Starting phenix.real_space_refine on Wed May 28 18:58:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jax_36137/05_2025/8jax_36137.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jax_36137/05_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_36137/05_2025/8jax_36137.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jax_36137/05_2025/8jax_36137.map" model { file = "/net/cci-nas-00/data/ceres_data/8jax_36137/05_2025/8jax_36137.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jax_36137/05_2025/8jax_36137.cif" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 36 7.16 5 S 96 5.16 5 C 20181 2.51 5 N 5446 2.21 5 O 6130 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 31889 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1313 Classifications: {'peptide': 162} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1293 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 156} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1318 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1305 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1310 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1304 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1304 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1304 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1299 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 156} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "J" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1318 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1318 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1307 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "N" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1310 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1315 Classifications: {'peptide': 162} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1305 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Q" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1318 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1310 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "T" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1315 Classifications: {'peptide': 162} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "U" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 154} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1318 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "W" Number of atoms: 1300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1300 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 156} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "X" Number of atoms: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1310 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'FE2': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 11 residue: pdb=" NB HEM B 201 " occ=0.04 ... (41 atoms not shown) pdb="FE HEM B 201 " occ=0.04 residue: pdb=" NB HEM D 201 " occ=0.00 ... (41 atoms not shown) pdb="FE HEM D 201 " occ=0.00 residue: pdb=" NB HEM F 202 " occ=0.00 ... (41 atoms not shown) pdb="FE HEM F 202 " occ=0.00 residue: pdb=" NB HEM H 202 " occ=0.03 ... (41 atoms not shown) pdb="FE HEM H 202 " occ=0.03 residue: pdb=" NB HEM K 201 " occ=0.44 ... (41 atoms not shown) pdb="FE HEM K 201 " occ=0.44 residue: pdb=" NB HEM P 202 " occ=0.32 ... (41 atoms not shown) pdb="FE HEM P 202 " occ=0.32 residue: pdb=" NB HEM R 201 " occ=0.03 ... (41 atoms not shown) pdb="FE HEM R 201 " occ=0.03 residue: pdb=" NB HEM S 202 " occ=0.06 ... (41 atoms not shown) pdb="FE HEM S 202 " occ=0.06 residue: pdb=" NB HEM U 202 " occ=0.04 ... (41 atoms not shown) pdb="FE HEM U 202 " occ=0.04 residue: pdb=" NB HEM V 202 " occ=0.40 ... (41 atoms not shown) pdb="FE HEM V 202 " occ=0.40 residue: pdb=" NB HEM X 201 " occ=0.05 ... (41 atoms not shown) pdb="FE HEM X 201 " occ=0.05 Time building chain proxies: 17.39, per 1000 atoms: 0.55 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: 8.57 Conformation dependent library (CDL) restraints added in 3.7 seconds 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7422 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 0 sheets defined 82.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 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: 9.10 Time building geometry restraints manager: 9.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.41: 13552 1.41 - 1.60: 18673 1.60 - 1.79: 108 1.79 - 1.98: 84 1.98 - 2.17: 48 Bond restraints: 32465 Sorted by residual: bond pdb=" CB MET N 52 " pdb=" CG MET N 52 " ideal model delta sigma weight residual 1.520 1.440 0.080 3.00e-02 1.11e+03 7.04e+00 bond pdb=" SD MET O 52 " pdb=" CE MET O 52 " ideal model delta sigma weight residual 1.791 1.731 0.060 2.50e-02 1.60e+03 5.83e+00 bond pdb=" CB MET O 52 " pdb=" CG MET O 52 " ideal model delta sigma weight residual 1.520 1.448 0.072 3.00e-02 1.11e+03 5.78e+00 bond pdb=" SD MET N 52 " pdb=" CE MET N 52 " ideal model delta sigma weight residual 1.791 1.735 0.056 2.50e-02 1.60e+03 5.03e+00 bond pdb=" CB MET X 52 " pdb=" CG MET X 52 " ideal model delta sigma weight residual 1.520 1.455 0.065 3.00e-02 1.11e+03 4.75e+00 ... (remaining 32460 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.85: 43962 5.85 - 11.70: 59 11.70 - 17.55: 17 17.55 - 23.40: 8 23.40 - 29.25: 6 Bond angle restraints: 44052 Sorted by residual: angle pdb=" CB MET O 52 " pdb=" CG MET O 52 " pdb=" SD MET O 52 " ideal model delta sigma weight residual 112.70 83.45 29.25 3.00e+00 1.11e-01 9.50e+01 angle pdb=" CB MET K 52 " pdb=" CG MET K 52 " pdb=" SD MET K 52 " ideal model delta sigma weight residual 112.70 141.19 -28.49 3.00e+00 1.11e-01 9.02e+01 angle pdb=" CB MET U 52 " pdb=" CG MET U 52 " pdb=" SD MET U 52 " ideal model delta sigma weight residual 112.70 89.62 23.08 3.00e+00 1.11e-01 5.92e+01 angle pdb=" CB MET W 52 " pdb=" CG MET W 52 " pdb=" SD MET W 52 " ideal model delta sigma weight residual 112.70 91.82 20.88 3.00e+00 1.11e-01 4.84e+01 angle pdb=" CB MET B 52 " pdb=" CG MET B 52 " pdb=" SD MET B 52 " ideal model delta sigma weight residual 112.70 93.10 19.60 3.00e+00 1.11e-01 4.27e+01 ... (remaining 44047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 16228 17.99 - 35.99: 2402 35.99 - 53.98: 621 53.98 - 71.98: 107 71.98 - 89.97: 79 Dihedral angle restraints: 19437 sinusoidal: 8062 harmonic: 11375 Sorted by residual: dihedral pdb=" CA MET K 52 " pdb=" C MET K 52 " pdb=" N ARG K 53 " pdb=" CA ARG K 53 " ideal model delta harmonic sigma weight residual 180.00 155.69 24.31 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA GLU F 94 " pdb=" C GLU F 94 " pdb=" N LEU F 95 " pdb=" CA LEU F 95 " ideal model delta harmonic sigma weight residual 180.00 157.74 22.26 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA GLU W 94 " pdb=" C GLU W 94 " pdb=" N LEU W 95 " pdb=" CA LEU W 95 " ideal model delta harmonic sigma weight residual 180.00 158.03 21.97 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 19434 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 4243 0.051 - 0.101: 564 0.101 - 0.152: 76 0.152 - 0.202: 7 0.202 - 0.253: 5 Chirality restraints: 4895 Sorted by residual: chirality pdb=" CA MET K 52 " pdb=" N MET K 52 " pdb=" C MET K 52 " pdb=" CB MET K 52 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA GLU W 94 " pdb=" N GLU W 94 " pdb=" C GLU W 94 " pdb=" CB GLU W 94 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA GLU F 94 " pdb=" N GLU F 94 " pdb=" C GLU F 94 " pdb=" CB GLU F 94 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 4892 not shown) Planarity restraints: 5697 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEM U 202 " 0.015 2.00e-02 2.50e+03 2.00e-02 8.99e+00 pdb=" C2C HEM U 202 " -0.001 2.00e-02 2.50e+03 pdb=" C3C HEM U 202 " 0.006 2.00e-02 2.50e+03 pdb=" C4C HEM U 202 " 0.013 2.00e-02 2.50e+03 pdb=" CAC HEM U 202 " 0.003 2.00e-02 2.50e+03 pdb=" CHC HEM U 202 " -0.029 2.00e-02 2.50e+03 pdb=" CHD HEM U 202 " -0.035 2.00e-02 2.50e+03 pdb=" CMC HEM U 202 " -0.004 2.00e-02 2.50e+03 pdb=" NC HEM U 202 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A HEM F 202 " -0.011 2.00e-02 2.50e+03 1.74e-02 6.79e+00 pdb=" C2A HEM F 202 " 0.027 2.00e-02 2.50e+03 pdb=" C3A HEM F 202 " 0.011 2.00e-02 2.50e+03 pdb=" C4A HEM F 202 " 0.004 2.00e-02 2.50e+03 pdb=" CAA HEM F 202 " -0.023 2.00e-02 2.50e+03 pdb=" CHA HEM F 202 " 0.019 2.00e-02 2.50e+03 pdb=" CHB HEM F 202 " 0.003 2.00e-02 2.50e+03 pdb=" CMA HEM F 202 " -0.002 2.00e-02 2.50e+03 pdb=" NA HEM F 202 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND HEM S 202 " -0.025 2.00e-02 2.50e+03 1.64e-02 6.03e+00 pdb=" C1D HEM S 202 " -0.016 2.00e-02 2.50e+03 pdb=" C2D HEM S 202 " -0.001 2.00e-02 2.50e+03 pdb=" C3D HEM S 202 " 0.007 2.00e-02 2.50e+03 pdb=" C4D HEM S 202 " -0.012 2.00e-02 2.50e+03 pdb=" CAD HEM S 202 " -0.007 2.00e-02 2.50e+03 pdb=" CHA HEM S 202 " 0.026 2.00e-02 2.50e+03 pdb=" CHD HEM S 202 " 0.025 2.00e-02 2.50e+03 pdb=" CMD HEM S 202 " 0.003 2.00e-02 2.50e+03 ... (remaining 5694 not shown) Histogram of nonbonded interaction distances: 1.14 - 1.89: 28 1.89 - 2.64: 614 2.64 - 3.40: 45679 3.40 - 4.15: 68932 4.15 - 4.90: 132269 Nonbonded interactions: 247522 Sorted by model distance: nonbonded pdb=" OE1 GLU W 18 " pdb=" OE1 GLU W 51 " model vdw 1.139 3.040 nonbonded pdb=" OE1 GLU F 18 " pdb=" OE1 GLU F 51 " model vdw 1.152 3.040 nonbonded pdb=" OE1 GLU T 18 " pdb=" OE1 GLU T 51 " model vdw 1.212 3.040 nonbonded pdb=" OE1 GLU Q 18 " pdb=" OE1 GLU Q 51 " model vdw 1.216 3.040 nonbonded pdb=" OE1 GLU X 18 " pdb=" OE1 GLU X 51 " model vdw 1.250 3.040 ... (remaining 247517 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 148 or (resid 149 and (name N or name CA or name \ C or name O or name CB )) or resid 150 through 156 or (resid 157 and (name N or \ name CA or name C or name O or name CB )))) selection = (chain 'B' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 157)) selection = (chain 'C' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 156 or (resid 157 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'E' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'F' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'G' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'H' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'I' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'J' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 156 or (resid 157 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'K' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'L' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 156 or (resid 157 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'M' and (resid 1 through 148 or (resid 149 and (name N or name CA or name \ C or name O or name CB )) or resid 150 through 157)) selection = (chain 'N' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'O' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 156 or (resid 157 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'P' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'Q' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 156 or (resid 157 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'R' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'S' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'T' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 156 or (resid 157 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'U' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'V' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 156 or (resid 157 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'W' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'X' and (resid 1 through 65 or (resid 66 and (name N or name CA or name C \ or name O or name CB )) or resid 67 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.200 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 62.190 Find NCS groups from input model: 2.010 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.689 32485 Z= 0.669 Angle : 0.834 29.248 44052 Z= 0.348 Chirality : 0.035 0.253 4895 Planarity : 0.003 0.042 5697 Dihedral : 18.674 89.974 12015 Min Nonbonded Distance : 1.139 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.44 % Favored : 97.38 % Rotamer: Outliers : 0.36 % Allowed : 25.34 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.13), residues: 3810 helix: 3.01 (0.08), residues: 3049 sheet: None (None), residues: 0 loop : -2.57 (0.20), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 37 HIS 0.005 0.001 HIS S 54 PHE 0.016 0.001 PHE O 26 TYR 0.009 0.001 TYR M 25 ARG 0.011 0.001 ARG M 53 Details of bonding type rmsd hydrogen bonds : bond 0.11872 ( 2633) hydrogen bonds : angle 4.01181 ( 7899) covalent geometry : bond 0.00497 (32465) covalent geometry : angle 0.83398 (44052) Misc. bond : bond 0.34938 ( 20) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 467 time to evaluate : 3.718 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: 0.4390 time to fit residues: 328.4970 Evaluate side-chains 455 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 450 time to evaluate : 3.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 156 GLN Chi-restraints excluded: chain L residue 160 ASP Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain T residue 22 ILE Chi-restraints excluded: chain V residue 141 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 321 optimal weight: 7.9990 chunk 288 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 7.9990 chunk 154 optimal weight: 9.9990 chunk 298 optimal weight: 7.9990 chunk 115 optimal weight: 9.9990 chunk 181 optimal weight: 0.8980 chunk 222 optimal weight: 5.9990 chunk 345 optimal weight: 3.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 81 GLN E 72 GLN E 118 ASN K 130 HIS L 72 GLN P 118 ASN T 130 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.087115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.073877 restraints weight = 64281.368| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.82 r_work: 0.2856 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 344 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.395 32485 Z= 0.238 Angle : 0.732 24.964 44052 Z= 0.324 Chirality : 0.037 0.279 4895 Planarity : 0.003 0.035 5697 Dihedral : 6.600 89.081 4300 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.73 % Favored : 97.09 % Rotamer: Outliers : 3.41 % Allowed : 22.67 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.38 (0.13), residues: 3810 helix: 3.25 (0.08), residues: 3084 sheet: None (None), residues: 0 loop : -2.74 (0.20), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP S 37 HIS 0.005 0.001 HIS U 54 PHE 0.013 0.001 PHE C 26 TYR 0.008 0.001 TYR G 71 ARG 0.003 0.000 ARG X 61 Details of bonding type rmsd hydrogen bonds : bond 0.09610 ( 2633) hydrogen bonds : angle 3.79837 ( 7899) covalent geometry : bond 0.00575 (32465) covalent geometry : angle 0.73182 (44052) Misc. bond : bond 0.09212 ( 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 550 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 436 time to evaluate : 3.644 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8346 (mp0) REVERT: D 56 GLU cc_start: 0.9307 (OUTLIER) cc_final: 0.8871 (tm-30) REVERT: G 150 LEU cc_start: 0.9663 (OUTLIER) cc_final: 0.9378 (mp) REVERT: H 105 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8442 (mt) REVERT: H 148 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9116 (tt) REVERT: O 52 MET cc_start: 0.8604 (mtt) cc_final: 0.8255 (mtt) REVERT: P 52 MET cc_start: 0.9024 (ttm) cc_final: 0.8652 (mtt) REVERT: T 52 MET cc_start: 0.8577 (mtt) cc_final: 0.8303 (mtt) REVERT: X 53 ARG cc_start: 0.8523 (mtm-85) cc_final: 0.8160 (mtm110) outliers start: 114 outliers final: 59 residues processed: 520 average time/residue: 0.4452 time to fit residues: 368.0244 Evaluate side-chains 472 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 408 time to evaluate : 3.513 ------------------------------------------------------------------------------- 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 83 VAL Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 141 ILE Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 119 VAL Chi-restraints excluded: chain J residue 52 MET Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain K residue 52 MET Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 160 ASP Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain M residue 141 ILE Chi-restraints excluded: chain N residue 52 MET Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain S residue 83 VAL Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain T residue 22 ILE Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 141 ILE Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 119 VAL Chi-restraints excluded: chain U residue 153 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 152 THR Chi-restraints excluded: chain W residue 131 ILE Chi-restraints excluded: chain X residue 52 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 114 optimal weight: 5.9990 chunk 56 optimal weight: 0.0470 chunk 156 optimal weight: 1.9990 chunk 273 optimal weight: 0.9990 chunk 209 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 362 optimal weight: 8.9990 chunk 292 optimal weight: 7.9990 chunk 145 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 overall best weight: 1.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 72 GLN L 72 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.091027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.077728 restraints weight = 63401.209| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.85 r_work: 0.2937 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 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 = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| r_final: 0.2935 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.188 32485 Z= 0.148 Angle : 0.592 19.465 44052 Z= 0.272 Chirality : 0.033 0.232 4895 Planarity : 0.003 0.033 5697 Dihedral : 6.484 85.437 4293 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.26 % Favored : 97.56 % Rotamer: Outliers : 2.69 % Allowed : 23.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.82 (0.13), residues: 3810 helix: 3.59 (0.08), residues: 3093 sheet: None (None), residues: 0 loop : -2.86 (0.19), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP T 37 HIS 0.003 0.000 HIS W 130 PHE 0.018 0.001 PHE H 26 TYR 0.006 0.001 TYR V 149 ARG 0.006 0.000 ARG K 53 Details of bonding type rmsd hydrogen bonds : bond 0.07052 ( 2633) hydrogen bonds : angle 3.37616 ( 7899) covalent geometry : bond 0.00306 (32465) covalent geometry : angle 0.59154 (44052) Misc. bond : bond 0.05473 ( 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 570 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 480 time to evaluate : 3.705 Fit side-chains 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: H 105 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8295 (mt) REVERT: H 148 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8907 (tt) REVERT: J 105 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8405 (mt) REVERT: P 39 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7530 (mttt) REVERT: P 52 MET cc_start: 0.9026 (ttm) cc_final: 0.8782 (mtt) REVERT: P 81 GLN cc_start: 0.8821 (mm-40) cc_final: 0.8570 (mm-40) REVERT: U 73 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.7917 (ptt90) REVERT: V 81 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8585 (mm110) REVERT: W 52 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.8786 (mtt) REVERT: W 73 ARG cc_start: 0.9118 (OUTLIER) cc_final: 0.8078 (ptt90) REVERT: W 85 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8018 (mp0) REVERT: X 53 ARG cc_start: 0.8405 (mtm-85) cc_final: 0.8017 (mtm110) outliers start: 90 outliers final: 31 residues processed: 547 average time/residue: 0.4341 time to fit residues: 379.7975 Evaluate side-chains 484 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 445 time to evaluate : 3.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 141 ILE 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 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 148 LEU Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain I residue 50 ASP Chi-restraints excluded: chain J residue 105 ILE Chi-restraints excluded: chain K residue 7 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 N residue 52 MET Chi-restraints excluded: chain P residue 39 LYS Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 153 VAL Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain T residue 22 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 V residue 141 ILE Chi-restraints excluded: chain W residue 52 MET Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain W residue 85 GLU Chi-restraints excluded: chain W residue 144 LEU Chi-restraints excluded: chain X residue 52 MET Chi-restraints excluded: chain X residue 141 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 295 optimal weight: 1.9990 chunk 204 optimal weight: 7.9990 chunk 239 optimal weight: 10.0000 chunk 196 optimal weight: 8.9990 chunk 125 optimal weight: 9.9990 chunk 187 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 176 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 360 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 HIS E 14 GLN E 72 GLN J 72 GLN L 72 GLN N 32 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.089154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.075778 restraints weight = 62686.326| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.82 r_work: 0.2856 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 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 = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| r_final: 0.2834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.1061 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= 0.189 Angle : 0.623 19.187 44052 Z= 0.286 Chirality : 0.034 0.178 4895 Planarity : 0.003 0.032 5697 Dihedral : 6.491 89.353 4293 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.49 % Favored : 97.32 % Rotamer: Outliers : 3.20 % Allowed : 22.91 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.71 (0.13), residues: 3810 helix: 3.50 (0.08), residues: 3074 sheet: None (None), residues: 0 loop : -2.62 (0.20), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 37 HIS 0.007 0.001 HIS F 130 PHE 0.012 0.001 PHE H 26 TYR 0.007 0.001 TYR G 71 ARG 0.003 0.000 ARG S 100 Details of bonding type rmsd hydrogen bonds : bond 0.08276 ( 2633) hydrogen bonds : angle 3.53303 ( 7899) covalent geometry : bond 0.00446 (32465) covalent geometry : angle 0.62315 (44052) Misc. bond : bond 0.07886 ( 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 557 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 450 time to evaluate : 3.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8138 (mp0) REVERT: H 105 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8352 (mt) REVERT: H 148 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9048 (tt) REVERT: J 52 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7576 (mtt) REVERT: N 4 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.8126 (m-30) REVERT: P 39 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.7755 (mttt) REVERT: R 4 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8253 (t0) REVERT: U 73 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8018 (ptt90) REVERT: V 1 MET cc_start: 0.7238 (tpp) cc_final: 0.6792 (ttm) REVERT: W 52 MET cc_start: 0.9130 (OUTLIER) cc_final: 0.8748 (mtt) REVERT: W 73 ARG cc_start: 0.9168 (OUTLIER) cc_final: 0.8128 (ptt90) REVERT: W 85 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8085 (mp0) REVERT: X 53 ARG cc_start: 0.8479 (mtm-85) cc_final: 0.8093 (mtm110) outliers start: 107 outliers final: 68 residues processed: 529 average time/residue: 0.4454 time to fit residues: 373.8579 Evaluate side-chains 501 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 422 time to evaluate : 3.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 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 77 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 2 GLN Chi-restraints excluded: chain D residue 50 ASP Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain G residue 77 VAL 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 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 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 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 79 VAL Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 116 SER Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain P residue 39 LYS Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 141 ILE Chi-restraints excluded: chain R residue 4 ASP Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain T residue 22 ILE Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 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 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 Chi-restraints excluded: chain X residue 52 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 262 optimal weight: 5.9990 chunk 147 optimal weight: 8.9990 chunk 242 optimal weight: 4.9990 chunk 184 optimal weight: 10.0000 chunk 171 optimal weight: 6.9990 chunk 258 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 267 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3209 r_free = 0.3209 target = 0.083538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.070085 restraints weight = 63786.834| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.85 r_work: 0.2795 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| r_final: 0.2773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.259 32485 Z= 0.208 Angle : 0.632 19.646 44052 Z= 0.294 Chirality : 0.035 0.187 4895 Planarity : 0.003 0.031 5697 Dihedral : 6.498 85.043 4293 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.70 % Favored : 97.14 % Rotamer: Outliers : 3.86 % Allowed : 23.15 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.67 (0.13), residues: 3810 helix: 3.48 (0.08), residues: 3080 sheet: None (None), residues: 0 loop : -2.78 (0.19), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP M 37 HIS 0.004 0.001 HIS U 54 PHE 0.013 0.001 PHE H 26 TYR 0.008 0.001 TYR G 71 ARG 0.004 0.000 ARG H 45 Details of bonding type rmsd hydrogen bonds : bond 0.09129 ( 2633) hydrogen bonds : angle 3.65145 ( 7899) covalent geometry : bond 0.00493 (32465) covalent geometry : angle 0.63157 (44052) Misc. bond : bond 0.07757 ( 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 574 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 445 time to evaluate : 3.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8282 (mp0) REVERT: B 73 ARG cc_start: 0.9272 (OUTLIER) cc_final: 0.8619 (ptt90) REVERT: G 135 GLU cc_start: 0.9056 (OUTLIER) cc_final: 0.8811 (mt-10) REVERT: H 81 GLN cc_start: 0.8950 (mp10) cc_final: 0.8678 (mp10) REVERT: H 148 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9024 (tt) REVERT: I 81 GLN cc_start: 0.8933 (mp10) cc_final: 0.8653 (mp10) REVERT: J 52 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.7613 (mtt) REVERT: N 4 ASP cc_start: 0.8470 (OUTLIER) cc_final: 0.8227 (m-30) REVERT: N 144 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8942 (mp) REVERT: P 39 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.7842 (mttt) REVERT: T 156 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8340 (pt0) REVERT: U 73 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.8013 (ptt90) REVERT: V 85 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8115 (mp0) REVERT: W 52 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8670 (mtt) REVERT: W 73 ARG cc_start: 0.9204 (OUTLIER) cc_final: 0.8159 (ptt90) REVERT: W 85 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8080 (mp0) REVERT: X 53 ARG cc_start: 0.8555 (mtm-85) cc_final: 0.8203 (mtm110) outliers start: 129 outliers final: 88 residues processed: 543 average time/residue: 0.4406 time to fit residues: 375.2795 Evaluate side-chains 513 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 411 time to evaluate : 3.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 2 GLN Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 78 ARG Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 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 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 J residue 83 VAL 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 L residue 83 VAL Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain L residue 160 ASP Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 141 ILE Chi-restraints excluded: chain N residue 4 ASP Chi-restraints excluded: chain N residue 52 MET Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 116 SER Chi-restraints excluded: chain N residue 144 LEU Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain O residue 141 ILE Chi-restraints excluded: chain O residue 153 VAL Chi-restraints excluded: chain P residue 39 LYS Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 144 LEU Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 152 THR Chi-restraints excluded: chain P residue 153 VAL Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain Q residue 116 SER Chi-restraints excluded: chain 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 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 83 VAL Chi-restraints excluded: chain U residue 137 GLN Chi-restraints excluded: chain U residue 152 THR Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 85 GLU Chi-restraints excluded: chain V residue 116 SER Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain V residue 152 THR Chi-restraints excluded: chain V residue 153 VAL Chi-restraints excluded: chain W residue 52 MET Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain W residue 78 ARG Chi-restraints excluded: chain W residue 85 GLU Chi-restraints excluded: chain W residue 131 ILE Chi-restraints excluded: chain X residue 52 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 4 optimal weight: 1.9990 chunk 259 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 205 optimal weight: 1.9990 chunk 363 optimal weight: 10.0000 chunk 114 optimal weight: 8.9990 chunk 380 optimal weight: 0.6980 chunk 40 optimal weight: 9.9990 chunk 247 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 159 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3309 r_free = 0.3309 target = 0.089300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.075868 restraints weight = 63013.211| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.84 r_work: 0.2916 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2912 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| r_final: 0.2912 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.202 32485 Z= 0.146 Angle : 0.586 23.569 44052 Z= 0.268 Chirality : 0.033 0.187 4895 Planarity : 0.003 0.035 5697 Dihedral : 6.449 87.717 4293 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.20 % Favored : 97.61 % Rotamer: Outliers : 2.69 % Allowed : 24.44 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.96 (0.13), residues: 3810 helix: 3.70 (0.08), residues: 3086 sheet: None (None), residues: 0 loop : -2.82 (0.19), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 37 HIS 0.002 0.000 HIS T 54 PHE 0.017 0.001 PHE H 26 TYR 0.005 0.001 TYR Q 43 ARG 0.003 0.000 ARG H 45 Details of bonding type rmsd hydrogen bonds : bond 0.07255 ( 2633) hydrogen bonds : angle 3.36812 ( 7899) covalent geometry : bond 0.00320 (32465) covalent geometry : angle 0.58632 (44052) Misc. bond : bond 0.06495 ( 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 559 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 469 time to evaluate : 3.758 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: 0.8609 (OUTLIER) cc_final: 0.8164 (mp0) REVERT: H 81 GLN cc_start: 0.8917 (mp10) cc_final: 0.8685 (mp10) REVERT: H 148 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8881 (tt) REVERT: I 81 GLN cc_start: 0.8882 (mp10) cc_final: 0.8631 (mp10) REVERT: J 52 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.7589 (mtt) REVERT: N 120 PHE cc_start: 0.9043 (OUTLIER) cc_final: 0.8817 (m-10) REVERT: P 39 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7600 (mttt) REVERT: R 4 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.8148 (t0) REVERT: U 73 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.7932 (ptt90) REVERT: W 52 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.8806 (mtt) REVERT: W 85 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8015 (mp0) REVERT: X 53 ARG cc_start: 0.8524 (mtm-85) cc_final: 0.8159 (mtm110) outliers start: 90 outliers final: 59 residues processed: 537 average time/residue: 0.4186 time to fit residues: 359.4387 Evaluate side-chains 509 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 441 time to evaluate : 3.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 2 GLN Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 78 ARG Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain G residue 72 GLN Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain I residue 50 ASP Chi-restraints excluded: chain J residue 52 MET Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain L residue 160 ASP Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain N residue 52 MET Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 116 SER Chi-restraints excluded: chain N residue 120 PHE 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 153 VAL Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 68 LEU Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain R residue 4 ASP Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 147 SER Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain T residue 22 ILE Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 152 THR 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 78 ARG Chi-restraints excluded: chain W residue 85 GLU Chi-restraints excluded: chain W residue 141 ILE Chi-restraints excluded: chain W residue 144 LEU Chi-restraints excluded: chain X residue 141 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 220 optimal weight: 3.9990 chunk 336 optimal weight: 10.0000 chunk 251 optimal weight: 2.9990 chunk 175 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 162 optimal weight: 6.9990 chunk 310 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 GLN E 72 GLN J 72 GLN K 130 HIS L 72 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.092581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.079595 restraints weight = 62286.986| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.70 r_work: 0.2866 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- 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 = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| r_final: 0.2864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.235 32485 Z= 0.176 Angle : 0.623 23.790 44052 Z= 0.281 Chirality : 0.034 0.190 4895 Planarity : 0.003 0.038 5697 Dihedral : 6.470 88.947 4293 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.62 % Favored : 97.19 % Rotamer: Outliers : 3.17 % Allowed : 24.59 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.84 (0.13), residues: 3810 helix: 3.62 (0.08), residues: 3077 sheet: None (None), residues: 0 loop : -2.79 (0.19), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 37 HIS 0.004 0.000 HIS U 54 PHE 0.013 0.001 PHE C 26 TYR 0.006 0.001 TYR M 43 ARG 0.006 0.000 ARG T 53 Details of bonding type rmsd hydrogen bonds : bond 0.08028 ( 2633) hydrogen bonds : angle 3.48100 ( 7899) covalent geometry : bond 0.00412 (32465) covalent geometry : angle 0.62294 (44052) Misc. bond : bond 0.07732 ( 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 551 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 445 time to evaluate : 3.743 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: 0.8686 (OUTLIER) cc_final: 0.8151 (mp0) REVERT: B 73 ARG cc_start: 0.9281 (OUTLIER) cc_final: 0.8638 (ptt90) REVERT: H 81 GLN cc_start: 0.8912 (mp10) cc_final: 0.8665 (mp10) REVERT: H 148 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8966 (tt) REVERT: I 81 GLN cc_start: 0.8962 (mp10) cc_final: 0.8694 (mp10) REVERT: J 52 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.7631 (mtt) REVERT: N 4 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.8100 (m-30) REVERT: P 39 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.7695 (mttt) REVERT: Q 73 ARG cc_start: 0.9257 (OUTLIER) cc_final: 0.8380 (ptt90) REVERT: R 4 ASP cc_start: 0.8482 (OUTLIER) cc_final: 0.8059 (t0) REVERT: U 73 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8027 (ptt90) REVERT: V 85 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8096 (mp0) REVERT: W 52 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8685 (mtt) REVERT: W 73 ARG cc_start: 0.9179 (OUTLIER) cc_final: 0.8226 (ptt90) REVERT: W 85 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8061 (mp0) REVERT: X 53 ARG cc_start: 0.8554 (mtm-85) cc_final: 0.8173 (mtm110) outliers start: 106 outliers final: 75 residues processed: 528 average time/residue: 0.4592 time to fit residues: 382.1646 Evaluate side-chains 515 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 427 time to evaluate : 3.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 2 GLN Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 78 ARG Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 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 I residue 119 VAL Chi-restraints excluded: chain J residue 52 MET Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain L residue 160 ASP Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 115 THR Chi-restraints excluded: chain 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 77 VAL Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 116 SER Chi-restraints excluded: chain O residue 2 GLN Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain P residue 39 LYS Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 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 4 ASP Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain R residue 147 SER Chi-restraints excluded: chain S residue 52 MET Chi-restraints excluded: chain S residue 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 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 85 GLU Chi-restraints excluded: chain V residue 116 SER Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain V residue 153 VAL Chi-restraints excluded: chain W residue 52 MET Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain W residue 78 ARG Chi-restraints excluded: chain W residue 85 GLU 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 131 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 265 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 231 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 359 optimal weight: 0.0370 chunk 364 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 196 optimal weight: 7.9990 overall best weight: 4.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 72 GLN P 81 GLN ** U 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.086377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.072945 restraints weight = 63063.231| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.81 r_work: 0.2806 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| r_final: 0.2764 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.255 32485 Z= 0.205 Angle : 0.658 27.235 44052 Z= 0.300 Chirality : 0.035 0.189 4895 Planarity : 0.003 0.031 5697 Dihedral : 6.472 83.225 4293 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.91 % Favored : 96.90 % Rotamer: Outliers : 3.35 % Allowed : 24.62 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.73 (0.13), residues: 3810 helix: 3.54 (0.08), residues: 3065 sheet: None (None), residues: 0 loop : -2.73 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 37 HIS 0.004 0.001 HIS U 54 PHE 0.015 0.001 PHE H 26 TYR 0.007 0.001 TYR G 71 ARG 0.009 0.000 ARG Q 53 Details of bonding type rmsd hydrogen bonds : bond 0.09085 ( 2633) hydrogen bonds : angle 3.64543 ( 7899) covalent geometry : bond 0.00488 (32465) covalent geometry : angle 0.65805 (44052) Misc. bond : bond 0.08056 ( 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 560 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 448 time to evaluate : 3.835 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 85 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8292 (mp0) REVERT: B 73 ARG cc_start: 0.9265 (OUTLIER) cc_final: 0.8582 (ptt90) REVERT: G 135 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8825 (mt-10) REVERT: H 81 GLN cc_start: 0.8947 (mp10) cc_final: 0.8702 (mp10) REVERT: H 148 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.8980 (tt) REVERT: I 81 GLN cc_start: 0.9013 (mp10) cc_final: 0.8751 (mp10) REVERT: J 52 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.7625 (mtt) REVERT: P 39 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.7817 (mttt) REVERT: Q 73 ARG cc_start: 0.9258 (OUTLIER) cc_final: 0.8356 (ptt90) REVERT: R 4 ASP cc_start: 0.8622 (OUTLIER) cc_final: 0.8271 (t0) REVERT: T 78 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8226 (ptp90) REVERT: U 73 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.8009 (ptt90) REVERT: V 85 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8091 (mp0) REVERT: W 52 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8714 (mtt) REVERT: W 73 ARG cc_start: 0.9168 (OUTLIER) cc_final: 0.8168 (ptt90) REVERT: W 85 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8054 (mp0) REVERT: X 53 ARG cc_start: 0.8605 (mtm-85) cc_final: 0.8277 (mtm110) outliers start: 112 outliers final: 84 residues processed: 535 average time/residue: 0.4608 time to fit residues: 385.2834 Evaluate side-chains 524 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 426 time to evaluate : 3.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 52 MET 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 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 F residue 78 ARG Chi-restraints excluded: chain F residue 83 VAL 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 119 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 135 GLU Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 147 SER Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain I residue 50 ASP Chi-restraints excluded: chain I residue 116 SER Chi-restraints excluded: chain I residue 119 VAL Chi-restraints excluded: chain J residue 52 MET Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 116 SER Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 141 ILE Chi-restraints excluded: chain N residue 52 MET Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 116 SER Chi-restraints excluded: chain O residue 68 LEU Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain P residue 39 LYS Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 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 4 ASP Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain R residue 147 SER Chi-restraints excluded: chain S residue 52 MET Chi-restraints excluded: chain S residue 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 78 ARG Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain U residue 7 VAL Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 77 VAL Chi-restraints excluded: chain U residue 141 ILE Chi-restraints excluded: chain U residue 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 W residue 52 MET Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain W residue 78 ARG Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 85 GLU Chi-restraints excluded: chain W residue 116 SER 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 103 optimal weight: 6.9990 chunk 207 optimal weight: 7.9990 chunk 204 optimal weight: 5.9990 chunk 340 optimal weight: 6.9990 chunk 353 optimal weight: 1.9990 chunk 357 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 311 optimal weight: 0.9990 chunk 253 optimal weight: 2.9990 chunk 232 optimal weight: 5.9990 chunk 209 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 72 GLN U 137 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.085459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.072035 restraints weight = 63558.526| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.85 r_work: 0.2835 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| r_final: 0.2815 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.233 32485 Z= 0.171 Angle : 0.639 24.059 44052 Z= 0.286 Chirality : 0.033 0.195 4895 Planarity : 0.003 0.038 5697 Dihedral : 6.438 84.583 4291 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.68 % Favored : 97.14 % Rotamer: Outliers : 2.90 % Allowed : 25.04 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.83 (0.13), residues: 3810 helix: 3.63 (0.08), residues: 3072 sheet: None (None), residues: 0 loop : -2.83 (0.19), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 37 HIS 0.002 0.000 HIS U 54 PHE 0.015 0.001 PHE H 26 TYR 0.007 0.001 TYR K 25 ARG 0.008 0.000 ARG H 45 Details of bonding type rmsd hydrogen bonds : bond 0.08300 ( 2633) hydrogen bonds : angle 3.54334 ( 7899) covalent geometry : bond 0.00391 (32465) covalent geometry : angle 0.63926 (44052) Misc. bond : bond 0.07467 ( 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 534 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 437 time to evaluate : 3.520 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: A 85 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8154 (mp0) REVERT: B 73 ARG cc_start: 0.9278 (OUTLIER) cc_final: 0.8640 (ptt90) REVERT: G 52 MET cc_start: 0.8501 (mtt) cc_final: 0.8034 (mtt) REVERT: H 81 GLN cc_start: 0.8931 (mp10) cc_final: 0.8679 (mp10) REVERT: H 148 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8921 (tt) REVERT: I 81 GLN cc_start: 0.9044 (mp10) cc_final: 0.8770 (mp10) REVERT: P 39 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.7731 (mttt) REVERT: Q 73 ARG cc_start: 0.9262 (OUTLIER) cc_final: 0.8379 (ptt90) REVERT: R 4 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.8149 (t0) REVERT: T 156 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8348 (pt0) REVERT: U 73 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8019 (ptt90) REVERT: V 85 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8089 (mp0) REVERT: W 52 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8712 (mtt) REVERT: W 73 ARG cc_start: 0.9178 (OUTLIER) cc_final: 0.8197 (ptt90) REVERT: W 85 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8085 (mp0) REVERT: X 53 ARG cc_start: 0.8615 (mtm-85) cc_final: 0.8285 (mtm110) outliers start: 97 outliers final: 74 residues processed: 514 average time/residue: 0.4328 time to fit residues: 351.9375 Evaluate side-chains 510 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 424 time to evaluate : 3.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 52 MET 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 C residue 119 VAL Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 78 ARG Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain G residue 72 GLN Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain H residue 141 ILE Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain H residue 152 THR Chi-restraints excluded: chain I residue 50 ASP 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 83 VAL Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 82 SER Chi-restraints excluded: chain M residue 115 THR Chi-restraints excluded: chain N residue 52 MET Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 116 SER Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain P residue 39 LYS Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 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 R residue 4 ASP Chi-restraints excluded: chain R residue 115 THR Chi-restraints excluded: chain R residue 147 SER Chi-restraints excluded: chain S residue 52 MET Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain 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 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 W residue 52 MET Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain W residue 78 ARG Chi-restraints excluded: chain W residue 83 VAL Chi-restraints excluded: chain W residue 85 GLU Chi-restraints excluded: chain W residue 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 61 optimal weight: 5.9990 chunk 272 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 353 optimal weight: 0.9980 chunk 357 optimal weight: 5.9990 chunk 302 optimal weight: 0.0010 chunk 81 optimal weight: 10.0000 chunk 118 optimal weight: 0.0040 chunk 164 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 243 optimal weight: 0.9980 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 HIS C 28 HIS G 88 GLN J 72 GLN N 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.092133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.078830 restraints weight = 62637.163| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.84 r_work: 0.2975 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.179 32485 Z= 0.141 Angle : 0.606 21.485 44052 Z= 0.276 Chirality : 0.033 0.217 4895 Planarity : 0.003 0.037 5697 Dihedral : 6.449 86.905 4291 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.41 % Favored : 97.43 % Rotamer: Outliers : 2.06 % Allowed : 25.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.97 (0.13), residues: 3810 helix: 3.73 (0.08), residues: 3078 sheet: None (None), residues: 0 loop : -2.86 (0.19), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 37 HIS 0.006 0.000 HIS Q 54 PHE 0.020 0.001 PHE H 26 TYR 0.009 0.001 TYR Q 43 ARG 0.017 0.001 ARG P 53 Details of bonding type rmsd hydrogen bonds : bond 0.06397 ( 2633) hydrogen bonds : angle 3.29301 ( 7899) covalent geometry : bond 0.00296 (32465) covalent geometry : angle 0.60556 (44052) Misc. bond : bond 0.06279 ( 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 534 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 465 time to evaluate : 3.654 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: A 2 GLN cc_start: 0.9043 (mm-40) cc_final: 0.8763 (mt0) REVERT: A 85 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8126 (mp0) REVERT: H 81 GLN cc_start: 0.8880 (mp10) cc_final: 0.8664 (mp10) REVERT: H 148 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8805 (tt) REVERT: J 52 MET cc_start: 0.8709 (mtt) cc_final: 0.8134 (mtt) REVERT: P 39 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7406 (mttt) REVERT: Q 73 ARG cc_start: 0.9227 (OUTLIER) cc_final: 0.8349 (ptt90) REVERT: R 4 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.8038 (t0) REVERT: T 52 MET cc_start: 0.8353 (mtt) cc_final: 0.7962 (mtt) REVERT: U 73 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.7924 (ptt90) REVERT: V 53 ARG cc_start: 0.8538 (mtm110) cc_final: 0.8305 (mtm-85) REVERT: X 53 ARG cc_start: 0.8580 (mtm-85) cc_final: 0.8230 (mtm110) outliers start: 69 outliers final: 45 residues processed: 519 average time/residue: 0.4182 time to fit residues: 346.1549 Evaluate side-chains 492 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 441 time to evaluate : 3.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain F residue 78 ARG Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain G residue 72 GLN Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain G residue 155 GLU Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 148 LEU Chi-restraints excluded: chain I residue 116 SER Chi-restraints excluded: chain J residue 78 ARG Chi-restraints excluded: chain K residue 7 VAL Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain L residue 115 THR Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 115 THR Chi-restraints excluded: chain N residue 52 MET Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 116 SER Chi-restraints excluded: chain O residue 158 GLN Chi-restraints excluded: chain P residue 39 LYS Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 153 VAL Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 73 ARG Chi-restraints excluded: chain Q residue 115 THR Chi-restraints excluded: chain R residue 4 ASP Chi-restraints excluded: chain R residue 39 LYS 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 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 154 ILE Chi-restraints excluded: chain V residue 141 ILE Chi-restraints excluded: chain W residue 78 ARG Chi-restraints excluded: chain W residue 131 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 47 optimal weight: 5.9990 chunk 328 optimal weight: 4.9990 chunk 315 optimal weight: 0.9980 chunk 366 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 chunk 376 optimal weight: 10.0000 chunk 251 optimal weight: 3.9990 chunk 177 optimal weight: 10.0000 chunk 211 optimal weight: 2.9990 chunk 349 optimal weight: 10.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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 N 156 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 = 0.3314 r_free = 0.3314 target = 0.091012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.077716 restraints weight = 62931.929| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.82 r_work: 0.2909 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- 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 = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 86 | |-----------------------------------------------------------------------------| r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.466 32485 Z= 0.164 Angle : 0.656 36.790 44052 Z= 0.284 Chirality : 0.033 0.198 4895 Planarity : 0.003 0.050 5697 Dihedral : 6.407 86.442 4291 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.65 % Favored : 97.17 % Rotamer: Outliers : 1.91 % Allowed : 26.11 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.82 (0.13), residues: 3810 helix: 3.61 (0.08), residues: 3080 sheet: None (None), residues: 0 loop : -2.84 (0.19), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 37 HIS 0.003 0.000 HIS I 54 PHE 0.013 0.001 PHE C 26 TYR 0.015 0.001 TYR U 149 ARG 0.009 0.000 ARG G 53 Details of bonding type rmsd hydrogen bonds : bond 0.07323 ( 2633) hydrogen bonds : angle 3.43195 ( 7899) covalent geometry : bond 0.00385 (32465) covalent geometry : angle 0.65573 (44052) Misc. bond : bond 0.12050 ( 20) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12298.25 seconds wall clock time: 214 minutes 19.11 seconds (12859.11 seconds total)