Starting phenix.real_space_refine on Thu Jun 26 13:49:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jb0_36139/06_2025/8jb0_36139.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jb0_36139/06_2025/8jb0_36139.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jb0_36139/06_2025/8jb0_36139.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jb0_36139/06_2025/8jb0_36139.map" model { file = "/net/cci-nas-00/data/ceres_data/8jb0_36139/06_2025/8jb0_36139.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jb0_36139/06_2025/8jb0_36139.cif" } resolution = 4.2 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= 0.002 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 19773 2.51 5 N 5397 2.21 5 O 6085 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 31387 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 1316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1316 Classifications: {'peptide': 162} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 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: 1310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1310 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 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: 1296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1296 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 156} Unresolved chain link angles: 1 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': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {'FE2': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {'FE2': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {'FE2': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {'FE2': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {'FE2': 2} 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {'FE2': 2} 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {'FE2': 2} 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {'FE2': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {'FE2': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {'FE2': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {'FE2': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {'FE2': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'FE2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 18.15, per 1000 atoms: 0.58 Number of scatterers: 31387 At special positions: 0 Unit cell: (130.416, 131.274, 130.416, 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 6085 8.00 N 5397 7.00 C 19773 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=0, symmetry=0 Time building additional restraints: 8.07 Conformation dependent library (CDL) restraints added in 3.5 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 81.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.22 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: 4.114A pdb=" N THR A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL A 153 " --> pdb=" O TYR A 149 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 36 Processing helix chain 'B' and resid 37 through 65 Processing helix chain 'B' and resid 82 through 111 removed outlier: 3.626A 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 removed outlier: 3.587A pdb=" N ILE C 8 " --> pdb=" O ASP C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 65 removed outlier: 3.812A pdb=" N LEU C 65 " --> pdb=" O ARG C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 110 removed outlier: 3.709A pdb=" N MET C 86 " --> pdb=" O SER C 82 " (cutoff:3.500A) 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 removed outlier: 3.666A pdb=" N ILE D 8 " --> pdb=" O ASP D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 65 removed outlier: 3.519A pdb=" N LEU D 65 " --> pdb=" O ARG D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 110 removed outlier: 3.571A pdb=" N MET D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 145 Processing helix chain 'D' and resid 146 through 154 Processing helix chain 'F' and resid 4 through 36 removed outlier: 3.546A pdb=" N ILE F 8 " --> pdb=" O ASP F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 65 Processing helix chain 'F' and resid 82 through 110 removed outlier: 3.919A 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: 3.741A pdb=" N ILE E 8 " --> pdb=" O ASP E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 65 Processing helix chain 'E' and resid 82 through 110 removed outlier: 3.502A pdb=" N MET E 86 " --> pdb=" O SER E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 145 Processing helix chain 'E' and resid 145 through 153 removed outlier: 3.735A pdb=" N VAL E 153 " --> pdb=" O TYR E 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 35 Processing helix chain 'G' and resid 38 through 65 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: 3.549A pdb=" N ILE H 8 " --> pdb=" O ASP H 4 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 65 removed outlier: 3.584A pdb=" N LEU H 65 " --> pdb=" O ARG H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 110 removed outlier: 3.820A 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 153 Processing helix chain 'I' and resid 4 through 36 Processing helix chain 'I' and resid 37 through 65 removed outlier: 3.718A pdb=" N LEU I 65 " --> pdb=" O ARG I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 110 removed outlier: 3.568A pdb=" N MET I 86 " --> pdb=" O SER I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 145 Processing helix chain 'I' and resid 145 through 153 removed outlier: 3.627A pdb=" N VAL I 153 " --> pdb=" O TYR I 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 35 removed outlier: 3.769A pdb=" N ILE J 8 " --> pdb=" O ASP J 4 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 65 removed outlier: 3.797A pdb=" N ALA J 41 " --> pdb=" O TRP J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 110 removed outlier: 3.608A pdb=" N MET J 86 " --> pdb=" O SER J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 145 Processing helix chain 'J' and resid 145 through 154 removed outlier: 3.613A pdb=" N THR J 152 " --> pdb=" O LEU J 148 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL J 153 " --> pdb=" O TYR J 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 35 removed outlier: 3.589A pdb=" N LYS K 35 " --> pdb=" O LEU K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 65 removed outlier: 3.573A pdb=" N LEU K 65 " --> pdb=" O ARG K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 111 removed outlier: 3.656A pdb=" N MET K 86 " --> pdb=" O SER K 82 " (cutoff:3.500A) 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: 3.583A pdb=" N ILE L 8 " --> pdb=" O ASP L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 65 Processing helix chain 'L' and resid 82 through 111 removed outlier: 4.041A pdb=" N MET L 86 " --> pdb=" O SER L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 145 removed outlier: 3.522A pdb=" N GLY L 145 " --> pdb=" O ILE L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 154 removed outlier: 3.929A pdb=" N THR L 152 " --> pdb=" O LEU L 148 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL L 153 " --> pdb=" O TYR L 149 " (cutoff:3.500A) removed outlier: 3.625A 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: 3.517A pdb=" N MET M 86 " --> pdb=" O SER M 82 " (cutoff:3.500A) removed outlier: 4.333A 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 146 through 152 removed outlier: 3.853A pdb=" N THR M 152 " --> pdb=" O LEU M 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 36 Processing helix chain 'N' and resid 37 through 65 removed outlier: 3.573A pdb=" N ALA N 41 " --> pdb=" O TRP N 37 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 110 removed outlier: 3.612A 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: 3.647A 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 removed outlier: 3.509A pdb=" N GLY O 145 " --> pdb=" O ILE O 141 " (cutoff:3.500A) Processing helix chain 'O' and resid 145 through 154 Processing helix chain 'P' and resid 4 through 35 removed outlier: 3.546A pdb=" N ILE P 8 " --> pdb=" O ASP P 4 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS P 35 " --> pdb=" O LEU P 31 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 65 Processing helix chain 'P' and resid 82 through 111 Processing helix chain 'P' and resid 114 through 145 Processing helix chain 'P' and resid 145 through 153 Processing helix chain 'Q' and resid 4 through 36 Processing helix chain 'Q' and resid 37 through 65 removed outlier: 3.627A pdb=" N LEU Q 65 " --> pdb=" O ARG Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 110 removed outlier: 3.577A pdb=" N MET Q 86 " --> pdb=" O SER Q 82 " (cutoff:3.500A) removed outlier: 4.167A 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: 3.675A 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 Processing helix chain 'R' and resid 82 through 111 removed outlier: 3.705A 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 153 removed outlier: 3.719A pdb=" N THR R 152 " --> pdb=" O LEU R 148 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL R 153 " --> pdb=" O TYR R 149 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 36 Processing helix chain 'S' and resid 37 through 65 removed outlier: 3.676A pdb=" N ALA S 41 " --> pdb=" O TRP S 37 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU S 65 " --> pdb=" O ARG S 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 110 removed outlier: 3.826A pdb=" N MET S 86 " --> pdb=" O SER S 82 " (cutoff:3.500A) removed outlier: 4.165A 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: 3.655A pdb=" N THR S 152 " --> pdb=" O LEU S 148 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 36 removed outlier: 3.735A pdb=" N ILE T 8 " --> pdb=" O ASP T 4 " (cutoff:3.500A) Processing helix chain 'T' and resid 37 through 65 Processing helix chain 'T' and resid 82 through 111 removed outlier: 3.666A 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 removed outlier: 3.652A pdb=" N ILE U 8 " --> pdb=" O ASP U 4 " (cutoff:3.500A) Processing helix chain 'U' and resid 38 through 65 removed outlier: 3.563A pdb=" N LEU U 65 " --> pdb=" O ARG U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 110 removed outlier: 3.621A pdb=" N MET U 86 " --> pdb=" O SER U 82 " (cutoff:3.500A) Processing helix chain 'U' and resid 114 through 145 Processing helix chain 'U' and resid 146 through 153 removed outlier: 3.706A pdb=" N VAL U 153 " --> pdb=" O TYR U 149 " (cutoff:3.500A) Processing helix chain 'V' and resid 4 through 36 removed outlier: 3.933A 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 removed outlier: 3.692A pdb=" N ILE W 8 " --> pdb=" O ASP W 4 " (cutoff:3.500A) Processing helix chain 'W' and resid 37 through 65 Processing helix chain 'W' and resid 82 through 110 removed outlier: 3.674A pdb=" N MET W 86 " --> pdb=" O SER W 82 " (cutoff:3.500A) Processing helix chain 'W' and resid 114 through 145 Processing helix chain 'W' and resid 145 through 154 removed outlier: 3.725A pdb=" N THR W 152 " --> pdb=" O LEU W 148 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL W 153 " --> pdb=" O TYR W 149 " (cutoff:3.500A) Processing helix chain 'X' and resid 4 through 36 removed outlier: 3.666A 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 removed outlier: 3.703A pdb=" N MET X 86 " --> pdb=" O SER X 82 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 145 Processing helix chain 'X' and resid 145 through 154 removed outlier: 3.526A pdb=" N THR X 152 " --> pdb=" O LEU X 148 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL X 153 " --> pdb=" O TYR X 149 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE X 154 " --> pdb=" O LEU X 150 " (cutoff:3.500A) 2606 hydrogen bonds defined for protein. 7818 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: 9.01 Time building geometry restraints manager: 9.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8003 1.33 - 1.45: 5808 1.45 - 1.57: 17864 1.57 - 1.69: 0 1.69 - 1.81: 192 Bond restraints: 31867 Sorted by residual: bond pdb=" C GLN W 158 " pdb=" O GLN W 158 " ideal model delta sigma weight residual 1.235 1.244 -0.009 4.70e-03 4.53e+04 4.08e+00 bond pdb=" CA ALA I 110 " pdb=" C ALA I 110 " ideal model delta sigma weight residual 1.522 1.554 -0.032 1.72e-02 3.38e+03 3.54e+00 bond pdb=" CD GLU H 121 " pdb=" OE1 GLU H 121 " ideal model delta sigma weight residual 1.249 1.214 0.035 1.90e-02 2.77e+03 3.47e+00 bond pdb=" CG LEU Q 27 " pdb=" CD1 LEU Q 27 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.22e+00 bond pdb=" CG GLU E 121 " pdb=" CD GLU E 121 " ideal model delta sigma weight residual 1.516 1.475 0.041 2.50e-02 1.60e+03 2.73e+00 ... (remaining 31862 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 42171 1.80 - 3.60: 748 3.60 - 5.41: 117 5.41 - 7.21: 28 7.21 - 9.01: 7 Bond angle restraints: 43071 Sorted by residual: angle pdb=" C VAL F 107 " pdb=" N MET F 108 " pdb=" CA MET F 108 " ideal model delta sigma weight residual 122.26 113.86 8.40 1.73e+00 3.34e-01 2.36e+01 angle pdb=" C VAL N 153 " pdb=" N ILE N 154 " pdb=" CA ILE N 154 " ideal model delta sigma weight residual 121.97 130.37 -8.40 1.80e+00 3.09e-01 2.18e+01 angle pdb=" N GLU D 121 " pdb=" CA GLU D 121 " pdb=" CB GLU D 121 " ideal model delta sigma weight residual 110.28 117.10 -6.82 1.55e+00 4.16e-01 1.94e+01 angle pdb=" N GLU E 121 " pdb=" CA GLU E 121 " pdb=" CB GLU E 121 " ideal model delta sigma weight residual 110.28 117.05 -6.77 1.55e+00 4.16e-01 1.91e+01 angle pdb=" N GLU H 121 " pdb=" CA GLU H 121 " pdb=" CB GLU H 121 " ideal model delta sigma weight residual 110.28 116.70 -6.42 1.55e+00 4.16e-01 1.71e+01 ... (remaining 43066 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 17017 17.93 - 35.85: 1869 35.85 - 53.78: 315 53.78 - 71.70: 67 71.70 - 89.63: 74 Dihedral angle restraints: 19342 sinusoidal: 7967 harmonic: 11375 Sorted by residual: dihedral pdb=" CA TRP X 37 " pdb=" C TRP X 37 " pdb=" N THR X 38 " pdb=" CA THR X 38 " ideal model delta harmonic sigma weight residual -180.00 -159.52 -20.48 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA LYS L 111 " pdb=" C LYS L 111 " pdb=" N HIS L 112 " pdb=" CA HIS L 112 " ideal model delta harmonic sigma weight residual 180.00 159.68 20.32 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA ASP A 113 " pdb=" C ASP A 113 " pdb=" N ILE A 114 " pdb=" CA ILE A 114 " ideal model delta harmonic sigma weight residual -180.00 -161.04 -18.96 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 19339 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 3801 0.040 - 0.079: 855 0.079 - 0.119: 205 0.119 - 0.159: 30 0.159 - 0.199: 4 Chirality restraints: 4895 Sorted by residual: chirality pdb=" CA GLN N 88 " pdb=" N GLN N 88 " pdb=" C GLN N 88 " pdb=" CB GLN N 88 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.85e-01 chirality pdb=" CA PHE H 120 " pdb=" N PHE H 120 " pdb=" C PHE H 120 " pdb=" CB PHE H 120 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" CA GLU H 121 " pdb=" N GLU H 121 " pdb=" C GLU H 121 " pdb=" CB GLU H 121 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.69e-01 ... (remaining 4892 not shown) Planarity restraints: 5626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA O 21 " -0.013 2.00e-02 2.50e+03 2.67e-02 7.13e+00 pdb=" C ALA O 21 " 0.046 2.00e-02 2.50e+03 pdb=" O ALA O 21 " -0.017 2.00e-02 2.50e+03 pdb=" N ILE O 22 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 66 " 0.010 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" CG ASP B 66 " -0.037 2.00e-02 2.50e+03 pdb=" OD1 ASP B 66 " 0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP B 66 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL N 153 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.43e+00 pdb=" C VAL N 153 " 0.036 2.00e-02 2.50e+03 pdb=" O VAL N 153 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE N 154 " -0.012 2.00e-02 2.50e+03 ... (remaining 5623 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2898 2.74 - 3.28: 34328 3.28 - 3.82: 54511 3.82 - 4.36: 57892 4.36 - 4.90: 99742 Nonbonded interactions: 249371 Sorted by model distance: nonbonded pdb=" OE1 GLN F 137 " pdb=" OH TYR F 149 " model vdw 2.196 3.040 nonbonded pdb=" O ARG V 109 " pdb=" NE ARG V 109 " model vdw 2.199 3.120 nonbonded pdb=" O HIS F 28 " pdb=" NE2 GLN F 32 " model vdw 2.203 3.120 nonbonded pdb=" OE1 GLN C 156 " pdb=" OG1 THR F 152 " model vdw 2.211 3.040 nonbonded pdb=" OD2 ASP B 113 " pdb=" OG SER B 116 " model vdw 2.217 3.040 ... (remaining 249366 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 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 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 'B' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 157)) selection = (chain 'C' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 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 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 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 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 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 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 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 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 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 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 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 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 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 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 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 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 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 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 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 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 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 'N' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 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 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 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 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 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 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 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 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 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 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 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 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 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 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 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 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 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 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 'X' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.030 Extract box with map and model: 1.320 Check model and map are aligned: 0.240 Set scattering table: 0.320 Process input model: 63.230 Find NCS groups from input model: 1.970 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: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 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 : 0.003 0.059 31867 Z= 0.166 Angle : 0.624 9.009 43071 Z= 0.355 Chirality : 0.037 0.199 4895 Planarity : 0.003 0.051 5626 Dihedral : 16.006 89.630 11920 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.81 % Favored : 97.03 % Rotamer: Outliers : 0.09 % Allowed : 0.45 % Favored : 99.46 % 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: 2.31 (0.13), residues: 3810 helix: 2.49 (0.09), residues: 3050 sheet: None (None), residues: 0 loop : -2.75 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP Q 37 HIS 0.010 0.001 HIS R 28 PHE 0.031 0.002 PHE L 120 TYR 0.025 0.002 TYR R 71 ARG 0.008 0.001 ARG H 53 Details of bonding type rmsd hydrogen bonds : bond 0.09531 ( 2606) hydrogen bonds : angle 4.31743 ( 7818) covalent geometry : bond 0.00343 (31867) covalent geometry : angle 0.62433 (43071) *********************** 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 519 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 516 time to evaluate : 7.411 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 TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8518 (t70) cc_final: 0.8241 (t0) REVERT: A 86 MET cc_start: 0.8989 (mmp) cc_final: 0.8732 (mmp) REVERT: C 70 ASN cc_start: 0.8591 (t0) cc_final: 0.8274 (t0) REVERT: F 99 ASP cc_start: 0.8471 (t0) cc_final: 0.8234 (t0) REVERT: G 108 MET cc_start: 0.8856 (mmt) cc_final: 0.8631 (mmm) REVERT: I 123 ILE cc_start: 0.8590 (mm) cc_final: 0.8240 (mm) REVERT: J 137 GLN cc_start: 0.8695 (pt0) cc_final: 0.7985 (tt0) REVERT: K 57 VAL cc_start: 0.9189 (p) cc_final: 0.8957 (p) REVERT: K 115 THR cc_start: 0.7105 (m) cc_final: 0.6874 (m) REVERT: P 52 MET cc_start: 0.7168 (ttm) cc_final: 0.6926 (ttm) REVERT: P 90 ASP cc_start: 0.8687 (m-30) cc_final: 0.8439 (m-30) REVERT: R 53 ARG cc_start: 0.8379 (ttm110) cc_final: 0.8118 (mtm110) REVERT: R 151 SER cc_start: 0.8842 (t) cc_final: 0.8637 (p) REVERT: S 76 HIS cc_start: 0.8610 (t-90) cc_final: 0.7580 (t-90) REVERT: S 113 ASP cc_start: 0.6746 (t0) cc_final: 0.6516 (t0) REVERT: T 22 ILE cc_start: 0.9457 (pt) cc_final: 0.9245 (pt) REVERT: T 32 GLN cc_start: 0.9127 (mp10) cc_final: 0.8685 (mp10) REVERT: T 60 ASP cc_start: 0.8120 (m-30) cc_final: 0.7546 (m-30) REVERT: T 90 ASP cc_start: 0.8842 (m-30) cc_final: 0.8565 (m-30) REVERT: U 114 ILE cc_start: 0.7730 (mm) cc_final: 0.7360 (mm) REVERT: V 86 MET cc_start: 0.7927 (mtm) cc_final: 0.7072 (mtt) REVERT: V 118 ASN cc_start: 0.8923 (m110) cc_final: 0.8555 (m-40) outliers start: 3 outliers final: 2 residues processed: 518 average time/residue: 0.5113 time to fit residues: 437.5744 Evaluate side-chains 345 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 343 time to evaluate : 4.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 321 optimal weight: 20.0000 chunk 288 optimal weight: 8.9990 chunk 160 optimal weight: 20.0000 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 8.9990 chunk 154 optimal weight: 20.0000 chunk 298 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 181 optimal weight: 7.9990 chunk 222 optimal weight: 3.9990 chunk 345 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 32 GLN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 HIS G 137 GLN H 137 GLN ** L 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 HIS M 28 HIS M 129 HIS ** N 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 23 ASN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 137 GLN W 118 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.060712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.052658 restraints weight = 182489.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.053926 restraints weight = 120840.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.054872 restraints weight = 87833.023| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 31867 Z= 0.177 Angle : 0.564 7.521 43071 Z= 0.315 Chirality : 0.036 0.158 4895 Planarity : 0.003 0.039 5626 Dihedral : 4.070 22.992 4193 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.15 % Favored : 96.69 % Rotamer: Outliers : 0.30 % Allowed : 5.77 % Favored : 93.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.13), residues: 3810 helix: 2.54 (0.08), residues: 3062 sheet: None (None), residues: 0 loop : -2.70 (0.20), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Q 37 HIS 0.007 0.001 HIS R 28 PHE 0.018 0.001 PHE I 10 TYR 0.021 0.002 TYR R 71 ARG 0.005 0.000 ARG X 61 Details of bonding type rmsd hydrogen bonds : bond 0.05991 ( 2606) hydrogen bonds : angle 3.79925 ( 7818) covalent geometry : bond 0.00383 (31867) covalent geometry : angle 0.56382 (43071) *********************** 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 509 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 499 time to evaluate : 4.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8606 (ttt) cc_final: 0.8371 (ttm) REVERT: A 66 ASP cc_start: 0.8628 (t70) cc_final: 0.8370 (t0) REVERT: C 70 ASN cc_start: 0.8522 (t0) cc_final: 0.8229 (t0) REVERT: C 108 MET cc_start: 0.8320 (tmm) cc_final: 0.8095 (tmm) REVERT: C 119 VAL cc_start: 0.9093 (m) cc_final: 0.8846 (p) REVERT: D 121 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7570 (pt0) REVERT: F 99 ASP cc_start: 0.8557 (t0) cc_final: 0.8333 (t0) REVERT: E 121 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8708 (mp0) REVERT: H 86 MET cc_start: 0.8075 (ptp) cc_final: 0.7805 (ptp) REVERT: H 95 LEU cc_start: 0.9110 (mt) cc_final: 0.8733 (pp) REVERT: J 14 GLN cc_start: 0.8712 (tp40) cc_final: 0.7743 (tp40) REVERT: J 137 GLN cc_start: 0.8617 (pt0) cc_final: 0.8038 (tt0) REVERT: J 144 LEU cc_start: 0.9074 (tt) cc_final: 0.8804 (tt) REVERT: K 115 THR cc_start: 0.7138 (m) cc_final: 0.6903 (m) REVERT: N 22 ILE cc_start: 0.9104 (mt) cc_final: 0.8833 (mm) REVERT: P 52 MET cc_start: 0.6989 (ttm) cc_final: 0.6771 (ttm) REVERT: Q 100 ARG cc_start: 0.8663 (ttm110) cc_final: 0.8361 (ttp-110) REVERT: R 151 SER cc_start: 0.8827 (t) cc_final: 0.8590 (p) REVERT: S 113 ASP cc_start: 0.6515 (t0) cc_final: 0.6263 (t0) REVERT: T 22 ILE cc_start: 0.9465 (pt) cc_final: 0.9259 (pt) REVERT: T 86 MET cc_start: 0.7829 (mtm) cc_final: 0.7098 (mtm) REVERT: T 90 ASP cc_start: 0.8945 (m-30) cc_final: 0.8720 (m-30) REVERT: U 37 TRP cc_start: 0.7389 (m-10) cc_final: 0.7155 (m-90) REVERT: U 86 MET cc_start: 0.8447 (mtm) cc_final: 0.8165 (mtm) REVERT: U 90 ASP cc_start: 0.8364 (m-30) cc_final: 0.8140 (m-30) REVERT: U 114 ILE cc_start: 0.7698 (mm) cc_final: 0.7413 (mm) REVERT: U 139 ASP cc_start: 0.8014 (m-30) cc_final: 0.7812 (m-30) REVERT: U 143 LYS cc_start: 0.8740 (tttt) cc_final: 0.8500 (tptm) REVERT: V 86 MET cc_start: 0.8041 (mtm) cc_final: 0.7400 (mtt) REVERT: V 114 ILE cc_start: 0.9100 (mm) cc_final: 0.8896 (mm) REVERT: V 118 ASN cc_start: 0.8966 (m110) cc_final: 0.8622 (m110) REVERT: W 108 MET cc_start: 0.8425 (tmm) cc_final: 0.8034 (tmm) outliers start: 10 outliers final: 3 residues processed: 506 average time/residue: 0.6180 time to fit residues: 512.8889 Evaluate side-chains 339 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 334 time to evaluate : 3.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 225 optimal weight: 20.0000 chunk 221 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 339 optimal weight: 7.9990 chunk 238 optimal weight: 0.0370 chunk 354 optimal weight: 6.9990 chunk 323 optimal weight: 7.9990 chunk 371 optimal weight: 10.0000 chunk 291 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 337 optimal weight: 10.0000 overall best weight: 4.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 ASN F 32 GLN E 32 GLN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN K 88 GLN L 23 ASN M 28 HIS M 32 GLN ** N 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 HIS P 23 ASN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.061037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.053155 restraints weight = 184972.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.054439 restraints weight = 120824.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.055326 restraints weight = 87122.528| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31867 Z= 0.154 Angle : 0.545 8.799 43071 Z= 0.303 Chirality : 0.035 0.150 4895 Planarity : 0.003 0.040 5626 Dihedral : 4.043 23.000 4193 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.83 % Favored : 97.01 % Rotamer: Outliers : 0.09 % Allowed : 3.86 % Favored : 96.05 % 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: 2.54 (0.13), residues: 3810 helix: 2.63 (0.08), residues: 3062 sheet: None (None), residues: 0 loop : -2.68 (0.20), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 37 HIS 0.012 0.001 HIS D 54 PHE 0.031 0.001 PHE W 120 TYR 0.035 0.002 TYR Q 71 ARG 0.007 0.000 ARG I 73 Details of bonding type rmsd hydrogen bonds : bond 0.05805 ( 2606) hydrogen bonds : angle 3.66106 ( 7818) covalent geometry : bond 0.00330 (31867) covalent geometry : angle 0.54522 (43071) *********************** 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 518 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 515 time to evaluate : 3.436 Fit side-chains revert: symmetry clash 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 TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8710 (ttt) cc_final: 0.8445 (ttm) REVERT: A 66 ASP cc_start: 0.8563 (t70) cc_final: 0.8310 (t0) REVERT: A 86 MET cc_start: 0.9083 (mmp) cc_final: 0.8858 (mmp) REVERT: A 111 LYS cc_start: 0.8687 (tppt) cc_final: 0.8399 (tppp) REVERT: B 90 ASP cc_start: 0.8816 (m-30) cc_final: 0.8575 (m-30) REVERT: C 70 ASN cc_start: 0.8543 (t0) cc_final: 0.8220 (t0) REVERT: C 119 VAL cc_start: 0.9094 (m) cc_final: 0.8837 (p) REVERT: F 99 ASP cc_start: 0.8542 (t0) cc_final: 0.8304 (t0) REVERT: H 86 MET cc_start: 0.8028 (ptp) cc_final: 0.7720 (ptp) REVERT: H 95 LEU cc_start: 0.9165 (mt) cc_final: 0.8697 (pp) REVERT: J 14 GLN cc_start: 0.8638 (tp40) cc_final: 0.8081 (tp40) REVERT: J 137 GLN cc_start: 0.8490 (pt0) cc_final: 0.7758 (tt0) REVERT: K 115 THR cc_start: 0.7104 (m) cc_final: 0.6887 (m) REVERT: M 88 GLN cc_start: 0.8661 (pp30) cc_final: 0.8227 (pp30) REVERT: P 90 ASP cc_start: 0.8970 (m-30) cc_final: 0.8732 (m-30) REVERT: Q 100 ARG cc_start: 0.8669 (ttm110) cc_final: 0.8390 (ttp-110) REVERT: T 22 ILE cc_start: 0.9497 (pt) cc_final: 0.9247 (pt) REVERT: T 86 MET cc_start: 0.7833 (mtm) cc_final: 0.7208 (mtt) REVERT: T 90 ASP cc_start: 0.8982 (m-30) cc_final: 0.8756 (m-30) REVERT: U 86 MET cc_start: 0.8436 (mtm) cc_final: 0.7861 (mtt) REVERT: U 114 ILE cc_start: 0.7765 (mm) cc_final: 0.7379 (mm) REVERT: U 143 LYS cc_start: 0.8772 (tttt) cc_final: 0.8540 (tptm) REVERT: V 86 MET cc_start: 0.7970 (mtm) cc_final: 0.7508 (mtt) outliers start: 3 outliers final: 3 residues processed: 517 average time/residue: 0.4259 time to fit residues: 356.7855 Evaluate side-chains 336 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 333 time to evaluate : 3.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 39 optimal weight: 20.0000 chunk 338 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 277 optimal weight: 20.0000 chunk 288 optimal weight: 20.0000 chunk 111 optimal weight: 7.9990 chunk 321 optimal weight: 20.0000 chunk 156 optimal weight: 9.9990 chunk 317 optimal weight: 6.9990 chunk 211 optimal weight: 5.9990 chunk 281 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 14 GLN E 32 GLN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** K 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 28 HIS ** N 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 23 ASN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 118 ASN X 23 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.059797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.051818 restraints weight = 184986.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.053089 restraints weight = 122005.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.054013 restraints weight = 88547.886| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31867 Z= 0.187 Angle : 0.573 7.763 43071 Z= 0.319 Chirality : 0.036 0.160 4895 Planarity : 0.003 0.033 5626 Dihedral : 4.099 22.426 4193 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.02 % Favored : 96.82 % Rotamer: Outliers : 0.06 % Allowed : 4.13 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.13), residues: 3810 helix: 2.53 (0.08), residues: 3054 sheet: None (None), residues: 0 loop : -2.66 (0.20), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 37 HIS 0.012 0.001 HIS D 54 PHE 0.020 0.002 PHE N 26 TYR 0.022 0.002 TYR Q 71 ARG 0.008 0.001 ARG X 53 Details of bonding type rmsd hydrogen bonds : bond 0.06026 ( 2606) hydrogen bonds : angle 3.79529 ( 7818) covalent geometry : bond 0.00408 (31867) covalent geometry : angle 0.57286 (43071) *********************** 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 475 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 473 time to evaluate : 3.808 Fit side-chains revert: symmetry clash revert: symmetry clash 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. TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8724 (ttt) cc_final: 0.8455 (ttm) REVERT: A 66 ASP cc_start: 0.8708 (t70) cc_final: 0.8391 (t0) REVERT: C 70 ASN cc_start: 0.8537 (t0) cc_final: 0.8212 (t0) REVERT: C 119 VAL cc_start: 0.9120 (m) cc_final: 0.8885 (p) REVERT: D 95 LEU cc_start: 0.9010 (mt) cc_final: 0.8736 (pp) REVERT: F 56 GLU cc_start: 0.8925 (tp30) cc_final: 0.8317 (mm-30) REVERT: F 99 ASP cc_start: 0.8647 (t0) cc_final: 0.8389 (t0) REVERT: F 108 MET cc_start: 0.8293 (ptp) cc_final: 0.7844 (ptp) REVERT: H 61 ARG cc_start: 0.8546 (tpt170) cc_final: 0.8202 (tpm170) REVERT: H 86 MET cc_start: 0.8001 (ptp) cc_final: 0.7515 (ptp) REVERT: H 95 LEU cc_start: 0.9200 (mt) cc_final: 0.8737 (pp) REVERT: J 14 GLN cc_start: 0.8699 (tp40) cc_final: 0.8193 (tp40) REVERT: J 137 GLN cc_start: 0.8603 (pt0) cc_final: 0.7943 (tt0) REVERT: K 86 MET cc_start: 0.7630 (ptp) cc_final: 0.7144 (ptp) REVERT: K 115 THR cc_start: 0.7279 (m) cc_final: 0.7063 (m) REVERT: M 95 LEU cc_start: 0.9015 (mt) cc_final: 0.8440 (mt) REVERT: N 1 MET cc_start: 0.7649 (tmm) cc_final: 0.7234 (tmm) REVERT: N 22 ILE cc_start: 0.9107 (mt) cc_final: 0.8799 (mm) REVERT: T 22 ILE cc_start: 0.9494 (pt) cc_final: 0.9277 (pt) REVERT: T 86 MET cc_start: 0.7953 (mtm) cc_final: 0.7466 (mtm) REVERT: T 90 ASP cc_start: 0.9111 (m-30) cc_final: 0.8811 (m-30) REVERT: T 126 ASP cc_start: 0.8764 (t70) cc_final: 0.8560 (t70) REVERT: U 86 MET cc_start: 0.8518 (mtm) cc_final: 0.7998 (mtt) REVERT: U 114 ILE cc_start: 0.7964 (mm) cc_final: 0.7649 (mm) REVERT: U 143 LYS cc_start: 0.8793 (tttt) cc_final: 0.8570 (tptm) REVERT: V 86 MET cc_start: 0.8021 (mtm) cc_final: 0.7411 (mtt) outliers start: 2 outliers final: 2 residues processed: 475 average time/residue: 0.4173 time to fit residues: 320.6768 Evaluate side-chains 322 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 320 time to evaluate : 3.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 300 optimal weight: 10.0000 chunk 123 optimal weight: 20.0000 chunk 121 optimal weight: 20.0000 chunk 169 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 319 optimal weight: 20.0000 chunk 38 optimal weight: 0.6980 chunk 161 optimal weight: 5.9990 chunk 212 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 308 optimal weight: 3.9990 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 28 HIS ** F 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN E 72 GLN G 72 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 112 HIS ** N 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 HIS P 23 ASN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 28 HIS ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 118 ASN X 23 ASN X 130 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.059840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.052062 restraints weight = 183625.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.053301 restraints weight = 121883.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.054159 restraints weight = 88757.258| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 31867 Z= 0.172 Angle : 0.568 9.189 43071 Z= 0.314 Chirality : 0.036 0.163 4895 Planarity : 0.003 0.034 5626 Dihedral : 4.081 23.269 4193 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.91 % Favored : 96.93 % Rotamer: Outliers : 0.21 % Allowed : 3.11 % Favored : 96.68 % 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: 2.47 (0.13), residues: 3810 helix: 2.58 (0.08), residues: 3066 sheet: None (None), residues: 0 loop : -2.71 (0.20), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 37 HIS 0.015 0.001 HIS M 112 PHE 0.042 0.002 PHE A 120 TYR 0.037 0.002 TYR Q 71 ARG 0.008 0.000 ARG X 53 Details of bonding type rmsd hydrogen bonds : bond 0.05991 ( 2606) hydrogen bonds : angle 3.69554 ( 7818) covalent geometry : bond 0.00361 (31867) covalent geometry : angle 0.56771 (43071) *********************** 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 499 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 492 time to evaluate : 3.442 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 TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8754 (ttt) cc_final: 0.8487 (ttm) REVERT: A 66 ASP cc_start: 0.8695 (t70) cc_final: 0.8419 (t0) REVERT: B 128 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7785 (mt-10) REVERT: C 70 ASN cc_start: 0.8535 (t0) cc_final: 0.8259 (t0) REVERT: C 119 VAL cc_start: 0.9147 (m) cc_final: 0.8897 (p) REVERT: D 95 LEU cc_start: 0.9064 (mt) cc_final: 0.8836 (pp) REVERT: F 56 GLU cc_start: 0.8900 (tp30) cc_final: 0.8278 (mm-30) REVERT: F 99 ASP cc_start: 0.8628 (t0) cc_final: 0.8379 (t0) REVERT: F 108 MET cc_start: 0.8242 (ptp) cc_final: 0.7735 (ptp) REVERT: G 108 MET cc_start: 0.8339 (mmm) cc_final: 0.7885 (mmt) REVERT: G 123 ILE cc_start: 0.8620 (mm) cc_final: 0.8377 (mm) REVERT: H 61 ARG cc_start: 0.8427 (tpt170) cc_final: 0.8211 (tpm170) REVERT: H 86 MET cc_start: 0.7988 (ptp) cc_final: 0.7522 (ptp) REVERT: H 95 LEU cc_start: 0.9218 (mt) cc_final: 0.8739 (pp) REVERT: I 52 MET cc_start: 0.7433 (ttm) cc_final: 0.7189 (ttm) REVERT: J 14 GLN cc_start: 0.8683 (tp40) cc_final: 0.8325 (tp40) REVERT: J 137 GLN cc_start: 0.8583 (pt0) cc_final: 0.7071 (pt0) REVERT: M 95 LEU cc_start: 0.8918 (mt) cc_final: 0.8467 (mt) REVERT: T 86 MET cc_start: 0.8098 (mtm) cc_final: 0.7614 (mtt) REVERT: T 90 ASP cc_start: 0.9048 (m-30) cc_final: 0.8817 (m-30) REVERT: U 86 MET cc_start: 0.8462 (mtm) cc_final: 0.7906 (mtt) REVERT: U 114 ILE cc_start: 0.8019 (mm) cc_final: 0.7660 (mm) REVERT: U 143 LYS cc_start: 0.8809 (tttt) cc_final: 0.8589 (tptm) REVERT: V 86 MET cc_start: 0.8159 (mtm) cc_final: 0.7703 (mtt) REVERT: W 150 LEU cc_start: 0.9411 (mt) cc_final: 0.9146 (tt) outliers start: 7 outliers final: 4 residues processed: 497 average time/residue: 0.3885 time to fit residues: 314.9079 Evaluate side-chains 329 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 325 time to evaluate : 3.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 65 optimal weight: 20.0000 chunk 130 optimal weight: 3.9990 chunk 356 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 47 optimal weight: 0.0070 chunk 351 optimal weight: 6.9990 chunk 230 optimal weight: 4.9990 chunk 151 optimal weight: 7.9990 chunk 141 optimal weight: 20.0000 chunk 142 optimal weight: 5.9990 chunk 282 optimal weight: 7.9990 overall best weight: 3.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 HIS C 88 GLN C 129 HIS D 28 HIS E 32 GLN G 137 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 23 ASN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 23 ASN Q 130 HIS ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 76 HIS T 158 GLN U 118 ASN X 23 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.060770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.052759 restraints weight = 183272.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.054058 restraints weight = 121195.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.055015 restraints weight = 87876.025| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31867 Z= 0.144 Angle : 0.552 8.564 43071 Z= 0.304 Chirality : 0.035 0.139 4895 Planarity : 0.003 0.037 5626 Dihedral : 3.989 21.715 4193 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.94 % Favored : 96.90 % Rotamer: Outliers : 0.12 % Allowed : 2.42 % Favored : 97.46 % 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: 2.56 (0.13), residues: 3810 helix: 2.63 (0.08), residues: 3067 sheet: None (None), residues: 0 loop : -2.66 (0.20), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 37 HIS 0.011 0.001 HIS O 28 PHE 0.028 0.001 PHE F 120 TYR 0.019 0.001 TYR Q 71 ARG 0.008 0.000 ARG O 45 Details of bonding type rmsd hydrogen bonds : bond 0.05718 ( 2606) hydrogen bonds : angle 3.61152 ( 7818) covalent geometry : bond 0.00307 (31867) covalent geometry : angle 0.55183 (43071) *********************** 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 502 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 498 time to evaluate : 4.054 Fit side-chains revert: symmetry clash 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. TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8745 (ttt) cc_final: 0.8472 (ttm) REVERT: A 66 ASP cc_start: 0.8802 (t70) cc_final: 0.8537 (t0) REVERT: B 18 GLU cc_start: 0.8023 (tt0) cc_final: 0.7097 (tm-30) REVERT: B 128 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7799 (mt-10) REVERT: C 70 ASN cc_start: 0.8486 (t0) cc_final: 0.8195 (t0) REVERT: C 119 VAL cc_start: 0.9148 (m) cc_final: 0.8914 (p) REVERT: D 1 MET cc_start: 0.6564 (pmm) cc_final: 0.6335 (pmm) REVERT: D 95 LEU cc_start: 0.9075 (mt) cc_final: 0.8840 (pp) REVERT: F 99 ASP cc_start: 0.8656 (t0) cc_final: 0.8388 (t0) REVERT: F 108 MET cc_start: 0.8369 (ptp) cc_final: 0.7820 (ptp) REVERT: G 108 MET cc_start: 0.8551 (mmm) cc_final: 0.8179 (mmt) REVERT: G 123 ILE cc_start: 0.8611 (mm) cc_final: 0.8347 (mm) REVERT: H 61 ARG cc_start: 0.8402 (tpt170) cc_final: 0.8187 (tpm170) REVERT: H 86 MET cc_start: 0.8065 (ptp) cc_final: 0.7495 (ptp) REVERT: H 95 LEU cc_start: 0.9202 (mt) cc_final: 0.8716 (pp) REVERT: I 52 MET cc_start: 0.7478 (ttm) cc_final: 0.7216 (ttm) REVERT: J 14 GLN cc_start: 0.8679 (tp40) cc_final: 0.8220 (tp40) REVERT: J 114 ILE cc_start: 0.6524 (mp) cc_final: 0.6286 (mp) REVERT: K 86 MET cc_start: 0.7663 (ptp) cc_final: 0.7122 (ptp) REVERT: M 132 ASP cc_start: 0.8657 (t0) cc_final: 0.8398 (t0) REVERT: S 76 HIS cc_start: 0.8546 (t70) cc_final: 0.7033 (t-90) REVERT: S 78 ARG cc_start: 0.8698 (ptp-110) cc_final: 0.8081 (ptp-110) REVERT: T 20 THR cc_start: 0.9513 (m) cc_final: 0.9297 (p) REVERT: T 86 MET cc_start: 0.8035 (mtm) cc_final: 0.7519 (mtt) REVERT: T 90 ASP cc_start: 0.9062 (m-30) cc_final: 0.8784 (m-30) REVERT: T 126 ASP cc_start: 0.8681 (t70) cc_final: 0.8451 (t70) REVERT: U 86 MET cc_start: 0.8414 (mtm) cc_final: 0.7878 (mtt) REVERT: U 114 ILE cc_start: 0.8094 (mm) cc_final: 0.7727 (mm) REVERT: U 143 LYS cc_start: 0.8817 (tttt) cc_final: 0.8601 (tptm) REVERT: V 86 MET cc_start: 0.8035 (mtm) cc_final: 0.7791 (mtt) REVERT: W 1 MET cc_start: 0.8132 (pmm) cc_final: 0.7705 (pmm) REVERT: W 150 LEU cc_start: 0.9420 (mt) cc_final: 0.9126 (tt) outliers start: 4 outliers final: 3 residues processed: 502 average time/residue: 0.3937 time to fit residues: 324.8594 Evaluate side-chains 332 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 329 time to evaluate : 4.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 87 optimal weight: 4.9990 chunk 105 optimal weight: 20.0000 chunk 50 optimal weight: 9.9990 chunk 338 optimal weight: 20.0000 chunk 211 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 294 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 HIS ** D 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 GLN ** F 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 137 GLN ** N 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 23 ASN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 HIS T 158 GLN U 118 ASN X 23 ASN X 130 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.059753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.051852 restraints weight = 184573.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.053103 restraints weight = 121992.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.053998 restraints weight = 88593.851| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 31867 Z= 0.173 Angle : 0.585 9.356 43071 Z= 0.323 Chirality : 0.036 0.151 4895 Planarity : 0.003 0.036 5626 Dihedral : 4.048 22.114 4193 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.07 % Favored : 96.77 % Rotamer: Outliers : 0.06 % Allowed : 1.76 % Favored : 98.18 % 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: 2.47 (0.13), residues: 3810 helix: 2.56 (0.08), residues: 3062 sheet: None (None), residues: 0 loop : -2.62 (0.20), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 37 HIS 0.020 0.001 HIS D 54 PHE 0.043 0.001 PHE A 120 TYR 0.025 0.002 TYR Q 71 ARG 0.009 0.000 ARG X 53 Details of bonding type rmsd hydrogen bonds : bond 0.05916 ( 2606) hydrogen bonds : angle 3.75502 ( 7818) covalent geometry : bond 0.00377 (31867) covalent geometry : angle 0.58452 (43071) *********************** 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 474 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 472 time to evaluate : 3.566 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. TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8748 (ttt) cc_final: 0.8491 (ttm) REVERT: A 66 ASP cc_start: 0.8809 (t70) cc_final: 0.8543 (t0) REVERT: B 18 GLU cc_start: 0.7873 (tt0) cc_final: 0.7326 (tm-30) REVERT: B 128 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7843 (mt-10) REVERT: C 70 ASN cc_start: 0.8502 (t0) cc_final: 0.8230 (t0) REVERT: C 119 VAL cc_start: 0.9185 (m) cc_final: 0.8945 (p) REVERT: D 1 MET cc_start: 0.6599 (pmm) cc_final: 0.6372 (pmm) REVERT: F 99 ASP cc_start: 0.8674 (t0) cc_final: 0.8415 (t0) REVERT: G 108 MET cc_start: 0.8536 (mmm) cc_final: 0.8185 (mmt) REVERT: G 123 ILE cc_start: 0.8726 (mm) cc_final: 0.8468 (mm) REVERT: H 61 ARG cc_start: 0.8369 (tpt170) cc_final: 0.8150 (tpm170) REVERT: H 86 MET cc_start: 0.8097 (ptp) cc_final: 0.7408 (ptp) REVERT: H 95 LEU cc_start: 0.9243 (mt) cc_final: 0.8764 (pp) REVERT: H 108 MET cc_start: 0.8008 (mtm) cc_final: 0.7707 (mtp) REVERT: I 52 MET cc_start: 0.7691 (ttm) cc_final: 0.7366 (ttm) REVERT: J 14 GLN cc_start: 0.8622 (tp40) cc_final: 0.8209 (tp40) REVERT: J 114 ILE cc_start: 0.6622 (mp) cc_final: 0.6397 (mp) REVERT: K 86 MET cc_start: 0.7723 (ptp) cc_final: 0.7190 (ptp) REVERT: K 108 MET cc_start: 0.8725 (tmm) cc_final: 0.8196 (tmm) REVERT: M 95 LEU cc_start: 0.8978 (mt) cc_final: 0.8411 (mt) REVERT: M 132 ASP cc_start: 0.8657 (t0) cc_final: 0.8372 (t0) REVERT: N 1 MET cc_start: 0.7328 (tmm) cc_final: 0.7068 (tmm) REVERT: O 52 MET cc_start: 0.6492 (ttm) cc_final: 0.6125 (ttm) REVERT: R 27 LEU cc_start: 0.8361 (mm) cc_final: 0.7848 (mm) REVERT: R 153 VAL cc_start: 0.6556 (m) cc_final: 0.6257 (t) REVERT: S 86 MET cc_start: 0.8487 (ppp) cc_final: 0.8269 (ppp) REVERT: T 86 MET cc_start: 0.8066 (mtm) cc_final: 0.7531 (mtt) REVERT: T 90 ASP cc_start: 0.9086 (m-30) cc_final: 0.8815 (m-30) REVERT: T 126 ASP cc_start: 0.8662 (t70) cc_final: 0.8461 (t70) REVERT: U 86 MET cc_start: 0.8387 (mtm) cc_final: 0.7831 (mtt) REVERT: U 114 ILE cc_start: 0.8129 (mm) cc_final: 0.7761 (mm) REVERT: U 143 LYS cc_start: 0.8801 (tttt) cc_final: 0.8593 (tptm) REVERT: W 1 MET cc_start: 0.8098 (pmm) cc_final: 0.7701 (pmm) REVERT: W 150 LEU cc_start: 0.9439 (mt) cc_final: 0.9107 (tt) outliers start: 2 outliers final: 2 residues processed: 474 average time/residue: 0.3871 time to fit residues: 301.0191 Evaluate side-chains 314 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 312 time to evaluate : 3.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 106 optimal weight: 20.0000 chunk 254 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 280 optimal weight: 7.9990 chunk 114 optimal weight: 9.9990 chunk 334 optimal weight: 5.9990 chunk 227 optimal weight: 5.9990 chunk 203 optimal weight: 7.9990 chunk 240 optimal weight: 20.0000 chunk 339 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN H 24 GLN H 118 ASN J 137 GLN ** N 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 23 ASN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 HIS U 118 ASN W 130 HIS X 23 ASN ** X 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 156 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.059165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.051272 restraints weight = 186127.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.052530 restraints weight = 122893.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.053441 restraints weight = 89468.723| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 31867 Z= 0.183 Angle : 0.616 8.519 43071 Z= 0.339 Chirality : 0.037 0.160 4895 Planarity : 0.003 0.034 5626 Dihedral : 4.104 21.343 4193 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.91 % Favored : 96.93 % Rotamer: Outliers : 0.09 % Allowed : 1.61 % Favored : 98.30 % 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: 2.34 (0.13), residues: 3810 helix: 2.45 (0.08), residues: 3074 sheet: None (None), residues: 0 loop : -2.65 (0.20), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 37 HIS 0.012 0.001 HIS D 54 PHE 0.038 0.002 PHE I 10 TYR 0.036 0.002 TYR K 25 ARG 0.007 0.000 ARG X 53 Details of bonding type rmsd hydrogen bonds : bond 0.06125 ( 2606) hydrogen bonds : angle 3.85336 ( 7818) covalent geometry : bond 0.00400 (31867) covalent geometry : angle 0.61588 (43071) *********************** 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 467 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 464 time to evaluate : 3.624 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 TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8774 (ttt) cc_final: 0.8521 (ttm) REVERT: A 60 ASP cc_start: 0.8289 (m-30) cc_final: 0.8085 (m-30) REVERT: A 66 ASP cc_start: 0.8791 (t70) cc_final: 0.8557 (t0) REVERT: B 52 MET cc_start: 0.7154 (ttt) cc_final: 0.6938 (ttt) REVERT: B 128 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7882 (mt-10) REVERT: C 70 ASN cc_start: 0.8478 (t0) cc_final: 0.8223 (t0) REVERT: D 52 MET cc_start: 0.7850 (ttt) cc_final: 0.7637 (ttt) REVERT: D 114 ILE cc_start: 0.8541 (pt) cc_final: 0.8275 (pt) REVERT: D 115 THR cc_start: 0.8967 (p) cc_final: 0.8586 (p) REVERT: G 108 MET cc_start: 0.8486 (mmm) cc_final: 0.8137 (mmt) REVERT: G 123 ILE cc_start: 0.8828 (mm) cc_final: 0.8568 (mm) REVERT: H 61 ARG cc_start: 0.8443 (tpt170) cc_final: 0.8035 (tpm170) REVERT: H 86 MET cc_start: 0.8004 (ptp) cc_final: 0.7419 (ptp) REVERT: H 108 MET cc_start: 0.8147 (mtm) cc_final: 0.7870 (mtp) REVERT: I 52 MET cc_start: 0.7874 (ttm) cc_final: 0.7552 (ttm) REVERT: J 14 GLN cc_start: 0.8630 (tp40) cc_final: 0.8268 (tp40) REVERT: J 114 ILE cc_start: 0.6691 (mp) cc_final: 0.6481 (mp) REVERT: L 111 LYS cc_start: 0.8661 (tppt) cc_final: 0.8346 (tppp) REVERT: M 95 LEU cc_start: 0.8865 (mt) cc_final: 0.8396 (mt) REVERT: M 132 ASP cc_start: 0.8672 (t0) cc_final: 0.8397 (t0) REVERT: N 43 TYR cc_start: 0.6221 (m-80) cc_final: 0.6010 (m-10) REVERT: O 52 MET cc_start: 0.6497 (ttm) cc_final: 0.6106 (ttm) REVERT: O 86 MET cc_start: 0.8166 (mtp) cc_final: 0.7951 (ttm) REVERT: O 149 TYR cc_start: 0.8702 (t80) cc_final: 0.8502 (t80) REVERT: P 86 MET cc_start: 0.8478 (mtt) cc_final: 0.8134 (mtt) REVERT: T 86 MET cc_start: 0.8078 (mtm) cc_final: 0.7534 (mtt) REVERT: T 90 ASP cc_start: 0.9072 (m-30) cc_final: 0.8756 (m-30) REVERT: U 86 MET cc_start: 0.8429 (mtm) cc_final: 0.7867 (mtt) REVERT: U 114 ILE cc_start: 0.8151 (mm) cc_final: 0.7789 (mm) REVERT: U 143 LYS cc_start: 0.8852 (tttt) cc_final: 0.8646 (tptm) REVERT: W 1 MET cc_start: 0.8098 (pmm) cc_final: 0.7709 (pmm) REVERT: W 150 LEU cc_start: 0.9457 (mt) cc_final: 0.9124 (tt) outliers start: 3 outliers final: 2 residues processed: 467 average time/residue: 0.4101 time to fit residues: 314.9749 Evaluate side-chains 322 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 320 time to evaluate : 3.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 340 optimal weight: 10.0000 chunk 239 optimal weight: 20.0000 chunk 281 optimal weight: 5.9990 chunk 349 optimal weight: 20.0000 chunk 171 optimal weight: 8.9990 chunk 152 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 chunk 193 optimal weight: 20.0000 chunk 223 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 chunk 86 optimal weight: 5.9990 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 GLN E 32 GLN G 12 ASN G 137 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 HIS K 28 HIS ** N 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 72 GLN P 14 GLN P 23 ASN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 HIS U 118 ASN V 129 HIS W 130 HIS X 23 ASN X 130 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.058730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.051044 restraints weight = 185846.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.052242 restraints weight = 123173.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.053126 restraints weight = 90113.905| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 31867 Z= 0.199 Angle : 0.640 8.967 43071 Z= 0.356 Chirality : 0.038 0.191 4895 Planarity : 0.003 0.034 5626 Dihedral : 4.179 22.221 4193 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.02 % Favored : 96.82 % Rotamer: Outliers : 0.09 % Allowed : 0.90 % Favored : 99.01 % 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: 2.20 (0.13), residues: 3810 helix: 2.36 (0.08), residues: 3068 sheet: None (None), residues: 0 loop : -2.68 (0.20), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F 37 HIS 0.012 0.001 HIS D 54 PHE 0.041 0.002 PHE A 120 TYR 0.025 0.002 TYR Q 71 ARG 0.007 0.001 ARG V 100 Details of bonding type rmsd hydrogen bonds : bond 0.06346 ( 2606) hydrogen bonds : angle 3.99979 ( 7818) covalent geometry : bond 0.00437 (31867) covalent geometry : angle 0.63968 (43071) *********************** 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 447 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 444 time to evaluate : 3.814 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 TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8848 (ttt) cc_final: 0.8579 (ttm) REVERT: A 66 ASP cc_start: 0.8845 (t70) cc_final: 0.8613 (t0) REVERT: A 86 MET cc_start: 0.9052 (mmp) cc_final: 0.8803 (mmp) REVERT: B 52 MET cc_start: 0.7088 (ttt) cc_final: 0.6826 (ttt) REVERT: B 128 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7876 (mt-10) REVERT: C 70 ASN cc_start: 0.8464 (t0) cc_final: 0.8218 (t0) REVERT: D 52 MET cc_start: 0.7959 (ttt) cc_final: 0.7710 (ttt) REVERT: D 114 ILE cc_start: 0.8633 (pt) cc_final: 0.8397 (pt) REVERT: D 115 THR cc_start: 0.9148 (p) cc_final: 0.8800 (p) REVERT: F 108 MET cc_start: 0.8361 (ptp) cc_final: 0.7826 (ptp) REVERT: G 108 MET cc_start: 0.8397 (mmm) cc_final: 0.8038 (mmt) REVERT: G 123 ILE cc_start: 0.8898 (mm) cc_final: 0.8622 (mm) REVERT: H 86 MET cc_start: 0.8091 (ptp) cc_final: 0.7474 (ptp) REVERT: H 108 MET cc_start: 0.8178 (mtm) cc_final: 0.7909 (mtp) REVERT: I 52 MET cc_start: 0.7996 (ttm) cc_final: 0.7646 (ttm) REVERT: J 14 GLN cc_start: 0.8602 (tp40) cc_final: 0.8313 (tp40) REVERT: K 108 MET cc_start: 0.8757 (tmm) cc_final: 0.8301 (tmm) REVERT: L 111 LYS cc_start: 0.8672 (tppt) cc_final: 0.8371 (tppp) REVERT: L 123 ILE cc_start: 0.8981 (pt) cc_final: 0.8601 (tt) REVERT: M 95 LEU cc_start: 0.8907 (mt) cc_final: 0.8431 (mt) REVERT: M 132 ASP cc_start: 0.8634 (t0) cc_final: 0.8363 (t0) REVERT: O 52 MET cc_start: 0.6555 (ttm) cc_final: 0.6092 (ttm) REVERT: O 149 TYR cc_start: 0.8694 (t80) cc_final: 0.8435 (t80) REVERT: T 86 MET cc_start: 0.8076 (mtm) cc_final: 0.7690 (mtt) REVERT: T 90 ASP cc_start: 0.9090 (m-30) cc_final: 0.8783 (m-30) REVERT: U 86 MET cc_start: 0.8442 (mtm) cc_final: 0.7871 (mtt) REVERT: U 114 ILE cc_start: 0.8202 (mm) cc_final: 0.7836 (mm) REVERT: U 143 LYS cc_start: 0.8879 (tttt) cc_final: 0.8648 (tptm) REVERT: W 1 MET cc_start: 0.8075 (pmm) cc_final: 0.7690 (pmm) REVERT: W 150 LEU cc_start: 0.9463 (mt) cc_final: 0.9199 (tt) outliers start: 3 outliers final: 2 residues processed: 447 average time/residue: 0.3923 time to fit residues: 290.5703 Evaluate side-chains 311 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 309 time to evaluate : 3.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 256 optimal weight: 4.9990 chunk 259 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 354 optimal weight: 7.9990 chunk 69 optimal weight: 20.0000 chunk 348 optimal weight: 3.9990 chunk 303 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 372 optimal weight: 9.9990 chunk 367 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 HIS ** D 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 28 HIS K 76 HIS L 28 HIS N 14 GLN P 23 ASN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 70 ASN W 130 HIS X 23 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.059877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.052112 restraints weight = 184097.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.053378 restraints weight = 121715.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.054298 restraints weight = 88301.295| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31867 Z= 0.158 Angle : 0.616 11.044 43071 Z= 0.338 Chirality : 0.037 0.184 4895 Planarity : 0.003 0.092 5626 Dihedral : 4.115 22.241 4193 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.91 % Favored : 96.93 % Rotamer: Outliers : 0.09 % Allowed : 0.39 % Favored : 99.52 % 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: 2.34 (0.13), residues: 3810 helix: 2.47 (0.09), residues: 3070 sheet: None (None), residues: 0 loop : -2.68 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 37 HIS 0.011 0.001 HIS D 54 PHE 0.025 0.001 PHE I 10 TYR 0.025 0.002 TYR Q 71 ARG 0.011 0.000 ARG X 53 Details of bonding type rmsd hydrogen bonds : bond 0.06005 ( 2606) hydrogen bonds : angle 3.82639 ( 7818) covalent geometry : bond 0.00340 (31867) covalent geometry : angle 0.61550 (43071) ********************** 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 470 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 467 time to evaluate : 4.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8892 (ttt) cc_final: 0.8622 (ttm) REVERT: A 60 ASP cc_start: 0.8304 (m-30) cc_final: 0.8085 (m-30) REVERT: A 66 ASP cc_start: 0.8816 (t70) cc_final: 0.8602 (t0) REVERT: A 86 MET cc_start: 0.9042 (mmp) cc_final: 0.8832 (mmp) REVERT: B 128 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7937 (mt-10) REVERT: C 70 ASN cc_start: 0.8516 (t0) cc_final: 0.8257 (t0) REVERT: D 52 MET cc_start: 0.7830 (ttt) cc_final: 0.7597 (ttt) REVERT: D 114 ILE cc_start: 0.8554 (pt) cc_final: 0.8315 (pt) REVERT: D 115 THR cc_start: 0.9121 (p) cc_final: 0.8724 (p) REVERT: F 108 MET cc_start: 0.8300 (ptp) cc_final: 0.8007 (ptp) REVERT: G 108 MET cc_start: 0.8396 (mmm) cc_final: 0.8061 (mmt) REVERT: G 123 ILE cc_start: 0.8853 (mm) cc_final: 0.8613 (mm) REVERT: H 2 GLN cc_start: 0.7926 (mm110) cc_final: 0.7110 (pm20) REVERT: H 86 MET cc_start: 0.7979 (ptp) cc_final: 0.7459 (ptp) REVERT: H 108 MET cc_start: 0.8144 (mtm) cc_final: 0.7896 (mtp) REVERT: I 52 MET cc_start: 0.7987 (ttm) cc_final: 0.7659 (ttm) REVERT: I 123 ILE cc_start: 0.8843 (mm) cc_final: 0.8555 (mm) REVERT: J 14 GLN cc_start: 0.8668 (tp40) cc_final: 0.8359 (tp40) REVERT: K 86 MET cc_start: 0.8095 (ptp) cc_final: 0.7500 (ptp) REVERT: K 108 MET cc_start: 0.8732 (tmm) cc_final: 0.8236 (tmm) REVERT: L 111 LYS cc_start: 0.8683 (tppt) cc_final: 0.8376 (tppp) REVERT: M 66 ASP cc_start: 0.8222 (t0) cc_final: 0.8005 (t0) REVERT: M 95 LEU cc_start: 0.8902 (mt) cc_final: 0.8452 (mt) REVERT: M 132 ASP cc_start: 0.8677 (t0) cc_final: 0.8401 (t0) REVERT: O 52 MET cc_start: 0.6473 (ttm) cc_final: 0.5991 (ttm) REVERT: O 149 TYR cc_start: 0.8766 (t80) cc_final: 0.8437 (t80) REVERT: P 154 ILE cc_start: 0.9355 (mm) cc_final: 0.9096 (mm) REVERT: T 86 MET cc_start: 0.8002 (mtm) cc_final: 0.7627 (mtt) REVERT: T 90 ASP cc_start: 0.9074 (m-30) cc_final: 0.8768 (m-30) REVERT: U 86 MET cc_start: 0.8430 (mtm) cc_final: 0.7905 (mtt) REVERT: U 90 ASP cc_start: 0.8619 (m-30) cc_final: 0.8211 (m-30) REVERT: U 143 LYS cc_start: 0.8851 (tttt) cc_final: 0.8615 (tptm) REVERT: W 1 MET cc_start: 0.8093 (pmm) cc_final: 0.7708 (pmm) REVERT: W 150 LEU cc_start: 0.9432 (mt) cc_final: 0.9116 (tt) outliers start: 3 outliers final: 2 residues processed: 470 average time/residue: 0.4089 time to fit residues: 316.9675 Evaluate side-chains 319 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 317 time to evaluate : 3.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 352 optimal weight: 5.9990 chunk 225 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 258 optimal weight: 7.9990 chunk 350 optimal weight: 9.9990 chunk 252 optimal weight: 7.9990 chunk 312 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 358 optimal weight: 10.0000 chunk 294 optimal weight: 6.9990 chunk 377 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 HIS K 76 HIS P 23 ASN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 129 HIS W 130 HIS X 23 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.059585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.051888 restraints weight = 186395.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.053150 restraints weight = 122816.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.054071 restraints weight = 88797.468| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31867 Z= 0.168 Angle : 0.617 10.786 43071 Z= 0.340 Chirality : 0.037 0.178 4895 Planarity : 0.003 0.036 5626 Dihedral : 4.110 21.890 4193 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.20 % Favored : 96.64 % Rotamer: Outliers : 0.06 % Allowed : 0.45 % Favored : 99.49 % 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: 2.29 (0.13), residues: 3810 helix: 2.43 (0.09), residues: 3074 sheet: None (None), residues: 0 loop : -2.71 (0.20), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 37 HIS 0.010 0.001 HIS D 54 PHE 0.024 0.002 PHE V 120 TYR 0.018 0.002 TYR L 149 ARG 0.011 0.000 ARG X 53 Details of bonding type rmsd hydrogen bonds : bond 0.05968 ( 2606) hydrogen bonds : angle 3.86952 ( 7818) covalent geometry : bond 0.00367 (31867) covalent geometry : angle 0.61741 (43071) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9317.99 seconds wall clock time: 166 minutes 10.75 seconds (9970.75 seconds total)