Starting phenix.real_space_refine on Sun Apr 14 14:04:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jax_36137/04_2024/8jax_36137_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jax_36137/04_2024/8jax_36137.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jax_36137/04_2024/8jax_36137.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jax_36137/04_2024/8jax_36137.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jax_36137/04_2024/8jax_36137_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jax_36137/04_2024/8jax_36137_updated.pdb" } resolution = 3.27 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 36 7.16 5 S 96 5.16 5 C 20181 2.51 5 N 5446 2.21 5 O 6130 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 60": "OD1" <-> "OD2" Residue "A ASP 99": "OD1" <-> "OD2" Residue "A GLU 127": "OE1" <-> "OE2" Residue "B ASP 60": "OD1" <-> "OD2" Residue "B ASP 126": "OD1" <-> "OD2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F ASP 113": "OD1" <-> "OD2" Residue "F GLU 127": "OE1" <-> "OE2" Residue "E TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 121": "OE1" <-> "OE2" Residue "G GLU 18": "OE1" <-> "OE2" Residue "G GLU 127": "OE1" <-> "OE2" Residue "H TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 121": "OE1" <-> "OE2" Residue "J TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 94": "OE1" <-> "OE2" Residue "M TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 51": "OE1" <-> "OE2" Residue "M ASP 99": "OD1" <-> "OD2" Residue "N TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 94": "OE1" <-> "OE2" Residue "Q TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 51": "OE1" <-> "OE2" Residue "R ASP 4": "OD1" <-> "OD2" Residue "R PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 121": "OE1" <-> "OE2" Residue "T GLU 94": "OE1" <-> "OE2" Residue "U TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 94": "OE1" <-> "OE2" Residue "X GLU 56": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 31889 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1313 Classifications: {'peptide': 162} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1293 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 156} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1318 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1305 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1310 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1304 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1304 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1304 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1299 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 156} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "J" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1318 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1318 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1307 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "N" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1310 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1315 Classifications: {'peptide': 162} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1305 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Q" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1318 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1310 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "T" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1315 Classifications: {'peptide': 162} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "U" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1318 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "W" Number of atoms: 1300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1300 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 156} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "X" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1310 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 11 residue: pdb=" NB HEM B 201 " occ=0.04 ... (41 atoms not shown) pdb="FE HEM B 201 " occ=0.04 residue: pdb=" NB HEM D 201 " occ=0.00 ... (41 atoms not shown) pdb="FE HEM D 201 " occ=0.00 residue: pdb=" NB HEM F 202 " occ=0.00 ... (41 atoms not shown) pdb="FE HEM F 202 " occ=0.00 residue: pdb=" NB HEM H 202 " occ=0.03 ... (41 atoms not shown) pdb="FE HEM H 202 " occ=0.03 residue: pdb=" NB HEM K 201 " occ=0.44 ... (41 atoms not shown) pdb="FE HEM K 201 " occ=0.44 residue: pdb=" NB HEM P 202 " occ=0.32 ... (41 atoms not shown) pdb="FE HEM P 202 " occ=0.32 residue: pdb=" NB HEM R 201 " occ=0.03 ... (41 atoms not shown) pdb="FE HEM R 201 " occ=0.03 residue: pdb=" NB HEM S 202 " occ=0.06 ... (41 atoms not shown) pdb="FE HEM S 202 " occ=0.06 residue: pdb=" NB HEM U 202 " occ=0.04 ... (41 atoms not shown) pdb="FE HEM U 202 " occ=0.04 residue: pdb=" NB HEM V 202 " occ=0.40 ... (41 atoms not shown) pdb="FE HEM V 202 " occ=0.40 residue: pdb=" NB HEM X 201 " occ=0.05 ... (41 atoms not shown) pdb="FE HEM X 201 " occ=0.05 Time building chain proxies: 16.26, per 1000 atoms: 0.51 Number of scatterers: 31889 At special positions: 0 Unit cell: (131.274, 131.274, 131.274, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 36 26.01 S 96 16.00 O 6130 8.00 N 5446 7.00 C 20181 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=21, symmetry=0 Number of additional bonds: simple=21, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.49 Conformation dependent library (CDL) restraints added in 5.7 seconds 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7422 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 0 sheets defined 77.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.54 Creating SS restraints... Processing helix chain 'A' and resid 5 through 35 Processing helix chain 'A' and resid 39 through 65 Processing helix chain 'A' and resid 83 through 110 Processing helix chain 'A' and resid 115 through 144 Processing helix chain 'A' and resid 146 through 153 removed outlier: 4.066A pdb=" N THR A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL A 153 " --> pdb=" O TYR A 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 35 removed outlier: 3.517A pdb=" N LYS B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 65 Processing helix chain 'B' and resid 83 through 110 Processing helix chain 'B' and resid 115 through 144 Processing helix chain 'B' and resid 146 through 153 Processing helix chain 'C' and resid 5 through 34 Processing helix chain 'C' and resid 38 through 65 removed outlier: 3.572A pdb=" N LEU C 65 " --> pdb=" O ARG C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 111 removed outlier: 3.674A pdb=" N LYS C 111 " --> pdb=" O VAL C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 144 Processing helix chain 'C' and resid 146 through 152 removed outlier: 3.817A pdb=" N THR C 152 " --> pdb=" O LEU C 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 35 Processing helix chain 'D' and resid 38 through 64 Processing helix chain 'D' and resid 83 through 111 removed outlier: 3.798A pdb=" N LYS D 111 " --> pdb=" O VAL D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 144 Processing helix chain 'D' and resid 146 through 153 Processing helix chain 'F' and resid 5 through 35 Processing helix chain 'F' and resid 39 through 64 Processing helix chain 'F' and resid 83 through 111 removed outlier: 3.506A pdb=" N LYS F 111 " --> pdb=" O VAL F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 144 Processing helix chain 'F' and resid 146 through 152 removed outlier: 3.796A pdb=" N THR F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 35 Processing helix chain 'E' and resid 38 through 64 Processing helix chain 'E' and resid 83 through 111 removed outlier: 3.729A pdb=" N LYS E 111 " --> pdb=" O VAL E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 144 Processing helix chain 'E' and resid 146 through 153 removed outlier: 3.767A pdb=" N VAL E 153 " --> pdb=" O TYR E 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 35 Processing helix chain 'G' and resid 38 through 64 Processing helix chain 'G' and resid 83 through 110 Processing helix chain 'G' and resid 115 through 144 Processing helix chain 'G' and resid 146 through 152 removed outlier: 4.027A pdb=" N THR G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 35 Processing helix chain 'H' and resid 38 through 64 Processing helix chain 'H' and resid 83 through 111 removed outlier: 3.697A pdb=" N LYS H 111 " --> pdb=" O VAL H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 144 Processing helix chain 'H' and resid 146 through 153 removed outlier: 3.609A pdb=" N VAL H 153 " --> pdb=" O TYR H 149 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 35 Processing helix chain 'I' and resid 38 through 64 Processing helix chain 'I' and resid 83 through 111 removed outlier: 3.733A pdb=" N LYS I 111 " --> pdb=" O VAL I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 115 through 144 Processing helix chain 'I' and resid 146 through 151 Processing helix chain 'J' and resid 5 through 35 Processing helix chain 'J' and resid 38 through 64 Processing helix chain 'J' and resid 83 through 111 removed outlier: 3.781A pdb=" N LYS J 111 " --> pdb=" O VAL J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 115 through 144 Processing helix chain 'J' and resid 146 through 152 removed outlier: 3.788A pdb=" N THR J 152 " --> pdb=" O LEU J 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 35 Processing helix chain 'K' and resid 38 through 64 Processing helix chain 'K' and resid 83 through 110 Processing helix chain 'K' and resid 115 through 144 Processing helix chain 'K' and resid 146 through 153 removed outlier: 3.703A pdb=" N VAL K 153 " --> pdb=" O TYR K 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 35 Processing helix chain 'L' and resid 38 through 64 Processing helix chain 'L' and resid 83 through 110 Processing helix chain 'L' and resid 115 through 144 Processing helix chain 'L' and resid 146 through 153 removed outlier: 3.930A pdb=" N THR L 152 " --> pdb=" O LEU L 148 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL L 153 " --> pdb=" O TYR L 149 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 35 Processing helix chain 'M' and resid 38 through 64 Processing helix chain 'M' and resid 83 through 111 removed outlier: 4.091A pdb=" N ALA M 110 " --> pdb=" O GLU M 106 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS M 111 " --> pdb=" O VAL M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 115 through 144 Processing helix chain 'M' and resid 146 through 152 removed outlier: 3.875A pdb=" N THR M 152 " --> pdb=" O LEU M 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 35 Processing helix chain 'N' and resid 39 through 64 Processing helix chain 'N' and resid 83 through 111 removed outlier: 3.632A pdb=" N LYS N 111 " --> pdb=" O VAL N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 115 through 144 Processing helix chain 'N' and resid 146 through 150 Processing helix chain 'O' and resid 5 through 35 Processing helix chain 'O' and resid 38 through 64 Processing helix chain 'O' and resid 83 through 111 removed outlier: 3.767A pdb=" N LYS O 111 " --> pdb=" O VAL O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 115 through 144 Processing helix chain 'O' and resid 146 through 153 Processing helix chain 'P' and resid 5 through 34 Processing helix chain 'P' and resid 38 through 64 Processing helix chain 'P' and resid 83 through 110 Processing helix chain 'P' and resid 115 through 144 Processing helix chain 'P' and resid 146 through 153 Processing helix chain 'Q' and resid 5 through 35 Processing helix chain 'Q' and resid 38 through 64 Processing helix chain 'Q' and resid 83 through 111 removed outlier: 4.124A pdb=" N ALA Q 110 " --> pdb=" O GLU Q 106 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LYS Q 111 " --> pdb=" O VAL Q 107 " (cutoff:3.500A) Processing helix chain 'Q' and resid 115 through 144 Processing helix chain 'Q' and resid 146 through 152 removed outlier: 3.869A pdb=" N THR Q 152 " --> pdb=" O LEU Q 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 35 Processing helix chain 'R' and resid 38 through 64 Processing helix chain 'R' and resid 83 through 110 Processing helix chain 'R' and resid 115 through 144 Processing helix chain 'R' and resid 146 through 151 Processing helix chain 'S' and resid 5 through 35 Processing helix chain 'S' and resid 38 through 64 Processing helix chain 'S' and resid 83 through 111 removed outlier: 4.293A pdb=" N ALA S 110 " --> pdb=" O GLU S 106 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LYS S 111 " --> pdb=" O VAL S 107 " (cutoff:3.500A) Processing helix chain 'S' and resid 115 through 144 Processing helix chain 'S' and resid 146 through 152 removed outlier: 3.820A pdb=" N THR S 152 " --> pdb=" O LEU S 148 " (cutoff:3.500A) Processing helix chain 'T' and resid 5 through 35 Processing helix chain 'T' and resid 38 through 64 Processing helix chain 'T' and resid 83 through 110 Processing helix chain 'T' and resid 115 through 144 Processing helix chain 'T' and resid 146 through 151 Processing helix chain 'U' and resid 5 through 35 Processing helix chain 'U' and resid 39 through 64 Processing helix chain 'U' and resid 83 through 111 removed outlier: 3.679A pdb=" N LYS U 111 " --> pdb=" O VAL U 107 " (cutoff:3.500A) Processing helix chain 'U' and resid 115 through 144 Processing helix chain 'U' and resid 146 through 153 Processing helix chain 'V' and resid 5 through 35 Processing helix chain 'V' and resid 38 through 64 Processing helix chain 'V' and resid 83 through 111 removed outlier: 3.726A pdb=" N LYS V 111 " --> pdb=" O VAL V 107 " (cutoff:3.500A) Processing helix chain 'V' and resid 115 through 144 Processing helix chain 'V' and resid 146 through 153 Processing helix chain 'W' and resid 5 through 35 Processing helix chain 'W' and resid 38 through 64 Processing helix chain 'W' and resid 83 through 111 removed outlier: 3.656A pdb=" N LYS W 111 " --> pdb=" O VAL W 107 " (cutoff:3.500A) Processing helix chain 'W' and resid 115 through 144 Processing helix chain 'W' and resid 146 through 152 removed outlier: 3.845A pdb=" N THR W 152 " --> pdb=" O LEU W 148 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 35 Processing helix chain 'X' and resid 38 through 64 Processing helix chain 'X' and resid 83 through 110 Processing helix chain 'X' and resid 115 through 144 Processing helix chain 'X' and resid 146 through 152 removed outlier: 3.838A pdb=" N THR X 152 " --> pdb=" O LEU X 148 " (cutoff:3.500A) 2454 hydrogen bonds defined for protein. 7362 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: 10.10 Time building geometry restraints manager: 14.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.41: 13552 1.41 - 1.60: 18673 1.60 - 1.79: 108 1.79 - 1.98: 84 1.98 - 2.17: 48 Bond restraints: 32465 Sorted by residual: bond pdb=" CB MET N 52 " pdb=" CG MET N 52 " ideal model delta sigma weight residual 1.520 1.440 0.080 3.00e-02 1.11e+03 7.04e+00 bond pdb=" SD MET O 52 " pdb=" CE MET O 52 " ideal model delta sigma weight residual 1.791 1.731 0.060 2.50e-02 1.60e+03 5.83e+00 bond pdb=" CB MET O 52 " pdb=" CG MET O 52 " ideal model delta sigma weight residual 1.520 1.448 0.072 3.00e-02 1.11e+03 5.78e+00 bond pdb=" SD MET N 52 " pdb=" CE MET N 52 " ideal model delta sigma weight residual 1.791 1.735 0.056 2.50e-02 1.60e+03 5.03e+00 bond pdb=" CB MET X 52 " pdb=" CG MET X 52 " ideal model delta sigma weight residual 1.520 1.455 0.065 3.00e-02 1.11e+03 4.75e+00 ... (remaining 32460 not shown) Histogram of bond angle deviations from ideal: 83.45 - 102.19: 145 102.19 - 120.93: 35295 120.93 - 139.67: 8587 139.67 - 158.41: 7 158.41 - 177.14: 18 Bond angle restraints: 44052 Sorted by residual: angle pdb=" CB MET O 52 " pdb=" CG MET O 52 " pdb=" SD MET O 52 " ideal model delta sigma weight residual 112.70 83.45 29.25 3.00e+00 1.11e-01 9.50e+01 angle pdb=" CB MET K 52 " pdb=" CG MET K 52 " pdb=" SD MET K 52 " ideal model delta sigma weight residual 112.70 141.19 -28.49 3.00e+00 1.11e-01 9.02e+01 angle pdb=" CB MET U 52 " pdb=" CG MET U 52 " pdb=" SD MET U 52 " ideal model delta sigma weight residual 112.70 89.62 23.08 3.00e+00 1.11e-01 5.92e+01 angle pdb=" CB MET W 52 " pdb=" CG MET W 52 " pdb=" SD MET W 52 " ideal model delta sigma weight residual 112.70 91.82 20.88 3.00e+00 1.11e-01 4.84e+01 angle pdb=" CB MET B 52 " pdb=" CG MET B 52 " pdb=" SD MET B 52 " ideal model delta sigma weight residual 112.70 93.10 19.60 3.00e+00 1.11e-01 4.27e+01 ... (remaining 44047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 16228 17.99 - 35.99: 2402 35.99 - 53.98: 621 53.98 - 71.98: 107 71.98 - 89.97: 79 Dihedral angle restraints: 19437 sinusoidal: 8062 harmonic: 11375 Sorted by residual: dihedral pdb=" CA MET K 52 " pdb=" C MET K 52 " pdb=" N ARG K 53 " pdb=" CA ARG K 53 " ideal model delta harmonic sigma weight residual 180.00 155.69 24.31 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA GLU F 94 " pdb=" C GLU F 94 " pdb=" N LEU F 95 " pdb=" CA LEU F 95 " ideal model delta harmonic sigma weight residual 180.00 157.74 22.26 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA GLU W 94 " pdb=" C GLU W 94 " pdb=" N LEU W 95 " pdb=" CA LEU W 95 " ideal model delta harmonic sigma weight residual 180.00 158.03 21.97 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 19434 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 4243 0.051 - 0.101: 564 0.101 - 0.152: 76 0.152 - 0.202: 7 0.202 - 0.253: 5 Chirality restraints: 4895 Sorted by residual: chirality pdb=" CA MET K 52 " pdb=" N MET K 52 " pdb=" C MET K 52 " pdb=" CB MET K 52 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA GLU W 94 " pdb=" N GLU W 94 " pdb=" C GLU W 94 " pdb=" CB GLU W 94 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA GLU F 94 " pdb=" N GLU F 94 " pdb=" C GLU F 94 " pdb=" CB GLU F 94 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 4892 not shown) Planarity restraints: 5697 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEM U 202 " 0.015 2.00e-02 2.50e+03 2.00e-02 8.99e+00 pdb=" C2C HEM U 202 " -0.001 2.00e-02 2.50e+03 pdb=" C3C HEM U 202 " 0.006 2.00e-02 2.50e+03 pdb=" C4C HEM U 202 " 0.013 2.00e-02 2.50e+03 pdb=" CAC HEM U 202 " 0.003 2.00e-02 2.50e+03 pdb=" CHC HEM U 202 " -0.029 2.00e-02 2.50e+03 pdb=" CHD HEM U 202 " -0.035 2.00e-02 2.50e+03 pdb=" CMC HEM U 202 " -0.004 2.00e-02 2.50e+03 pdb=" NC HEM U 202 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A HEM F 202 " -0.011 2.00e-02 2.50e+03 1.74e-02 6.79e+00 pdb=" C2A HEM F 202 " 0.027 2.00e-02 2.50e+03 pdb=" C3A HEM F 202 " 0.011 2.00e-02 2.50e+03 pdb=" C4A HEM F 202 " 0.004 2.00e-02 2.50e+03 pdb=" CAA HEM F 202 " -0.023 2.00e-02 2.50e+03 pdb=" CHA HEM F 202 " 0.019 2.00e-02 2.50e+03 pdb=" CHB HEM F 202 " 0.003 2.00e-02 2.50e+03 pdb=" CMA HEM F 202 " -0.002 2.00e-02 2.50e+03 pdb=" NA HEM F 202 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND HEM S 202 " -0.025 2.00e-02 2.50e+03 1.64e-02 6.03e+00 pdb=" C1D HEM S 202 " -0.016 2.00e-02 2.50e+03 pdb=" C2D HEM S 202 " -0.001 2.00e-02 2.50e+03 pdb=" C3D HEM S 202 " 0.007 2.00e-02 2.50e+03 pdb=" C4D HEM S 202 " -0.012 2.00e-02 2.50e+03 pdb=" CAD HEM S 202 " -0.007 2.00e-02 2.50e+03 pdb=" CHA HEM S 202 " 0.026 2.00e-02 2.50e+03 pdb=" CHD HEM S 202 " 0.025 2.00e-02 2.50e+03 pdb=" CMD HEM S 202 " 0.003 2.00e-02 2.50e+03 ... (remaining 5694 not shown) Histogram of nonbonded interaction distances: 1.14 - 1.89: 28 1.89 - 2.64: 614 2.64 - 3.40: 45825 3.40 - 4.15: 69286 4.15 - 4.90: 132479 Nonbonded interactions: 248232 Sorted by model distance: nonbonded pdb=" OE1 GLU W 18 " pdb=" OE1 GLU W 51 " model vdw 1.139 3.040 nonbonded pdb=" OE1 GLU F 18 " pdb=" OE1 GLU F 51 " model vdw 1.152 3.040 nonbonded pdb=" OE1 GLU T 18 " pdb=" OE1 GLU T 51 " model vdw 1.212 3.040 nonbonded pdb=" OE1 GLU Q 18 " pdb=" OE1 GLU Q 51 " model vdw 1.216 3.040 nonbonded pdb=" OE1 GLU X 18 " pdb=" OE1 GLU X 51 " model vdw 1.250 3.040 ... (remaining 248227 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 148 or (resid 149 and (name N or name CA or name \ C or name O or name CB )) or resid 150 through 156 or (resid 157 and (name N or \ name CA or name C or name O or name CB )))) selection = (chain 'B' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 157)) selection = (chain 'C' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 156 or (resid 157 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'E' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'F' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'G' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'H' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'I' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'J' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 156 or (resid 157 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'K' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'L' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 156 or (resid 157 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'M' and (resid 1 through 148 or (resid 149 and (name N or name CA or name \ C or name O or name CB )) or resid 150 through 157)) selection = (chain 'N' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'O' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 156 or (resid 157 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'P' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'Q' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 156 or (resid 157 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'R' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'S' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'T' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 156 or (resid 157 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'U' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'V' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 156 or (resid 157 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'W' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'X' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) } 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=0.99 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: 1.280 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: 0.040 Extract box with map and model: 5.810 Check model and map are aligned: 0.500 Set scattering table: 0.310 Process input model: 81.230 Find NCS groups from input model: 2.690 Set up NCS constraints: 0.120 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: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 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 : 0.005 0.095 32465 Z= 0.324 Angle : 0.834 29.248 44052 Z= 0.348 Chirality : 0.035 0.253 4895 Planarity : 0.003 0.042 5697 Dihedral : 18.674 89.974 12015 Min Nonbonded Distance : 1.139 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.44 % Favored : 97.38 % Rotamer: Outliers : 0.36 % Allowed : 25.34 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.04 (0.13), residues: 3810 helix: 3.01 (0.08), residues: 3049 sheet: None (None), residues: 0 loop : -2.57 (0.20), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 37 HIS 0.005 0.001 HIS S 54 PHE 0.016 0.001 PHE O 26 TYR 0.009 0.001 TYR M 25 ARG 0.011 0.001 ARG M 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 467 time to evaluate : 3.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 473 average time/residue: 0.4660 time to fit residues: 347.4763 Evaluate side-chains 455 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 450 time to evaluate : 4.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 156 GLN Chi-restraints excluded: chain L residue 160 ASP Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain T residue 22 ILE Chi-restraints excluded: chain V residue 141 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 321 optimal weight: 9.9990 chunk 288 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 7.9990 chunk 154 optimal weight: 8.9990 chunk 298 optimal weight: 8.9990 chunk 115 optimal weight: 9.9990 chunk 181 optimal weight: 3.9990 chunk 222 optimal weight: 10.0000 chunk 345 optimal weight: 0.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 81 GLN E 118 ASN K 130 HIS L 72 GLN O 156 GLN O 158 GLN P 118 ASN T 130 HIS X 2 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 32465 Z= 0.422 Angle : 0.747 25.088 44052 Z= 0.329 Chirality : 0.037 0.279 4895 Planarity : 0.003 0.033 5697 Dihedral : 6.587 87.109 4300 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.73 % Favored : 97.09 % Rotamer: Outliers : 3.62 % Allowed : 23.27 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.29 (0.13), residues: 3810 helix: 3.21 (0.08), residues: 3062 sheet: None (None), residues: 0 loop : -2.71 (0.20), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP S 37 HIS 0.006 0.001 HIS U 54 PHE 0.013 0.001 PHE C 26 TYR 0.010 0.001 TYR G 71 ARG 0.004 0.000 ARG H 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 440 time to evaluate : 3.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 56 GLU cc_start: 0.9194 (OUTLIER) cc_final: 0.8886 (tt0) REVERT: G 52 MET cc_start: 0.8487 (mtt) cc_final: 0.8203 (mtt) REVERT: G 150 LEU cc_start: 0.9669 (OUTLIER) cc_final: 0.9362 (mp) REVERT: H 105 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8370 (mt) REVERT: H 148 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9110 (tt) REVERT: I 39 LYS cc_start: 0.8781 (mppt) cc_final: 0.8576 (mttm) REVERT: I 81 GLN cc_start: 0.8915 (mp10) cc_final: 0.8664 (mp10) REVERT: K 81 GLN cc_start: 0.8924 (mp10) cc_final: 0.8689 (mp10) REVERT: P 52 MET cc_start: 0.8910 (ttm) cc_final: 0.8620 (mtt) REVERT: P 144 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8764 (mp) REVERT: T 94 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8327 (mm-30) REVERT: T 120 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.8818 (m-10) REVERT: W 52 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7945 (mtt) REVERT: W 94 GLU cc_start: 0.8235 (pt0) cc_final: 0.8020 (mt-10) REVERT: X 53 ARG cc_start: 0.8441 (mtm-85) cc_final: 0.8057 (mtm110) outliers start: 121 outliers final: 84 residues processed: 531 average time/residue: 0.4571 time to fit residues: 382.1848 Evaluate side-chains 505 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 413 time to evaluate : 3.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 151 SER Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 119 VAL Chi-restraints excluded: chain J residue 52 MET Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain J residue 152 THR Chi-restraints excluded: chain K residue 52 MET Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 160 ASP Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 141 ILE Chi-restraints excluded: chain N residue 52 MET Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 160 ASP Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain O residue 116 SER Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain O residue 158 GLN Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 144 LEU Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 152 THR Chi-restraints excluded: chain T residue 4 ASP Chi-restraints excluded: chain T residue 22 ILE Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 83 VAL Chi-restraints excluded: chain T residue 94 GLU Chi-restraints excluded: chain T residue 120 PHE Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 119 VAL Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 152 THR Chi-restraints excluded: chain W residue 52 MET Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 119 VAL Chi-restraints excluded: chain W residue 131 ILE Chi-restraints excluded: chain W residue 152 THR Chi-restraints excluded: chain X residue 52 MET Chi-restraints excluded: chain X residue 83 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 192 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 287 optimal weight: 7.9990 chunk 235 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 346 optimal weight: 3.9990 chunk 374 optimal weight: 6.9990 chunk 308 optimal weight: 2.9990 chunk 343 optimal weight: 0.9990 chunk 118 optimal weight: 9.9990 chunk 278 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 72 GLN ** O 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 32465 Z= 0.254 Angle : 0.614 19.540 44052 Z= 0.281 Chirality : 0.033 0.246 4895 Planarity : 0.003 0.031 5697 Dihedral : 6.522 88.407 4293 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.41 % Favored : 97.40 % Rotamer: Outliers : 3.26 % Allowed : 24.35 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.64 (0.13), residues: 3810 helix: 3.50 (0.08), residues: 3028 sheet: None (None), residues: 0 loop : -2.51 (0.20), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 37 HIS 0.003 0.000 HIS U 54 PHE 0.015 0.001 PHE C 26 TYR 0.005 0.001 TYR V 149 ARG 0.003 0.000 ARG K 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 463 time to evaluate : 4.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLN cc_start: 0.9153 (mm-40) cc_final: 0.8904 (mt0) REVERT: B 73 ARG cc_start: 0.9202 (OUTLIER) cc_final: 0.8020 (ptt90) REVERT: B 81 GLN cc_start: 0.9017 (mm-40) cc_final: 0.8774 (mm-40) REVERT: F 81 GLN cc_start: 0.8998 (mm-40) cc_final: 0.8793 (mm-40) REVERT: G 150 LEU cc_start: 0.9650 (OUTLIER) cc_final: 0.9393 (mp) REVERT: H 81 GLN cc_start: 0.8846 (mp10) cc_final: 0.8591 (mp10) REVERT: H 105 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8316 (mt) REVERT: H 148 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.8960 (tt) REVERT: I 81 GLN cc_start: 0.8912 (mp10) cc_final: 0.8664 (mp10) REVERT: J 105 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8347 (mt) REVERT: K 52 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8111 (pmm) REVERT: K 81 GLN cc_start: 0.8907 (mp10) cc_final: 0.8644 (mp10) REVERT: N 86 MET cc_start: 0.8083 (mtm) cc_final: 0.7855 (mtt) REVERT: T 94 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8357 (mm-30) REVERT: U 73 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.7964 (ptt90) REVERT: X 53 ARG cc_start: 0.8355 (mtm-85) cc_final: 0.7992 (mtm110) REVERT: X 81 GLN cc_start: 0.9007 (mm-40) cc_final: 0.8806 (mm-40) outliers start: 109 outliers final: 60 residues processed: 546 average time/residue: 0.4727 time to fit residues: 409.1920 Evaluate side-chains 490 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 422 time to evaluate : 4.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 151 SER Chi-restraints excluded: chain H residue 4 ASP Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 119 VAL Chi-restraints excluded: chain J residue 4 ASP Chi-restraints excluded: chain J residue 52 MET Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain K residue 52 MET Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain L residue 160 ASP Chi-restraints excluded: chain N residue 52 MET Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 116 SER Chi-restraints excluded: chain O residue 2 GLN Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain P residue 4 ASP Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain T residue 22 ILE Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 94 GLU Chi-restraints excluded: chain U residue 4 ASP Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 119 VAL Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 152 THR Chi-restraints excluded: chain V residue 4 ASP Chi-restraints excluded: chain V residue 119 VAL Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain V residue 152 THR Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain W residue 78 ARG Chi-restraints excluded: chain W residue 108 MET Chi-restraints excluded: chain W residue 131 ILE Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain X residue 52 MET Chi-restraints excluded: chain X residue 141 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 342 optimal weight: 10.0000 chunk 260 optimal weight: 4.9990 chunk 179 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 165 optimal weight: 0.9980 chunk 232 optimal weight: 0.9990 chunk 347 optimal weight: 4.9990 chunk 368 optimal weight: 0.8980 chunk 181 optimal weight: 0.7980 chunk 329 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 130 HIS E 14 GLN L 72 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 32465 Z= 0.200 Angle : 0.569 19.024 44052 Z= 0.261 Chirality : 0.032 0.216 4895 Planarity : 0.003 0.045 5697 Dihedral : 6.472 89.474 4293 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.15 % Favored : 97.66 % Rotamer: Outliers : 3.35 % Allowed : 23.84 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.84 (0.13), residues: 3810 helix: 3.66 (0.08), residues: 3046 sheet: None (None), residues: 0 loop : -2.68 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP H 37 HIS 0.003 0.000 HIS L 130 PHE 0.015 0.001 PHE C 26 TYR 0.006 0.001 TYR P 149 ARG 0.008 0.000 ARG H 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 479 time to evaluate : 3.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 150 LEU cc_start: 0.9644 (OUTLIER) cc_final: 0.9386 (mp) REVERT: H 81 GLN cc_start: 0.8830 (mp10) cc_final: 0.8585 (mp10) REVERT: H 148 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8881 (tt) REVERT: I 81 GLN cc_start: 0.8879 (mp10) cc_final: 0.8640 (mp10) REVERT: J 105 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8319 (mt) REVERT: K 52 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8110 (pmm) REVERT: K 81 GLN cc_start: 0.8870 (mp10) cc_final: 0.8607 (mp10) REVERT: N 108 MET cc_start: 0.8228 (mtp) cc_final: 0.8014 (mtp) REVERT: P 39 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7757 (mttt) REVERT: U 73 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.7960 (ptt90) REVERT: X 53 ARG cc_start: 0.8368 (mtm-85) cc_final: 0.7990 (mtm110) outliers start: 112 outliers final: 65 residues processed: 566 average time/residue: 0.4405 time to fit residues: 396.9861 Evaluate side-chains 515 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 444 time to evaluate : 3.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 4 ASP Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 119 VAL Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain J residue 4 ASP Chi-restraints excluded: chain J residue 52 MET Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain K residue 52 MET Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain L residue 160 ASP Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain N residue 52 MET Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 116 SER Chi-restraints excluded: chain N residue 160 ASP Chi-restraints excluded: chain O residue 2 GLN Chi-restraints excluded: chain O residue 116 SER Chi-restraints excluded: chain P residue 4 ASP Chi-restraints excluded: chain P residue 39 LYS Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain Q residue 73 ARG Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 116 SER Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain T residue 22 ILE Chi-restraints excluded: chain T residue 116 SER Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 77 VAL Chi-restraints excluded: chain U residue 119 VAL Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain V residue 4 ASP Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 116 SER Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain V residue 153 VAL Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain W residue 144 LEU Chi-restraints excluded: chain X residue 4 ASP Chi-restraints excluded: chain X residue 119 VAL Chi-restraints excluded: chain X residue 141 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 306 optimal weight: 0.7980 chunk 209 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 274 optimal weight: 0.9980 chunk 151 optimal weight: 7.9990 chunk 314 optimal weight: 0.9980 chunk 254 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 188 optimal weight: 9.9990 chunk 330 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 72 GLN N 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 32465 Z= 0.179 Angle : 0.549 19.124 44052 Z= 0.250 Chirality : 0.032 0.210 4895 Planarity : 0.002 0.032 5697 Dihedral : 6.423 89.095 4293 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.07 % Favored : 97.74 % Rotamer: Outliers : 2.48 % Allowed : 25.28 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.94 (0.13), residues: 3810 helix: 3.73 (0.08), residues: 3042 sheet: None (None), residues: 0 loop : -2.62 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP E 37 HIS 0.002 0.000 HIS W 130 PHE 0.015 0.001 PHE C 26 TYR 0.006 0.001 TYR F 43 ARG 0.010 0.000 ARG H 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 485 time to evaluate : 4.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 ARG cc_start: 0.9142 (OUTLIER) cc_final: 0.8005 (ptt90) REVERT: G 150 LEU cc_start: 0.9633 (OUTLIER) cc_final: 0.9397 (mp) REVERT: H 81 GLN cc_start: 0.8825 (mp10) cc_final: 0.8608 (mp10) REVERT: H 148 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8828 (tt) REVERT: I 81 GLN cc_start: 0.8860 (mp10) cc_final: 0.8628 (mp10) REVERT: J 105 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8278 (mt) REVERT: K 52 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8190 (pmm) REVERT: K 81 GLN cc_start: 0.8851 (mp10) cc_final: 0.8592 (mp10) REVERT: P 39 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7552 (mttt) REVERT: R 4 ASP cc_start: 0.8747 (OUTLIER) cc_final: 0.8492 (t0) REVERT: T 81 GLN cc_start: 0.8784 (mp10) cc_final: 0.8573 (mp10) REVERT: U 73 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.7960 (ptt90) outliers start: 83 outliers final: 46 residues processed: 549 average time/residue: 0.4440 time to fit residues: 388.2185 Evaluate side-chains 510 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 456 time to evaluate : 3.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 141 ILE Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 151 SER Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain I residue 50 ASP Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain J residue 4 ASP Chi-restraints excluded: chain J residue 52 MET Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain K residue 52 MET Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain L residue 160 ASP Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain N residue 52 MET Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 116 SER Chi-restraints excluded: chain O residue 2 GLN Chi-restraints excluded: chain P residue 4 ASP Chi-restraints excluded: chain P residue 39 LYS Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 73 ARG Chi-restraints excluded: chain R residue 4 ASP Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 147 SER Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain T residue 22 ILE Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain U residue 119 VAL Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain W residue 78 ARG Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain W residue 144 LEU Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 141 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 123 optimal weight: 2.9990 chunk 331 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 216 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 368 optimal weight: 3.9990 chunk 306 optimal weight: 0.9990 chunk 170 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 193 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 72 GLN O 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 32465 Z= 0.236 Angle : 0.581 18.800 44052 Z= 0.265 Chirality : 0.033 0.211 4895 Planarity : 0.003 0.034 5697 Dihedral : 6.392 89.411 4293 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.36 % Favored : 97.45 % Rotamer: Outliers : 3.11 % Allowed : 25.28 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.80 (0.13), residues: 3810 helix: 3.62 (0.08), residues: 3047 sheet: None (None), residues: 0 loop : -2.67 (0.20), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N 37 HIS 0.003 0.000 HIS U 54 PHE 0.011 0.001 PHE C 26 TYR 0.007 0.001 TYR N 25 ARG 0.004 0.000 ARG C 53 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 465 time to evaluate : 3.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLN cc_start: 0.9188 (mt0) cc_final: 0.8973 (mt0) REVERT: B 73 ARG cc_start: 0.9154 (OUTLIER) cc_final: 0.7907 (ptt90) REVERT: G 150 LEU cc_start: 0.9651 (OUTLIER) cc_final: 0.9374 (mp) REVERT: H 81 GLN cc_start: 0.8849 (mp10) cc_final: 0.8628 (mp10) REVERT: H 148 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8905 (tt) REVERT: I 81 GLN cc_start: 0.8892 (mp10) cc_final: 0.8681 (mp10) REVERT: K 52 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8361 (pmm) REVERT: K 81 GLN cc_start: 0.8872 (mp10) cc_final: 0.8614 (mp10) REVERT: N 108 MET cc_start: 0.8351 (mtp) cc_final: 0.8117 (mtp) REVERT: P 39 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.7810 (mttt) REVERT: R 4 ASP cc_start: 0.8739 (OUTLIER) cc_final: 0.8479 (t0) REVERT: T 81 GLN cc_start: 0.8852 (mp10) cc_final: 0.8633 (mp10) REVERT: U 73 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.8025 (ptt90) REVERT: X 53 ARG cc_start: 0.8441 (mtm-85) cc_final: 0.8092 (mtm110) outliers start: 104 outliers final: 77 residues processed: 557 average time/residue: 0.4723 time to fit residues: 419.2501 Evaluate side-chains 532 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 448 time to evaluate : 3.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 4 ASP Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 2 GLN Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 151 SER Chi-restraints excluded: chain H residue 60 ASP Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 119 VAL Chi-restraints excluded: chain I residue 148 LEU Chi-restraints excluded: chain J residue 4 ASP Chi-restraints excluded: chain J residue 52 MET Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain K residue 52 MET Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain L residue 4 ASP Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain L residue 147 SER Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 160 ASP Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain N residue 52 MET Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 116 SER Chi-restraints excluded: chain N residue 160 ASP Chi-restraints excluded: chain O residue 2 GLN Chi-restraints excluded: chain O residue 116 SER Chi-restraints excluded: chain P residue 4 ASP Chi-restraints excluded: chain P residue 39 LYS Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 73 ARG Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 116 SER Chi-restraints excluded: chain R residue 4 ASP Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 147 SER Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain T residue 22 ILE Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain U residue 4 ASP Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 77 VAL Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain U residue 119 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 116 SER Chi-restraints excluded: chain V residue 119 VAL Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain V residue 153 VAL Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain W residue 78 ARG Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 119 VAL Chi-restraints excluded: chain W residue 131 ILE Chi-restraints excluded: chain W residue 144 LEU Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 116 SER Chi-restraints excluded: chain X residue 119 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 355 optimal weight: 8.9990 chunk 41 optimal weight: 9.9990 chunk 210 optimal weight: 2.9990 chunk 269 optimal weight: 6.9990 chunk 208 optimal weight: 5.9990 chunk 310 optimal weight: 10.0000 chunk 205 optimal weight: 10.0000 chunk 367 optimal weight: 7.9990 chunk 229 optimal weight: 8.9990 chunk 223 optimal weight: 10.0000 chunk 169 optimal weight: 4.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 72 GLN ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 32465 Z= 0.392 Angle : 0.664 19.614 44052 Z= 0.314 Chirality : 0.036 0.233 4895 Planarity : 0.003 0.056 5697 Dihedral : 6.476 87.349 4293 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.76 % Favored : 97.06 % Rotamer: Outliers : 4.07 % Allowed : 24.17 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.53 (0.13), residues: 3810 helix: 3.42 (0.08), residues: 3034 sheet: None (None), residues: 0 loop : -2.61 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 37 HIS 0.006 0.001 HIS U 54 PHE 0.022 0.001 PHE V 120 TYR 0.009 0.001 TYR G 71 ARG 0.011 0.000 ARG H 45 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 443 time to evaluate : 4.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 81 GLN cc_start: 0.8986 (mp10) cc_final: 0.8585 (mp10) REVERT: G 150 LEU cc_start: 0.9671 (OUTLIER) cc_final: 0.9375 (mp) REVERT: H 81 GLN cc_start: 0.8884 (mp10) cc_final: 0.8653 (mp10) REVERT: H 144 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8959 (mp) REVERT: H 148 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9017 (tt) REVERT: I 81 GLN cc_start: 0.8960 (mp10) cc_final: 0.8736 (mp10) REVERT: K 81 GLN cc_start: 0.8918 (mp10) cc_final: 0.8649 (mp10) REVERT: N 108 MET cc_start: 0.8674 (mtp) cc_final: 0.8468 (mtp) REVERT: N 144 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8941 (mp) REVERT: P 39 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8196 (mttt) REVERT: R 4 ASP cc_start: 0.8871 (OUTLIER) cc_final: 0.8576 (t0) REVERT: R 105 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8448 (mt) REVERT: S 114 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8042 (mm) REVERT: T 4 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.7501 (p0) REVERT: T 81 GLN cc_start: 0.8904 (mp10) cc_final: 0.8677 (mp10) REVERT: T 156 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.8490 (pt0) REVERT: U 73 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.8044 (ptt90) REVERT: X 53 ARG cc_start: 0.8473 (mtm-85) cc_final: 0.8200 (mtm110) outliers start: 136 outliers final: 108 residues processed: 556 average time/residue: 0.4844 time to fit residues: 417.7659 Evaluate side-chains 539 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 420 time to evaluate : 3.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 4 ASP Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 2 GLN Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain F residue 78 ARG Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 151 SER Chi-restraints excluded: chain H residue 60 ASP Chi-restraints excluded: chain H residue 83 VAL Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 119 VAL Chi-restraints excluded: chain I residue 148 LEU Chi-restraints excluded: chain J residue 4 ASP Chi-restraints excluded: chain J residue 52 MET Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain L residue 4 ASP Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain L residue 147 SER Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 141 ILE Chi-restraints excluded: chain N residue 52 MET Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 116 SER Chi-restraints excluded: chain N residue 144 LEU Chi-restraints excluded: chain N residue 160 ASP Chi-restraints excluded: chain O residue 2 GLN Chi-restraints excluded: chain O residue 68 LEU Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain O residue 116 SER Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain O residue 153 VAL Chi-restraints excluded: chain O residue 158 GLN Chi-restraints excluded: chain P residue 4 ASP Chi-restraints excluded: chain P residue 39 LYS Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 73 ARG Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 116 SER Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain R residue 4 ASP Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain R residue 147 SER Chi-restraints excluded: chain S residue 52 MET Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 114 ILE Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain T residue 4 ASP Chi-restraints excluded: chain T residue 22 ILE Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 83 VAL Chi-restraints excluded: chain T residue 116 SER Chi-restraints excluded: chain T residue 156 GLN Chi-restraints excluded: chain U residue 4 ASP Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 77 VAL Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain U residue 119 VAL Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 116 SER Chi-restraints excluded: chain V residue 119 VAL Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain W residue 78 ARG Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 119 VAL Chi-restraints excluded: chain W residue 131 ILE Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 116 SER Chi-restraints excluded: chain X residue 119 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 227 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 chunk 219 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 233 optimal weight: 9.9990 chunk 250 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 288 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 72 GLN ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 32465 Z= 0.265 Angle : 0.639 26.520 44052 Z= 0.285 Chirality : 0.033 0.187 4895 Planarity : 0.003 0.048 5697 Dihedral : 6.478 87.811 4291 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.36 % Favored : 97.48 % Rotamer: Outliers : 3.50 % Allowed : 24.89 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.76 (0.13), residues: 3810 helix: 3.64 (0.08), residues: 3013 sheet: None (None), residues: 0 loop : -2.59 (0.20), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 37 HIS 0.003 0.000 HIS U 54 PHE 0.014 0.001 PHE H 26 TYR 0.007 0.001 TYR V 149 ARG 0.014 0.000 ARG I 53 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 453 time to evaluate : 3.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 ARG cc_start: 0.9191 (OUTLIER) cc_final: 0.7978 (ptt90) REVERT: B 81 GLN cc_start: 0.9066 (mm-40) cc_final: 0.8847 (mm110) REVERT: G 150 LEU cc_start: 0.9651 (OUTLIER) cc_final: 0.9397 (mp) REVERT: H 81 GLN cc_start: 0.8867 (mp10) cc_final: 0.8642 (mp10) REVERT: H 148 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8927 (tt) REVERT: I 81 GLN cc_start: 0.8949 (mp10) cc_final: 0.8722 (mp10) REVERT: I 153 VAL cc_start: 0.9017 (OUTLIER) cc_final: 0.8747 (m) REVERT: K 81 GLN cc_start: 0.8912 (mp10) cc_final: 0.8642 (mp10) REVERT: N 108 MET cc_start: 0.8585 (mtp) cc_final: 0.8384 (mtp) REVERT: P 39 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.7969 (mttt) REVERT: R 4 ASP cc_start: 0.8868 (OUTLIER) cc_final: 0.8581 (t0) REVERT: R 81 GLN cc_start: 0.8810 (mp10) cc_final: 0.8394 (mp10) REVERT: S 114 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.7973 (mm) REVERT: T 4 ASP cc_start: 0.8204 (OUTLIER) cc_final: 0.7468 (p0) REVERT: T 81 GLN cc_start: 0.8891 (mp10) cc_final: 0.8671 (mp10) REVERT: U 73 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.7966 (ptt90) REVERT: X 53 ARG cc_start: 0.8495 (mtm-85) cc_final: 0.8248 (mtm110) outliers start: 117 outliers final: 87 residues processed: 556 average time/residue: 0.4517 time to fit residues: 396.6279 Evaluate side-chains 526 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 430 time to evaluate : 4.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 4 ASP Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain F residue 78 ARG Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 151 SER Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 119 VAL Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain J residue 4 ASP Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 4 ASP Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain M residue 141 ILE Chi-restraints excluded: chain N residue 52 MET Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 116 SER Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 160 ASP Chi-restraints excluded: chain O residue 2 GLN Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain O residue 116 SER Chi-restraints excluded: chain O residue 153 VAL Chi-restraints excluded: chain P residue 39 LYS Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 73 ARG Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 116 SER Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain R residue 4 ASP Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 147 SER Chi-restraints excluded: chain S residue 52 MET Chi-restraints excluded: chain S residue 114 ILE Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain T residue 4 ASP Chi-restraints excluded: chain T residue 22 ILE Chi-restraints excluded: chain T residue 116 SER Chi-restraints excluded: chain U residue 4 ASP Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 77 VAL Chi-restraints excluded: chain U residue 119 VAL Chi-restraints excluded: chain U residue 137 GLN Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 116 SER Chi-restraints excluded: chain V residue 119 VAL Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain W residue 78 ARG Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 116 SER Chi-restraints excluded: chain W residue 119 VAL Chi-restraints excluded: chain W residue 131 ILE Chi-restraints excluded: chain X residue 4 ASP Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 116 SER Chi-restraints excluded: chain X residue 119 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 334 optimal weight: 6.9990 chunk 351 optimal weight: 7.9990 chunk 320 optimal weight: 9.9990 chunk 342 optimal weight: 3.9990 chunk 205 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 268 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 chunk 309 optimal weight: 7.9990 chunk 323 optimal weight: 5.9990 chunk 341 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 81 GLN K 130 HIS L 72 GLN ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 32465 Z= 0.318 Angle : 0.659 23.138 44052 Z= 0.295 Chirality : 0.034 0.197 4895 Planarity : 0.003 0.059 5697 Dihedral : 6.464 86.291 4291 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.62 % Favored : 97.22 % Rotamer: Outliers : 3.56 % Allowed : 25.16 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.64 (0.13), residues: 3810 helix: 3.55 (0.08), residues: 3013 sheet: None (None), residues: 0 loop : -2.63 (0.19), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 37 HIS 0.004 0.001 HIS U 54 PHE 0.014 0.001 PHE V 120 TYR 0.006 0.001 TYR G 71 ARG 0.007 0.000 ARG H 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 442 time to evaluate : 3.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 ARG cc_start: 0.9196 (OUTLIER) cc_final: 0.7962 (ptt90) REVERT: B 81 GLN cc_start: 0.9078 (mm-40) cc_final: 0.8850 (mm110) REVERT: G 150 LEU cc_start: 0.9665 (OUTLIER) cc_final: 0.9385 (mp) REVERT: H 81 GLN cc_start: 0.8883 (mp10) cc_final: 0.8661 (mp10) REVERT: H 148 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.8965 (tt) REVERT: I 81 GLN cc_start: 0.8965 (mp10) cc_final: 0.8733 (mp10) REVERT: I 153 VAL cc_start: 0.9039 (OUTLIER) cc_final: 0.8781 (m) REVERT: J 52 MET cc_start: 0.8360 (mtt) cc_final: 0.7873 (mtt) REVERT: K 81 GLN cc_start: 0.8912 (mp10) cc_final: 0.8638 (mp10) REVERT: P 39 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8059 (mttt) REVERT: R 4 ASP cc_start: 0.8867 (OUTLIER) cc_final: 0.8582 (t0) REVERT: R 105 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8371 (mt) REVERT: T 4 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.7535 (p0) REVERT: T 78 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8029 (ptp90) REVERT: T 81 GLN cc_start: 0.8915 (mp10) cc_final: 0.8694 (mp10) REVERT: U 73 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.7997 (ptt90) REVERT: X 53 ARG cc_start: 0.8511 (mtm-85) cc_final: 0.8275 (mtm110) outliers start: 119 outliers final: 101 residues processed: 542 average time/residue: 0.4717 time to fit residues: 398.2503 Evaluate side-chains 542 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 431 time to evaluate : 3.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 4 ASP Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain F residue 78 ARG Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 151 SER Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain I residue 78 ARG Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 119 VAL Chi-restraints excluded: chain I residue 148 LEU Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain J residue 4 ASP Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain L residue 4 ASP Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain M residue 141 ILE Chi-restraints excluded: chain N residue 52 MET Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 116 SER Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 160 ASP Chi-restraints excluded: chain O residue 2 GLN Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain O residue 116 SER Chi-restraints excluded: chain O residue 153 VAL Chi-restraints excluded: chain P residue 4 ASP Chi-restraints excluded: chain P residue 39 LYS Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 73 ARG Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 116 SER Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain R residue 4 ASP Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 147 SER Chi-restraints excluded: chain S residue 2 GLN Chi-restraints excluded: chain S residue 52 MET Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain T residue 4 ASP Chi-restraints excluded: chain T residue 22 ILE Chi-restraints excluded: chain T residue 78 ARG Chi-restraints excluded: chain T residue 116 SER Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 77 VAL Chi-restraints excluded: chain U residue 119 VAL Chi-restraints excluded: chain U residue 137 GLN Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 152 THR Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 116 SER Chi-restraints excluded: chain V residue 119 VAL Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain W residue 78 ARG Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 116 SER Chi-restraints excluded: chain W residue 119 VAL Chi-restraints excluded: chain W residue 131 ILE Chi-restraints excluded: chain X residue 4 ASP Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 224 optimal weight: 1.9990 chunk 361 optimal weight: 5.9990 chunk 220 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 chunk 251 optimal weight: 5.9990 chunk 379 optimal weight: 1.9990 chunk 349 optimal weight: 10.0000 chunk 302 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 233 optimal weight: 4.9990 chunk 185 optimal weight: 9.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 HIS L 72 GLN ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 32465 Z= 0.235 Angle : 0.602 22.448 44052 Z= 0.278 Chirality : 0.033 0.206 4895 Planarity : 0.003 0.081 5697 Dihedral : 6.437 87.976 4291 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.31 % Favored : 97.53 % Rotamer: Outliers : 3.14 % Allowed : 25.67 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.80 (0.13), residues: 3810 helix: 3.67 (0.08), residues: 3029 sheet: None (None), residues: 0 loop : -2.73 (0.19), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP R 37 HIS 0.003 0.000 HIS K 54 PHE 0.015 0.001 PHE H 26 TYR 0.007 0.001 TYR V 149 ARG 0.018 0.000 ARG H 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 449 time to evaluate : 3.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 ARG cc_start: 0.9184 (OUTLIER) cc_final: 0.7986 (ptt90) REVERT: B 81 GLN cc_start: 0.9059 (mm-40) cc_final: 0.8822 (mm110) REVERT: F 81 GLN cc_start: 0.9059 (mm-40) cc_final: 0.8857 (mm110) REVERT: G 150 LEU cc_start: 0.9647 (OUTLIER) cc_final: 0.9402 (mp) REVERT: H 81 GLN cc_start: 0.8876 (mp10) cc_final: 0.8654 (mp10) REVERT: H 148 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8865 (tt) REVERT: I 81 GLN cc_start: 0.8951 (mp10) cc_final: 0.8720 (mp10) REVERT: I 153 VAL cc_start: 0.8985 (OUTLIER) cc_final: 0.8706 (m) REVERT: J 52 MET cc_start: 0.8373 (mtt) cc_final: 0.7929 (mtt) REVERT: K 81 GLN cc_start: 0.8905 (mp10) cc_final: 0.8652 (mp10) REVERT: P 39 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.7912 (mttt) REVERT: R 4 ASP cc_start: 0.8839 (OUTLIER) cc_final: 0.8580 (t0) REVERT: T 4 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7467 (p0) REVERT: T 78 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.7974 (ptp90) REVERT: T 81 GLN cc_start: 0.8869 (mp10) cc_final: 0.8651 (mp10) REVERT: T 156 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8485 (pt0) REVERT: U 73 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.7972 (ptt90) REVERT: X 53 ARG cc_start: 0.8496 (mtm-85) cc_final: 0.8241 (mtm110) outliers start: 105 outliers final: 87 residues processed: 537 average time/residue: 0.4588 time to fit residues: 390.8572 Evaluate side-chains 534 residues out of total 3426 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 437 time to evaluate : 4.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 4 ASP Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain F residue 78 ARG Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 151 SER Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain I residue 78 ARG Chi-restraints excluded: chain I residue 119 VAL Chi-restraints excluded: chain I residue 148 LEU Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain J residue 4 ASP Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain L residue 4 ASP Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain M residue 141 ILE Chi-restraints excluded: chain N residue 52 MET Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 116 SER Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 160 ASP Chi-restraints excluded: chain O residue 2 GLN Chi-restraints excluded: chain O residue 116 SER Chi-restraints excluded: chain O residue 153 VAL Chi-restraints excluded: chain P residue 4 ASP Chi-restraints excluded: chain P residue 39 LYS Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 73 ARG Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 116 SER Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain R residue 4 ASP Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 147 SER Chi-restraints excluded: chain S residue 52 MET Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain T residue 4 ASP Chi-restraints excluded: chain T residue 22 ILE Chi-restraints excluded: chain T residue 78 ARG Chi-restraints excluded: chain T residue 116 SER Chi-restraints excluded: chain T residue 156 GLN Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 119 VAL Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 116 SER Chi-restraints excluded: chain V residue 119 VAL Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain W residue 78 ARG Chi-restraints excluded: chain W residue 116 SER Chi-restraints excluded: chain W residue 119 VAL Chi-restraints excluded: chain W residue 131 ILE Chi-restraints excluded: chain X residue 4 ASP Chi-restraints excluded: chain X residue 83 VAL Chi-restraints excluded: chain X residue 116 SER Chi-restraints excluded: chain X residue 119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 240 optimal weight: 2.9990 chunk 321 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 278 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 302 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 310 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 72 GLN N 156 GLN ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.088246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.075072 restraints weight = 64678.558| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.85 r_work: 0.2875 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2884 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2884 r_free = 0.2884 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 344 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| r_final: 0.2850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 32465 Z= 0.270 Angle : 0.618 22.935 44052 Z= 0.282 Chirality : 0.033 0.204 4895 Planarity : 0.003 0.110 5697 Dihedral : 6.417 87.361 4291 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.44 % Favored : 97.40 % Rotamer: Outliers : 3.26 % Allowed : 25.64 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.73 (0.13), residues: 3810 helix: 3.62 (0.08), residues: 3017 sheet: None (None), residues: 0 loop : -2.65 (0.19), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP H 37 HIS 0.004 0.000 HIS W 54 PHE 0.013 0.001 PHE H 26 TYR 0.008 0.001 TYR M 25 ARG 0.012 0.000 ARG H 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7233.14 seconds wall clock time: 132 minutes 25.55 seconds (7945.55 seconds total)