Starting phenix.real_space_refine on Thu Jun 26 23:00:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jax_36137/06_2025/8jax_36137.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jax_36137/06_2025/8jax_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/cci-nas-00/data/ceres_data/8jax_36137/06_2025/8jax_36137.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jax_36137/06_2025/8jax_36137.map" model { file = "/net/cci-nas-00/data/ceres_data/8jax_36137/06_2025/8jax_36137.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jax_36137/06_2025/8jax_36137.cif" } 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. Time to flip 34 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 20.04, per 1000 atoms: 0.63 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 - 3.00 Amino acid : True - 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=20, symmetry=0 Number of additional bonds: simple=20, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.70 Conformation dependent library (CDL) restraints added in 4.1 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... Secondary structure from input PDB file: 120 helices and 0 sheets defined 82.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.67 Creating SS restraints... Processing helix chain 'A' and resid 4 through 36 Processing helix chain 'A' and resid 38 through 65 Processing helix chain 'A' and resid 82 through 111 Processing helix chain 'A' and resid 114 through 145 Processing helix chain 'A' and resid 145 through 154 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) removed outlier: 3.771A pdb=" N ILE A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 36 removed outlier: 3.517A pdb=" N LYS B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 65 Processing helix chain 'B' and resid 82 through 111 removed outlier: 3.586A pdb=" N MET B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 145 Processing helix chain 'B' and resid 145 through 154 Processing helix chain 'C' and resid 4 through 35 Processing helix chain 'C' and resid 37 through 65 removed outlier: 3.903A pdb=" N ALA C 41 " --> pdb=" O TRP C 37 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU C 65 " --> pdb=" O ARG C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 110 Processing helix chain 'C' and resid 114 through 145 Processing helix chain 'C' and resid 145 through 151 Processing helix chain 'D' and resid 4 through 36 Processing helix chain 'D' and resid 37 through 65 Processing helix chain 'D' and resid 82 through 110 Processing helix chain 'D' and resid 114 through 145 Processing helix chain 'D' and resid 145 through 154 Processing helix chain 'F' and resid 4 through 36 Processing helix chain 'F' and resid 38 through 65 Processing helix chain 'F' and resid 82 through 110 removed outlier: 3.544A pdb=" N MET F 86 " --> pdb=" O SER F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 145 Processing helix chain 'F' and resid 145 through 151 Processing helix chain 'E' and resid 4 through 36 removed outlier: 3.533A pdb=" N ILE E 8 " --> pdb=" O ASP E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 65 removed outlier: 3.550A pdb=" N ALA E 41 " --> pdb=" O TRP E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 110 Processing helix chain 'E' and resid 114 through 145 Processing helix chain 'E' and resid 145 through 154 removed outlier: 3.767A pdb=" N VAL E 153 " --> pdb=" O TYR E 149 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE E 154 " --> pdb=" O LEU E 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 36 removed outlier: 3.541A pdb=" N GLY G 36 " --> pdb=" O GLN G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 65 removed outlier: 3.826A pdb=" N ALA G 41 " --> pdb=" O TRP G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 111 Processing helix chain 'G' and resid 114 through 145 Processing helix chain 'G' and resid 145 through 151 Processing helix chain 'H' and resid 4 through 36 removed outlier: 3.551A pdb=" N GLY H 36 " --> pdb=" O GLN H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 65 removed outlier: 3.897A pdb=" N ALA H 41 " --> pdb=" O TRP H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 110 removed outlier: 3.526A pdb=" N MET H 86 " --> pdb=" O SER H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 145 Processing helix chain 'H' and resid 145 through 154 removed outlier: 3.609A pdb=" N VAL H 153 " --> pdb=" O TYR H 149 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 36 Processing helix chain 'I' and resid 37 through 65 removed outlier: 3.565A pdb=" N LEU I 65 " --> pdb=" O ARG I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 110 Processing helix chain 'I' and resid 114 through 145 Processing helix chain 'I' and resid 145 through 152 Processing helix chain 'J' and resid 4 through 36 Processing helix chain 'J' and resid 37 through 65 removed outlier: 3.837A pdb=" N ALA J 41 " --> pdb=" O TRP J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 110 Processing helix chain 'J' and resid 114 through 145 Processing helix chain 'J' and resid 145 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 4 through 36 Processing helix chain 'K' and resid 37 through 65 Processing helix chain 'K' and resid 82 through 111 Processing helix chain 'K' and resid 114 through 145 Processing helix chain 'K' and resid 145 through 152 Processing helix chain 'L' and resid 4 through 36 removed outlier: 3.546A pdb=" N ILE L 8 " --> pdb=" O ASP L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 65 removed outlier: 3.829A pdb=" N ALA L 41 " --> pdb=" O TRP L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 111 removed outlier: 3.591A pdb=" N MET L 86 " --> pdb=" O SER L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 145 Processing helix chain 'L' and resid 145 through 154 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) removed outlier: 3.781A pdb=" N ILE L 154 " --> pdb=" O LEU L 150 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 36 Processing helix chain 'M' and resid 37 through 65 Processing helix chain 'M' and resid 82 through 110 removed outlier: 4.091A pdb=" N ALA M 110 " --> pdb=" O GLU M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 114 through 145 Processing helix chain 'M' and resid 145 through 151 Processing helix chain 'N' and resid 4 through 36 Processing helix chain 'N' and resid 38 through 65 Processing helix chain 'N' and resid 82 through 110 removed outlier: 3.590A pdb=" N MET N 86 " --> pdb=" O SER N 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 114 through 145 Processing helix chain 'N' and resid 145 through 151 Processing helix chain 'O' and resid 4 through 36 Processing helix chain 'O' and resid 37 through 65 removed outlier: 3.625A pdb=" N ALA O 41 " --> pdb=" O TRP O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 110 Processing helix chain 'O' and resid 114 through 145 Processing helix chain 'O' and resid 145 through 154 Processing helix chain 'P' and resid 4 through 35 removed outlier: 3.682A pdb=" N LYS P 35 " --> pdb=" O LEU P 31 " (cutoff:3.500A) Processing helix chain 'P' and resid 37 through 65 removed outlier: 3.692A pdb=" N ALA P 41 " --> pdb=" O TRP P 37 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 111 removed outlier: 3.522A pdb=" N MET P 86 " --> pdb=" O SER P 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 114 through 145 Processing helix chain 'P' and resid 145 through 154 Processing helix chain 'Q' and resid 4 through 36 Processing helix chain 'Q' and resid 37 through 65 removed outlier: 3.506A pdb=" N LEU Q 65 " --> pdb=" O ARG Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 110 removed outlier: 4.124A pdb=" N ALA Q 110 " --> pdb=" O GLU Q 106 " (cutoff:3.500A) Processing helix chain 'Q' and resid 114 through 145 Processing helix chain 'Q' and resid 145 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 4 through 36 Processing helix chain 'R' and resid 37 through 65 removed outlier: 3.527A pdb=" N ALA R 41 " --> pdb=" O TRP R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 111 removed outlier: 3.546A pdb=" N MET R 86 " --> pdb=" O SER R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 114 through 145 Processing helix chain 'R' and resid 145 through 152 removed outlier: 3.747A pdb=" N THR R 152 " --> pdb=" O LEU R 148 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 36 Processing helix chain 'S' and resid 37 through 65 removed outlier: 3.501A pdb=" N LEU S 65 " --> pdb=" O ARG S 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 110 removed outlier: 3.517A pdb=" N MET S 86 " --> pdb=" O SER S 82 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ALA S 110 " --> pdb=" O GLU S 106 " (cutoff:3.500A) Processing helix chain 'S' and resid 114 through 145 Processing helix chain 'S' and resid 145 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 4 through 36 Processing helix chain 'T' and resid 37 through 65 removed outlier: 3.597A pdb=" N ALA T 41 " --> pdb=" O TRP T 37 " (cutoff:3.500A) Processing helix chain 'T' and resid 82 through 111 removed outlier: 3.507A pdb=" N MET T 86 " --> pdb=" O SER T 82 " (cutoff:3.500A) Processing helix chain 'T' and resid 114 through 145 Processing helix chain 'T' and resid 145 through 152 Processing helix chain 'U' and resid 4 through 36 Processing helix chain 'U' and resid 38 through 65 Processing helix chain 'U' and resid 82 through 110 Processing helix chain 'U' and resid 114 through 145 Processing helix chain 'U' and resid 145 through 154 Processing helix chain 'V' and resid 4 through 36 removed outlier: 3.632A pdb=" N ILE V 8 " --> pdb=" O ASP V 4 " (cutoff:3.500A) Processing helix chain 'V' and resid 37 through 65 Processing helix chain 'V' and resid 82 through 110 Processing helix chain 'V' and resid 114 through 145 Processing helix chain 'V' and resid 145 through 154 Processing helix chain 'W' and resid 4 through 36 Processing helix chain 'W' and resid 37 through 65 Processing helix chain 'W' and resid 82 through 110 Processing helix chain 'W' and resid 114 through 145 Processing helix chain 'W' and resid 145 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 4 through 36 removed outlier: 3.505A pdb=" N ILE X 8 " --> pdb=" O ASP X 4 " (cutoff:3.500A) Processing helix chain 'X' and resid 37 through 65 Processing helix chain 'X' and resid 82 through 111 Processing helix chain 'X' and resid 114 through 145 Processing helix chain 'X' and resid 145 through 152 removed outlier: 3.838A pdb=" N THR X 152 " --> pdb=" O LEU X 148 " (cutoff:3.500A) 2633 hydrogen bonds defined for protein. 7899 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: 10.79 Time building geometry restraints manager: 10.70 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: 0.00 - 5.85: 43962 5.85 - 11.70: 59 11.70 - 17.55: 17 17.55 - 23.40: 8 23.40 - 29.25: 6 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: 45679 3.40 - 4.15: 68932 4.15 - 4.90: 132269 Nonbonded interactions: 247522 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 247517 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 0.690 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: 0.020 Extract box with map and model: 1.310 Check model and map are aligned: 0.240 Set scattering table: 0.310 Process input model: 71.970 Find NCS groups from input model: 2.280 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.890 ------------------------------------------------------------------------------- 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 : 0.010 0.689 32485 Z= 0.669 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 Details of bonding type rmsd hydrogen bonds : bond 0.11872 ( 2633) hydrogen bonds : angle 4.01181 ( 7899) covalent geometry : bond 0.00497 (32465) covalent geometry : angle 0.83398 (44052) Misc. bond : bond 0.34938 ( 20) *********************** 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 to be fit. rotamer outliers: 12 poor density : 467 time to evaluate : 3.530 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: 0.4375 time to fit residues: 327.6556 Evaluate side-chains 455 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 450 time to evaluate : 3.741 ------------------------------------------------------------------------------- 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: 7.9990 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: 9.9990 chunk 298 optimal weight: 7.9990 chunk 115 optimal weight: 9.9990 chunk 181 optimal weight: 0.8980 chunk 222 optimal weight: 5.9990 chunk 345 optimal weight: 3.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 81 GLN E 72 GLN E 118 ASN K 130 HIS L 72 GLN P 118 ASN T 130 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.087187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.073947 restraints weight = 64237.128| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.82 r_work: 0.2858 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 344 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| r_final: 0.2829 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 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 : 0.006 0.400 32485 Z= 0.238 Angle : 0.730 24.842 44052 Z= 0.324 Chirality : 0.037 0.286 4895 Planarity : 0.003 0.037 5697 Dihedral : 6.600 89.256 4300 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.73 % Favored : 97.09 % Rotamer: Outliers : 3.38 % Allowed : 22.67 % Favored : 73.95 % 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: 3.39 (0.13), residues: 3810 helix: 3.25 (0.08), residues: 3084 sheet: None (None), residues: 0 loop : -2.74 (0.20), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP S 37 HIS 0.005 0.001 HIS U 54 PHE 0.013 0.001 PHE C 26 TYR 0.008 0.001 TYR G 71 ARG 0.003 0.000 ARG X 61 Details of bonding type rmsd hydrogen bonds : bond 0.09578 ( 2633) hydrogen bonds : angle 3.79800 ( 7899) covalent geometry : bond 0.00574 (32465) covalent geometry : angle 0.73006 (44052) Misc. bond : bond 0.09313 ( 20) *********************** 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 551 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 438 time to evaluate : 3.427 Fit side-chains 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: A 85 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8345 (mp0) REVERT: D 56 GLU cc_start: 0.9308 (OUTLIER) cc_final: 0.8873 (tm-30) REVERT: G 150 LEU cc_start: 0.9664 (OUTLIER) cc_final: 0.9379 (mp) REVERT: H 105 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8441 (mt) REVERT: H 148 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9115 (tt) REVERT: O 52 MET cc_start: 0.8590 (mtt) cc_final: 0.8241 (mtt) REVERT: P 52 MET cc_start: 0.9036 (ttm) cc_final: 0.8668 (mtt) REVERT: T 52 MET cc_start: 0.8569 (mtt) cc_final: 0.8296 (mtt) REVERT: X 53 ARG cc_start: 0.8509 (mtm-85) cc_final: 0.8132 (mtm110) outliers start: 113 outliers final: 59 residues processed: 520 average time/residue: 0.4349 time to fit residues: 358.4944 Evaluate side-chains 473 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 409 time to evaluate : 3.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 154 ILE 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 C residue 141 ILE Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain F residue 141 ILE 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 116 SER Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 141 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 52 MET Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain K residue 52 MET 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 82 SER 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 141 ILE Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain P residue 141 ILE 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 115 THR Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain T residue 22 ILE Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 119 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 152 THR Chi-restraints excluded: chain W residue 131 ILE Chi-restraints excluded: chain X residue 52 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 114 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 156 optimal weight: 6.9990 chunk 273 optimal weight: 2.9990 chunk 209 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 362 optimal weight: 8.9990 chunk 292 optimal weight: 10.0000 chunk 145 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 72 GLN L 72 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.086959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.073550 restraints weight = 63849.201| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.85 r_work: 0.2856 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| r_final: 0.2869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.202 32485 Z= 0.165 Angle : 0.610 19.361 44052 Z= 0.280 Chirality : 0.033 0.241 4895 Planarity : 0.003 0.030 5697 Dihedral : 6.522 88.766 4293 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.47 % Favored : 97.35 % Rotamer: Outliers : 3.23 % Allowed : 22.73 % Favored : 74.04 % 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: 3.72 (0.13), residues: 3810 helix: 3.52 (0.08), residues: 3078 sheet: None (None), residues: 0 loop : -2.75 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP T 37 HIS 0.003 0.000 HIS W 130 PHE 0.016 0.001 PHE C 26 TYR 0.005 0.001 TYR M 43 ARG 0.004 0.000 ARG I 53 Details of bonding type rmsd hydrogen bonds : bond 0.08209 ( 2633) hydrogen bonds : angle 3.54076 ( 7899) covalent geometry : bond 0.00361 (32465) covalent geometry : angle 0.61019 (44052) Misc. bond : bond 0.06077 ( 20) *********************** 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 568 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 460 time to evaluate : 4.178 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: B 56 GLU cc_start: 0.9192 (OUTLIER) cc_final: 0.8926 (tt0) REVERT: H 105 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8342 (mt) REVERT: H 148 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8999 (tt) REVERT: I 81 GLN cc_start: 0.8919 (mp10) cc_final: 0.8610 (mp10) REVERT: K 52 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.8126 (pmm) REVERT: P 39 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.7713 (mttt) REVERT: P 52 MET cc_start: 0.9051 (ttm) cc_final: 0.8777 (mtt) REVERT: Q 52 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8419 (mtt) REVERT: U 73 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.7944 (ptt90) REVERT: W 52 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8676 (mtt) REVERT: W 73 ARG cc_start: 0.9149 (OUTLIER) cc_final: 0.8093 (ptt90) REVERT: W 85 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8051 (mp0) REVERT: X 53 ARG cc_start: 0.8461 (mtm-85) cc_final: 0.8101 (mtm110) outliers start: 108 outliers final: 52 residues processed: 541 average time/residue: 0.4714 time to fit residues: 401.6689 Evaluate side-chains 488 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 426 time to evaluate : 3.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 7 VAL Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 77 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 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 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 H residue 52 MET Chi-restraints excluded: chain H residue 60 ASP Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 136 THR 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 50 ASP Chi-restraints excluded: chain J residue 52 MET Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain K residue 7 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 M residue 77 VAL Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain N residue 52 MET Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain P residue 39 LYS Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain P residue 153 VAL Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 52 MET 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 141 ILE Chi-restraints excluded: chain T residue 22 ILE Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 152 THR Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain W residue 52 MET Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain W residue 85 GLU Chi-restraints excluded: chain W residue 131 ILE Chi-restraints excluded: chain W residue 144 LEU Chi-restraints excluded: chain X residue 52 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 295 optimal weight: 1.9990 chunk 204 optimal weight: 10.0000 chunk 239 optimal weight: 10.0000 chunk 196 optimal weight: 5.9990 chunk 125 optimal weight: 0.9980 chunk 187 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 176 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 360 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 14 GLN E 72 GLN J 72 GLN L 72 GLN N 32 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.084037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.070558 restraints weight = 63947.836| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.85 r_work: 0.2809 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| r_final: 0.2803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.254 32485 Z= 0.201 Angle : 0.640 18.817 44052 Z= 0.294 Chirality : 0.035 0.235 4895 Planarity : 0.003 0.034 5697 Dihedral : 6.514 89.965 4293 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.62 % Favored : 97.19 % Rotamer: Outliers : 3.98 % Allowed : 22.55 % Favored : 73.47 % 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: 3.62 (0.13), residues: 3810 helix: 3.44 (0.08), residues: 3070 sheet: None (None), residues: 0 loop : -2.67 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 37 HIS 0.004 0.001 HIS U 54 PHE 0.013 0.001 PHE H 26 TYR 0.008 0.001 TYR G 71 ARG 0.005 0.000 ARG H 45 Details of bonding type rmsd hydrogen bonds : bond 0.09011 ( 2633) hydrogen bonds : angle 3.65036 ( 7899) covalent geometry : bond 0.00473 (32465) covalent geometry : angle 0.63999 (44052) Misc. bond : bond 0.08108 ( 20) *********************** 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 575 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 442 time to evaluate : 4.020 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: A 85 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8322 (mp0) REVERT: B 56 GLU cc_start: 0.9229 (OUTLIER) cc_final: 0.8980 (tt0) REVERT: B 73 ARG cc_start: 0.9284 (OUTLIER) cc_final: 0.8645 (ptt90) REVERT: H 148 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9039 (tt) REVERT: N 4 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.8254 (m-30) REVERT: P 39 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.7820 (mttt) REVERT: P 52 MET cc_start: 0.9158 (ttm) cc_final: 0.8857 (mtt) REVERT: U 73 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.7982 (ptt90) REVERT: W 52 MET cc_start: 0.9157 (OUTLIER) cc_final: 0.8739 (mtt) REVERT: W 73 ARG cc_start: 0.9187 (OUTLIER) cc_final: 0.8122 (ptt90) REVERT: W 85 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8063 (mp0) REVERT: X 53 ARG cc_start: 0.8520 (mtm-85) cc_final: 0.8120 (mtm110) outliers start: 133 outliers final: 86 residues processed: 542 average time/residue: 0.4542 time to fit residues: 389.3806 Evaluate side-chains 505 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 409 time to evaluate : 3.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 85 GLU 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 7 VAL Chi-restraints excluded: chain B residue 56 GLU 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 93 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 2 GLN Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 52 MET 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 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 116 SER Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 147 SER Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain I residue 50 ASP 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 141 ILE 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 83 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 M residue 83 VAL Chi-restraints excluded: chain M residue 141 ILE Chi-restraints excluded: chain N residue 4 ASP Chi-restraints excluded: chain N residue 52 MET Chi-restraints excluded: chain N residue 63 LEU 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 39 LYS Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 148 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 115 THR Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 152 THR Chi-restraints excluded: chain T residue 22 ILE Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain U residue 7 VAL 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 137 GLN Chi-restraints excluded: chain U residue 152 THR Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 116 SER Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain V residue 152 THR Chi-restraints excluded: chain V residue 153 VAL Chi-restraints excluded: chain W residue 52 MET 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 85 GLU Chi-restraints excluded: chain W residue 131 ILE Chi-restraints excluded: chain X residue 52 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 262 optimal weight: 8.9990 chunk 147 optimal weight: 0.9990 chunk 242 optimal weight: 4.9990 chunk 184 optimal weight: 9.9990 chunk 171 optimal weight: 10.0000 chunk 258 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 267 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 HIS F 130 HIS E 72 GLN J 72 GLN L 72 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.085598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.072157 restraints weight = 63550.122| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.85 r_work: 0.2844 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.234 32485 Z= 0.169 Angle : 0.619 20.618 44052 Z= 0.279 Chirality : 0.033 0.181 4895 Planarity : 0.003 0.032 5697 Dihedral : 6.476 89.505 4293 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.57 % Favored : 97.27 % Rotamer: Outliers : 3.56 % Allowed : 23.57 % Favored : 72.87 % 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: 3.78 (0.13), residues: 3810 helix: 3.56 (0.08), residues: 3081 sheet: None (None), residues: 0 loop : -2.78 (0.19), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 37 HIS 0.003 0.000 HIS U 54 PHE 0.014 0.001 PHE C 26 TYR 0.005 0.001 TYR M 43 ARG 0.003 0.000 ARG T 53 Details of bonding type rmsd hydrogen bonds : bond 0.08362 ( 2633) hydrogen bonds : angle 3.53786 ( 7899) covalent geometry : bond 0.00383 (32465) covalent geometry : angle 0.61898 (44052) Misc. bond : bond 0.07178 ( 20) *********************** 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 to be fit. rotamer outliers: 119 poor density : 449 time to evaluate : 3.805 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: A 85 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8338 (mp0) REVERT: B 56 GLU cc_start: 0.9231 (OUTLIER) cc_final: 0.8967 (tt0) REVERT: B 73 ARG cc_start: 0.9284 (OUTLIER) cc_final: 0.8660 (ptt90) REVERT: G 135 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8787 (mt-10) REVERT: H 148 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8963 (tt) REVERT: N 4 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.8194 (m-30) REVERT: P 39 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.7756 (mttt) REVERT: P 52 MET cc_start: 0.9221 (ttm) cc_final: 0.8972 (mtt) REVERT: T 52 MET cc_start: 0.8770 (mtt) cc_final: 0.8496 (mtt) REVERT: T 156 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8313 (pt0) REVERT: U 73 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.7946 (ptt90) REVERT: W 52 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.8776 (mtt) REVERT: W 73 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8141 (ptt90) REVERT: W 85 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8070 (mp0) REVERT: X 53 ARG cc_start: 0.8534 (mtm-85) cc_final: 0.8194 (mtm110) outliers start: 119 outliers final: 82 residues processed: 543 average time/residue: 0.4639 time to fit residues: 398.6577 Evaluate side-chains 514 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 420 time to evaluate : 3.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 144 LEU 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 7 VAL Chi-restraints excluded: chain B residue 56 GLU 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 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 2 GLN Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 78 ARG 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 83 VAL 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 135 GLU Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 147 SER Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain I residue 50 ASP 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 78 ARG Chi-restraints excluded: chain K residue 7 VAL 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 M residue 83 VAL Chi-restraints excluded: chain N residue 4 ASP 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 144 LEU Chi-restraints excluded: chain O residue 2 GLN Chi-restraints excluded: chain O residue 83 VAL 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 144 LEU Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain P residue 153 VAL 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 116 SER Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 147 SER Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain T residue 22 ILE Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 156 GLN Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 73 ARG 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 116 SER Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain V residue 152 THR Chi-restraints excluded: chain V residue 153 VAL Chi-restraints excluded: chain W residue 52 MET Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain W residue 78 ARG Chi-restraints excluded: chain W residue 85 GLU Chi-restraints excluded: chain W residue 131 ILE Chi-restraints excluded: chain W residue 144 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 4 optimal weight: 3.9990 chunk 259 optimal weight: 1.9990 chunk 127 optimal weight: 10.0000 chunk 205 optimal weight: 2.9990 chunk 363 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 380 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 247 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 159 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 GLN E 72 GLN J 72 GLN L 72 GLN P 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.087632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.074280 restraints weight = 63696.829| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.84 r_work: 0.2870 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.216 32485 Z= 0.156 Angle : 0.597 22.820 44052 Z= 0.270 Chirality : 0.033 0.184 4895 Planarity : 0.003 0.030 5697 Dihedral : 6.464 89.499 4293 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.52 % Favored : 97.32 % Rotamer: Outliers : 3.38 % Allowed : 24.17 % Favored : 72.45 % 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: 3.87 (0.13), residues: 3810 helix: 3.64 (0.08), residues: 3078 sheet: None (None), residues: 0 loop : -2.78 (0.19), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 37 HIS 0.002 0.000 HIS U 54 PHE 0.014 0.001 PHE C 26 TYR 0.006 0.001 TYR Q 43 ARG 0.004 0.000 ARG C 53 Details of bonding type rmsd hydrogen bonds : bond 0.07680 ( 2633) hydrogen bonds : angle 3.42955 ( 7899) covalent geometry : bond 0.00349 (32465) covalent geometry : angle 0.59728 (44052) Misc. bond : bond 0.06956 ( 20) *********************** 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 571 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 458 time to evaluate : 3.741 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: A 85 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8177 (mp0) REVERT: B 56 GLU cc_start: 0.9247 (OUTLIER) cc_final: 0.8977 (tt0) REVERT: G 135 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8771 (mt-10) REVERT: H 148 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8917 (tt) REVERT: N 4 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.8119 (m-30) REVERT: N 81 GLN cc_start: 0.8951 (mm-40) cc_final: 0.8744 (mm110) REVERT: N 120 PHE cc_start: 0.9098 (OUTLIER) cc_final: 0.8879 (m-10) REVERT: P 39 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.7680 (mttt) REVERT: R 4 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8336 (t0) REVERT: U 73 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.7974 (ptt90) REVERT: V 85 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8090 (mp0) REVERT: W 52 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8826 (mtt) REVERT: W 73 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.8122 (ptt90) REVERT: W 85 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8033 (mp0) REVERT: X 52 MET cc_start: 0.7497 (mtt) cc_final: 0.7211 (mtt) REVERT: X 53 ARG cc_start: 0.8556 (mtm-85) cc_final: 0.8180 (mtm110) outliers start: 113 outliers final: 77 residues processed: 547 average time/residue: 0.4455 time to fit residues: 390.1173 Evaluate side-chains 516 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 426 time to evaluate : 3.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU 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 7 VAL Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 77 VAL 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 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 152 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 78 ARG 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 72 GLN Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 147 SER Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain I residue 50 ASP Chi-restraints excluded: chain I residue 119 VAL Chi-restraints excluded: chain J residue 52 MET Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 116 SER 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 M residue 83 VAL Chi-restraints excluded: chain N residue 4 ASP Chi-restraints excluded: chain N residue 52 MET Chi-restraints excluded: chain N residue 72 GLN 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 120 PHE Chi-restraints excluded: chain N residue 144 LEU Chi-restraints excluded: chain O residue 2 GLN Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain P residue 39 LYS Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain P residue 153 VAL Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 83 VAL 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 52 MET Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain T residue 22 ILE Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 85 GLU Chi-restraints excluded: chain V residue 116 SER Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain V residue 152 THR Chi-restraints excluded: chain V residue 153 VAL Chi-restraints excluded: chain W residue 52 MET Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain W residue 78 ARG Chi-restraints excluded: chain W residue 85 GLU Chi-restraints excluded: chain W residue 131 ILE Chi-restraints excluded: chain W residue 144 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 220 optimal weight: 2.9990 chunk 336 optimal weight: 9.9990 chunk 251 optimal weight: 0.9990 chunk 175 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 199 optimal weight: 0.0020 chunk 107 optimal weight: 6.9990 chunk 162 optimal weight: 6.9990 chunk 310 optimal weight: 0.0870 chunk 83 optimal weight: 9.9990 overall best weight: 1.4172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 72 GLN J 72 GLN K 130 HIS L 72 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.090732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.077441 restraints weight = 63089.356| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.84 r_work: 0.2949 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2944 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.190 32485 Z= 0.140 Angle : 0.578 21.958 44052 Z= 0.265 Chirality : 0.032 0.190 4895 Planarity : 0.003 0.027 5697 Dihedral : 6.444 89.646 4293 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.28 % Favored : 97.56 % Rotamer: Outliers : 2.96 % Allowed : 24.86 % Favored : 72.18 % 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: 3.96 (0.13), residues: 3810 helix: 3.70 (0.08), residues: 3093 sheet: None (None), residues: 0 loop : -2.88 (0.19), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 37 HIS 0.003 0.000 HIS W 130 PHE 0.015 0.001 PHE C 26 TYR 0.008 0.001 TYR K 25 ARG 0.007 0.000 ARG I 53 Details of bonding type rmsd hydrogen bonds : bond 0.06762 ( 2633) hydrogen bonds : angle 3.29802 ( 7899) covalent geometry : bond 0.00305 (32465) covalent geometry : angle 0.57827 (44052) Misc. bond : bond 0.06439 ( 20) *********************** 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 556 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 457 time to evaluate : 4.000 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: A 2 GLN cc_start: 0.9057 (mm-40) cc_final: 0.8792 (mt0) REVERT: A 85 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8140 (mp0) REVERT: B 73 ARG cc_start: 0.9264 (OUTLIER) cc_final: 0.8654 (ptt90) REVERT: G 135 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8569 (mm-30) REVERT: H 148 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8851 (tt) REVERT: N 4 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.8073 (m-30) REVERT: O 158 GLN cc_start: 0.6136 (OUTLIER) cc_final: 0.5888 (mp10) REVERT: P 39 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7540 (mttt) REVERT: P 52 MET cc_start: 0.8933 (mtt) cc_final: 0.8662 (mtt) REVERT: R 4 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.8216 (t0) REVERT: T 156 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8295 (pt0) REVERT: U 73 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.7966 (ptt90) REVERT: V 53 ARG cc_start: 0.8449 (mtm110) cc_final: 0.8226 (mtm-85) REVERT: V 85 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8061 (mp0) REVERT: W 52 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8577 (mtt) REVERT: W 73 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.8073 (ptt90) REVERT: W 85 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8001 (mp0) REVERT: X 53 ARG cc_start: 0.8580 (mtm-85) cc_final: 0.8197 (mtm110) outliers start: 99 outliers final: 60 residues processed: 536 average time/residue: 0.4316 time to fit residues: 369.3468 Evaluate side-chains 514 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 440 time to evaluate : 3.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 144 LEU 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 7 VAL 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 116 SER 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 152 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain F residue 78 ARG Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain G residue 72 GLN Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 147 SER Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain I residue 116 SER Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain L residue 115 THR 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 115 THR Chi-restraints excluded: chain N residue 4 ASP 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 O residue 2 GLN Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain O residue 158 GLN Chi-restraints excluded: chain P residue 39 LYS Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain P residue 153 VAL Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 68 LEU 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 S residue 52 MET Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain T residue 22 ILE Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 156 GLN Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 85 GLU 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 52 MET Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain W residue 85 GLU Chi-restraints excluded: chain W residue 131 ILE Chi-restraints excluded: chain W residue 144 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 131 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 265 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 231 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 359 optimal weight: 0.6980 chunk 364 optimal weight: 0.0050 chunk 106 optimal weight: 2.9990 chunk 196 optimal weight: 8.9990 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 GLN E 72 GLN G 88 GLN J 72 GLN L 72 GLN P 81 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.093802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.080337 restraints weight = 60914.421| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.68 r_work: 0.2927 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.168 32485 Z= 0.132 Angle : 0.562 20.802 44052 Z= 0.260 Chirality : 0.032 0.194 4895 Planarity : 0.003 0.038 5697 Dihedral : 6.434 89.192 4293 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.55 % Favored : 97.30 % Rotamer: Outliers : 2.33 % Allowed : 25.19 % Favored : 72.48 % 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: 3.98 (0.13), residues: 3810 helix: 3.73 (0.08), residues: 3084 sheet: None (None), residues: 0 loop : -2.85 (0.19), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 37 HIS 0.002 0.000 HIS T 54 PHE 0.015 0.001 PHE C 26 TYR 0.008 0.001 TYR K 25 ARG 0.008 0.000 ARG Q 53 Details of bonding type rmsd hydrogen bonds : bond 0.06005 ( 2633) hydrogen bonds : angle 3.22039 ( 7899) covalent geometry : bond 0.00286 (32465) covalent geometry : angle 0.56242 (44052) Misc. bond : bond 0.06030 ( 20) *********************** 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 532 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 454 time to evaluate : 3.568 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: A 2 GLN cc_start: 0.9025 (mm-40) cc_final: 0.8746 (mt0) REVERT: A 85 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8197 (mp0) REVERT: B 73 ARG cc_start: 0.9245 (OUTLIER) cc_final: 0.8705 (ptt90) REVERT: H 148 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8873 (tt) REVERT: J 52 MET cc_start: 0.8374 (mtt) cc_final: 0.7852 (mtt) REVERT: P 39 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7414 (mttt) REVERT: R 4 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.8049 (t0) REVERT: R 105 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8476 (mt) REVERT: U 73 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8046 (ptt90) REVERT: V 85 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8032 (mp0) REVERT: W 73 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.8166 (ptt90) REVERT: X 53 ARG cc_start: 0.8591 (mtm-85) cc_final: 0.8256 (mtm110) outliers start: 78 outliers final: 54 residues processed: 515 average time/residue: 0.4354 time to fit residues: 355.9995 Evaluate side-chains 501 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 438 time to evaluate : 4.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 154 ILE 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 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 G residue 77 VAL Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 147 SER Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain I residue 116 SER Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain K residue 7 VAL 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 115 THR Chi-restraints excluded: chain N residue 52 MET Chi-restraints excluded: chain N residue 116 SER Chi-restraints excluded: chain O residue 2 GLN Chi-restraints excluded: chain O residue 153 VAL Chi-restraints excluded: chain P residue 39 LYS Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 153 VAL Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 68 LEU 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 105 ILE Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain S residue 52 MET Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain T residue 22 ILE Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain U residue 153 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 85 GLU 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 85 GLU Chi-restraints excluded: chain W residue 131 ILE Chi-restraints excluded: chain W residue 144 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 103 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 204 optimal weight: 7.9990 chunk 340 optimal weight: 8.9990 chunk 353 optimal weight: 0.9980 chunk 357 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 311 optimal weight: 10.0000 chunk 253 optimal weight: 3.9990 chunk 232 optimal weight: 5.9990 chunk 209 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 81 GLN E 72 GLN J 72 GLN N 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.088622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.075152 restraints weight = 62974.974| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.82 r_work: 0.2858 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.395 32485 Z= 0.197 Angle : 0.679 34.879 44052 Z= 0.298 Chirality : 0.034 0.194 4895 Planarity : 0.003 0.041 5697 Dihedral : 6.455 88.718 4291 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.81 % Favored : 97.03 % Rotamer: Outliers : 2.63 % Allowed : 25.37 % Favored : 72.00 % 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: 3.60 (0.08), residues: 3059 sheet: None (None), residues: 0 loop : -2.67 (0.20), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 37 HIS 0.005 0.001 HIS T 54 PHE 0.016 0.001 PHE V 120 TYR 0.009 0.001 TYR N 25 ARG 0.014 0.000 ARG I 53 Details of bonding type rmsd hydrogen bonds : bond 0.08233 ( 2633) hydrogen bonds : angle 3.52053 ( 7899) covalent geometry : bond 0.00475 (32465) covalent geometry : angle 0.67910 (44052) Misc. bond : bond 0.10970 ( 20) *********************** 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 519 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 431 time to evaluate : 3.744 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: A 85 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8244 (mp0) REVERT: B 56 GLU cc_start: 0.9226 (OUTLIER) cc_final: 0.8982 (tt0) REVERT: B 73 ARG cc_start: 0.9289 (OUTLIER) cc_final: 0.8640 (ptt90) REVERT: H 148 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8965 (tt) REVERT: J 52 MET cc_start: 0.8390 (mtt) cc_final: 0.7697 (mtt) REVERT: P 39 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.7786 (mttt) REVERT: Q 53 ARG cc_start: 0.8608 (mtm-85) cc_final: 0.8405 (mtm110) REVERT: R 4 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8263 (t0) REVERT: U 73 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.8025 (ptt90) REVERT: V 85 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8110 (mp0) REVERT: W 73 ARG cc_start: 0.9143 (OUTLIER) cc_final: 0.8114 (ptt90) REVERT: W 85 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8074 (mp0) REVERT: X 53 ARG cc_start: 0.8618 (mtm-85) cc_final: 0.8295 (mtm110) outliers start: 88 outliers final: 62 residues processed: 505 average time/residue: 0.4554 time to fit residues: 361.2339 Evaluate side-chains 491 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 419 time to evaluate : 3.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 56 GLU 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 116 SER 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 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 G residue 77 VAL Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 147 SER 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 116 SER Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 115 THR Chi-restraints excluded: chain N residue 52 MET Chi-restraints excluded: chain N residue 63 LEU Chi-restraints excluded: chain N residue 116 SER Chi-restraints excluded: chain N residue 144 LEU Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain P residue 39 LYS Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 153 VAL Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 68 LEU 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 52 MET Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain T residue 22 ILE Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 77 VAL Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 153 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 85 GLU Chi-restraints excluded: chain V residue 152 THR 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 85 GLU Chi-restraints excluded: chain W residue 131 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 61 optimal weight: 3.9990 chunk 272 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 353 optimal weight: 0.9990 chunk 357 optimal weight: 4.9990 chunk 302 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 118 optimal weight: 0.7980 chunk 164 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 243 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 72 GLN J 72 GLN P 81 GLN ** U 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.087005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.073543 restraints weight = 63252.349| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.86 r_work: 0.2872 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.295 32485 Z= 0.168 Angle : 0.649 30.607 44052 Z= 0.286 Chirality : 0.033 0.192 4895 Planarity : 0.003 0.037 5697 Dihedral : 6.413 85.154 4291 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.78 % Favored : 97.06 % Rotamer: Outliers : 2.18 % Allowed : 25.79 % Favored : 72.03 % 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: 3.87 (0.13), residues: 3810 helix: 3.65 (0.08), residues: 3075 sheet: None (None), residues: 0 loop : -2.81 (0.19), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP N 37 HIS 0.003 0.000 HIS S 130 PHE 0.013 0.001 PHE H 26 TYR 0.005 0.001 TYR V 43 ARG 0.007 0.000 ARG V 53 Details of bonding type rmsd hydrogen bonds : bond 0.07904 ( 2633) hydrogen bonds : angle 3.47096 ( 7899) covalent geometry : bond 0.00388 (32465) covalent geometry : angle 0.64939 (44052) Misc. bond : bond 0.08959 ( 20) ********************** 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 502 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 429 time to evaluate : 3.642 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: A 2 GLN cc_start: 0.9125 (mm-40) cc_final: 0.8885 (mt0) REVERT: A 85 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8104 (mp0) REVERT: B 56 GLU cc_start: 0.9236 (OUTLIER) cc_final: 0.8982 (tt0) REVERT: B 73 ARG cc_start: 0.9294 (OUTLIER) cc_final: 0.8665 (ptt90) REVERT: H 148 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8893 (tt) REVERT: J 52 MET cc_start: 0.8498 (mtt) cc_final: 0.7949 (mtt) REVERT: P 39 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.7727 (mttt) REVERT: R 4 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8284 (t0) REVERT: U 73 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.8030 (ptt90) REVERT: V 53 ARG cc_start: 0.8494 (mtm110) cc_final: 0.8271 (mtm-85) REVERT: V 85 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8097 (mp0) REVERT: W 73 ARG cc_start: 0.9156 (OUTLIER) cc_final: 0.8116 (ptt90) REVERT: W 85 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8067 (mp0) REVERT: X 53 ARG cc_start: 0.8647 (mtm-85) cc_final: 0.8313 (mtm110) outliers start: 73 outliers final: 57 residues processed: 491 average time/residue: 0.4432 time to fit residues: 342.0388 Evaluate side-chains 491 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 424 time to evaluate : 3.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 56 GLU 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 116 SER 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 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 G residue 77 VAL Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 147 SER Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 116 SER Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 115 THR Chi-restraints excluded: chain N residue 52 MET Chi-restraints excluded: chain N residue 116 SER Chi-restraints excluded: chain O residue 68 LEU Chi-restraints excluded: chain P residue 39 LYS Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain P residue 153 VAL Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 68 LEU 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 S residue 52 MET Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain T residue 22 ILE Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 77 VAL Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 153 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 85 GLU 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 85 GLU Chi-restraints excluded: chain W residue 131 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 47 optimal weight: 5.9990 chunk 328 optimal weight: 0.8980 chunk 315 optimal weight: 0.9990 chunk 366 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 376 optimal weight: 8.9990 chunk 251 optimal weight: 0.8980 chunk 177 optimal weight: 5.9990 chunk 211 optimal weight: 1.9990 chunk 349 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 81 GLN E 72 GLN J 72 GLN N 81 GLN U 137 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.090033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.076620 restraints weight = 62686.457| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.83 r_work: 0.2930 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2925 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.271 32485 Z= 0.148 Angle : 0.621 30.166 44052 Z= 0.279 Chirality : 0.033 0.204 4895 Planarity : 0.003 0.035 5697 Dihedral : 6.358 86.230 4291 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.52 % Favored : 97.32 % Rotamer: Outliers : 2.18 % Allowed : 25.93 % Favored : 71.88 % 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: 3.97 (0.13), residues: 3810 helix: 3.70 (0.08), residues: 3081 sheet: None (None), residues: 0 loop : -2.76 (0.19), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 37 HIS 0.003 0.000 HIS P 54 PHE 0.021 0.001 PHE H 26 TYR 0.007 0.001 TYR Q 43 ARG 0.010 0.000 ARG Q 53 Details of bonding type rmsd hydrogen bonds : bond 0.06989 ( 2633) hydrogen bonds : angle 3.35604 ( 7899) covalent geometry : bond 0.00330 (32465) covalent geometry : angle 0.62063 (44052) Misc. bond : bond 0.08113 ( 20) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13792.62 seconds wall clock time: 239 minutes 15.92 seconds (14355.92 seconds total)