Starting phenix.real_space_refine on Mon Aug 25 22:02:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jax_36137/08_2025/8jax_36137.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jax_36137/08_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_36137/08_2025/8jax_36137.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jax_36137/08_2025/8jax_36137.map" model { file = "/net/cci-nas-00/data/ceres_data/8jax_36137/08_2025/8jax_36137.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jax_36137/08_2025/8jax_36137.cif" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASP:plan': 2, 'GLN:plan1': 1} 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: 6.90, per 1000 atoms: 0.22 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: 2.67 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.76 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: 4.50 Time building geometry restraints manager: 3.52 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 24.810 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.080 ------------------------------------------------------------------------------- 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 : 7.79 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.011 0.001 ARG M 53 TYR 0.009 0.001 TYR M 25 PHE 0.016 0.001 PHE O 26 TRP 0.005 0.001 TRP A 37 HIS 0.005 0.001 HIS S 54 Details of bonding type rmsd covalent geometry : bond 0.00497 (32465) covalent geometry : angle 0.83398 (44052) hydrogen bonds : bond 0.11872 ( 2633) hydrogen bonds : angle 4.01181 ( 7899) 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 : 1.129 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: 0.1969 time to fit residues: 146.7834 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 : 1.229 ------------------------------------------------------------------------------- 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 197 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 T 130 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.089257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.076016 restraints weight = 64556.967| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.83 r_work: 0.2897 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 344 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| r_final: 0.2861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.402 32485 Z= 0.203 Angle : 0.708 25.034 44052 Z= 0.309 Chirality : 0.035 0.257 4895 Planarity : 0.003 0.041 5697 Dihedral : 6.566 87.240 4300 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.68 % Favored : 97.14 % Rotamer: Outliers : 3.08 % Allowed : 22.73 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.50 (0.13), residues: 3810 helix: 3.33 (0.08), residues: 3078 sheet: None (None), residues: 0 loop : -2.62 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG X 61 TYR 0.007 0.001 TYR V 43 PHE 0.014 0.001 PHE C 26 TRP 0.004 0.001 TRP A 37 HIS 0.004 0.001 HIS U 54 Details of bonding type rmsd covalent geometry : bond 0.00480 (32465) covalent geometry : angle 0.70835 (44052) hydrogen bonds : bond 0.08914 ( 2633) hydrogen bonds : angle 3.68460 ( 7899) Misc. bond : bond 0.09327 ( 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 562 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 459 time to evaluate : 0.929 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: A 85 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8191 (mp0) REVERT: G 150 LEU cc_start: 0.9656 (OUTLIER) cc_final: 0.9383 (mp) REVERT: H 105 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8431 (mt) REVERT: H 148 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9080 (tt) REVERT: O 52 MET cc_start: 0.8565 (mtt) cc_final: 0.8179 (mtt) REVERT: P 52 MET cc_start: 0.9008 (ttm) cc_final: 0.8676 (mtt) REVERT: T 52 MET cc_start: 0.8554 (mtt) cc_final: 0.8277 (mtt) REVERT: X 53 ARG cc_start: 0.8471 (mtm-85) cc_final: 0.8111 (mtm110) outliers start: 103 outliers final: 47 residues processed: 536 average time/residue: 0.1914 time to fit residues: 163.7147 Evaluate side-chains 473 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 422 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 98 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 52 MET Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain E residue 119 VAL 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 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 141 ILE Chi-restraints excluded: chain K residue 52 MET 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 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 366 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 285 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 210 optimal weight: 0.9980 chunk 221 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 chunk 344 optimal weight: 6.9990 chunk 226 optimal weight: 5.9990 chunk 181 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 HIS E 72 GLN L 72 GLN P 118 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.085172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.071721 restraints weight = 64002.868| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.87 r_work: 0.2829 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| r_final: 0.2804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.197 32485 Z= 0.188 Angle : 0.633 20.568 44052 Z= 0.293 Chirality : 0.035 0.227 4895 Planarity : 0.003 0.036 5697 Dihedral : 6.537 89.583 4293 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.55 % Favored : 97.27 % Rotamer: Outliers : 3.65 % Allowed : 22.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.63 (0.13), residues: 3810 helix: 3.44 (0.08), residues: 3071 sheet: None (None), residues: 0 loop : -2.62 (0.20), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 45 TYR 0.007 0.001 TYR G 71 PHE 0.015 0.001 PHE C 26 TRP 0.003 0.001 TRP S 37 HIS 0.004 0.001 HIS U 54 Details of bonding type rmsd covalent geometry : bond 0.00437 (32465) covalent geometry : angle 0.63260 (44052) hydrogen bonds : bond 0.08848 ( 2633) hydrogen bonds : angle 3.62600 ( 7899) Misc. bond : bond 0.06196 ( 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 579 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 457 time to evaluate : 1.196 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: 0.9206 (OUTLIER) cc_final: 0.8946 (tt0) REVERT: G 150 LEU cc_start: 0.9650 (OUTLIER) cc_final: 0.9396 (mp) REVERT: H 105 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8372 (mt) REVERT: H 148 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9051 (tt) REVERT: I 81 GLN cc_start: 0.8926 (mp10) cc_final: 0.8627 (mp10) REVERT: P 39 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.7806 (mttt) REVERT: P 52 MET cc_start: 0.9053 (ttm) cc_final: 0.8739 (mtt) REVERT: P 81 GLN cc_start: 0.8891 (mm-40) cc_final: 0.8681 (mm-40) REVERT: Q 52 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8425 (mtt) REVERT: U 73 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.7973 (ptt90) REVERT: W 52 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8739 (mtt) REVERT: W 73 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.8099 (ptt90) REVERT: W 85 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8095 (mp0) REVERT: X 53 ARG cc_start: 0.8479 (mtm-85) cc_final: 0.8130 (mtm110) outliers start: 122 outliers final: 71 residues processed: 548 average time/residue: 0.2040 time to fit residues: 177.0659 Evaluate side-chains 499 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 418 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 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 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 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 57 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain H residue 60 ASP Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 141 ILE 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 J residue 52 MET 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 K residue 83 VAL Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain L residue 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 52 MET Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 116 SER 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 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 S residue 152 THR 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 73 ARG 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 W residue 52 MET Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 85 GLU Chi-restraints excluded: chain W residue 108 MET 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 15 optimal weight: 0.0270 chunk 46 optimal weight: 3.9990 chunk 167 optimal weight: 4.9990 chunk 306 optimal weight: 0.9980 chunk 263 optimal weight: 4.9990 chunk 247 optimal weight: 0.9990 chunk 338 optimal weight: 10.0000 chunk 228 optimal weight: 6.9990 chunk 201 optimal weight: 6.9990 chunk 145 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 overall best weight: 2.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 130 HIS E 14 GLN 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 = 0.3286 r_free = 0.3286 target = 0.087894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.074526 restraints weight = 63235.948| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.84 r_work: 0.2894 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 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 = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| r_final: 0.2876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.217 32485 Z= 0.155 Angle : 0.606 22.557 44052 Z= 0.272 Chirality : 0.033 0.183 4895 Planarity : 0.003 0.035 5697 Dihedral : 6.474 88.374 4293 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.31 % Favored : 97.51 % Rotamer: Outliers : 2.99 % Allowed : 23.72 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.85 (0.13), residues: 3810 helix: 3.61 (0.08), residues: 3078 sheet: None (None), residues: 0 loop : -2.72 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 100 TYR 0.006 0.001 TYR M 43 PHE 0.015 0.001 PHE C 26 TRP 0.003 0.001 TRP B 37 HIS 0.005 0.000 HIS F 130 Details of bonding type rmsd covalent geometry : bond 0.00343 (32465) covalent geometry : angle 0.60574 (44052) hydrogen bonds : bond 0.07737 ( 2633) hydrogen bonds : angle 3.44196 ( 7899) Misc. bond : bond 0.07073 ( 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 551 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 451 time to evaluate : 1.326 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: 0.8634 (OUTLIER) cc_final: 0.8182 (mp0) REVERT: B 56 GLU cc_start: 0.9206 (OUTLIER) cc_final: 0.8940 (tt0) REVERT: B 73 ARG cc_start: 0.9275 (OUTLIER) cc_final: 0.8670 (ptt90) REVERT: H 105 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8369 (mt) REVERT: H 148 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8961 (tt) REVERT: N 4 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8184 (m-30) REVERT: P 39 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.7643 (mttt) REVERT: R 81 GLN cc_start: 0.8948 (mm-40) cc_final: 0.8716 (mp10) REVERT: U 73 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.7939 (ptt90) REVERT: W 52 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8502 (mtt) REVERT: W 73 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.8107 (ptt90) REVERT: W 85 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8057 (mp0) REVERT: X 53 ARG cc_start: 0.8456 (mtm-85) cc_final: 0.8056 (mtm110) REVERT: X 156 GLN cc_start: 0.8567 (tp-100) cc_final: 0.8342 (tp40) outliers start: 100 outliers final: 59 residues processed: 524 average time/residue: 0.2170 time to fit residues: 180.4141 Evaluate side-chains 494 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 424 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain B residue 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 93 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 2 GLN Chi-restraints excluded: chain D residue 50 ASP 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 83 VAL 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 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 K residue 7 VAL Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain L residue 160 ASP Chi-restraints excluded: chain M residue 77 VAL 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 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 119 VAL 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 R residue 115 THR 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 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 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 85 GLU Chi-restraints excluded: chain W residue 131 ILE Chi-restraints excluded: chain W residue 144 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 179 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 79 optimal weight: 0.0370 chunk 297 optimal weight: 6.9990 chunk 248 optimal weight: 9.9990 chunk 272 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 316 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 367 optimal weight: 6.9990 chunk 189 optimal weight: 7.9990 overall best weight: 2.2064 ------------------------------------------------------------------------------- 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 L 72 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.091183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.077639 restraints weight = 61373.873| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.82 r_work: 0.2907 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2905 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.219 32485 Z= 0.151 Angle : 0.598 20.760 44052 Z= 0.268 Chirality : 0.033 0.178 4895 Planarity : 0.003 0.029 5697 Dihedral : 6.481 89.248 4293 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.44 % Favored : 97.40 % Rotamer: Outliers : 3.08 % Allowed : 23.81 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.88 (0.13), residues: 3810 helix: 3.64 (0.08), residues: 3084 sheet: None (None), residues: 0 loop : -2.77 (0.19), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 45 TYR 0.006 0.001 TYR M 43 PHE 0.014 0.001 PHE C 26 TRP 0.003 0.001 TRP B 37 HIS 0.003 0.000 HIS W 130 Details of bonding type rmsd covalent geometry : bond 0.00337 (32465) covalent geometry : angle 0.59816 (44052) hydrogen bonds : bond 0.07423 ( 2633) hydrogen bonds : angle 3.38299 ( 7899) Misc. bond : bond 0.07067 ( 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 562 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 459 time to evaluate : 1.331 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 2 GLN cc_start: 0.9056 (mm-40) cc_final: 0.8793 (mt0) REVERT: A 85 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8142 (mp0) REVERT: B 56 GLU cc_start: 0.9238 (OUTLIER) cc_final: 0.8966 (tt0) REVERT: B 73 ARG cc_start: 0.9258 (OUTLIER) cc_final: 0.8650 (ptt90) REVERT: E 52 MET cc_start: 0.8471 (mtt) cc_final: 0.7939 (mtt) REVERT: H 105 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8294 (mt) REVERT: H 148 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8910 (tt) REVERT: N 4 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.8074 (m-30) REVERT: P 39 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7615 (mttt) REVERT: T 52 MET cc_start: 0.8815 (mtt) cc_final: 0.8568 (mtt) REVERT: T 156 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8337 (pt0) REVERT: U 73 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.7942 (ptt90) REVERT: W 52 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.8757 (mtt) REVERT: W 73 ARG cc_start: 0.9141 (OUTLIER) cc_final: 0.8105 (ptt90) REVERT: W 85 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8027 (mp0) REVERT: X 53 ARG cc_start: 0.8506 (mtm-85) cc_final: 0.8070 (mtm110) outliers start: 103 outliers final: 64 residues processed: 538 average time/residue: 0.2155 time to fit residues: 184.7993 Evaluate side-chains 509 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 433 time to evaluate : 1.290 ------------------------------------------------------------------------------- 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 116 SER Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain B residue 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 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 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 77 VAL Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain H residue 52 MET 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 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 K residue 7 VAL Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain L residue 160 ASP Chi-restraints excluded: chain M residue 77 VAL 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 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 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 R residue 115 THR 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 156 GLN 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 V residue 77 VAL 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 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 166 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 310 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 chunk 200 optimal weight: 9.9990 chunk 334 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 ** U 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.092696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.079641 restraints weight = 61839.911| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.72 r_work: 0.2868 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.238 32485 Z= 0.175 Angle : 0.626 22.589 44052 Z= 0.279 Chirality : 0.034 0.182 4895 Planarity : 0.003 0.036 5697 Dihedral : 6.480 89.222 4293 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.65 % Favored : 97.19 % Rotamer: Outliers : 3.56 % Allowed : 23.51 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.81 (0.13), residues: 3810 helix: 3.59 (0.08), residues: 3077 sheet: None (None), residues: 0 loop : -2.73 (0.20), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 45 TYR 0.006 0.001 TYR G 71 PHE 0.012 0.001 PHE H 26 TRP 0.002 0.001 TRP F 37 HIS 0.004 0.000 HIS W 130 Details of bonding type rmsd covalent geometry : bond 0.00412 (32465) covalent geometry : angle 0.62619 (44052) hydrogen bonds : bond 0.08063 ( 2633) hydrogen bonds : angle 3.47805 ( 7899) Misc. bond : bond 0.07668 ( 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 574 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 455 time to evaluate : 1.054 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 2 GLN cc_start: 0.9067 (mm-40) cc_final: 0.8805 (mt0) REVERT: A 85 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8168 (mp0) REVERT: B 56 GLU cc_start: 0.9232 (OUTLIER) cc_final: 0.8963 (tt0) REVERT: B 73 ARG cc_start: 0.9270 (OUTLIER) cc_final: 0.8642 (ptt90) REVERT: G 135 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8756 (mt-10) REVERT: H 105 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8343 (mt) REVERT: H 148 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8962 (tt) REVERT: N 4 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.8098 (m-30) REVERT: P 39 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7721 (mttt) REVERT: Q 73 ARG cc_start: 0.9251 (OUTLIER) cc_final: 0.8352 (ptt90) REVERT: T 156 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.8323 (pt0) REVERT: U 73 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.7984 (ptt90) REVERT: V 85 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8119 (mp0) REVERT: W 52 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8670 (mtt) REVERT: W 73 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.8108 (ptt90) REVERT: W 85 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8054 (mp0) REVERT: X 53 ARG cc_start: 0.8538 (mtm-85) cc_final: 0.8179 (mtm110) outliers start: 119 outliers final: 80 residues processed: 551 average time/residue: 0.2262 time to fit residues: 196.3285 Evaluate side-chains 522 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 427 time to evaluate : 1.252 ------------------------------------------------------------------------------- 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 116 SER 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 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 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 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 141 ILE Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 105 ILE 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 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 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 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 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 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 73 ARG 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 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 77 VAL Chi-restraints excluded: chain U residue 152 THR 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 221 optimal weight: 0.5980 chunk 86 optimal weight: 8.9990 chunk 290 optimal weight: 2.9990 chunk 345 optimal weight: 6.9990 chunk 206 optimal weight: 8.9990 chunk 331 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- 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 ** U 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.089184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.075865 restraints weight = 62229.223| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.78 r_work: 0.2873 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 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 = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.068 | | 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: 0.8889 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.231 32485 Z= 0.165 Angle : 0.622 22.017 44052 Z= 0.276 Chirality : 0.033 0.187 4895 Planarity : 0.003 0.039 5697 Dihedral : 6.480 88.720 4293 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.68 % Favored : 97.17 % Rotamer: Outliers : 3.38 % Allowed : 24.14 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.85 (0.13), residues: 3810 helix: 3.62 (0.08), residues: 3078 sheet: None (None), residues: 0 loop : -2.74 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 53 TYR 0.005 0.001 TYR V 43 PHE 0.013 0.001 PHE C 26 TRP 0.003 0.001 TRP B 37 HIS 0.003 0.000 HIS U 54 Details of bonding type rmsd covalent geometry : bond 0.00378 (32465) covalent geometry : angle 0.62206 (44052) hydrogen bonds : bond 0.07932 ( 2633) hydrogen bonds : angle 3.45837 ( 7899) Misc. bond : bond 0.07373 ( 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 555 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 442 time to evaluate : 1.318 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 2 GLN cc_start: 0.9059 (mm-40) cc_final: 0.8795 (mt0) REVERT: A 85 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8155 (mp0) REVERT: B 56 GLU cc_start: 0.9238 (OUTLIER) cc_final: 0.8965 (tt0) REVERT: B 73 ARG cc_start: 0.9267 (OUTLIER) cc_final: 0.8651 (ptt90) REVERT: G 135 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8764 (mt-10) REVERT: H 148 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8935 (tt) REVERT: P 39 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.7712 (mttt) REVERT: Q 73 ARG cc_start: 0.9250 (OUTLIER) cc_final: 0.8359 (ptt90) REVERT: T 52 MET cc_start: 0.8902 (mtt) cc_final: 0.8671 (mtt) REVERT: T 156 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8307 (pt0) REVERT: U 73 ARG cc_start: 0.9079 (OUTLIER) cc_final: 0.7971 (ptt90) REVERT: V 85 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8116 (mp0) REVERT: W 52 MET cc_start: 0.9128 (OUTLIER) cc_final: 0.8781 (mtt) REVERT: W 73 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.8100 (ptt90) REVERT: W 85 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8051 (mp0) REVERT: X 53 ARG cc_start: 0.8557 (mtm-85) cc_final: 0.8208 (mtm110) outliers start: 113 outliers final: 84 residues processed: 532 average time/residue: 0.2139 time to fit residues: 178.5155 Evaluate side-chains 521 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 424 time to evaluate : 1.229 ------------------------------------------------------------------------------- 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 116 SER 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 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 119 VAL Chi-restraints excluded: chain D residue 2 GLN Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 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 F residue 141 ILE 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 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 116 SER Chi-restraints excluded: chain I residue 119 VAL Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain K residue 7 VAL 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 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 M residue 141 ILE 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 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 73 ARG 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 S residue 52 MET 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 77 VAL 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 116 SER Chi-restraints excluded: chain W residue 131 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 275 optimal weight: 8.9990 chunk 209 optimal weight: 8.9990 chunk 346 optimal weight: 0.9990 chunk 378 optimal weight: 1.9990 chunk 252 optimal weight: 0.9990 chunk 377 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 212 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 88 GLN J 72 GLN L 72 GLN U 137 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.091168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.077858 restraints weight = 62853.314| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.83 r_work: 0.2955 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.189 32485 Z= 0.141 Angle : 0.603 27.566 44052 Z= 0.269 Chirality : 0.032 0.202 4895 Planarity : 0.003 0.033 5697 Dihedral : 6.432 86.040 4293 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.28 % Favored : 97.56 % Rotamer: Outliers : 2.45 % Allowed : 25.04 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.99 (0.13), residues: 3810 helix: 3.73 (0.08), residues: 3087 sheet: None (None), residues: 0 loop : -2.84 (0.19), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG P 53 TYR 0.007 0.001 TYR Q 43 PHE 0.015 0.001 PHE C 26 TRP 0.005 0.001 TRP B 37 HIS 0.003 0.000 HIS D 112 Details of bonding type rmsd covalent geometry : bond 0.00312 (32465) covalent geometry : angle 0.60268 (44052) hydrogen bonds : bond 0.06695 ( 2633) hydrogen bonds : angle 3.28770 ( 7899) Misc. bond : bond 0.06379 ( 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 542 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 460 time to evaluate : 1.367 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: 0.9048 (mm-40) cc_final: 0.8777 (mt0) REVERT: A 85 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8120 (mp0) REVERT: E 52 MET cc_start: 0.8718 (mtt) cc_final: 0.8297 (mtt) REVERT: H 148 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8848 (tt) REVERT: J 52 MET cc_start: 0.8363 (mtt) cc_final: 0.7814 (mtt) REVERT: P 39 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7504 (mttt) REVERT: T 52 MET cc_start: 0.8907 (mtt) cc_final: 0.8704 (mtt) REVERT: T 156 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8300 (pt0) REVERT: U 73 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.7954 (ptt90) REVERT: V 85 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8088 (mp0) REVERT: W 73 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.8048 (ptt90) REVERT: W 85 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8023 (mp0) REVERT: X 53 ARG cc_start: 0.8566 (mtm-85) cc_final: 0.8205 (mtm110) outliers start: 82 outliers final: 53 residues processed: 525 average time/residue: 0.2128 time to fit residues: 177.7215 Evaluate side-chains 495 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 434 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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 116 SER Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 2 GLN Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 153 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 155 GLU Chi-restraints excluded: chain H residue 52 MET 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 I residue 116 SER Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 116 SER 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 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 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 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 156 GLN 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 266 optimal weight: 1.9990 chunk 263 optimal weight: 4.9990 chunk 293 optimal weight: 8.9990 chunk 141 optimal weight: 0.9990 chunk 192 optimal weight: 5.9990 chunk 241 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 248 optimal weight: 7.9990 chunk 63 optimal weight: 8.9990 chunk 376 optimal weight: 7.9990 chunk 201 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 GLN J 72 GLN L 72 GLN P 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.090714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.077576 restraints weight = 62207.253| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.79 r_work: 0.2818 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 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 = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 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 : 0.006 0.419 32485 Z= 0.206 Angle : 0.669 22.785 44052 Z= 0.302 Chirality : 0.035 0.178 4895 Planarity : 0.003 0.051 5697 Dihedral : 6.460 89.841 4291 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.70 % Favored : 97.14 % Rotamer: Outliers : 2.72 % Allowed : 24.89 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.74 (0.13), residues: 3810 helix: 3.55 (0.08), residues: 3071 sheet: None (None), residues: 0 loop : -2.76 (0.20), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 53 TYR 0.009 0.001 TYR M 25 PHE 0.016 0.001 PHE V 120 TRP 0.005 0.001 TRP J 37 HIS 0.004 0.001 HIS U 54 Details of bonding type rmsd covalent geometry : bond 0.00489 (32465) covalent geometry : angle 0.66907 (44052) hydrogen bonds : bond 0.08788 ( 2633) hydrogen bonds : angle 3.61333 ( 7899) Misc. bond : bond 0.11654 ( 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 528 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 437 time to evaluate : 1.375 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: A 85 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8281 (mp0) REVERT: B 73 ARG cc_start: 0.9302 (OUTLIER) cc_final: 0.8683 (ptt90) REVERT: G 135 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8806 (mt-10) REVERT: H 148 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8982 (tt) REVERT: J 52 MET cc_start: 0.8582 (mtt) cc_final: 0.7932 (mtt) REVERT: P 39 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.7840 (mttt) REVERT: Q 73 ARG cc_start: 0.9249 (OUTLIER) cc_final: 0.8340 (ptt90) REVERT: T 156 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8318 (pt0) REVERT: U 73 ARG cc_start: 0.9101 (OUTLIER) cc_final: 0.8051 (ptt90) REVERT: V 85 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8095 (mp0) REVERT: W 73 ARG cc_start: 0.9173 (OUTLIER) cc_final: 0.8195 (ptt90) REVERT: W 85 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8089 (mp0) REVERT: X 53 ARG cc_start: 0.8624 (mtm-85) cc_final: 0.8301 (mtm110) outliers start: 91 outliers final: 70 residues processed: 511 average time/residue: 0.2291 time to fit residues: 181.9953 Evaluate side-chains 502 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 421 time to evaluate : 1.275 ------------------------------------------------------------------------------- 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 116 SER Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 144 LEU 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 119 VAL Chi-restraints excluded: chain D residue 2 GLN 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 141 ILE Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 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 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 116 SER Chi-restraints excluded: chain I residue 119 VAL 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 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 115 THR Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain 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 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 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 73 ARG 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 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 156 GLN 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 152 THR 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 116 SER 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 243 optimal weight: 3.9990 chunk 369 optimal weight: 6.9990 chunk 346 optimal weight: 0.9990 chunk 374 optimal weight: 10.0000 chunk 164 optimal weight: 3.9990 chunk 329 optimal weight: 3.9990 chunk 217 optimal weight: 10.0000 chunk 43 optimal weight: 0.0010 chunk 181 optimal weight: 7.9990 chunk 253 optimal weight: 0.1980 chunk 146 optimal weight: 3.9990 overall best weight: 1.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 72 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.088681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.075320 restraints weight = 63056.710| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.84 r_work: 0.2903 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2898 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| r_final: 0.2897 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.519 32485 Z= 0.153 Angle : 0.631 23.207 44052 Z= 0.282 Chirality : 0.033 0.203 4895 Planarity : 0.003 0.051 5697 Dihedral : 6.402 83.733 4291 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.44 % Favored : 97.40 % Rotamer: Outliers : 1.85 % Allowed : 25.90 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.92 (0.13), residues: 3810 helix: 3.69 (0.08), residues: 3076 sheet: None (None), residues: 0 loop : -2.82 (0.19), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 45 TYR 0.006 0.001 TYR Q 43 PHE 0.015 0.001 PHE C 26 TRP 0.005 0.001 TRP B 37 HIS 0.003 0.000 HIS W 54 Details of bonding type rmsd covalent geometry : bond 0.00331 (32465) covalent geometry : angle 0.63092 (44052) hydrogen bonds : bond 0.07393 ( 2633) hydrogen bonds : angle 3.40457 ( 7899) Misc. bond : bond 0.12961 ( 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: 62 poor density : 440 time to evaluate : 1.300 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: 0.9051 (mm-40) cc_final: 0.8778 (mt0) REVERT: A 85 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8137 (mp0) REVERT: B 73 ARG cc_start: 0.9262 (OUTLIER) cc_final: 0.8655 (ptt90) REVERT: H 148 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8858 (tt) REVERT: J 52 MET cc_start: 0.8564 (mtt) cc_final: 0.7943 (mtt) REVERT: N 81 GLN cc_start: 0.9092 (mm-40) cc_final: 0.8883 (mm110) REVERT: P 39 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7637 (mttt) REVERT: Q 73 ARG cc_start: 0.9216 (OUTLIER) cc_final: 0.8311 (ptt90) REVERT: T 52 MET cc_start: 0.8861 (mtt) cc_final: 0.8580 (mtt) REVERT: T 156 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8310 (pt0) REVERT: U 73 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.7954 (ptt90) REVERT: V 53 ARG cc_start: 0.8488 (mtm110) cc_final: 0.8254 (mtm-85) REVERT: V 85 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8072 (mp0) REVERT: W 73 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.8091 (ptt90) REVERT: W 85 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8035 (mp0) REVERT: X 53 ARG cc_start: 0.8615 (mtm-85) cc_final: 0.8266 (mtm110) outliers start: 62 outliers final: 49 residues processed: 492 average time/residue: 0.2142 time to fit residues: 166.4096 Evaluate side-chains 490 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 431 time to evaluate : 1.212 ------------------------------------------------------------------------------- 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 116 SER Chi-restraints excluded: chain A residue 144 LEU 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 78 ARG Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 153 VAL 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 52 MET 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 116 SER Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 116 SER 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 N residue 52 MET Chi-restraints excluded: chain N residue 116 SER 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 73 ARG 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 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 156 GLN 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 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 116 SER 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 362 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 368 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 241 optimal weight: 9.9990 chunk 171 optimal weight: 5.9990 chunk 249 optimal weight: 4.9990 chunk 157 optimal weight: 0.9980 chunk 259 optimal weight: 4.9990 chunk 312 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 81 GLN J 72 GLN P 81 GLN S 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.086720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.073395 restraints weight = 63641.675| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.84 r_work: 0.2867 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2864 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| r_final: 0.2865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.525 32485 Z= 0.173 Angle : 0.638 22.314 44052 Z= 0.286 Chirality : 0.034 0.212 4895 Planarity : 0.003 0.061 5697 Dihedral : 6.384 86.239 4291 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.68 % Favored : 97.17 % Rotamer: Outliers : 2.36 % Allowed : 25.55 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.84 (0.13), residues: 3810 helix: 3.63 (0.08), residues: 3072 sheet: None (None), residues: 0 loop : -2.78 (0.20), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG W 53 TYR 0.006 0.001 TYR N 25 PHE 0.013 0.001 PHE V 120 TRP 0.003 0.001 TRP J 37 HIS 0.003 0.000 HIS K 54 Details of bonding type rmsd covalent geometry : bond 0.00400 (32465) covalent geometry : angle 0.63832 (44052) hydrogen bonds : bond 0.07908 ( 2633) hydrogen bonds : angle 3.49054 ( 7899) Misc. bond : bond 0.13310 ( 20) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6050.73 seconds wall clock time: 104 minutes 50.27 seconds (6290.27 seconds total)