Starting phenix.real_space_refine on Wed May 28 10:31:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jb0_36139/05_2025/8jb0_36139.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jb0_36139/05_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_36139/05_2025/8jb0_36139.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jb0_36139/05_2025/8jb0_36139.map" model { file = "/net/cci-nas-00/data/ceres_data/8jb0_36139/05_2025/8jb0_36139.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jb0_36139/05_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): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 18.71, per 1000 atoms: 0.60 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: 8.34 Conformation dependent library (CDL) restraints added in 3.7 seconds 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7422 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 0 sheets defined 81.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.26 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: 9.04 Time building geometry restraints manager: 9.47 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.280 Check model and map are aligned: 0.230 Set scattering table: 0.310 Process input model: 63.430 Find NCS groups from input model: 2.080 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.920 ------------------------------------------------------------------------------- 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 : 3.468 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: 0.3883 time to fit residues: 328.0958 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 : 3.908 ------------------------------------------------------------------------------- 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 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.060707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.052649 restraints weight = 182493.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.053921 restraints weight = 120847.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.054862 restraints weight = 87840.444| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1151 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 : 0.565 7.490 43071 Z= 0.315 Chirality : 0.037 0.157 4895 Planarity : 0.003 0.038 5626 Dihedral : 4.073 22.998 4193 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.84 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 0.016 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 0.05994 ( 2606) hydrogen bonds : angle 3.79784 ( 7818) covalent geometry : bond 0.00383 (31867) covalent geometry : angle 0.56465 (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 511 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 501 time to evaluate : 3.731 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: 0.8603 (ttt) cc_final: 0.8368 (ttm) REVERT: A 66 ASP cc_start: 0.8615 (t70) cc_final: 0.8359 (t0) REVERT: A 111 LYS cc_start: 0.8673 (tppt) cc_final: 0.8443 (tppp) REVERT: C 70 ASN cc_start: 0.8511 (t0) cc_final: 0.8225 (t0) REVERT: C 108 MET cc_start: 0.8319 (tmm) cc_final: 0.8087 (tmm) REVERT: C 119 VAL cc_start: 0.9088 (m) cc_final: 0.8843 (p) REVERT: D 121 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7577 (pt0) REVERT: F 99 ASP cc_start: 0.8540 (t0) cc_final: 0.8315 (t0) REVERT: E 121 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8712 (mp0) REVERT: H 86 MET cc_start: 0.8060 (ptp) cc_final: 0.7795 (ptp) REVERT: H 95 LEU cc_start: 0.9111 (mt) cc_final: 0.8734 (pp) REVERT: J 14 GLN cc_start: 0.8695 (tp40) cc_final: 0.7739 (tp40) REVERT: J 137 GLN cc_start: 0.8608 (pt0) cc_final: 0.8047 (tt0) REVERT: J 144 LEU cc_start: 0.9084 (tt) cc_final: 0.8815 (tt) REVERT: K 115 THR cc_start: 0.7129 (m) cc_final: 0.6891 (m) REVERT: N 22 ILE cc_start: 0.9107 (mt) cc_final: 0.8836 (mm) REVERT: P 52 MET cc_start: 0.7009 (ttm) cc_final: 0.6782 (ttm) REVERT: Q 100 ARG cc_start: 0.8663 (ttm110) cc_final: 0.8362 (ttp-110) REVERT: R 151 SER cc_start: 0.8824 (t) cc_final: 0.8588 (p) REVERT: S 113 ASP cc_start: 0.6519 (t0) cc_final: 0.6271 (t0) REVERT: T 22 ILE cc_start: 0.9464 (pt) cc_final: 0.9258 (pt) REVERT: T 86 MET cc_start: 0.7833 (mtm) cc_final: 0.7104 (mtm) REVERT: T 90 ASP cc_start: 0.8938 (m-30) cc_final: 0.8711 (m-30) REVERT: U 37 TRP cc_start: 0.7398 (m-10) cc_final: 0.7176 (m-90) REVERT: U 86 MET cc_start: 0.8425 (mtm) cc_final: 0.8139 (mtm) REVERT: U 90 ASP cc_start: 0.8355 (m-30) cc_final: 0.8130 (m-30) REVERT: U 114 ILE cc_start: 0.7695 (mm) cc_final: 0.7404 (mm) REVERT: U 139 ASP cc_start: 0.8004 (m-30) cc_final: 0.7803 (m-30) REVERT: U 143 LYS cc_start: 0.8740 (tttt) cc_final: 0.8496 (tptm) REVERT: V 86 MET cc_start: 0.8033 (mtm) cc_final: 0.7382 (mtt) REVERT: V 114 ILE cc_start: 0.9093 (mm) cc_final: 0.8892 (mm) REVERT: V 118 ASN cc_start: 0.8966 (m110) cc_final: 0.8624 (m110) REVERT: W 108 MET cc_start: 0.8402 (tmm) cc_final: 0.8014 (tmm) outliers start: 10 outliers final: 3 residues processed: 507 average time/residue: 0.4061 time to fit residues: 333.4240 Evaluate side-chains 338 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 333 time to evaluate : 3.415 ------------------------------------------------------------------------------- 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: 3.9990 chunk 148 optimal weight: 1.9990 chunk 339 optimal weight: 0.0010 chunk 238 optimal weight: 5.9990 chunk 354 optimal weight: 9.9990 chunk 323 optimal weight: 7.9990 chunk 371 optimal weight: 8.9990 chunk 291 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 337 optimal weight: 10.0000 overall best weight: 3.9994 ------------------------------------------------------------------------------- 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 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** V 137 GLN ** 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 = 0.3311 r_free = 0.3311 target = 0.061327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.053427 restraints weight = 184628.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.054724 restraints weight = 120554.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.055665 restraints weight = 86865.748| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 31867 Z= 0.147 Angle : 0.540 9.147 43071 Z= 0.299 Chirality : 0.035 0.179 4895 Planarity : 0.003 0.031 5626 Dihedral : 4.035 22.730 4193 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.78 % Favored : 97.06 % Rotamer: Outliers : 0.15 % Allowed : 3.68 % Favored : 96.17 % 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: 2.64 (0.08), residues: 3062 sheet: None (None), residues: 0 loop : -2.67 (0.20), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 37 HIS 0.013 0.001 HIS D 54 PHE 0.033 0.001 PHE W 120 TYR 0.033 0.002 TYR Q 71 ARG 0.009 0.000 ARG N 102 Details of bonding type rmsd hydrogen bonds : bond 0.05757 ( 2606) hydrogen bonds : angle 3.63952 ( 7818) covalent geometry : bond 0.00315 (31867) covalent geometry : angle 0.54008 (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 529 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 524 time to evaluate : 3.439 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: A 52 MET cc_start: 0.8711 (ttt) cc_final: 0.8279 (ttt) REVERT: A 66 ASP cc_start: 0.8543 (t70) cc_final: 0.8281 (t0) REVERT: A 86 MET cc_start: 0.9084 (mmp) cc_final: 0.8841 (mmp) REVERT: B 90 ASP cc_start: 0.8804 (m-30) cc_final: 0.8567 (m-30) REVERT: C 70 ASN cc_start: 0.8584 (t0) cc_final: 0.8255 (t0) REVERT: C 119 VAL cc_start: 0.9080 (m) cc_final: 0.8827 (p) REVERT: F 99 ASP cc_start: 0.8531 (t0) cc_final: 0.8292 (t0) REVERT: G 108 MET cc_start: 0.8753 (mmt) cc_final: 0.8545 (mmt) REVERT: H 86 MET cc_start: 0.8005 (ptp) cc_final: 0.7704 (ptp) REVERT: H 95 LEU cc_start: 0.9157 (mt) cc_final: 0.8698 (pp) REVERT: J 14 GLN cc_start: 0.8636 (tp40) cc_final: 0.8054 (tp40) REVERT: J 137 GLN cc_start: 0.8502 (pt0) cc_final: 0.7728 (tt0) REVERT: K 115 THR cc_start: 0.7071 (m) cc_final: 0.6854 (m) REVERT: M 88 GLN cc_start: 0.8658 (pp30) cc_final: 0.8230 (pp30) REVERT: P 90 ASP cc_start: 0.8951 (m-30) cc_final: 0.8716 (m-30) REVERT: Q 100 ARG cc_start: 0.8652 (ttm110) cc_final: 0.8376 (ttp-110) REVERT: T 22 ILE cc_start: 0.9491 (pt) cc_final: 0.9241 (pt) REVERT: T 86 MET cc_start: 0.7831 (mtm) cc_final: 0.7212 (mtt) REVERT: T 90 ASP cc_start: 0.8958 (m-30) cc_final: 0.8734 (m-30) REVERT: T 108 MET cc_start: 0.7256 (mtt) cc_final: 0.6927 (mtm) REVERT: U 86 MET cc_start: 0.8427 (mtm) cc_final: 0.7864 (mtt) REVERT: U 114 ILE cc_start: 0.7773 (mm) cc_final: 0.7385 (mm) REVERT: U 143 LYS cc_start: 0.8785 (tttt) cc_final: 0.8561 (tptm) REVERT: V 86 MET cc_start: 0.7986 (mtm) cc_final: 0.7447 (mtt) outliers start: 5 outliers final: 4 residues processed: 527 average time/residue: 0.4018 time to fit residues: 344.5621 Evaluate side-chains 336 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 332 time to evaluate : 3.595 ------------------------------------------------------------------------------- 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: 9.9990 chunk 338 optimal weight: 6.9990 chunk 26 optimal weight: 30.0000 chunk 277 optimal weight: 20.0000 chunk 288 optimal weight: 9.9990 chunk 111 optimal weight: 7.9990 chunk 321 optimal weight: 9.9990 chunk 156 optimal weight: 10.0000 chunk 317 optimal weight: 3.9990 chunk 211 optimal weight: 10.0000 chunk 281 optimal weight: 20.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- 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 72 GLN G 156 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** K 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 156 GLN 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 V 137 GLN X 23 ASN ** X 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.059327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.051370 restraints weight = 182844.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.052634 restraints weight = 120292.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.053519 restraints weight = 87221.396| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 31867 Z= 0.200 Angle : 0.599 7.640 43071 Z= 0.333 Chirality : 0.038 0.209 4895 Planarity : 0.003 0.038 5626 Dihedral : 4.159 22.534 4193 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.12 % Favored : 96.72 % Rotamer: Outliers : 0.06 % Allowed : 4.31 % Favored : 95.63 % 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: 2.27 (0.13), residues: 3810 helix: 2.42 (0.08), residues: 3068 sheet: None (None), residues: 0 loop : -2.69 (0.20), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 37 HIS 0.018 0.001 HIS R 28 PHE 0.020 0.002 PHE N 120 TYR 0.025 0.002 TYR Q 71 ARG 0.008 0.001 ARG X 53 Details of bonding type rmsd hydrogen bonds : bond 0.06157 ( 2606) hydrogen bonds : angle 3.87924 ( 7818) covalent geometry : bond 0.00432 (31867) covalent geometry : angle 0.59889 (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 476 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 474 time to evaluate : 3.748 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. TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8697 (ttt) cc_final: 0.8426 (ttm) REVERT: A 66 ASP cc_start: 0.8708 (t70) cc_final: 0.8394 (t0) REVERT: C 70 ASN cc_start: 0.8576 (t0) cc_final: 0.8251 (t0) REVERT: C 119 VAL cc_start: 0.9123 (m) cc_final: 0.8889 (p) REVERT: D 95 LEU cc_start: 0.9010 (mt) cc_final: 0.8741 (pp) REVERT: F 99 ASP cc_start: 0.8646 (t0) cc_final: 0.8384 (t0) REVERT: H 61 ARG cc_start: 0.8526 (tpt170) cc_final: 0.8172 (tpm170) REVERT: H 86 MET cc_start: 0.8001 (ptp) cc_final: 0.7491 (ptp) REVERT: H 95 LEU cc_start: 0.9212 (mt) cc_final: 0.8750 (pp) REVERT: J 14 GLN cc_start: 0.8677 (tp40) cc_final: 0.8179 (tp40) REVERT: J 137 GLN cc_start: 0.8566 (pt0) cc_final: 0.7887 (tt0) REVERT: K 86 MET cc_start: 0.7638 (ptp) cc_final: 0.7070 (ptp) REVERT: K 115 THR cc_start: 0.7314 (m) cc_final: 0.7078 (m) REVERT: M 95 LEU cc_start: 0.9009 (mt) cc_final: 0.8421 (mt) REVERT: N 22 ILE cc_start: 0.9122 (mt) cc_final: 0.8816 (mm) REVERT: T 22 ILE cc_start: 0.9501 (pt) cc_final: 0.9283 (pt) REVERT: T 86 MET cc_start: 0.7964 (mtm) cc_final: 0.7477 (mtm) REVERT: T 90 ASP cc_start: 0.9107 (m-30) cc_final: 0.8814 (m-30) REVERT: T 126 ASP cc_start: 0.8753 (t70) cc_final: 0.8548 (t70) REVERT: U 86 MET cc_start: 0.8515 (mtm) cc_final: 0.7996 (mtt) REVERT: U 114 ILE cc_start: 0.7961 (mm) cc_final: 0.7658 (mm) REVERT: U 143 LYS cc_start: 0.8815 (tttt) cc_final: 0.8578 (tptm) REVERT: V 86 MET cc_start: 0.8017 (mtm) cc_final: 0.7398 (mtt) REVERT: X 94 GLU cc_start: 0.8851 (mp0) cc_final: 0.8599 (mp0) outliers start: 2 outliers final: 2 residues processed: 476 average time/residue: 0.4025 time to fit residues: 313.8140 Evaluate side-chains 320 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 318 time to evaluate : 3.738 ------------------------------------------------------------------------------- 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: 30.0000 chunk 121 optimal weight: 20.0000 chunk 169 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 319 optimal weight: 20.0000 chunk 38 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 chunk 212 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 308 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 GLN C 129 HIS D 28 HIS E 32 GLN E 72 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 28 HIS M 112 HIS ** N 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 HIS O 156 GLN P 23 ASN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.059716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.051843 restraints weight = 183785.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.053106 restraints weight = 121109.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.054044 restraints weight = 87717.946| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 31867 Z= 0.172 Angle : 0.568 8.438 43071 Z= 0.314 Chirality : 0.036 0.160 4895 Planarity : 0.003 0.034 5626 Dihedral : 4.107 22.639 4193 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.91 % Favored : 96.93 % Rotamer: Outliers : 0.15 % Allowed : 3.02 % Favored : 96.83 % 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: 2.53 (0.08), residues: 3066 sheet: None (None), residues: 0 loop : -2.70 (0.20), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 37 HIS 0.013 0.001 HIS M 112 PHE 0.038 0.002 PHE A 120 TYR 0.027 0.002 TYR Q 71 ARG 0.009 0.000 ARG X 53 Details of bonding type rmsd hydrogen bonds : bond 0.06075 ( 2606) hydrogen bonds : angle 3.76871 ( 7818) covalent geometry : bond 0.00373 (31867) covalent geometry : angle 0.56847 (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 490 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 485 time to evaluate : 3.648 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: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8739 (ttt) cc_final: 0.8482 (ttm) REVERT: A 66 ASP cc_start: 0.8699 (t70) cc_final: 0.8423 (t0) REVERT: B 128 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7769 (mt-10) REVERT: C 70 ASN cc_start: 0.8522 (t0) cc_final: 0.8213 (t0) REVERT: C 119 VAL cc_start: 0.9141 (m) cc_final: 0.8888 (p) REVERT: D 95 LEU cc_start: 0.9052 (mt) cc_final: 0.8829 (pp) REVERT: F 56 GLU cc_start: 0.8902 (tp30) cc_final: 0.8282 (mm-30) REVERT: F 99 ASP cc_start: 0.8599 (t0) cc_final: 0.8350 (t0) REVERT: F 108 MET cc_start: 0.8235 (ptp) cc_final: 0.7711 (ptp) REVERT: G 123 ILE cc_start: 0.8591 (mm) cc_final: 0.8370 (mm) REVERT: H 61 ARG cc_start: 0.8406 (tpt170) cc_final: 0.8148 (tpm170) REVERT: H 86 MET cc_start: 0.8024 (ptp) cc_final: 0.7485 (ptp) REVERT: H 95 LEU cc_start: 0.9226 (mt) cc_final: 0.8744 (pp) REVERT: I 52 MET cc_start: 0.7518 (ttm) cc_final: 0.7257 (ttm) REVERT: J 137 GLN cc_start: 0.8559 (pt0) cc_final: 0.7920 (tt0) REVERT: P 52 MET cc_start: 0.6945 (ttm) cc_final: 0.6731 (ttm) REVERT: P 90 ASP cc_start: 0.9091 (m-30) cc_final: 0.8883 (m-30) REVERT: T 86 MET cc_start: 0.8013 (mtm) cc_final: 0.7552 (mtt) REVERT: T 90 ASP cc_start: 0.9048 (m-30) cc_final: 0.8819 (m-30) REVERT: U 86 MET cc_start: 0.8452 (mtm) cc_final: 0.7920 (mtt) REVERT: U 114 ILE cc_start: 0.8007 (mm) cc_final: 0.7648 (mm) REVERT: U 143 LYS cc_start: 0.8824 (tttt) cc_final: 0.8592 (tptm) REVERT: U 154 ILE cc_start: 0.9086 (mm) cc_final: 0.8884 (mt) REVERT: V 86 MET cc_start: 0.8153 (mtm) cc_final: 0.7270 (mtt) REVERT: W 150 LEU cc_start: 0.9396 (mt) cc_final: 0.9138 (tt) outliers start: 5 outliers final: 4 residues processed: 489 average time/residue: 0.3964 time to fit residues: 315.8507 Evaluate side-chains 322 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 318 time to evaluate : 3.670 ------------------------------------------------------------------------------- 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: 8.9990 chunk 130 optimal weight: 7.9990 chunk 356 optimal weight: 4.9990 chunk 123 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 351 optimal weight: 7.9990 chunk 230 optimal weight: 10.0000 chunk 151 optimal weight: 8.9990 chunk 141 optimal weight: 20.0000 chunk 142 optimal weight: 9.9990 chunk 282 optimal weight: 0.8980 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 28 HIS E 32 GLN G 137 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 23 ASN ** 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 ** 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 = 0.3258 r_free = 0.3258 target = 0.059697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.051765 restraints weight = 184769.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.053041 restraints weight = 122032.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.053976 restraints weight = 88423.615| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 31867 Z= 0.168 Angle : 0.573 8.230 43071 Z= 0.317 Chirality : 0.036 0.144 4895 Planarity : 0.003 0.039 5626 Dihedral : 4.069 22.092 4193 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.94 % Favored : 96.90 % Rotamer: Outliers : 0.09 % Allowed : 2.75 % Favored : 97.16 % 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: 2.51 (0.08), residues: 3066 sheet: None (None), residues: 0 loop : -2.69 (0.20), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 37 HIS 0.009 0.001 HIS D 54 PHE 0.031 0.001 PHE F 120 TYR 0.033 0.002 TYR Q 71 ARG 0.007 0.000 ARG O 45 Details of bonding type rmsd hydrogen bonds : bond 0.06029 ( 2606) hydrogen bonds : angle 3.76994 ( 7818) covalent geometry : bond 0.00365 (31867) covalent geometry : angle 0.57276 (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 475 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 472 time to evaluate : 3.556 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: symmetry clash REVERT: A 52 MET cc_start: 0.8759 (ttt) cc_final: 0.8488 (ttm) REVERT: A 66 ASP cc_start: 0.8796 (t70) cc_final: 0.8545 (t0) REVERT: B 128 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7812 (mt-10) REVERT: C 70 ASN cc_start: 0.8539 (t0) cc_final: 0.8266 (t0) REVERT: C 119 VAL cc_start: 0.9155 (m) cc_final: 0.8918 (p) REVERT: D 1 MET cc_start: 0.6636 (pmm) cc_final: 0.6430 (pmm) REVERT: D 95 LEU cc_start: 0.9080 (mt) cc_final: 0.8858 (pp) REVERT: F 99 ASP cc_start: 0.8627 (t0) cc_final: 0.8372 (t0) REVERT: G 123 ILE cc_start: 0.8675 (mm) cc_final: 0.8433 (mm) REVERT: H 86 MET cc_start: 0.8069 (ptp) cc_final: 0.7473 (ptp) REVERT: H 95 LEU cc_start: 0.9239 (mt) cc_final: 0.8751 (pp) REVERT: J 137 GLN cc_start: 0.8607 (pt0) cc_final: 0.7265 (pt0) REVERT: K 86 MET cc_start: 0.7640 (ptp) cc_final: 0.7222 (ptp) REVERT: M 95 LEU cc_start: 0.9005 (mt) cc_final: 0.8426 (mt) REVERT: M 132 ASP cc_start: 0.8648 (t0) cc_final: 0.8388 (t0) REVERT: N 1 MET cc_start: 0.7467 (tmm) cc_final: 0.7238 (tmm) REVERT: S 86 MET cc_start: 0.8399 (ppp) cc_final: 0.8156 (ppp) REVERT: T 86 MET cc_start: 0.8075 (mtm) cc_final: 0.7584 (mtt) REVERT: T 90 ASP cc_start: 0.9070 (m-30) cc_final: 0.8791 (m-30) REVERT: U 86 MET cc_start: 0.8375 (mtm) cc_final: 0.7804 (mtt) REVERT: U 114 ILE cc_start: 0.8066 (mm) cc_final: 0.7714 (mm) REVERT: U 143 LYS cc_start: 0.8823 (tttt) cc_final: 0.8590 (tptm) REVERT: V 86 MET cc_start: 0.7998 (mtm) cc_final: 0.7754 (mtt) REVERT: W 1 MET cc_start: 0.8215 (pmm) cc_final: 0.7731 (pmm) REVERT: W 150 LEU cc_start: 0.9418 (mt) cc_final: 0.9111 (tt) outliers start: 3 outliers final: 3 residues processed: 475 average time/residue: 0.3841 time to fit residues: 298.7008 Evaluate side-chains 317 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 314 time to evaluate : 3.525 ------------------------------------------------------------------------------- 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: 8.9990 chunk 105 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 chunk 338 optimal weight: 20.0000 chunk 211 optimal weight: 8.9990 chunk 138 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 55 optimal weight: 30.0000 chunk 14 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 294 optimal weight: 5.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 GLN E 32 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 23 ASN ** 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** ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 118 ASN W 130 HIS X 23 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.058670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.050920 restraints weight = 185598.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.052160 restraints weight = 122739.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.053004 restraints weight = 89024.660| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31867 Z= 0.198 Angle : 0.622 8.953 43071 Z= 0.344 Chirality : 0.038 0.155 4895 Planarity : 0.003 0.038 5626 Dihedral : 4.160 22.547 4193 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.18 % Favored : 96.67 % Rotamer: Outliers : 0.06 % Allowed : 2.18 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.13), residues: 3810 helix: 2.36 (0.08), residues: 3075 sheet: None (None), residues: 0 loop : -2.72 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 37 HIS 0.016 0.001 HIS D 54 PHE 0.039 0.002 PHE A 120 TYR 0.039 0.002 TYR Q 71 ARG 0.012 0.001 ARG X 53 Details of bonding type rmsd hydrogen bonds : bond 0.06339 ( 2606) hydrogen bonds : angle 3.93405 ( 7818) covalent geometry : bond 0.00434 (31867) covalent geometry : angle 0.62200 (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 465 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 463 time to evaluate : 3.518 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: symmetry clash REVERT: A 52 MET cc_start: 0.8778 (ttt) cc_final: 0.8520 (ttm) REVERT: A 66 ASP cc_start: 0.8825 (t70) cc_final: 0.8571 (t0) REVERT: B 18 GLU cc_start: 0.7852 (tt0) cc_final: 0.7483 (tm-30) REVERT: B 128 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7838 (mt-10) REVERT: C 70 ASN cc_start: 0.8556 (t0) cc_final: 0.8294 (t0) REVERT: C 119 VAL cc_start: 0.9221 (m) cc_final: 0.8997 (p) REVERT: D 1 MET cc_start: 0.6629 (pmm) cc_final: 0.6428 (pmm) REVERT: D 52 MET cc_start: 0.7826 (ttt) cc_final: 0.7605 (ttt) REVERT: F 99 ASP cc_start: 0.8662 (t0) cc_final: 0.8410 (t0) REVERT: F 108 MET cc_start: 0.8341 (ptp) cc_final: 0.7823 (ptp) REVERT: G 123 ILE cc_start: 0.8812 (mm) cc_final: 0.8563 (mm) REVERT: H 61 ARG cc_start: 0.8396 (tpt170) cc_final: 0.8047 (tpm170) REVERT: H 86 MET cc_start: 0.8122 (ptp) cc_final: 0.7424 (ptp) REVERT: H 108 MET cc_start: 0.7925 (mtm) cc_final: 0.7688 (mtp) REVERT: K 108 MET cc_start: 0.8793 (tmm) cc_final: 0.8251 (tmm) REVERT: M 95 LEU cc_start: 0.8873 (mt) cc_final: 0.8409 (mt) REVERT: M 132 ASP cc_start: 0.8651 (t0) cc_final: 0.8381 (t0) REVERT: O 52 MET cc_start: 0.6521 (ttm) cc_final: 0.6134 (ttm) REVERT: R 153 VAL cc_start: 0.6791 (m) cc_final: 0.6539 (t) REVERT: S 86 MET cc_start: 0.8541 (ppp) cc_final: 0.8229 (ppp) REVERT: T 86 MET cc_start: 0.8073 (mtm) cc_final: 0.7568 (mtt) REVERT: T 90 ASP cc_start: 0.9078 (m-30) cc_final: 0.8812 (m-30) REVERT: U 86 MET cc_start: 0.8353 (mtm) cc_final: 0.7803 (mtt) REVERT: U 143 LYS cc_start: 0.8864 (tttt) cc_final: 0.8612 (tptm) REVERT: V 86 MET cc_start: 0.8138 (mtm) cc_final: 0.7927 (mtt) REVERT: W 1 MET cc_start: 0.8169 (pmm) cc_final: 0.7715 (pmm) REVERT: W 150 LEU cc_start: 0.9446 (mt) cc_final: 0.9108 (tt) outliers start: 2 outliers final: 2 residues processed: 465 average time/residue: 0.3795 time to fit residues: 291.1879 Evaluate side-chains 303 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 301 time to evaluate : 3.483 ------------------------------------------------------------------------------- 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: 10.0000 chunk 17 optimal weight: 9.9990 chunk 280 optimal weight: 0.8980 chunk 114 optimal weight: 10.0000 chunk 334 optimal weight: 7.9990 chunk 227 optimal weight: 10.0000 chunk 203 optimal weight: 30.0000 chunk 240 optimal weight: 20.0000 chunk 339 optimal weight: 20.0000 chunk 2 optimal weight: 7.9990 overall best weight: 7.3790 ------------------------------------------------------------------------------- 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 G 137 GLN H 24 GLN H 118 ASN J 137 GLN ** K 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 28 HIS N 72 GLN P 23 ASN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 129 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 = 0.3228 r_free = 0.3228 target = 0.058556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.050782 restraints weight = 186915.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.052056 restraints weight = 122714.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.052966 restraints weight = 88559.957| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 31867 Z= 0.194 Angle : 0.624 9.291 43071 Z= 0.345 Chirality : 0.038 0.156 4895 Planarity : 0.003 0.035 5626 Dihedral : 4.183 22.813 4193 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.02 % Favored : 96.82 % Rotamer: Outliers : 0.12 % Allowed : 1.73 % Favored : 98.15 % 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: 2.18 (0.13), residues: 3810 helix: 2.35 (0.08), residues: 3071 sheet: None (None), residues: 0 loop : -2.74 (0.20), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 37 HIS 0.013 0.001 HIS D 54 PHE 0.034 0.002 PHE I 10 TYR 0.033 0.002 TYR Q 71 ARG 0.008 0.001 ARG S 53 Details of bonding type rmsd hydrogen bonds : bond 0.06417 ( 2606) hydrogen bonds : angle 3.96793 ( 7818) covalent geometry : bond 0.00427 (31867) covalent geometry : angle 0.62351 (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 454 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 450 time to evaluate : 3.530 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: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8770 (ttt) cc_final: 0.8516 (ttm) REVERT: A 60 ASP cc_start: 0.8334 (m-30) cc_final: 0.8125 (m-30) REVERT: A 66 ASP cc_start: 0.8831 (t70) cc_final: 0.8607 (t0) REVERT: B 128 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7862 (mt-10) REVERT: C 70 ASN cc_start: 0.8470 (t0) cc_final: 0.8219 (t0) REVERT: D 1 MET cc_start: 0.6772 (pmm) cc_final: 0.6559 (pmm) REVERT: D 52 MET cc_start: 0.7824 (ttt) cc_final: 0.7608 (ttt) REVERT: F 108 MET cc_start: 0.8294 (ptp) cc_final: 0.7968 (ptp) REVERT: E 52 MET cc_start: 0.7933 (mtt) cc_final: 0.7423 (mtp) REVERT: G 123 ILE cc_start: 0.8891 (mm) cc_final: 0.8646 (mm) REVERT: H 24 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8602 (mm-40) REVERT: H 86 MET cc_start: 0.8141 (ptp) cc_final: 0.7436 (ptp) REVERT: H 108 MET cc_start: 0.8080 (mtm) cc_final: 0.7875 (mtp) REVERT: L 123 ILE cc_start: 0.8913 (pt) cc_final: 0.8486 (tt) REVERT: M 95 LEU cc_start: 0.8935 (mt) cc_final: 0.8465 (mt) REVERT: M 132 ASP cc_start: 0.8660 (t0) cc_final: 0.8384 (t0) REVERT: O 52 MET cc_start: 0.6457 (ttm) cc_final: 0.6017 (ttm) REVERT: O 86 MET cc_start: 0.8435 (mtp) cc_final: 0.8063 (ttm) REVERT: O 149 TYR cc_start: 0.8722 (t80) cc_final: 0.8509 (t80) REVERT: T 86 MET cc_start: 0.8084 (mtm) cc_final: 0.7527 (mtm) REVERT: T 90 ASP cc_start: 0.9081 (m-30) cc_final: 0.8774 (m-30) REVERT: U 86 MET cc_start: 0.8404 (mtm) cc_final: 0.7852 (mtt) REVERT: U 143 LYS cc_start: 0.8890 (tttt) cc_final: 0.8641 (tptm) REVERT: W 1 MET cc_start: 0.8144 (pmm) cc_final: 0.7704 (pmm) REVERT: W 150 LEU cc_start: 0.9463 (mt) cc_final: 0.9197 (tt) outliers start: 4 outliers final: 2 residues processed: 454 average time/residue: 0.3770 time to fit residues: 282.1870 Evaluate side-chains 306 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 303 time to evaluate : 3.857 ------------------------------------------------------------------------------- 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: 6.9990 chunk 239 optimal weight: 20.0000 chunk 281 optimal weight: 6.9990 chunk 349 optimal weight: 20.0000 chunk 171 optimal weight: 0.0270 chunk 152 optimal weight: 8.9990 chunk 81 optimal weight: 20.0000 chunk 193 optimal weight: 20.0000 chunk 223 optimal weight: 20.0000 chunk 63 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 overall best weight: 5.2046 ------------------------------------------------------------------------------- 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 E 32 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 28 HIS P 23 ASN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 HIS ** S 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 23 ASN X 156 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.059311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.051558 restraints weight = 184236.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.052817 restraints weight = 121958.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.053718 restraints weight = 88544.088| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 31867 Z= 0.169 Angle : 0.611 9.597 43071 Z= 0.337 Chirality : 0.037 0.192 4895 Planarity : 0.003 0.059 5626 Dihedral : 4.146 22.949 4193 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.02 % Favored : 96.82 % Rotamer: Outliers : 0.06 % Allowed : 0.93 % 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: 2.26 (0.13), residues: 3810 helix: 2.40 (0.08), residues: 3074 sheet: None (None), residues: 0 loop : -2.71 (0.20), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 37 HIS 0.011 0.001 HIS D 54 PHE 0.039 0.002 PHE A 120 TYR 0.022 0.002 TYR Q 71 ARG 0.007 0.000 ARG V 100 Details of bonding type rmsd hydrogen bonds : bond 0.06206 ( 2606) hydrogen bonds : angle 3.89955 ( 7818) covalent geometry : bond 0.00370 (31867) covalent geometry : angle 0.61121 (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 473 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 471 time to evaluate : 3.854 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: 0.8822 (ttt) cc_final: 0.8562 (ttm) REVERT: A 60 ASP cc_start: 0.8330 (m-30) cc_final: 0.8114 (m-30) REVERT: A 66 ASP cc_start: 0.8864 (t70) cc_final: 0.8634 (t0) REVERT: B 128 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7906 (mt-10) REVERT: C 70 ASN cc_start: 0.8490 (t0) cc_final: 0.8162 (t0) REVERT: D 52 MET cc_start: 0.7980 (ttt) cc_final: 0.7740 (ttt) REVERT: G 123 ILE cc_start: 0.8839 (mm) cc_final: 0.8585 (mm) REVERT: H 2 GLN cc_start: 0.7907 (mm110) cc_final: 0.7066 (pm20) REVERT: H 86 MET cc_start: 0.8154 (ptp) cc_final: 0.7471 (ptp) REVERT: H 108 MET cc_start: 0.8117 (mtm) cc_final: 0.7896 (mtp) REVERT: K 108 MET cc_start: 0.8706 (tmm) cc_final: 0.8204 (tmm) REVERT: L 123 ILE cc_start: 0.8895 (pt) cc_final: 0.8534 (tt) REVERT: L 156 GLN cc_start: 0.5837 (tp-100) cc_final: 0.5393 (tp-100) REVERT: M 95 LEU cc_start: 0.8901 (mt) cc_final: 0.8432 (mt) REVERT: M 132 ASP cc_start: 0.8668 (t0) cc_final: 0.8368 (t0) REVERT: O 52 MET cc_start: 0.6264 (ttm) cc_final: 0.5889 (ttm) REVERT: O 86 MET cc_start: 0.8453 (mtp) cc_final: 0.8116 (ttm) REVERT: O 149 TYR cc_start: 0.8795 (t80) cc_final: 0.8509 (t80) REVERT: P 154 ILE cc_start: 0.9357 (mm) cc_final: 0.9105 (mm) REVERT: R 27 LEU cc_start: 0.8550 (mm) cc_final: 0.8308 (tp) REVERT: T 86 MET cc_start: 0.8064 (mtm) cc_final: 0.7695 (mtt) REVERT: T 90 ASP cc_start: 0.9095 (m-30) cc_final: 0.8797 (m-30) REVERT: T 126 ASP cc_start: 0.8722 (t70) cc_final: 0.8501 (t70) REVERT: U 86 MET cc_start: 0.8464 (mtm) cc_final: 0.7967 (mtt) REVERT: U 90 ASP cc_start: 0.8668 (m-30) cc_final: 0.8270 (m-30) REVERT: U 114 ILE cc_start: 0.8125 (mm) cc_final: 0.7870 (mm) REVERT: U 143 LYS cc_start: 0.8863 (tttt) cc_final: 0.8614 (tptm) REVERT: W 1 MET cc_start: 0.8129 (pmm) cc_final: 0.7687 (pmm) REVERT: W 150 LEU cc_start: 0.9449 (mt) cc_final: 0.9196 (tt) outliers start: 2 outliers final: 2 residues processed: 473 average time/residue: 0.4026 time to fit residues: 314.5270 Evaluate side-chains 310 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 308 time to evaluate : 3.708 ------------------------------------------------------------------------------- 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: 5.9990 chunk 259 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 354 optimal weight: 0.8980 chunk 69 optimal weight: 20.0000 chunk 348 optimal weight: 0.8980 chunk 303 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 372 optimal weight: 9.9990 chunk 367 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 HIS E 32 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 HIS L 28 HIS P 14 GLN P 23 ASN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 76 HIS V 129 HIS X 23 ASN ** X 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.060527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.052668 restraints weight = 183909.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.053955 restraints weight = 121093.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.054829 restraints weight = 87541.869| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31867 Z= 0.147 Angle : 0.595 10.254 43071 Z= 0.325 Chirality : 0.036 0.177 4895 Planarity : 0.003 0.041 5626 Dihedral : 4.064 22.551 4193 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.07 % Favored : 96.77 % Rotamer: Outliers : 0.06 % Allowed : 0.42 % 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: 2.40 (0.13), residues: 3810 helix: 2.49 (0.09), residues: 3075 sheet: None (None), residues: 0 loop : -2.65 (0.20), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 37 HIS 0.009 0.001 HIS R 28 PHE 0.025 0.001 PHE I 10 TYR 0.018 0.002 TYR K 25 ARG 0.012 0.000 ARG X 53 Details of bonding type rmsd hydrogen bonds : bond 0.05648 ( 2606) hydrogen bonds : angle 3.75714 ( 7818) covalent geometry : bond 0.00312 (31867) covalent geometry : angle 0.59451 (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 477 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 475 time to evaluate : 3.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash 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: 0.8814 (ttt) cc_final: 0.8527 (ttm) REVERT: A 60 ASP cc_start: 0.8296 (m-30) cc_final: 0.8061 (m-30) REVERT: A 66 ASP cc_start: 0.8812 (t70) cc_final: 0.8612 (t0) REVERT: B 128 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7902 (mt-10) REVERT: C 70 ASN cc_start: 0.8459 (t0) cc_final: 0.8169 (t0) REVERT: D 52 MET cc_start: 0.7808 (ttt) cc_final: 0.7599 (ttt) REVERT: F 108 MET cc_start: 0.8285 (ptp) cc_final: 0.7972 (ptp) REVERT: G 123 ILE cc_start: 0.8791 (mm) cc_final: 0.8528 (mm) REVERT: G 149 TYR cc_start: 0.8149 (t80) cc_final: 0.7855 (t80) REVERT: H 2 GLN cc_start: 0.7922 (mm110) cc_final: 0.7108 (pm20) REVERT: H 86 MET cc_start: 0.8023 (ptp) cc_final: 0.7596 (ptp) REVERT: H 95 LEU cc_start: 0.9036 (mt) cc_final: 0.8750 (pp) REVERT: K 108 MET cc_start: 0.8666 (tmm) cc_final: 0.8148 (tmm) REVERT: M 95 LEU cc_start: 0.8917 (mt) cc_final: 0.8467 (mt) REVERT: M 132 ASP cc_start: 0.8653 (t0) cc_final: 0.8390 (t0) REVERT: O 52 MET cc_start: 0.6272 (ttm) cc_final: 0.5844 (ttm) REVERT: O 86 MET cc_start: 0.8378 (mtp) cc_final: 0.8019 (ttm) REVERT: O 149 TYR cc_start: 0.8767 (t80) cc_final: 0.8484 (t80) REVERT: P 154 ILE cc_start: 0.9362 (mm) cc_final: 0.9109 (mm) REVERT: T 86 MET cc_start: 0.7984 (mtm) cc_final: 0.7530 (mtt) REVERT: T 90 ASP cc_start: 0.9069 (m-30) cc_final: 0.8807 (m-30) REVERT: T 94 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7575 (mt-10) REVERT: T 126 ASP cc_start: 0.8677 (t70) cc_final: 0.8466 (t70) REVERT: U 86 MET cc_start: 0.8493 (mtm) cc_final: 0.7981 (mtt) REVERT: U 90 ASP cc_start: 0.8607 (m-30) cc_final: 0.8247 (m-30) REVERT: W 1 MET cc_start: 0.8108 (pmm) cc_final: 0.7690 (pmm) REVERT: W 150 LEU cc_start: 0.9424 (mt) cc_final: 0.9109 (tt) outliers start: 2 outliers final: 2 residues processed: 477 average time/residue: 0.3968 time to fit residues: 310.8036 Evaluate side-chains 340 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 338 time to evaluate : 3.542 ------------------------------------------------------------------------------- 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: 10.0000 chunk 225 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 258 optimal weight: 20.0000 chunk 350 optimal weight: 20.0000 chunk 252 optimal weight: 6.9990 chunk 312 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 358 optimal weight: 5.9990 chunk 294 optimal weight: 8.9990 chunk 377 optimal weight: 3.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 HIS E 32 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 HIS H 112 HIS ** K 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 HIS P 23 ASN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 23 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.058830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.050851 restraints weight = 183464.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.052121 restraints weight = 121164.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.052995 restraints weight = 88191.713| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31867 Z= 0.182 Angle : 0.628 10.903 43071 Z= 0.347 Chirality : 0.038 0.190 4895 Planarity : 0.003 0.042 5626 Dihedral : 4.134 21.696 4193 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.25 % Favored : 96.59 % Rotamer: Outliers : 0.06 % Allowed : 0.60 % Favored : 99.34 % 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: 2.26 (0.13), residues: 3810 helix: 2.42 (0.08), residues: 3071 sheet: None (None), residues: 0 loop : -2.80 (0.20), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 37 HIS 0.008 0.001 HIS D 54 PHE 0.025 0.002 PHE V 120 TYR 0.022 0.002 TYR K 25 ARG 0.011 0.001 ARG X 53 Details of bonding type rmsd hydrogen bonds : bond 0.05998 ( 2606) hydrogen bonds : angle 3.89822 ( 7818) covalent geometry : bond 0.00401 (31867) covalent geometry : angle 0.62845 (43071) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8461.63 seconds wall clock time: 149 minutes 34.14 seconds (8974.14 seconds total)