Starting phenix.real_space_refine on Wed Nov 22 06:28:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sht_10205/11_2023/6sht_10205_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sht_10205/11_2023/6sht_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_10205/11_2023/6sht_10205.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sht_10205/11_2023/6sht_10205.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sht_10205/11_2023/6sht_10205_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sht_10205/11_2023/6sht_10205_neut.pdb" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 24 7.16 5 Mg 24 5.21 5 S 192 5.16 5 C 22296 2.51 5 N 6264 2.21 5 O 8352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 60": "NH1" <-> "NH2" Residue "A ARG 60": "NH1" <-> "NH2" Residue "A ASP 89": "OD1" <-> "OD2" Residue "B PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 60": "NH1" <-> "NH2" Residue "B ARG 60": "NH1" <-> "NH2" Residue "B ASP 89": "OD1" <-> "OD2" Residue "C PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 60": "NH1" <-> "NH2" Residue "C ARG 60": "NH1" <-> "NH2" Residue "C ASP 89": "OD1" <-> "OD2" Residue "D PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "D ASP 89": "OD1" <-> "OD2" Residue "E PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 60": "NH1" <-> "NH2" Residue "E ARG 60": "NH1" <-> "NH2" Residue "E ASP 89": "OD1" <-> "OD2" Residue "F PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 60": "NH1" <-> "NH2" Residue "F ARG 60": "NH1" <-> "NH2" Residue "F ASP 89": "OD1" <-> "OD2" Residue "G PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 60": "NH1" <-> "NH2" Residue "G ARG 60": "NH1" <-> "NH2" Residue "G ASP 89": "OD1" <-> "OD2" Residue "H PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 60": "NH1" <-> "NH2" Residue "H ARG 60": "NH1" <-> "NH2" Residue "H ASP 89": "OD1" <-> "OD2" Residue "I PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 60": "NH1" <-> "NH2" Residue "I ARG 60": "NH1" <-> "NH2" Residue "I ASP 89": "OD1" <-> "OD2" Residue "J PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 60": "NH1" <-> "NH2" Residue "J ARG 60": "NH1" <-> "NH2" Residue "J ASP 89": "OD1" <-> "OD2" Residue "K PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 60": "NH1" <-> "NH2" Residue "K ARG 60": "NH1" <-> "NH2" Residue "K ASP 89": "OD1" <-> "OD2" Residue "L PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ASP 89": "OD1" <-> "OD2" Residue "M PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 60": "NH1" <-> "NH2" Residue "M ARG 60": "NH1" <-> "NH2" Residue "M ASP 89": "OD1" <-> "OD2" Residue "N PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 60": "NH1" <-> "NH2" Residue "N ARG 60": "NH1" <-> "NH2" Residue "N ASP 89": "OD1" <-> "OD2" Residue "O PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 60": "NH1" <-> "NH2" Residue "O ARG 60": "NH1" <-> "NH2" Residue "O ASP 89": "OD1" <-> "OD2" Residue "P PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 60": "NH1" <-> "NH2" Residue "P ARG 60": "NH1" <-> "NH2" Residue "P ASP 89": "OD1" <-> "OD2" Residue "Q PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 60": "NH1" <-> "NH2" Residue "Q ARG 60": "NH1" <-> "NH2" Residue "Q ASP 89": "OD1" <-> "OD2" Residue "R PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 60": "NH1" <-> "NH2" Residue "R ARG 60": "NH1" <-> "NH2" Residue "R ASP 89": "OD1" <-> "OD2" Residue "S PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 60": "NH1" <-> "NH2" Residue "S ARG 60": "NH1" <-> "NH2" Residue "S ASP 89": "OD1" <-> "OD2" Residue "T PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 60": "NH1" <-> "NH2" Residue "T ARG 60": "NH1" <-> "NH2" Residue "T ASP 89": "OD1" <-> "OD2" Residue "U PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 60": "NH1" <-> "NH2" Residue "U ARG 60": "NH1" <-> "NH2" Residue "U ASP 89": "OD1" <-> "OD2" Residue "V PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 60": "NH1" <-> "NH2" Residue "V ARG 60": "NH1" <-> "NH2" Residue "V ASP 89": "OD1" <-> "OD2" Residue "W PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 60": "NH1" <-> "NH2" Residue "W ARG 60": "NH1" <-> "NH2" Residue "W ASP 89": "OD1" <-> "OD2" Residue "X PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 60": "NH1" <-> "NH2" Residue "X ARG 60": "NH1" <-> "NH2" Residue "X ASP 89": "OD1" <-> "OD2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 34.79, per 1000 atoms: 0.94 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: 15.49 Conformation dependent library (CDL) restraints added in 11.8 seconds 8640 Ramachandran restraints generated. 4320 Oldfield, 0 Emsley, 4320 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8400 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 77.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.83 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: 10.82 Time building geometry restraints manager: 16.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 9888 1.33 - 1.46: 8088 1.46 - 1.58: 17976 1.58 - 1.71: 48 1.71 - 1.84: 312 Bond restraints: 36312 Sorted by residual: bond pdb=" CA ALA D 157 " pdb=" CB ALA D 157 " ideal model delta sigma weight residual 1.530 1.465 0.064 1.46e-02 4.69e+03 1.94e+01 bond pdb=" CA ALA M 157 " pdb=" CB ALA M 157 " ideal model delta sigma weight residual 1.530 1.465 0.064 1.46e-02 4.69e+03 1.94e+01 bond pdb=" CA ALA B 157 " pdb=" CB ALA B 157 " ideal model delta sigma weight residual 1.530 1.465 0.064 1.46e-02 4.69e+03 1.94e+01 bond pdb=" CA ALA E 157 " pdb=" CB ALA E 157 " ideal model delta sigma weight residual 1.530 1.465 0.064 1.46e-02 4.69e+03 1.94e+01 bond pdb=" CA ALA K 157 " pdb=" CB ALA K 157 " ideal model delta sigma weight residual 1.530 1.465 0.064 1.46e-02 4.69e+03 1.94e+01 ... (remaining 36307 not shown) Histogram of bond angle deviations from ideal: 99.84 - 106.68: 1032 106.68 - 113.53: 18624 113.53 - 120.37: 16008 120.37 - 127.21: 13080 127.21 - 134.06: 360 Bond angle restraints: 49104 Sorted by residual: angle pdb=" N HIS B 170 " pdb=" CA HIS B 170 " pdb=" C HIS B 170 " ideal model delta sigma weight residual 111.69 118.63 -6.94 1.23e+00 6.61e-01 3.18e+01 angle pdb=" N HIS D 170 " pdb=" CA HIS D 170 " pdb=" C HIS D 170 " ideal model delta sigma weight residual 111.69 118.63 -6.94 1.23e+00 6.61e-01 3.18e+01 angle pdb=" N HIS Q 170 " pdb=" CA HIS Q 170 " pdb=" C HIS Q 170 " ideal model delta sigma weight residual 111.69 118.63 -6.94 1.23e+00 6.61e-01 3.18e+01 angle pdb=" N HIS U 170 " pdb=" CA HIS U 170 " pdb=" C HIS U 170 " ideal model delta sigma weight residual 111.69 118.63 -6.94 1.23e+00 6.61e-01 3.18e+01 angle pdb=" N HIS J 170 " pdb=" CA HIS J 170 " pdb=" C HIS J 170 " ideal model delta sigma weight residual 111.69 118.63 -6.94 1.23e+00 6.61e-01 3.18e+01 ... (remaining 49099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 21504 35.95 - 71.90: 1032 71.90 - 107.85: 24 107.85 - 143.80: 0 143.80 - 179.75: 24 Dihedral angle restraints: 22584 sinusoidal: 9456 harmonic: 13128 Sorted by residual: dihedral pdb=" CD BARG A 60 " pdb=" NE BARG A 60 " pdb=" CZ BARG A 60 " pdb=" NH1BARG A 60 " ideal model delta sinusoidal sigma weight residual 0.00 179.75 -179.75 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD BARG C 60 " pdb=" NE BARG C 60 " pdb=" CZ BARG C 60 " pdb=" NH1BARG C 60 " ideal model delta sinusoidal sigma weight residual 0.00 179.75 -179.75 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD BARG D 60 " pdb=" NE BARG D 60 " pdb=" CZ BARG D 60 " pdb=" NH1BARG D 60 " ideal model delta sinusoidal sigma weight residual 0.00 179.75 -179.75 1 1.00e+01 1.00e-02 1.92e+02 ... (remaining 22581 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.054: 2664 0.054 - 0.105: 1848 0.105 - 0.157: 504 0.157 - 0.209: 72 0.209 - 0.261: 24 Chirality restraints: 5112 Sorted by residual: chirality pdb=" CA VAL I 43 " pdb=" N VAL I 43 " pdb=" C VAL I 43 " pdb=" CB VAL I 43 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA VAL C 43 " pdb=" N VAL C 43 " pdb=" C VAL C 43 " pdb=" CB VAL C 43 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA VAL K 43 " pdb=" N VAL K 43 " pdb=" C VAL K 43 " pdb=" CB VAL K 43 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 5109 not shown) Planarity restraints: 6480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 134 " -0.038 2.00e-02 2.50e+03 1.99e-02 7.93e+00 pdb=" CG TYR F 134 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR F 134 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR F 134 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR F 134 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR F 134 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR F 134 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR F 134 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 134 " -0.038 2.00e-02 2.50e+03 1.99e-02 7.93e+00 pdb=" CG TYR L 134 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR L 134 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR L 134 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR L 134 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR L 134 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR L 134 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR L 134 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 134 " -0.038 2.00e-02 2.50e+03 1.99e-02 7.93e+00 pdb=" CG TYR G 134 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR G 134 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR G 134 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR G 134 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR G 134 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR G 134 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR G 134 " -0.018 2.00e-02 2.50e+03 ... (remaining 6477 not shown) Histogram of nonbonded interaction distances: 0.00 - 0.98: 60 0.98 - 1.96: 48 1.96 - 2.94: 16140 2.94 - 3.92: 107076 3.92 - 4.90: 208788 Warning: very small nonbonded interaction distances. Nonbonded interactions: 332112 Sorted by model distance: nonbonded pdb="FE FE D 201 " pdb="FE FE J 201 " model vdw 0.000 1.480 nonbonded pdb="FE FE D 201 " pdb="FE FE M 201 " model vdw 0.000 1.480 nonbonded pdb="FE FE D 201 " pdb="FE FE V 201 " model vdw 0.000 1.480 nonbonded pdb="FE FE J 201 " pdb="FE FE M 201 " model vdw 0.000 1.480 nonbonded pdb="FE FE J 201 " pdb="FE FE V 201 " model vdw 0.000 1.480 ... (remaining 332107 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'B' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'C' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'D' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'E' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'F' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'G' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'H' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'I' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'J' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'K' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'L' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'M' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'N' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'O' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'P' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'Q' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'R' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'S' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'T' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'U' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'V' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'W' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) selection = (chain 'X' and (resid 1 through 49 or resid 51 through 53 or resid 55 through 59 \ or resid 61 through 129 or resid 131 through 135 or resid 138 through 152 or re \ sid 154 through 168 or resid 170 through 202)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.93 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 5.680 Check model and map are aligned: 0.540 Set scattering table: 0.320 Process input model: 113.560 Find NCS groups from input model: 2.590 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.083 36312 Z= 0.990 Angle : 1.547 10.740 49104 Z= 1.010 Chirality : 0.070 0.261 5112 Planarity : 0.007 0.040 6480 Dihedral : 19.276 179.750 14184 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.58 % Allowed : 0.58 % Favored : 98.84 % Rotamer: Outliers : 5.56 % Allowed : 13.58 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.11), residues: 4320 helix: -1.81 (0.07), residues: 3384 sheet: None (None), residues: 0 loop : -1.17 (0.22), residues: 936 *********************** 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 : 4.222 Fit side-chains outliers start: 192 outliers final: 24 residues processed: 1392 average time/residue: 1.8593 time to fit residues: 3016.5970 Evaluate side-chains 978 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 954 time to evaluate : 4.160 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 5.6125 ------------------------------------------------------------------------------- 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: 0.9980 chunk 436 optimal weight: 8.9990 chunk 242 optimal weight: 0.9980 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: 0.8980 chunk 274 optimal weight: 3.9990 chunk 336 optimal weight: 5.9990 chunk 523 optimal weight: 50.0000 overall best weight: 1.3840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 55 GLN B 57 HIS B 72 GLN B 95 ASN C 72 GLN ** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 HIS F 62 HIS F 72 GLN G 57 HIS G 72 GLN G 108 ASN I 72 GLN I 108 ASN ** J 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 55 GLN K 72 GLN K 95 ASN L 72 GLN M 55 GLN M 95 ASN M 108 ASN N 8 ASN N 57 HIS N 62 HIS O 108 ASN P 72 GLN Q 72 GLN R 72 GLN R 108 ASN S 57 HIS S 72 GLN ** S 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 55 GLN T 57 HIS T 72 GLN U 57 HIS U 72 GLN U 151 ASN V 72 GLN W 57 HIS W 95 ASN X 72 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.290 36312 Z= 0.680 Angle : 1.968 40.348 49104 Z= 0.996 Chirality : 0.076 0.723 5112 Planarity : 0.017 0.175 6480 Dihedral : 13.696 179.984 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.68 % Allowed : 3.05 % Favored : 96.27 % Rotamer: Outliers : 7.64 % Allowed : 18.34 % Favored : 74.02 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.11), residues: 4320 helix: -0.67 (0.07), residues: 3384 sheet: None (None), residues: 0 loop : -1.56 (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 1359 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 1094 time to evaluate : 3.937 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 265 outliers final: 69 residues processed: 1162 average time/residue: 1.5792 time to fit residues: 2160.0289 Evaluate side-chains 1055 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 986 time to evaluate : 2.553 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 10 residues processed: 59 average time/residue: 0.6580 time to fit residues: 54.3293 ------------------------------------------------------------------------------- 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: 0.8980 chunk 162 optimal weight: 50.0000 chunk 435 optimal weight: 2.9990 chunk 356 optimal weight: 50.0000 chunk 144 optimal weight: 0.8980 chunk 524 optimal weight: 50.0000 chunk 566 optimal weight: 0.9980 chunk 466 optimal weight: 2.9990 chunk 519 optimal weight: 6.9990 chunk 178 optimal weight: 7.9990 chunk 420 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 C 72 GLN C 95 ASN D 55 GLN D 95 ASN D 109 GLN E 55 GLN E 72 GLN F 95 ASN G 95 ASN G 108 ASN H 72 GLN I 55 GLN I 108 ASN J 55 GLN K 72 GLN L 55 GLN L 72 GLN M 10 HIS M 22 ASN M 108 ASN ** M 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 55 GLN N 102 HIS O 72 GLN O 108 ASN P 72 GLN Q 72 GLN R 72 GLN R 95 ASN R 108 ASN R 115 HIS S 55 GLN S 72 GLN S 95 ASN T 72 GLN T 95 ASN U 72 GLN U 95 ASN U 108 ASN V 72 GLN V 95 ASN W 72 GLN X 72 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 36312 Z= 0.197 Angle : 0.551 7.371 49104 Z= 0.303 Chirality : 0.039 0.140 5112 Planarity : 0.004 0.055 6480 Dihedral : 13.007 179.974 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.48 % Allowed : 0.92 % Favored : 98.59 % Rotamer: Outliers : 3.76 % Allowed : 22.94 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.29 (0.12), residues: 4320 helix: 2.89 (0.08), residues: 3408 sheet: None (None), residues: 0 loop : -0.78 (0.20), residues: 912 *********************** 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 1141 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 1024 time to evaluate : 4.400 Fit side-chains outliers start: 117 outliers final: 32 residues processed: 1062 average time/residue: 1.2220 time to fit residues: 1543.3256 Evaluate side-chains 920 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 888 time to evaluate : 2.523 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 26 residues processed: 12 average time/residue: 0.3101 time to fit residues: 9.5486 ------------------------------------------------------------------------------- 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: 3.9990 chunk 271 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 250 optimal weight: 4.9990 chunk 351 optimal weight: 3.9990 chunk 525 optimal weight: 50.0000 chunk 556 optimal weight: 0.9980 chunk 274 optimal weight: 0.9980 chunk 498 optimal weight: 50.0000 chunk 150 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 95 ASN A 102 HIS ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 ASN B 102 HIS C 102 HIS ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 ASN D 102 HIS E 62 HIS E 95 ASN E 102 HIS ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 ASN F 62 HIS F 102 HIS G 8 ASN G 102 HIS H 8 ASN H 95 ASN H 102 HIS ** H 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 8 ASN I 102 HIS ** I 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 95 ASN J 102 HIS K 8 ASN ** K 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 102 HIS ** L 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 10 HIS M 102 HIS ** M 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 ASN N 102 HIS ** N 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 102 HIS O 108 ASN P 8 ASN P 102 HIS ** P 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 102 HIS ** Q 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 102 HIS S 102 HIS T 8 ASN T 102 HIS ** T 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 8 ASN U 102 HIS ** 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 8 ASN X 95 ASN X 102 HIS ** X 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 36312 Z= 0.212 Angle : 0.511 6.929 49104 Z= 0.280 Chirality : 0.038 0.126 5112 Planarity : 0.003 0.038 6480 Dihedral : 12.980 179.736 4968 Min Nonbonded Distance : 0.000 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.46 % Allowed : 1.07 % Favored : 98.47 % Rotamer: Outliers : 3.16 % Allowed : 25.31 % Favored : 71.53 % 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: 4.53 (0.12), residues: 4320 helix: 3.78 (0.08), residues: 3432 sheet: None (None), residues: 0 loop : -0.50 (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 1031 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 938 time to evaluate : 4.058 Fit side-chains outliers start: 93 outliers final: 53 residues processed: 985 average time/residue: 1.2936 time to fit residues: 1526.6905 Evaluate side-chains 954 residues out of total 3504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 901 time to evaluate : 5.097 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 34 residues processed: 24 average time/residue: 0.4922 time to fit residues: 21.9577 ------------------------------------------------------------------------------- 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: 6.9990 chunk 316 optimal weight: 10.0000 chunk 8 optimal weight: 0.0670 chunk 414 optimal weight: 0.8980 chunk 229 optimal weight: 0.9980 chunk 475 optimal weight: 50.0000 chunk 384 optimal weight: 0.9980 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: 1.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: