttpp) cc_final: 0.8370 (ttmm) REVERT: M 68 LYS cc_start: 0.8842 (mtpp) cc_final: 0.8392 (ttpp) REVERT: M 76 ARG cc_start: 0.9187 (mmt-90) cc_final: 0.8716 (mmt180) REVERT: N 42 ASP cc_start: 0.9190 (p0) cc_final: 0.8895 (p0) REVERT: N 68 LYS cc_start: 0.8891 (mtpp) cc_final: 0.8467 (ttpp) REVERT: N 76 ARG cc_start: 0.9143 (mmt-90) cc_final: 0.8777 (mpt180) REVERT: O 42 ASP cc_start: 0.9150 (p0) cc_final: 0.8821 (p0) REVERT: O 68 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8467 (ttpp) REVERT: P 42 ASP cc_start: 0.9107 (p0) cc_final: 0.8831 (p0) REVERT: P 68 LYS cc_start: 0.8794 (mtpp) cc_final: 0.8443 (ttpp) REVERT: Q 42 ASP cc_start: 0.9066 (p0) cc_final: 0.8779 (p0) REVERT: Q 68 LYS cc_start: 0.8824 (mtpp) cc_final: 0.8425 (ttpp) REVERT: R 68 LYS cc_start: 0.8824 (mtpp) cc_final: 0.8423 (ttpp) REVERT: S 42 ASP cc_start: 0.9177 (p0) cc_final: 0.8736 (p0) REVERT: S 46 LYS cc_start: 0.8757 (ttpp) cc_final: 0.8524 (ttmm) REVERT: S 68 LYS cc_start: 0.8851 (mtpp) cc_final: 0.8386 (ttpp) REVERT: S 76 ARG cc_start: 0.9115 (mmt-90) cc_final: 0.8759 (mpt180) REVERT: T 68 LYS cc_start: 0.8830 (mtpp) cc_final: 0.8423 (ttpp) REVERT: T 76 ARG cc_start: 0.9198 (mmt-90) cc_final: 0.8708 (mpt180) REVERT: U 42 ASP cc_start: 0.9169 (p0) cc_final: 0.8793 (p0) REVERT: U 46 LYS cc_start: 0.8866 (ttpp) cc_final: 0.8463 (ttmm) REVERT: U 68 LYS cc_start: 0.8802 (mtpp) cc_final: 0.8383 (ttpp) REVERT: U 76 ARG cc_start: 0.9192 (mmt-90) cc_final: 0.8693 (mmt180) REVERT: V 42 ASP cc_start: 0.9186 (p0) cc_final: 0.8887 (p0) REVERT: V 68 LYS cc_start: 0.8889 (mtpp) cc_final: 0.8425 (ttpp) REVERT: W 42 ASP cc_start: 0.9128 (p0) cc_final: 0.8775 (p0) REVERT: W 68 LYS cc_start: 0.8831 (mtpp) cc_final: 0.8392 (ttpp) REVERT: X 42 ASP cc_start: 0.9159 (p0) cc_final: 0.8789 (p0) REVERT: X 68 LYS cc_start: 0.8834 (mtpp) cc_final: 0.8445 (ttpp) outliers start: 156 outliers final: 75 residues processed: 991 average time/residue: 1.6719 time to fit residues: 1966.0165 Evaluate side-chains 1015 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 939 time to evaluate : 3.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 174 HIS Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain D residue 174 HIS Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 174 HIS Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 116 LYS Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain J residue 174 HIS Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 116 LYS Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 174 HIS Chi-restraints excluded: chain L residue 67 MET Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 110 SER Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain M residue 81 ASP Chi-restraints excluded: chain M residue 116 LYS Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain N residue 41 ASP Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 58 GLU Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 174 HIS Chi-restraints excluded: chain S residue 81 ASP Chi-restraints excluded: chain S residue 119 THR Chi-restraints excluded: chain S residue 174 HIS Chi-restraints excluded: chain T residue 81 ASP Chi-restraints excluded: chain T residue 116 LYS Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain T residue 164 GLU Chi-restraints excluded: chain T residue 174 HIS Chi-restraints excluded: chain U residue 81 ASP Chi-restraints excluded: chain U residue 119 THR Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain V residue 81 ASP Chi-restraints excluded: chain V residue 119 THR Chi-restraints excluded: chain W residue 81 ASP Chi-restraints excluded: chain W residue 86 ASP Chi-restraints excluded: chain W residue 87 ARG Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain X residue 81 ASP Chi-restraints excluded: chain X residue 119 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 537 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 317 optimal weight: 1.9990 chunk 406 optimal weight: 50.0000 chunk 315 optimal weight: 0.8980 chunk 469 optimal weight: 2.9990 chunk 311 optimal weight: 50.0000 chunk 555 optimal weight: 4.9990 chunk 347 optimal weight: 0.9990 chunk 338 optimal weight: 0.9980 chunk 256 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 102 HIS B 102 HIS C 102 HIS D 102 HIS E 102 HIS F 8 ASN F 102 HIS G 8 ASN G 102 HIS H 102 HIS I 95 ASN I 102 HIS J 102 HIS L 8 ASN L 102 HIS N 8 ASN N 102 HIS O 8 ASN O 102 HIS P 102 HIS Q 102 HIS R 102 HIS S 8 ASN S 102 HIS T 102 HIS V 8 ASN V 102 HIS W 102 HIS X 8 ASN X 102 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 36312 Z= 0.149 Angle : 0.455 5.565 49104 Z= 0.253 Chirality : 0.036 0.115 5112 Planarity : 0.003 0.036 6480 Dihedral : 12.953 179.557 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.39 % Allowed : 1.48 % Favored : 98.13 % Rotamer: Outliers : 3.14 % Allowed : 25.72 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 5.24 (0.12), residues: 4320 helix: 4.29 (0.08), residues: 3432 sheet: None (None), residues: 0 loop : -0.35 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 90 HIS 0.006 0.001 HIS C 102 PHE 0.013 0.002 PHE E 38 TYR 0.018 0.001 TYR I 37 ARG 0.001 0.000 ARG Q 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1030 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 940 time to evaluate : 4.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8635 (p0) cc_final: 0.7847 (p0) REVERT: A 42 ASP cc_start: 0.8682 (p0) cc_final: 0.8418 (p0) REVERT: A 46 LYS cc_start: 0.8351 (ttpp) cc_final: 0.8087 (ttmm) REVERT: A 68 LYS cc_start: 0.8545 (mtpp) cc_final: 0.8213 (ttpp) REVERT: B 41 ASP cc_start: 0.8611 (p0) cc_final: 0.7848 (p0) REVERT: B 68 LYS cc_start: 0.8495 (mtpp) cc_final: 0.8126 (ttpp) REVERT: B 76 ARG cc_start: 0.9099 (mmt180) cc_final: 0.8755 (mpt180) REVERT: C 41 ASP cc_start: 0.8559 (p0) cc_final: 0.7838 (p0) REVERT: C 46 LYS cc_start: 0.8417 (ttpp) cc_final: 0.8112 (ttmm) REVERT: C 68 LYS cc_start: 0.8516 (mtpp) cc_final: 0.8149 (ttpp) REVERT: D 41 ASP cc_start: 0.8557 (p0) cc_final: 0.7802 (p0) REVERT: D 46 LYS cc_start: 0.8373 (ttpp) cc_final: 0.8056 (ttmm) REVERT: D 68 LYS cc_start: 0.8462 (mtpp) cc_final: 0.8178 (ttpp) REVERT: E 41 ASP cc_start: 0.8665 (p0) cc_final: 0.7861 (p0) REVERT: E 46 LYS cc_start: 0.8338 (ttpp) cc_final: 0.8082 (ttmm) REVERT: E 68 LYS cc_start: 0.8396 (mtpp) cc_final: 0.8062 (ttpp) REVERT: F 41 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.7849 (p0) REVERT: F 68 LYS cc_start: 0.8506 (mtpp) cc_final: 0.8132 (ttpp) REVERT: G 41 ASP cc_start: 0.8617 (p0) cc_final: 0.7828 (p0) REVERT: G 42 ASP cc_start: 0.8635 (p0) cc_final: 0.8432 (p0) REVERT: G 46 LYS cc_start: 0.8351 (ttpp) cc_final: 0.8061 (mttp) REVERT: G 68 LYS cc_start: 0.8424 (mtpp) cc_final: 0.8108 (ttpp) REVERT: H 41 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.7875 (p0) REVERT: H 68 LYS cc_start: 0.8394 (mtpp) cc_final: 0.8121 (ttpp) REVERT: H 76 ARG cc_start: 0.9135 (mmt-90) cc_final: 0.8777 (mpt180) REVERT: I 41 ASP cc_start: 0.8686 (OUTLIER) cc_final: 0.7890 (p0) REVERT: I 42 ASP cc_start: 0.8693 (p0) cc_final: 0.8478 (p0) REVERT: I 46 LYS cc_start: 0.8457 (ttpp) cc_final: 0.8178 (mttp) REVERT: I 68 LYS cc_start: 0.8509 (mtpp) cc_final: 0.8148 (ttpp) REVERT: I 76 ARG cc_start: 0.9183 (mmt-90) cc_final: 0.8714 (mmt180) REVERT: J 41 ASP cc_start: 0.8623 (p0) cc_final: 0.7919 (p0) REVERT: J 68 LYS cc_start: 0.8595 (mtpp) cc_final: 0.8222 (ttpp) REVERT: K 41 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.7853 (p0) REVERT: K 46 LYS cc_start: 0.8367 (ttpp) cc_final: 0.8043 (ttmm) REVERT: K 68 LYS cc_start: 0.8492 (mtpp) cc_final: 0.8124 (ttpp) REVERT: K 76 ARG cc_start: 0.9116 (mmt-90) cc_final: 0.8775 (mpt180) REVERT: L 41 ASP cc_start: 0.8628 (p0) cc_final: 0.7818 (p0) REVERT: L 46 LYS cc_start: 0.8332 (ttpp) cc_final: 0.8072 (ttmm) REVERT: L 68 LYS cc_start: 0.8490 (mtpp) cc_final: 0.8113 (ttpp) REVERT: M 41 ASP cc_start: 0.8624 (p0) cc_final: 0.7769 (p0) REVERT: M 42 ASP cc_start: 0.8618 (p0) cc_final: 0.8349 (p0) REVERT: M 46 LYS cc_start: 0.8334 (ttpp) cc_final: 0.8105 (mttm) REVERT: M 68 LYS cc_start: 0.8563 (mtpp) cc_final: 0.8181 (ttpp) REVERT: M 76 ARG cc_start: 0.9202 (mmt-90) cc_final: 0.8742 (mmt180) REVERT: N 41 ASP cc_start: 0.8653 (OUTLIER) cc_final: 0.7942 (p0) REVERT: N 46 LYS cc_start: 0.8385 (ttpp) cc_final: 0.8070 (ttmm) REVERT: N 68 LYS cc_start: 0.8496 (mtpp) cc_final: 0.8135 (ttpp) REVERT: N 76 ARG cc_start: 0.9193 (mmt-90) cc_final: 0.8780 (mpt180) REVERT: O 41 ASP cc_start: 0.8651 (p0) cc_final: 0.7875 (p0) REVERT: O 68 LYS cc_start: 0.8537 (mtpp) cc_final: 0.8129 (ttpp) REVERT: O 76 ARG cc_start: 0.9170 (mmt-90) cc_final: 0.8847 (mpt180) REVERT: P 41 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.7853 (p0) REVERT: P 46 LYS cc_start: 0.8409 (ttpp) cc_final: 0.8167 (mttp) REVERT: Q 41 ASP cc_start: 0.8607 (p0) cc_final: 0.7853 (p0) REVERT: Q 46 LYS cc_start: 0.8356 (ttpp) cc_final: 0.8080 (ttmm) REVERT: Q 68 LYS cc_start: 0.8408 (mtpp) cc_final: 0.8093 (ttpp) REVERT: R 41 ASP cc_start: 0.8539 (p0) cc_final: 0.7779 (p0) REVERT: R 46 LYS cc_start: 0.8326 (ttmm) cc_final: 0.8119 (mttp) REVERT: R 68 LYS cc_start: 0.8413 (mtpp) cc_final: 0.8096 (ttpp) REVERT: S 41 ASP cc_start: 0.8667 (p0) cc_final: 0.7872 (p0) REVERT: S 42 ASP cc_start: 0.8654 (p0) cc_final: 0.8386 (p0) REVERT: S 46 LYS cc_start: 0.8319 (ttpp) cc_final: 0.8094 (ttmm) REVERT: S 68 LYS cc_start: 0.8578 (mtpp) cc_final: 0.8170 (ttpp) REVERT: S 76 ARG cc_start: 0.9161 (mmt-90) cc_final: 0.8805 (mpt180) REVERT: T 41 ASP cc_start: 0.8591 (p0) cc_final: 0.7872 (p0) REVERT: T 68 LYS cc_start: 0.8415 (mtpp) cc_final: 0.8091 (ttpp) REVERT: T 76 ARG cc_start: 0.9193 (mmt-90) cc_final: 0.8678 (mpt180) REVERT: U 41 ASP cc_start: 0.8615 (p0) cc_final: 0.7781 (p0) REVERT: U 46 LYS cc_start: 0.8346 (ttpp) cc_final: 0.8072 (mttp) REVERT: U 68 LYS cc_start: 0.8416 (mtpp) cc_final: 0.8082 (ttpp) REVERT: U 76 ARG cc_start: 0.9184 (mmt-90) cc_final: 0.8736 (mmt180) REVERT: V 41 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.7849 (p0) REVERT: V 46 LYS cc_start: 0.8358 (ttpp) cc_final: 0.8039 (ttmm) REVERT: V 68 LYS cc_start: 0.8489 (mtpp) cc_final: 0.8133 (ttpp) REVERT: W 41 ASP cc_start: 0.8625 (p0) cc_final: 0.7816 (p0) REVERT: W 46 LYS cc_start: 0.8311 (ttpp) cc_final: 0.8043 (ttmm) REVERT: W 65 LYS cc_start: 0.8730 (tttm) cc_final: 0.8497 (tttt) REVERT: W 68 LYS cc_start: 0.8432 (mtpp) cc_final: 0.8113 (ttpp) REVERT: X 41 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.7825 (p0) REVERT: X 46 LYS cc_start: 0.8350 (ttpp) cc_final: 0.8094 (ttmm) REVERT: X 68 LYS cc_start: 0.8466 (mtpp) cc_final: 0.8185 (ttpp) outliers start: 90 outliers final: 39 residues processed: 970 average time/residue: 1.6442 time to fit residues: 1896.1702 Evaluate side-chains 959 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 912 time to evaluate : 4.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 12 ASP Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 116 LYS Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 159 GLU Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain N residue 41 ASP Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain P residue 41 ASP Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain S residue 119 THR Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain U residue 81 ASP Chi-restraints excluded: chain U residue 119 THR Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain V residue 119 THR Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain X residue 41 ASP Chi-restraints excluded: chain X residue 81 ASP Chi-restraints excluded: chain X residue 119 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 343 optimal weight: 5.9990 chunk 221 optimal weight: 5.9990 chunk 331 optimal weight: 50.0000 chunk 167 optimal weight: 50.0000 chunk 109 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 352 optimal weight: 3.9990 chunk 378 optimal weight: 50.0000 chunk 274 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 436 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 102 HIS B 8 ASN B 102 HIS C 102 HIS D 8 ASN D 102 HIS E 102 HIS F 8 ASN F 102 HIS G 8 ASN G 55 GLN G 102 HIS H 8 ASN H 102 HIS I 8 ASN I 62 HIS I 102 HIS J 102 HIS K 8 ASN K 102 HIS L 8 ASN L 102 HIS M 102 HIS N 8 ASN N 102 HIS O 8 ASN O 102 HIS P 8 ASN P 102 HIS Q 102 HIS R 102 HIS S 8 ASN S 102 HIS T 8 ASN T 102 HIS U 8 ASN U 102 HIS V 8 ASN V 102 HIS W 102 HIS X 8 ASN X 102 HIS Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 36312 Z= 0.304 Angle : 0.539 6.008 49104 Z= 0.294 Chirality : 0.040 0.131 5112 Planarity : 0.003 0.034 6480 Dihedral : 13.004 179.749 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.39 % Allowed : 1.38 % Favored : 98.23 % Rotamer: Outliers : 3.65 % Allowed : 24.51 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 4.92 (0.12), residues: 4320 helix: 4.02 (0.08), residues: 3432 sheet: None (None), residues: 0 loop : -0.24 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 90 HIS 0.007 0.001 HIS C 102 PHE 0.019 0.002 PHE B 38 TYR 0.016 0.002 TYR P 134 ARG 0.004 0.000 ARG Q 76 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1022 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 912 time to evaluate : 4.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.9031 (p0) cc_final: 0.8694 (p0) REVERT: A 46 LYS cc_start: 0.8738 (ttpp) cc_final: 0.8420 (ttmm) REVERT: A 68 LYS cc_start: 0.8809 (mtpp) cc_final: 0.8413 (ttpp) REVERT: B 68 LYS cc_start: 0.8835 (mtpp) cc_final: 0.8413 (ttpp) REVERT: C 46 LYS cc_start: 0.8723 (ttpp) cc_final: 0.8414 (ttmm) REVERT: C 68 LYS cc_start: 0.8844 (mtpp) cc_final: 0.8423 (ttpp) REVERT: C 110 SER cc_start: 0.9356 (t) cc_final: 0.9101 (m) REVERT: D 46 LYS cc_start: 0.8724 (ttpp) cc_final: 0.8387 (ttmm) REVERT: D 68 LYS cc_start: 0.8765 (mtpp) cc_final: 0.8385 (ttpp) REVERT: E 46 LYS cc_start: 0.8733 (ttpp) cc_final: 0.8427 (ttmm) REVERT: E 68 LYS cc_start: 0.8773 (mtpp) cc_final: 0.8377 (ttpp) REVERT: E 110 SER cc_start: 0.9286 (t) cc_final: 0.9049 (m) REVERT: F 46 LYS cc_start: 0.8663 (ttpp) cc_final: 0.8377 (ttmm) REVERT: F 68 LYS cc_start: 0.8834 (mtpp) cc_final: 0.8403 (ttpp) REVERT: G 42 ASP cc_start: 0.9024 (p0) cc_final: 0.8771 (p0) REVERT: G 46 LYS cc_start: 0.8732 (ttpp) cc_final: 0.8397 (ttmm) REVERT: G 68 LYS cc_start: 0.8787 (mtpp) cc_final: 0.8427 (ttpp) REVERT: H 41 ASP cc_start: 0.8810 (OUTLIER) cc_final: 0.8109 (p0) REVERT: H 42 ASP cc_start: 0.8864 (p0) cc_final: 0.8656 (p0) REVERT: H 68 LYS cc_start: 0.8755 (mtpp) cc_final: 0.8393 (ttpp) REVERT: I 41 ASP cc_start: 0.8903 (OUTLIER) cc_final: 0.8128 (p0) REVERT: I 42 ASP cc_start: 0.9043 (p0) cc_final: 0.8756 (p0) REVERT: I 68 LYS cc_start: 0.8829 (mtpp) cc_final: 0.8406 (ttpp) REVERT: I 76 ARG cc_start: 0.9194 (mmt-90) cc_final: 0.8711 (mmt180) REVERT: J 68 LYS cc_start: 0.8849 (mtpp) cc_final: 0.8455 (ttpp) REVERT: J 110 SER cc_start: 0.9307 (t) cc_final: 0.9063 (m) REVERT: K 41 ASP cc_start: 0.8903 (OUTLIER) cc_final: 0.8121 (p0) REVERT: K 46 LYS cc_start: 0.8734 (ttpp) cc_final: 0.8416 (ttmm) REVERT: K 68 LYS cc_start: 0.8837 (mtpp) cc_final: 0.8409 (ttpp) REVERT: K 76 ARG cc_start: 0.9118 (mmt-90) cc_final: 0.8761 (mpt180) REVERT: L 46 LYS cc_start: 0.8719 (ttpp) cc_final: 0.8423 (ttmm) REVERT: L 68 LYS cc_start: 0.8840 (mtpp) cc_final: 0.8412 (ttpp) REVERT: M 42 ASP cc_start: 0.9003 (p0) cc_final: 0.8662 (p0) REVERT: M 46 LYS cc_start: 0.8720 (ttpp) cc_final: 0.8364 (ttmm) REVERT: M 68 LYS cc_start: 0.8788 (mtpp) cc_final: 0.8418 (ttpp) REVERT: M 76 ARG cc_start: 0.9204 (mmt-90) cc_final: 0.8729 (mmt180) REVERT: M 78 PHE cc_start: 0.9202 (m-80) cc_final: 0.8996 (m-80) REVERT: N 46 LYS cc_start: 0.8740 (ttpp) cc_final: 0.8397 (ttmm) REVERT: N 68 LYS cc_start: 0.8831 (mtpp) cc_final: 0.8416 (ttpp) REVERT: N 76 ARG cc_start: 0.9152 (mmt-90) cc_final: 0.8790 (mpt180) REVERT: O 68 LYS cc_start: 0.8839 (mtpp) cc_final: 0.8422 (ttpp) REVERT: O 76 ARG cc_start: 0.9159 (mmt-90) cc_final: 0.8832 (mpt180) REVERT: O 110 SER cc_start: 0.9310 (t) cc_final: 0.9078 (m) REVERT: P 41 ASP cc_start: 0.8843 (OUTLIER) cc_final: 0.8112 (p0) REVERT: P 46 LYS cc_start: 0.8784 (ttpp) cc_final: 0.8396 (ttmm) REVERT: P 110 SER cc_start: 0.9335 (t) cc_final: 0.9085 (m) REVERT: Q 46 LYS cc_start: 0.8718 (ttpp) cc_final: 0.8412 (ttmm) REVERT: Q 68 LYS cc_start: 0.8778 (mtpp) cc_final: 0.8387 (ttpp) REVERT: Q 110 SER cc_start: 0.9318 (t) cc_final: 0.9075 (m) REVERT: R 68 LYS cc_start: 0.8779 (mtpp) cc_final: 0.8375 (ttpp) REVERT: S 42 ASP cc_start: 0.9047 (p0) cc_final: 0.8643 (p0) REVERT: S 46 LYS cc_start: 0.8706 (ttpp) cc_final: 0.8439 (ttmm) REVERT: S 68 LYS cc_start: 0.8814 (mtpp) cc_final: 0.8344 (ttpp) REVERT: S 76 ARG cc_start: 0.9173 (mmt-90) cc_final: 0.8843 (mpt180) REVERT: S 110 SER cc_start: 0.9311 (t) cc_final: 0.9079 (m) REVERT: T 68 LYS cc_start: 0.8783 (mtpp) cc_final: 0.8423 (ttpp) REVERT: T 76 ARG cc_start: 0.9223 (mmt-90) cc_final: 0.8756 (mpt180) REVERT: U 46 LYS cc_start: 0.8717 (ttpp) cc_final: 0.8333 (ttmm) REVERT: U 68 LYS cc_start: 0.8782 (mtpp) cc_final: 0.8408 (ttpp) REVERT: U 76 ARG cc_start: 0.9170 (mmt-90) cc_final: 0.8683 (mmt180) REVERT: U 110 SER cc_start: 0.9322 (t) cc_final: 0.9096 (m) REVERT: V 41 ASP cc_start: 0.8890 (OUTLIER) cc_final: 0.8180 (p0) REVERT: V 46 LYS cc_start: 0.8745 (ttpp) cc_final: 0.8373 (ttmm) REVERT: V 68 LYS cc_start: 0.8805 (mtpp) cc_final: 0.8430 (ttpp) REVERT: W 46 LYS cc_start: 0.8706 (ttpp) cc_final: 0.8408 (ttmm) REVERT: W 68 LYS cc_start: 0.8789 (mtpp) cc_final: 0.8390 (ttpp) REVERT: X 41 ASP cc_start: 0.8886 (OUTLIER) cc_final: 0.8167 (p0) REVERT: X 46 LYS cc_start: 0.8748 (ttpp) cc_final: 0.8437 (ttmm) REVERT: X 68 LYS cc_start: 0.8770 (mtpp) cc_final: 0.8377 (ttpp) outliers start: 110 outliers final: 83 residues processed: 958 average time/residue: 1.5817 time to fit residues: 1810.4397 Evaluate side-chains 997 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 908 time to evaluate : 4.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain E residue 12 ASP Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 67 MET Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain G residue 67 MET Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 67 MET Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 116 LYS Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 159 GLU Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 159 GLU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 159 GLU Chi-restraints excluded: chain L residue 67 MET Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 159 GLU Chi-restraints excluded: chain N residue 41 ASP Chi-restraints excluded: chain N residue 67 MET Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain N residue 110 SER Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain O residue 67 MET Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain P residue 41 ASP Chi-restraints excluded: chain P residue 67 MET Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Q residue 67 MET Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain Q residue 164 GLU Chi-restraints excluded: chain R residue 67 MET Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain S residue 119 THR Chi-restraints excluded: chain T residue 67 MET Chi-restraints excluded: chain T residue 110 SER Chi-restraints excluded: chain T residue 116 LYS Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain T residue 164 GLU Chi-restraints excluded: chain U residue 67 MET Chi-restraints excluded: chain U residue 81 ASP Chi-restraints excluded: chain U residue 119 THR Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain V residue 67 MET Chi-restraints excluded: chain V residue 88 ASP Chi-restraints excluded: chain V residue 110 SER Chi-restraints excluded: chain V residue 119 THR Chi-restraints excluded: chain V residue 159 GLU Chi-restraints excluded: chain W residue 67 MET Chi-restraints excluded: chain W residue 86 ASP Chi-restraints excluded: chain W residue 116 LYS Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain X residue 41 ASP Chi-restraints excluded: chain X residue 81 ASP Chi-restraints excluded: chain X residue 110 SER Chi-restraints excluded: chain X residue 119 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 505 optimal weight: 1.9990 chunk 531 optimal weight: 0.9990 chunk 485 optimal weight: 3.9990 chunk 517 optimal weight: 3.9990 chunk 311 optimal weight: 50.0000 chunk 225 optimal weight: 1.9990 chunk 406 optimal weight: 50.0000 chunk 158 optimal weight: 2.9990 chunk 467 optimal weight: 2.9990 chunk 489 optimal weight: 5.9990 chunk 515 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 102 HIS B 8 ASN B 102 HIS C 102 HIS D 8 ASN D 102 HIS E 102 HIS F 8 ASN F 102 HIS G 8 ASN G 102 HIS H 8 ASN H 102 HIS I 8 ASN I 62 HIS I 102 HIS J 102 HIS K 8 ASN K 102 HIS L 8 ASN L 102 HIS M 8 ASN M 102 HIS N 8 ASN N 102 HIS O 8 ASN O 102 HIS P 8 ASN P 102 HIS Q 102 HIS R 102 HIS S 8 ASN S 102 HIS T 8 ASN T 102 HIS U 8 ASN U 102 HIS V 8 ASN V 102 HIS W 102 HIS X 8 ASN X 102 HIS Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 36312 Z= 0.216 Angle : 0.497 5.531 49104 Z= 0.273 Chirality : 0.037 0.121 5112 Planarity : 0.003 0.037 6480 Dihedral : 13.018 179.990 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.34 % Allowed : 1.55 % Favored : 98.11 % Rotamer: Outliers : 3.24 % Allowed : 25.33 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 5.10 (0.12), residues: 4320 helix: 4.15 (0.08), residues: 3432 sheet: None (None), residues: 0 loop : -0.17 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP Q 90 HIS 0.006 0.001 HIS C 102 PHE 0.015 0.002 PHE B 38 TYR 0.015 0.001 TYR P 134 ARG 0.003 0.000 ARG Q 76 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1037 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 942 time to evaluate : 4.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.8913 (p0) cc_final: 0.8563 (p0) REVERT: A 46 LYS cc_start: 0.8605 (ttpp) cc_final: 0.8294 (ttmm) REVERT: A 68 LYS cc_start: 0.8703 (mtpp) cc_final: 0.8318 (ttpp) REVERT: B 41 ASP cc_start: 0.8768 (p0) cc_final: 0.8083 (p0) REVERT: B 68 LYS cc_start: 0.8687 (mtpp) cc_final: 0.8313 (ttpp) REVERT: B 76 ARG cc_start: 0.9122 (mmt180) cc_final: 0.8795 (mpt180) REVERT: C 41 ASP cc_start: 0.8798 (p0) cc_final: 0.8061 (p0) REVERT: C 46 LYS cc_start: 0.8590 (ttpp) cc_final: 0.8283 (ttmm) REVERT: C 68 LYS cc_start: 0.8704 (mtpp) cc_final: 0.8301 (ttpp) REVERT: C 110 SER cc_start: 0.9314 (t) cc_final: 0.9051 (m) REVERT: D 41 ASP cc_start: 0.8734 (p0) cc_final: 0.8062 (p0) REVERT: D 46 LYS cc_start: 0.8610 (ttpp) cc_final: 0.8269 (ttmm) REVERT: D 68 LYS cc_start: 0.8619 (mtpp) cc_final: 0.8249 (ttpp) REVERT: E 41 ASP cc_start: 0.8794 (OUTLIER) cc_final: 0.8082 (p0) REVERT: E 46 LYS cc_start: 0.8604 (ttpp) cc_final: 0.8298 (ttmm) REVERT: E 68 LYS cc_start: 0.8641 (mtpp) cc_final: 0.8239 (ttpp) REVERT: F 41 ASP cc_start: 0.8806 (p0) cc_final: 0.8087 (p0) REVERT: F 46 LYS cc_start: 0.8497 (ttpp) cc_final: 0.8208 (ttmm) REVERT: F 68 LYS cc_start: 0.8662 (mtpp) cc_final: 0.8264 (ttpp) REVERT: G 41 ASP cc_start: 0.8829 (p0) cc_final: 0.8060 (p0) REVERT: G 42 ASP cc_start: 0.8872 (p0) cc_final: 0.8645 (p0) REVERT: G 46 LYS cc_start: 0.8617 (ttpp) cc_final: 0.8285 (ttmm) REVERT: G 68 LYS cc_start: 0.8657 (mtpp) cc_final: 0.8298 (ttpp) REVERT: H 68 LYS cc_start: 0.8592 (mtpp) cc_final: 0.8263 (ttpp) REVERT: I 41 ASP cc_start: 0.8833 (OUTLIER) cc_final: 0.8056 (p0) REVERT: I 42 ASP cc_start: 0.8901 (p0) cc_final: 0.8651 (p0) REVERT: I 46 LYS cc_start: 0.8668 (ttpp) cc_final: 0.8280 (ttmm) REVERT: I 68 LYS cc_start: 0.8684 (mtpp) cc_final: 0.8304 (ttpp) REVERT: I 76 ARG cc_start: 0.9195 (mmt-90) cc_final: 0.8728 (mmt180) REVERT: J 68 LYS cc_start: 0.8735 (mtpp) cc_final: 0.8332 (ttpp) REVERT: K 41 ASP cc_start: 0.8776 (OUTLIER) cc_final: 0.8010 (p0) REVERT: K 46 LYS cc_start: 0.8599 (ttpp) cc_final: 0.8280 (ttmm) REVERT: K 68 LYS cc_start: 0.8665 (mtpp) cc_final: 0.8269 (ttpp) REVERT: K 76 ARG cc_start: 0.9123 (mmt-90) cc_final: 0.8764 (mpt180) REVERT: L 41 ASP cc_start: 0.8783 (p0) cc_final: 0.8038 (p0) REVERT: L 46 LYS cc_start: 0.8577 (ttpp) cc_final: 0.8278 (ttmm) REVERT: L 68 LYS cc_start: 0.8713 (mtpp) cc_final: 0.8275 (ttpp) REVERT: M 41 ASP cc_start: 0.8784 (OUTLIER) cc_final: 0.8005 (p0) REVERT: M 42 ASP cc_start: 0.8858 (p0) cc_final: 0.8513 (p0) REVERT: M 46 LYS cc_start: 0.8591 (ttpp) cc_final: 0.8313 (mttm) REVERT: M 68 LYS cc_start: 0.8651 (mtpp) cc_final: 0.8278 (ttpp) REVERT: M 76 ARG cc_start: 0.9208 (mmt-90) cc_final: 0.8709 (mmt180) REVERT: N 41 ASP cc_start: 0.8812 (OUTLIER) cc_final: 0.8106 (p0) REVERT: N 46 LYS cc_start: 0.8607 (ttpp) cc_final: 0.8299 (ttmm) REVERT: N 68 LYS cc_start: 0.8636 (mtpp) cc_final: 0.8244 (ttpp) REVERT: N 76 ARG cc_start: 0.9152 (mmt-90) cc_final: 0.8762 (mpt180) REVERT: O 68 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8346 (ttpp) REVERT: O 76 ARG cc_start: 0.9160 (mmt-90) cc_final: 0.8814 (mpt180) REVERT: P 41 ASP cc_start: 0.8766 (OUTLIER) cc_final: 0.8010 (p0) REVERT: P 46 LYS cc_start: 0.8645 (ttpp) cc_final: 0.8302 (ttmm) REVERT: Q 41 ASP cc_start: 0.8756 (p0) cc_final: 0.8077 (p0) REVERT: Q 46 LYS cc_start: 0.8603 (ttpp) cc_final: 0.8297 (ttmm) REVERT: Q 68 LYS cc_start: 0.8641 (mtpp) cc_final: 0.8268 (ttpp) REVERT: R 68 LYS cc_start: 0.8608 (mtpp) cc_final: 0.8222 (ttpp) REVERT: S 41 ASP cc_start: 0.8796 (OUTLIER) cc_final: 0.8001 (p0) REVERT: S 42 ASP cc_start: 0.8881 (p0) cc_final: 0.8484 (p0) REVERT: S 46 LYS cc_start: 0.8550 (ttpp) cc_final: 0.8294 (ttmm) REVERT: S 68 LYS cc_start: 0.8733 (mtpp) cc_final: 0.8289 (ttpp) REVERT: S 76 ARG cc_start: 0.9176 (mmt-90) cc_final: 0.8855 (mpt180) REVERT: S 110 SER cc_start: 0.9261 (t) cc_final: 0.9037 (m) REVERT: T 68 LYS cc_start: 0.8682 (mtpp) cc_final: 0.8302 (ttpp) REVERT: T 76 ARG cc_start: 0.9213 (mmt-90) cc_final: 0.8669 (mpt180) REVERT: U 41 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.8035 (p0) REVERT: U 46 LYS cc_start: 0.8566 (ttpp) cc_final: 0.8180 (ttmm) REVERT: U 68 LYS cc_start: 0.8651 (mtpp) cc_final: 0.8250 (ttpp) REVERT: U 76 ARG cc_start: 0.9184 (mmt-90) cc_final: 0.8704 (mmt180) REVERT: U 110 SER cc_start: 0.9292 (t) cc_final: 0.9071 (m) REVERT: V 41 ASP cc_start: 0.8785 (OUTLIER) cc_final: 0.8032 (p0) REVERT: V 46 LYS cc_start: 0.8617 (ttpp) cc_final: 0.8290 (ttmm) REVERT: V 68 LYS cc_start: 0.8685 (mtpp) cc_final: 0.8288 (ttpp) REVERT: W 46 LYS cc_start: 0.8574 (ttpp) cc_final: 0.8283 (ttmm) REVERT: W 68 LYS cc_start: 0.8650 (mtpp) cc_final: 0.8284 (ttpp) REVERT: X 41 ASP cc_start: 0.8788 (OUTLIER) cc_final: 0.8073 (p0) REVERT: X 46 LYS cc_start: 0.8619 (ttpp) cc_final: 0.8308 (ttmm) REVERT: X 68 LYS cc_start: 0.8636 (mtpp) cc_final: 0.8260 (ttpp) outliers start: 95 outliers final: 66 residues processed: 977 average time/residue: 1.5881 time to fit residues: 1854.1798 Evaluate side-chains 990 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 913 time to evaluate : 4.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain E residue 12 ASP Chi-restraints excluded: chain E residue 41 ASP Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 116 LYS Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 159 GLU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 159 GLU Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 110 SER Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 159 GLU Chi-restraints excluded: chain N residue 41 ASP Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain N residue 159 GLU Chi-restraints excluded: chain O residue 67 MET Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain P residue 41 ASP Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain Q residue 164 GLU Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain S residue 41 ASP Chi-restraints excluded: chain S residue 119 THR Chi-restraints excluded: chain T residue 110 SER Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain T residue 164 GLU Chi-restraints excluded: chain U residue 41 ASP Chi-restraints excluded: chain U residue 81 ASP Chi-restraints excluded: chain U residue 119 THR Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain V residue 67 MET Chi-restraints excluded: chain V residue 110 SER Chi-restraints excluded: chain V residue 119 THR Chi-restraints excluded: chain W residue 86 ASP Chi-restraints excluded: chain W residue 116 LYS Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain X residue 41 ASP Chi-restraints excluded: chain X residue 67 MET Chi-restraints excluded: chain X residue 81 ASP Chi-restraints excluded: chain X residue 110 SER Chi-restraints excluded: chain X residue 119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 339 optimal weight: 0.8980 chunk 547 optimal weight: 50.0000 chunk 333 optimal weight: 50.0000 chunk 259 optimal weight: 50.0000 chunk 380 optimal weight: 50.0000 chunk 573 optimal weight: 50.0000 chunk 528 optimal weight: 5.9990 chunk 456 optimal weight: 0.0270 chunk 47 optimal weight: 50.0000 chunk 352 optimal weight: 7.9990 chunk 280 optimal weight: 0.4980 overall best weight: 3.0842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 102 HIS B 8 ASN B 102 HIS C 102 HIS D 8 ASN D 102 HIS E 102 HIS F 8 ASN F 102 HIS G 8 ASN G 102 HIS H 8 ASN H 102 HIS I 8 ASN I 62 HIS I 102 HIS J 102 HIS K 8 ASN K 102 HIS L 8 ASN L 102 HIS M 8 ASN M 102 HIS N 8 ASN N 102 HIS O 8 ASN O 102 HIS P 8 ASN P 102 HIS Q 102 HIS R 102 HIS S 8 ASN S 102 HIS T 8 ASN T 102 HIS U 8 ASN U 102 HIS V 8 ASN V 102 HIS W 102 HIS X 8 ASN X 102 HIS Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 36312 Z= 0.295 Angle : 0.544 6.093 49104 Z= 0.297 Chirality : 0.039 0.129 5112 Planarity : 0.003 0.035 6480 Dihedral : 12.994 179.742 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.34 % Allowed : 1.45 % Favored : 98.21 % Rotamer: Outliers : 3.40 % Allowed : 25.13 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 4.88 (0.12), residues: 4320 helix: 3.97 (0.08), residues: 3432 sheet: None (None), residues: 0 loop : -0.13 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 90 HIS 0.006 0.001 HIS G 102 PHE 0.017 0.002 PHE B 38 TYR 0.015 0.002 TYR P 134 ARG 0.003 0.000 ARG Q 76 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1021 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 920 time to evaluate : 4.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.9025 (p0) cc_final: 0.8713 (p0) REVERT: A 46 LYS cc_start: 0.8725 (ttpp) cc_final: 0.8407 (ttmm) REVERT: A 68 LYS cc_start: 0.8799 (mtpp) cc_final: 0.8406 (ttpp) REVERT: B 68 LYS cc_start: 0.8792 (mtpp) cc_final: 0.8359 (ttpp) REVERT: B 110 SER cc_start: 0.9334 (t) cc_final: 0.9073 (m) REVERT: C 46 LYS cc_start: 0.8701 (ttpp) cc_final: 0.8393 (ttmm) REVERT: C 68 LYS cc_start: 0.8837 (mtpp) cc_final: 0.8416 (ttpp) REVERT: C 110 SER cc_start: 0.9344 (t) cc_final: 0.9080 (m) REVERT: D 46 LYS cc_start: 0.8719 (ttpp) cc_final: 0.8380 (ttmm) REVERT: D 68 LYS cc_start: 0.8761 (mtpp) cc_final: 0.8371 (ttpp) REVERT: E 46 LYS cc_start: 0.8706 (ttpp) cc_final: 0.8396 (ttmm) REVERT: E 68 LYS cc_start: 0.8735 (mtpp) cc_final: 0.8328 (ttpp) REVERT: E 110 SER cc_start: 0.9297 (t) cc_final: 0.9046 (m) REVERT: F 46 LYS cc_start: 0.8644 (ttpp) cc_final: 0.8355 (ttmm) REVERT: F 68 LYS cc_start: 0.8805 (mtpp) cc_final: 0.8367 (ttpp) REVERT: G 42 ASP cc_start: 0.9012 (p0) cc_final: 0.8751 (p0) REVERT: G 46 LYS cc_start: 0.8724 (ttpp) cc_final: 0.8390 (ttmm) REVERT: G 68 LYS cc_start: 0.8773 (mtpp) cc_final: 0.8415 (ttpp) REVERT: H 68 LYS cc_start: 0.8750 (mtpp) cc_final: 0.8387 (ttpp) REVERT: I 41 ASP cc_start: 0.8890 (OUTLIER) cc_final: 0.8112 (p0) REVERT: I 42 ASP cc_start: 0.9022 (p0) cc_final: 0.8721 (p0) REVERT: I 46 LYS cc_start: 0.8789 (ttpp) cc_final: 0.8403 (ttmm) REVERT: I 68 LYS cc_start: 0.8814 (mtpp) cc_final: 0.8395 (ttpp) REVERT: I 76 ARG cc_start: 0.9192 (mmt-90) cc_final: 0.8708 (mmt180) REVERT: J 68 LYS cc_start: 0.8847 (mtpp) cc_final: 0.8450 (ttpp) REVERT: J 110 SER cc_start: 0.9318 (t) cc_final: 0.9067 (m) REVERT: K 41 ASP cc_start: 0.8865 (OUTLIER) cc_final: 0.8123 (p0) REVERT: K 46 LYS cc_start: 0.8715 (ttpp) cc_final: 0.8395 (ttmm) REVERT: K 68 LYS cc_start: 0.8825 (mtpp) cc_final: 0.8396 (ttpp) REVERT: K 76 ARG cc_start: 0.9132 (mmt-90) cc_final: 0.8776 (mpt180) REVERT: L 46 LYS cc_start: 0.8695 (ttpp) cc_final: 0.8392 (ttmm) REVERT: L 68 LYS cc_start: 0.8823 (mtpp) cc_final: 0.8393 (ttpp) REVERT: M 42 ASP cc_start: 0.8993 (p0) cc_final: 0.8646 (p0) REVERT: M 46 LYS cc_start: 0.8696 (ttpp) cc_final: 0.8340 (ttmm) REVERT: M 68 LYS cc_start: 0.8758 (mtpp) cc_final: 0.8398 (ttpp) REVERT: M 76 ARG cc_start: 0.9193 (mmt-90) cc_final: 0.8695 (mmt180) REVERT: N 41 ASP cc_start: 0.8823 (OUTLIER) cc_final: 0.8116 (p0) REVERT: N 46 LYS cc_start: 0.8715 (ttpp) cc_final: 0.8400 (ttmm) REVERT: N 68 LYS cc_start: 0.8820 (mtpp) cc_final: 0.8405 (ttpp) REVERT: N 76 ARG cc_start: 0.9148 (mmt-90) cc_final: 0.8782 (mpt180) REVERT: O 68 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8423 (ttpp) REVERT: O 76 ARG cc_start: 0.9158 (mmt-90) cc_final: 0.8807 (mpt180) REVERT: O 110 SER cc_start: 0.9326 (t) cc_final: 0.9080 (m) REVERT: P 41 ASP cc_start: 0.8834 (OUTLIER) cc_final: 0.8109 (p0) REVERT: P 46 LYS cc_start: 0.8763 (ttpp) cc_final: 0.8375 (ttmm) REVERT: P 110 SER cc_start: 0.9324 (t) cc_final: 0.9073 (m) REVERT: Q 46 LYS cc_start: 0.8705 (ttpp) cc_final: 0.8393 (ttmm) REVERT: Q 68 LYS cc_start: 0.8758 (mtpp) cc_final: 0.8401 (ttpp) REVERT: Q 110 SER cc_start: 0.9342 (t) cc_final: 0.9090 (m) REVERT: R 68 LYS cc_start: 0.8766 (mtpp) cc_final: 0.8359 (ttpp) REVERT: S 42 ASP cc_start: 0.9034 (p0) cc_final: 0.8649 (p0) REVERT: S 46 LYS cc_start: 0.8677 (ttpp) cc_final: 0.8412 (ttmm) REVERT: S 68 LYS cc_start: 0.8802 (mtpp) cc_final: 0.8376 (ttpp) REVERT: S 76 ARG cc_start: 0.9158 (mmt-90) cc_final: 0.8844 (mpt180) REVERT: S 110 SER cc_start: 0.9307 (t) cc_final: 0.9080 (m) REVERT: T 68 LYS cc_start: 0.8778 (mtpp) cc_final: 0.8381 (ttpp) REVERT: T 76 ARG cc_start: 0.9217 (mmt-90) cc_final: 0.8751 (mpt180) REVERT: U 41 ASP cc_start: 0.8823 (OUTLIER) cc_final: 0.8058 (p0) REVERT: U 46 LYS cc_start: 0.8720 (ttpp) cc_final: 0.8315 (ttmm) REVERT: U 68 LYS cc_start: 0.8736 (mtpp) cc_final: 0.8364 (ttpp) REVERT: U 76 ARG cc_start: 0.9181 (mmt-90) cc_final: 0.8685 (mmt180) REVERT: U 110 SER cc_start: 0.9323 (t) cc_final: 0.9103 (m) REVERT: V 41 ASP cc_start: 0.8843 (OUTLIER) cc_final: 0.8154 (p0) REVERT: V 46 LYS cc_start: 0.8728 (ttpp) cc_final: 0.8366 (ttmm) REVERT: V 68 LYS cc_start: 0.8793 (mtpp) cc_final: 0.8419 (ttpp) REVERT: W 46 LYS cc_start: 0.8683 (ttpp) cc_final: 0.8385 (ttmm) REVERT: W 68 LYS cc_start: 0.8771 (mtpp) cc_final: 0.8409 (ttpp) REVERT: X 41 ASP cc_start: 0.8854 (OUTLIER) cc_final: 0.8158 (p0) REVERT: X 46 LYS cc_start: 0.8722 (ttpp) cc_final: 0.8406 (ttmm) REVERT: X 68 LYS cc_start: 0.8781 (mtpp) cc_final: 0.8374 (ttpp) outliers start: 101 outliers final: 83 residues processed: 957 average time/residue: 1.6235 time to fit residues: 1853.0613 Evaluate side-chains 1009 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 918 time to evaluate : 4.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 159 GLU Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain H residue 67 MET Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 116 LYS Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 159 GLU Chi-restraints excluded: chain J residue 81 ASP Chi-restraints excluded: chain J residue 119 THR Chi-restraints excluded: chain J residue 159 GLU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain K residue 41 ASP Chi-restraints excluded: chain K residue 67 MET Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 159 GLU Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 110 SER Chi-restraints excluded: chain L residue 116 LYS Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain M residue 81 ASP Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 159 GLU Chi-restraints excluded: chain N residue 41 ASP Chi-restraints excluded: chain N residue 67 MET Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain N residue 159 GLU Chi-restraints excluded: chain O residue 67 MET Chi-restraints excluded: chain O residue 68 LYS Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain P residue 41 ASP Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 81 ASP Chi-restraints excluded: chain Q residue 86 ASP Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain Q residue 164 GLU Chi-restraints excluded: chain R residue 81 ASP Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain S residue 81 ASP Chi-restraints excluded: chain S residue 119 THR Chi-restraints excluded: chain T residue 110 SER Chi-restraints excluded: chain T residue 116 LYS Chi-restraints excluded: chain T residue 119 THR Chi-restraints excluded: chain T residue 164 GLU Chi-restraints excluded: chain U residue 41 ASP Chi-restraints excluded: chain U residue 81 ASP Chi-restraints excluded: chain U residue 119 THR Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain V residue 67 MET Chi-restraints excluded: chain V residue 88 ASP Chi-restraints excluded: chain V residue 110 SER Chi-restraints excluded: chain V residue 119 THR Chi-restraints excluded: chain W residue 81 ASP Chi-restraints excluded: chain W residue 86 ASP Chi-restraints excluded: chain W residue 116 LYS Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain X residue 41 ASP Chi-restraints excluded: chain X residue 67 MET Chi-restraints excluded: chain X residue 81 ASP Chi-restraints excluded: chain X residue 110 SER Chi-restraints excluded: chain X residue 119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 362 optimal weight: 2.9990 chunk 486 optimal weight: 4.9990 chunk 139 optimal weight: 50.0000 chunk 421 optimal weight: 3.9990 chunk 67 optimal weight: 50.0000 chunk 126 optimal weight: 2.9990 chunk 457 optimal weight: 0.7980 chunk 191 optimal weight: 50.0000 chunk 469 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 84 optimal weight: 0.1980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 102 HIS B 8 ASN B 102 HIS C 102 HIS D 8 ASN D 102 HIS E 102 HIS F 8 ASN F 102 HIS G 8 ASN G 102 HIS H 8 ASN H 102 HIS I 8 ASN I 102 HIS J 102 HIS K 8 ASN K 102 HIS L 8 ASN L 102 HIS M 102 HIS N 8 ASN N 102 HIS O 8 ASN O 102 HIS P 8 ASN P 102 HIS Q 102 HIS R 102 HIS S 8 ASN S 102 HIS T 8 ASN T 102 HIS U 8 ASN U 102 HIS V 8 ASN V 102 HIS W 102 HIS X 8 ASN X 102 HIS Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.108420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.085608 restraints weight = 309790.111| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 3.84 r_work: 0.2559 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2519 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2519 r_free = 0.2519 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1464 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2517 r_free = 0.2517 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1468 | |-----------------------------------------------------------------------------| r_final: 0.2517 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 36312 Z= 0.189 Angle : 0.482 5.487 49104 Z= 0.266 Chirality : 0.037 0.117 5112 Planarity : 0.003 0.038 6480 Dihedral : 12.985 179.997 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.34 % Allowed : 1.82 % Favored : 97.84 % Rotamer: Outliers : 3.14 % Allowed : 25.41 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 5.24 (0.12), residues: 4320 helix: 4.24 (0.08), residues: 3432 sheet: None (None), residues: 0 loop : -0.08 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP Q 90 HIS 0.007 0.001 HIS I 102 PHE 0.015 0.002 PHE B 38 TYR 0.014 0.001 TYR P 134 ARG 0.002 0.000 ARG Q 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23572.24 seconds wall clock time: 423 minutes 59.58 seconds (25439.58 seconds total)