Starting phenix.real_space_refine (version: dev) on Tue Dec 20 04:04:49 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sht_10205/12_2022/6sht_10205_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sht_10205/12_2022/6sht_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_10205/12_2022/6sht_10205.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sht_10205/12_2022/6sht_10205.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sht_10205/12_2022/6sht_10205_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sht_10205/12_2022/6sht_10205_neut.pdb" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 89": "OD1" <-> "OD2" Residue "C PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 89": "OD1" <-> "OD2" Residue "E PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 89": "OD1" <-> "OD2" Residue "G PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 89": "OD1" <-> "OD2" Residue "I PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 89": "OD1" <-> "OD2" Residue "K PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 89": "OD1" <-> "OD2" Residue "M PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 89": "OD1" <-> "OD2" Residue "O PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 89": "OD1" <-> "OD2" Residue "Q PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 89": "OD1" <-> "OD2" Residue "S PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 89": "OD1" <-> "OD2" Residue "U PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 89": "OD1" <-> "OD2" Residue "W PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 89": "OD1" <-> "OD2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 36.09, per 1000 atoms: 0.97 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: 15.77 Conformation dependent library (CDL) restraints added in 10.1 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: 0.86 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: 11.41 Time building geometry restraints manager: 16.91 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 V 170 " pdb=" CA HIS V 170 " pdb=" C HIS V 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 - 15.24: 18912 15.24 - 30.48: 2208 30.48 - 45.72: 984 45.72 - 60.95: 336 60.95 - 76.19: 144 Dihedral angle restraints: 22584 sinusoidal: 9456 harmonic: 13128 Sorted by residual: dihedral pdb=" CA ASP E 89 " pdb=" CB ASP E 89 " pdb=" CG ASP E 89 " pdb=" OD1 ASP E 89 " ideal model delta sinusoidal sigma weight residual -30.00 -85.86 55.86 1 2.00e+01 2.50e-03 1.05e+01 dihedral pdb=" CA ASP S 89 " pdb=" CB ASP S 89 " pdb=" CG ASP S 89 " pdb=" OD1 ASP S 89 " ideal model delta sinusoidal sigma weight residual -30.00 -85.86 55.86 1 2.00e+01 2.50e-03 1.05e+01 dihedral pdb=" CA ASP G 89 " pdb=" CB ASP G 89 " pdb=" CG ASP G 89 " pdb=" OD1 ASP G 89 " ideal model delta sinusoidal sigma weight residual -30.00 -85.86 55.86 1 2.00e+01 2.50e-03 1.05e+01 ... (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 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. 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: 1.300 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: 0.050 Extract box with map and model: 7.260 Check model and map are aligned: 0.500 Convert atoms to be neutral: 0.270 Process input model: 112.560 Find NCS groups from input model: 2.760 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9067 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 : 1.546 10.740 49104 Z= 1.008 Chirality : 0.070 0.261 5112 Planarity : 0.007 0.040 6480 Dihedral : 17.801 76.191 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 % 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 *********************** 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 : 4.257 Fit side-chains outliers start: 192 outliers final: 24 residues processed: 1392 average time/residue: 1.6709 time to fit residues: 2738.9720 Evaluate side-chains 978 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 954 time to evaluate : 4.148 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 5.5317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 486 optimal weight: 0.9990 chunk 436 optimal weight: 8.9990 chunk 242 optimal weight: 1.9990 chunk 149 optimal weight: 0.0270 chunk 294 optimal weight: 5.9990 chunk 233 optimal weight: 4.9990 chunk 451 optimal weight: 50.0000 chunk 174 optimal weight: 7.9990 chunk 274 optimal weight: 3.9990 chunk 336 optimal weight: 5.9990 chunk 523 optimal weight: 50.0000 overall best weight: 2.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 HIS B 72 GLN B 95 ASN ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN C 95 ASN C 138 GLN ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 HIS E 62 HIS ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 108 ASN H 20 GLN H 72 GLN H 138 GLN I 72 GLN I 108 ASN ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 GLN K 72 GLN K 95 ASN ** K 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 GLN M 55 GLN M 95 ASN M 108 ASN ** M 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 8 ASN N 57 HIS N 62 HIS O 57 HIS O 108 ASN P 8 ASN P 72 GLN ** P 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 GLN ** Q 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 72 GLN R 95 ASN S 57 HIS S 72 GLN S 138 GLN T 55 GLN T 57 HIS T 72 GLN ** T 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 57 HIS U 72 GLN U 151 ASN V 8 ASN V 72 GLN ** V 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 55 GLN W 57 HIS W 95 ASN ** W 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 72 GLN ** X 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.177 36312 Z= 0.592 Angle : 1.871 40.116 49104 Z= 0.950 Chirality : 0.073 0.660 5112 Planarity : 0.017 0.173 6480 Dihedral : 6.017 35.698 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.78 % Allowed : 3.90 % Favored : 95.32 % Rotamer Outliers : 7.69 % Cbeta Deviations : 0.17 % 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: -1.65 (0.11), residues: 4320 helix: -0.76 (0.08), residues: 3384 sheet: None (None), residues: 0 loop : -1.76 (0.20), residues: 936 *********************** 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 1401 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 1134 time to evaluate : 4.274 Fit side-chains outliers start: 267 outliers final: 63 residues processed: 1212 average time/residue: 1.5964 time to fit residues: 2300.8171 Evaluate side-chains 1058 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 995 time to evaluate : 4.082 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 10 residues processed: 54 average time/residue: 0.7568 time to fit residues: 62.5159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 290 optimal weight: 1.9990 chunk 162 optimal weight: 50.0000 chunk 435 optimal weight: 4.9990 chunk 356 optimal weight: 50.0000 chunk 144 optimal weight: 5.9990 chunk 524 optimal weight: 50.0000 chunk 566 optimal weight: 6.9990 chunk 466 optimal weight: 1.9990 chunk 519 optimal weight: 0.9990 chunk 178 optimal weight: 4.9990 chunk 420 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 108 ASN ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN C 102 HIS D 55 GLN D 95 ASN E 8 ASN E 55 GLN E 95 ASN F 95 ASN F 102 HIS G 72 GLN G 108 ASN H 20 GLN H 22 ASN H 108 ASN I 55 GLN I 108 ASN J 55 GLN J 102 HIS J 109 GLN K 10 HIS K 72 GLN L 55 GLN L 72 GLN L 95 ASN L 102 HIS M 22 ASN M 108 ASN ** M 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 8 ASN N 55 GLN N 102 HIS N 138 GLN O 72 GLN O 108 ASN P 72 GLN Q 72 GLN R 10 HIS R 72 GLN R 115 HIS S 55 GLN S 72 GLN S 95 ASN T 72 GLN T 102 HIS V 72 GLN V 95 ASN W 22 ASN W 72 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 36312 Z= 0.266 Angle : 0.589 7.033 49104 Z= 0.323 Chirality : 0.041 0.143 5112 Planarity : 0.004 0.036 6480 Dihedral : 4.109 37.900 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.46 % Allowed : 1.14 % Favored : 98.40 % Rotamer Outliers : 3.78 % 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: 2.86 (0.12), residues: 4320 helix: 2.55 (0.08), residues: 3432 sheet: None (None), residues: 0 loop : -0.88 (0.20), residues: 888 *********************** 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 1157 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 1040 time to evaluate : 4.720 Fit side-chains outliers start: 117 outliers final: 49 residues processed: 1086 average time/residue: 1.5345 time to fit residues: 1997.8008 Evaluate side-chains 963 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 914 time to evaluate : 4.079 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 30 residues processed: 22 average time/residue: 0.4398 time to fit residues: 21.6707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 517 optimal weight: 5.9990 chunk 393 optimal weight: 2.9990 chunk 271 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 250 optimal weight: 3.9990 chunk 351 optimal weight: 0.7980 chunk 525 optimal weight: 50.0000 chunk 556 optimal weight: 6.9990 chunk 274 optimal weight: 2.9990 chunk 498 optimal weight: 50.0000 chunk 150 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 102 HIS ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 ASN B 102 HIS B 138 GLN C 102 HIS D 102 HIS E 62 HIS ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 ASN F 102 HIS G 8 ASN G 102 HIS H 95 ASN H 102 HIS I 8 ASN I 62 HIS I 102 HIS J 102 HIS K 8 ASN K 138 GLN L 102 HIS ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 8 ASN M 95 ASN M 102 HIS M 138 GLN N 102 HIS O 8 ASN O 102 HIS O 108 ASN P 8 ASN P 102 HIS ** P 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 95 ASN Q 102 HIS ** Q 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 102 HIS T 8 ASN T 102 HIS ** T 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 95 ASN ** U 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 8 ASN V 102 HIS ** V 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 102 HIS ** W 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 95 ASN X 102 HIS ** X 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 36312 Z= 0.237 Angle : 0.524 6.528 49104 Z= 0.288 Chirality : 0.039 0.129 5112 Planarity : 0.003 0.033 6480 Dihedral : 3.804 34.737 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.46 % Allowed : 1.09 % Favored : 98.45 % Rotamer Outliers : 3.42 % 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: 4.33 (0.12), residues: 4320 helix: 3.64 (0.08), residues: 3432 sheet: None (None), residues: 0 loop : -0.61 (0.20), residues: 888 *********************** 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 1069 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 965 time to evaluate : 4.272 Fit side-chains outliers start: 104 outliers final: 72 residues processed: 1008 average time/residue: 1.4683 time to fit residues: 1788.2513 Evaluate side-chains 973 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 901 time to evaluate : 4.074 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 37 residues processed: 38 average time/residue: 0.6350 time to fit residues: 40.6774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 463 optimal weight: 2.9990 chunk 316 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 414 optimal weight: 6.9990 chunk 229 optimal weight: 5.9990 chunk 475 optimal weight: 50.0000 chunk 384 optimal weight: 3.9990 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: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 HIS A 138 GLN B 102 HIS C 62 HIS C 102 HIS D 102 HIS E 138 GLN F 8 ASN F 62 HIS F 102 HIS G 8 ASN G 95 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 L 8 ASN L 102 HIS L 138 GLN M 8 ASN M 102 HIS N 62 HIS N 102 HIS O 8 ASN O 102 HIS P 8 ASN P 55 GLN P 95 ASN P 102 HIS P 138 GLN Q 102 HIS Q 138 GLN R 55 GLN S 102 HIS T 8 ASN T 95 ASN T 102 HIS T 138 GLN U 55 GLN U 138 GLN V 8 ASN V 102 HIS V 138 GLN W 102 HIS W 138 GLN X 55 GLN X 102 HIS X 138 GLN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.039 36312 Z= 0.374 Angle : 0.590 6.778 49104 Z= 0.320 Chirality : 0.043 0.136 5112 Planarity : 0.004 0.033 6480 Dihedral : 3.893 35.653 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.41 % Allowed : 1.24 % Favored : 98.35 % Rotamer Outliers : 4.71 % 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: 4.35 (0.12), residues: 4320 helix: 3.64 (0.08), residues: 3432 sheet: None (None), residues: 0 loop : -0.51 (0.20), residues: 888 *********************** 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 1077 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 924 time to evaluate : 4.358 Fit side-chains outliers start: 153 outliers final: 59 residues processed: 978 average time/residue: 1.5055 time to fit residues: 1777.5346 Evaluate side-chains 980 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 921 time to evaluate : 4.403 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 16 residues processed: 43 average time/residue: 0.8000 time to fit residues: 53.9951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 326 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 chunk 557 optimal weight: 4.9990 chunk 462 optimal weight: 3.9990 chunk 258 optimal weight: 50.0000 chunk 46 optimal weight: 50.0000 chunk 184 optimal weight: 0.9990 chunk 292 optimal weight: 7.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 F 8 ASN F 102 HIS ** F 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 ASN G 102 HIS H 55 GLN H 102 HIS I 8 ASN I 102 HIS J 102 HIS K 8 ASN L 8 ASN L 102 HIS M 8 ASN M 102 HIS N 8 ASN N 62 HIS N 102 HIS O 8 ASN O 102 HIS P 8 ASN P 102 HIS Q 102 HIS S 102 HIS T 8 ASN T 102 HIS V 8 ASN V 102 HIS W 102 HIS X 102 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 36312 Z= 0.266 Angle : 0.526 6.011 49104 Z= 0.287 Chirality : 0.039 0.125 5112 Planarity : 0.003 0.034 6480 Dihedral : 3.763 34.014 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.41 % Allowed : 1.19 % Favored : 98.40 % Rotamer Outliers : 4.30 % 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: 4.75 (0.12), residues: 4320 helix: 3.92 (0.08), residues: 3432 sheet: None (None), residues: 0 loop : -0.39 (0.20), residues: 888 *********************** 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 1061 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 925 time to evaluate : 5.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 136 outliers final: 71 residues processed: 983 average time/residue: 1.4775 time to fit residues: 1755.6294 Evaluate side-chains 976 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 905 time to evaluate : 4.216 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 36 residues processed: 35 average time/residue: 0.8352 time to fit residues: 45.4035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 537 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 317 optimal weight: 5.9990 chunk 406 optimal weight: 50.0000 chunk 315 optimal weight: 5.9990 chunk 469 optimal weight: 4.9990 chunk 311 optimal weight: 50.0000 chunk 555 optimal weight: 0.9980 chunk 347 optimal weight: 5.9990 chunk 338 optimal weight: 2.9990 chunk 256 optimal weight: 8.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 F 8 ASN F 102 HIS ** F 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 ASN G 102 HIS H 8 ASN H 102 HIS I 8 ASN I 102 HIS J 95 ASN J 102 HIS K 8 ASN 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 S 8 ASN S 102 HIS T 8 ASN 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: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.3291 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= 0.344 Angle : 0.571 6.189 49104 Z= 0.310 Chirality : 0.041 0.134 5112 Planarity : 0.004 0.034 6480 Dihedral : 3.834 35.577 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.39 % Allowed : 1.65 % Favored : 97.97 % Rotamer Outliers : 4.32 % 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: 4.61 (0.12), residues: 4320 helix: 3.80 (0.08), residues: 3432 sheet: None (None), residues: 0 loop : -0.35 (0.20), residues: 888 *********************** 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 1060 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 924 time to evaluate : 4.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 136 outliers final: 79 residues processed: 975 average time/residue: 1.4412 time to fit residues: 1700.2724 Evaluate side-chains 983 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 904 time to evaluate : 4.502 Switching outliers to nearest non-outliers outliers start: 79 outliers final: 32 residues processed: 48 average time/residue: 0.6206 time to fit residues: 50.3611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 343 optimal weight: 0.7980 chunk 221 optimal weight: 0.9990 chunk 331 optimal weight: 50.0000 chunk 167 optimal weight: 50.0000 chunk 109 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 352 optimal weight: 3.9990 chunk 378 optimal weight: 50.0000 chunk 274 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 436 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 ** F 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 ASN G 102 HIS H 102 HIS I 95 ASN I 102 HIS J 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 8 ASN Q 102 HIS S 8 ASN S 102 HIS T 8 ASN 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: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 36312 Z= 0.149 Angle : 0.451 5.527 49104 Z= 0.251 Chirality : 0.035 0.115 5112 Planarity : 0.003 0.033 6480 Dihedral : 3.548 31.351 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.36 % Allowed : 1.21 % Favored : 98.43 % Rotamer Outliers : 2.91 % 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: 5.39 (0.12), residues: 4320 helix: 4.39 (0.08), residues: 3432 sheet: None (None), residues: 0 loop : -0.26 (0.20), residues: 888 *********************** 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 1010 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 929 time to evaluate : 4.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 34 residues processed: 962 average time/residue: 1.4859 time to fit residues: 1725.5994 Evaluate side-chains 933 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 899 time to evaluate : 3.916 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 30 residues processed: 5 average time/residue: 1.3662 time to fit residues: 13.6776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 505 optimal weight: 5.9990 chunk 531 optimal weight: 0.9980 chunk 485 optimal weight: 5.9990 chunk 517 optimal weight: 5.9990 chunk 311 optimal weight: 50.0000 chunk 225 optimal weight: 0.7980 chunk 406 optimal weight: 50.0000 chunk 158 optimal weight: 1.9990 chunk 467 optimal weight: 1.9990 chunk 489 optimal weight: 8.9990 chunk 515 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 ** F 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 ASN G 102 HIS H 8 ASN H 102 HIS I 8 ASN I 102 HIS J 102 HIS K 8 ASN 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 V 8 ASN V 102 HIS W 102 HIS X 8 ASN X 102 HIS Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 36312 Z= 0.172 Angle : 0.462 5.518 49104 Z= 0.254 Chirality : 0.036 0.115 5112 Planarity : 0.003 0.032 6480 Dihedral : 3.508 31.255 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.36 % Allowed : 1.38 % Favored : 98.26 % Rotamer Outliers : 2.26 % 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: 5.51 (0.12), residues: 4320 helix: 4.46 (0.08), residues: 3432 sheet: None (None), residues: 0 loop : -0.13 (0.20), residues: 888 *********************** 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 964 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 908 time to evaluate : 4.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 38 residues processed: 936 average time/residue: 1.4956 time to fit residues: 1697.2662 Evaluate side-chains 923 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 885 time to evaluate : 4.209 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 29 residues processed: 10 average time/residue: 1.4321 time to fit residues: 23.4453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 339 optimal weight: 2.9990 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: 8.9990 chunk 456 optimal weight: 0.2980 chunk 47 optimal weight: 50.0000 chunk 352 optimal weight: 7.9990 chunk 280 optimal weight: 3.9990 overall best weight: 4.8588 ------------------------------------------------------------------------------- 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 8 ASN H 102 HIS I 8 ASN I 102 HIS J 62 HIS J 102 HIS K 8 ASN K 102 HIS L 8 ASN L 102 HIS M 8 ASN M 62 HIS M 102 HIS N 8 ASN N 102 HIS O 8 ASN O 102 HIS P 8 ASN P 102 HIS Q 55 GLN Q 62 HIS Q 102 HIS R 102 HIS S 8 ASN S 102 HIS T 8 ASN T 102 HIS U 102 HIS V 8 ASN V 62 HIS V 102 HIS W 102 HIS X 8 ASN X 102 HIS Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.044 36312 Z= 0.428 Angle : 0.610 6.649 49104 Z= 0.330 Chirality : 0.044 0.148 5112 Planarity : 0.004 0.035 6480 Dihedral : 3.787 34.886 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.34 % Allowed : 1.70 % Favored : 97.97 % Rotamer Outliers : 2.57 % 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: 4.75 (0.12), residues: 4320 helix: 3.87 (0.08), residues: 3432 sheet: None (None), residues: 0 loop : -0.15 (0.20), residues: 888 ********************** 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 975 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 907 time to evaluate : 4.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 58 residues processed: 941 average time/residue: 1.4497 time to fit residues: 1654.5611 Evaluate side-chains 970 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 912 time to evaluate : 4.622 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 30 residues processed: 28 average time/residue: 1.5372 time to fit residues: 56.9071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 362 optimal weight: 1.9990 chunk 486 optimal weight: 3.9990 chunk 139 optimal weight: 50.0000 chunk 421 optimal weight: 2.9990 chunk 67 optimal weight: 50.0000 chunk 126 optimal weight: 2.9990 chunk 457 optimal weight: 7.9990 chunk 191 optimal weight: 50.0000 chunk 469 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 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 55 GLN 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 8 ASN H 102 HIS I 8 ASN I 102 HIS J 102 HIS K 8 ASN L 8 ASN L 102 HIS M 8 ASN M 102 HIS N 8 ASN N 102 HIS O 8 ASN O 55 GLN 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 102 HIS V 8 ASN V 102 HIS W 102 HIS X 8 ASN X 102 HIS Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.104090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.081488 restraints weight = 310501.029| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 3.82 r_work: 0.2529 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1464 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1467 | |-----------------------------------------------------------------------------| r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3469 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= 0.304 Angle : 0.550 5.967 49104 Z= 0.301 Chirality : 0.040 0.128 5112 Planarity : 0.003 0.035 6480 Dihedral : 3.745 34.619 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.34 % Allowed : 1.57 % Favored : 98.09 % Rotamer Outliers : 1.98 % 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: 4.81 (0.12), residues: 4320 helix: 3.92 (0.08), residues: 3432 sheet: None (None), residues: 0 loop : -0.15 (0.20), residues: 888 =============================================================================== Job complete usr+sys time: 22794.29 seconds wall clock time: 398 minutes 14.26 seconds (23894.26 seconds total)