Starting phenix.real_space_refine on Mon Aug 25 20:36:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jb0_36139/08_2025/8jb0_36139.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jb0_36139/08_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_36139/08_2025/8jb0_36139.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jb0_36139/08_2025/8jb0_36139.map" model { file = "/net/cci-nas-00/data/ceres_data/8jb0_36139/08_2025/8jb0_36139.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jb0_36139/08_2025/8jb0_36139.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 8.21, per 1000 atoms: 0.26 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: 2.83 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7422 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 0 sheets defined 81.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 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: 5.37 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8003 1.33 - 1.45: 5808 1.45 - 1.57: 17864 1.57 - 1.69: 0 1.69 - 1.81: 192 Bond restraints: 31867 Sorted by residual: bond pdb=" C GLN W 158 " pdb=" O GLN W 158 " ideal model delta sigma weight residual 1.235 1.244 -0.009 4.70e-03 4.53e+04 4.08e+00 bond pdb=" CA ALA I 110 " pdb=" C ALA I 110 " ideal model delta sigma weight residual 1.522 1.554 -0.032 1.72e-02 3.38e+03 3.54e+00 bond pdb=" CD GLU H 121 " pdb=" OE1 GLU H 121 " ideal model delta sigma weight residual 1.249 1.214 0.035 1.90e-02 2.77e+03 3.47e+00 bond pdb=" CG LEU Q 27 " pdb=" CD1 LEU Q 27 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.22e+00 bond pdb=" CG GLU E 121 " pdb=" CD GLU E 121 " ideal model delta sigma weight residual 1.516 1.475 0.041 2.50e-02 1.60e+03 2.73e+00 ... (remaining 31862 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 42171 1.80 - 3.60: 748 3.60 - 5.41: 117 5.41 - 7.21: 28 7.21 - 9.01: 7 Bond angle restraints: 43071 Sorted by residual: angle pdb=" C VAL F 107 " pdb=" N MET F 108 " pdb=" CA MET F 108 " ideal model delta sigma weight residual 122.26 113.86 8.40 1.73e+00 3.34e-01 2.36e+01 angle pdb=" C VAL N 153 " pdb=" N ILE N 154 " pdb=" CA ILE N 154 " ideal model delta sigma weight residual 121.97 130.37 -8.40 1.80e+00 3.09e-01 2.18e+01 angle pdb=" N GLU D 121 " pdb=" CA GLU D 121 " pdb=" CB GLU D 121 " ideal model delta sigma weight residual 110.28 117.10 -6.82 1.55e+00 4.16e-01 1.94e+01 angle pdb=" N GLU E 121 " pdb=" CA GLU E 121 " pdb=" CB GLU E 121 " ideal model delta sigma weight residual 110.28 117.05 -6.77 1.55e+00 4.16e-01 1.91e+01 angle pdb=" N GLU H 121 " pdb=" CA GLU H 121 " pdb=" CB GLU H 121 " ideal model delta sigma weight residual 110.28 116.70 -6.42 1.55e+00 4.16e-01 1.71e+01 ... (remaining 43066 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 17017 17.93 - 35.85: 1869 35.85 - 53.78: 315 53.78 - 71.70: 67 71.70 - 89.63: 74 Dihedral angle restraints: 19342 sinusoidal: 7967 harmonic: 11375 Sorted by residual: dihedral pdb=" CA TRP X 37 " pdb=" C TRP X 37 " pdb=" N THR X 38 " pdb=" CA THR X 38 " ideal model delta harmonic sigma weight residual -180.00 -159.52 -20.48 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA LYS L 111 " pdb=" C LYS L 111 " pdb=" N HIS L 112 " pdb=" CA HIS L 112 " ideal model delta harmonic sigma weight residual 180.00 159.68 20.32 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA ASP A 113 " pdb=" C ASP A 113 " pdb=" N ILE A 114 " pdb=" CA ILE A 114 " ideal model delta harmonic sigma weight residual -180.00 -161.04 -18.96 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 19339 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 3801 0.040 - 0.079: 855 0.079 - 0.119: 205 0.119 - 0.159: 30 0.159 - 0.199: 4 Chirality restraints: 4895 Sorted by residual: chirality pdb=" CA GLN N 88 " pdb=" N GLN N 88 " pdb=" C GLN N 88 " pdb=" CB GLN N 88 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.85e-01 chirality pdb=" CA PHE H 120 " pdb=" N PHE H 120 " pdb=" C PHE H 120 " pdb=" CB PHE H 120 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.17e-01 chirality pdb=" CA GLU H 121 " pdb=" N GLU H 121 " pdb=" C GLU H 121 " pdb=" CB GLU H 121 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.69e-01 ... (remaining 4892 not shown) Planarity restraints: 5626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA O 21 " -0.013 2.00e-02 2.50e+03 2.67e-02 7.13e+00 pdb=" C ALA O 21 " 0.046 2.00e-02 2.50e+03 pdb=" O ALA O 21 " -0.017 2.00e-02 2.50e+03 pdb=" N ILE O 22 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 66 " 0.010 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" CG ASP B 66 " -0.037 2.00e-02 2.50e+03 pdb=" OD1 ASP B 66 " 0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP B 66 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL N 153 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.43e+00 pdb=" C VAL N 153 " 0.036 2.00e-02 2.50e+03 pdb=" O VAL N 153 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE N 154 " -0.012 2.00e-02 2.50e+03 ... (remaining 5623 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2898 2.74 - 3.28: 34328 3.28 - 3.82: 54511 3.82 - 4.36: 57892 4.36 - 4.90: 99742 Nonbonded interactions: 249371 Sorted by model distance: nonbonded pdb=" OE1 GLN F 137 " pdb=" OH TYR F 149 " model vdw 2.196 3.040 nonbonded pdb=" O ARG V 109 " pdb=" NE ARG V 109 " model vdw 2.199 3.120 nonbonded pdb=" O HIS F 28 " pdb=" NE2 GLN F 32 " model vdw 2.203 3.120 nonbonded pdb=" OE1 GLN C 156 " pdb=" OG1 THR F 152 " model vdw 2.211 3.040 nonbonded pdb=" OD2 ASP B 113 " pdb=" OG SER B 116 " model vdw 2.217 3.040 ... (remaining 249366 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 156 or (resid 157 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'B' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 157)) selection = (chain 'C' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 156 or (resid 157 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'E' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'F' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'G' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'H' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'I' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'J' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 156 or (resid 157 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'K' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'L' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 156 or (resid 157 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'M' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'N' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'O' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 156 or (resid 157 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'P' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'Q' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 156 or (resid 157 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'R' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'S' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'T' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 156 or (resid 157 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'U' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) selection = (chain 'V' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 156 or (resid 157 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'W' and (resid 1 through 148 or (resid 149 and (name N or name CA or name \ C or name O or name CB )) or resid 150 through 157)) selection = (chain 'X' and (resid 1 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 148 or (resid 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 157)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 28.440 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.070 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.310 ------------------------------------------------------------------------------- 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 : 13.61 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.008 0.001 ARG H 53 TYR 0.025 0.002 TYR R 71 PHE 0.031 0.002 PHE L 120 TRP 0.021 0.002 TRP Q 37 HIS 0.010 0.001 HIS R 28 Details of bonding type rmsd covalent geometry : bond 0.00343 (31867) covalent geometry : angle 0.62433 (43071) hydrogen bonds : bond 0.09531 ( 2606) hydrogen bonds : angle 4.31743 ( 7818) *********************** 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 : 1.299 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: 0.8240 (t0) REVERT: A 86 MET cc_start: 0.8989 (mmp) cc_final: 0.8730 (mmp) REVERT: C 70 ASN cc_start: 0.8591 (t0) cc_final: 0.8273 (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: 0.8632 (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: 0.7907 (tt0) REVERT: K 57 VAL cc_start: 0.9189 (p) cc_final: 0.8958 (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: 0.6925 (ttm) REVERT: P 90 ASP cc_start: 0.8687 (m-30) cc_final: 0.8440 (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: 0.8639 (p) REVERT: S 76 HIS cc_start: 0.8610 (t-90) cc_final: 0.7579 (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: 0.9246 (pt) REVERT: T 32 GLN cc_start: 0.9127 (mp10) cc_final: 0.8684 (mp10) REVERT: T 60 ASP cc_start: 0.8120 (m-30) cc_final: 0.7548 (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: 0.7359 (mm) REVERT: V 86 MET cc_start: 0.7927 (mtm) cc_final: 0.7078 (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: 0.1991 time to fit residues: 168.4907 Evaluate side-chains 344 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 342 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 30.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 5.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- 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 H 137 GLN ** L 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 HIS M 28 HIS M 129 HIS ** N 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 23 ASN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 137 GLN W 118 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.061385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.053276 restraints weight = 181857.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.054569 restraints weight = 120135.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.055526 restraints weight = 87157.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.056229 restraints weight = 67451.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.056710 restraints weight = 55002.960| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31867 Z= 0.160 Angle : 0.545 7.797 43071 Z= 0.304 Chirality : 0.036 0.153 4895 Planarity : 0.003 0.039 5626 Dihedral : 4.025 22.392 4193 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.02 % Favored : 96.82 % Rotamer: Outliers : 0.27 % Allowed : 5.17 % Favored : 94.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.51 (0.13), residues: 3810 helix: 2.61 (0.08), residues: 3060 sheet: None (None), residues: 0 loop : -2.69 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 73 TYR 0.020 0.001 TYR R 71 PHE 0.020 0.001 PHE T 87 TRP 0.016 0.002 TRP Q 37 HIS 0.007 0.001 HIS R 28 Details of bonding type rmsd covalent geometry : bond 0.00343 (31867) covalent geometry : angle 0.54527 (43071) hydrogen bonds : bond 0.05832 ( 2606) hydrogen bonds : angle 3.74466 ( 7818) *********************** 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 523 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 514 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash 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: 0.8633 (ttt) cc_final: 0.8161 (ttt) REVERT: A 66 ASP cc_start: 0.8550 (t70) cc_final: 0.8283 (t0) REVERT: B 90 ASP cc_start: 0.8783 (m-30) cc_final: 0.8339 (m-30) REVERT: C 70 ASN cc_start: 0.8491 (t0) cc_final: 0.8113 (t0) REVERT: C 108 MET cc_start: 0.8261 (tmm) cc_final: 0.8037 (tmm) REVERT: C 119 VAL cc_start: 0.9083 (m) cc_final: 0.8824 (p) REVERT: D 121 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7511 (pt0) REVERT: F 99 ASP cc_start: 0.8553 (t0) cc_final: 0.8338 (t0) REVERT: E 121 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8631 (mp0) REVERT: H 86 MET cc_start: 0.8070 (ptp) cc_final: 0.7840 (ptp) REVERT: H 95 LEU cc_start: 0.9108 (mt) cc_final: 0.8732 (pp) REVERT: I 123 ILE cc_start: 0.8492 (mm) cc_final: 0.8072 (mm) REVERT: J 14 GLN cc_start: 0.8709 (tp40) cc_final: 0.7718 (tp40) REVERT: J 137 GLN cc_start: 0.8610 (pt0) cc_final: 0.8055 (tt0) REVERT: K 115 THR cc_start: 0.7027 (m) cc_final: 0.6778 (m) REVERT: M 88 GLN cc_start: 0.8738 (pp30) cc_final: 0.8194 (pp30) REVERT: N 52 MET cc_start: 0.6942 (mtp) cc_final: 0.6623 (mtp) REVERT: P 52 MET cc_start: 0.6975 (ttm) cc_final: 0.6730 (ttm) REVERT: R 151 SER cc_start: 0.8702 (t) cc_final: 0.8483 (p) REVERT: S 113 ASP cc_start: 0.6479 (t0) cc_final: 0.6242 (t0) REVERT: T 22 ILE cc_start: 0.9453 (pt) cc_final: 0.9235 (pt) REVERT: T 32 GLN cc_start: 0.9073 (mp10) cc_final: 0.8683 (mp10) REVERT: T 86 MET cc_start: 0.7883 (mtm) cc_final: 0.7102 (mtm) REVERT: T 90 ASP cc_start: 0.8873 (m-30) cc_final: 0.8660 (m-30) REVERT: U 37 TRP cc_start: 0.7296 (m-10) cc_final: 0.7086 (m-90) REVERT: U 86 MET cc_start: 0.8451 (mtm) cc_final: 0.8062 (mtm) REVERT: U 114 ILE cc_start: 0.7642 (mm) cc_final: 0.7324 (mm) REVERT: U 143 LYS cc_start: 0.8745 (tttt) cc_final: 0.8510 (tptm) REVERT: V 86 MET cc_start: 0.8013 (mtm) cc_final: 0.7426 (mtt) REVERT: V 118 ASN cc_start: 0.8953 (m110) cc_final: 0.8613 (m-40) REVERT: W 108 MET cc_start: 0.8360 (tmm) cc_final: 0.7966 (tmm) outliers start: 9 outliers final: 3 residues processed: 520 average time/residue: 0.1939 time to fit residues: 163.1459 Evaluate side-chains 341 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 336 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 119 optimal weight: 20.0000 chunk 308 optimal weight: 7.9990 chunk 302 optimal weight: 7.9990 chunk 131 optimal weight: 20.0000 chunk 223 optimal weight: 30.0000 chunk 2 optimal weight: 9.9990 chunk 263 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 306 optimal weight: 1.9990 chunk 133 optimal weight: 20.0000 chunk 265 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 32 GLN E 32 GLN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 GLN L 23 ASN M 28 HIS M 32 GLN ** N 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 HIS P 23 ASN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 137 GLN ** X 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 130 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 = 0.3282 r_free = 0.3282 target = 0.060259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.052464 restraints weight = 185944.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.053729 restraints weight = 121551.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.054653 restraints weight = 87633.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.055304 restraints weight = 67748.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.055834 restraints weight = 55118.157| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 31867 Z= 0.180 Angle : 0.576 9.575 43071 Z= 0.322 Chirality : 0.037 0.167 4895 Planarity : 0.003 0.051 5626 Dihedral : 4.078 23.147 4193 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.91 % Favored : 96.93 % Rotamer: Outliers : 0.18 % Allowed : 4.61 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.42 (0.13), residues: 3810 helix: 2.53 (0.08), residues: 3065 sheet: None (None), residues: 0 loop : -2.68 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 102 TYR 0.036 0.002 TYR Q 71 PHE 0.033 0.001 PHE W 120 TRP 0.030 0.002 TRP A 37 HIS 0.013 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00391 (31867) covalent geometry : angle 0.57616 (43071) hydrogen bonds : bond 0.06008 ( 2606) hydrogen bonds : angle 3.76921 ( 7818) *********************** 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 511 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 505 time to evaluate : 1.243 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: 0.8707 (ttt) cc_final: 0.8431 (ttm) REVERT: A 66 ASP cc_start: 0.8558 (t70) cc_final: 0.8317 (t0) REVERT: A 86 MET cc_start: 0.9045 (mmp) cc_final: 0.8839 (mmp) REVERT: A 111 LYS cc_start: 0.8698 (tppt) cc_final: 0.8423 (tppp) REVERT: B 90 ASP cc_start: 0.8800 (m-30) cc_final: 0.8518 (m-30) REVERT: C 70 ASN cc_start: 0.8559 (t0) cc_final: 0.8244 (t0) REVERT: C 119 VAL cc_start: 0.9095 (m) cc_final: 0.8836 (p) REVERT: F 99 ASP cc_start: 0.8504 (t0) cc_final: 0.8260 (t0) REVERT: H 86 MET cc_start: 0.8087 (ptp) cc_final: 0.7726 (ptp) REVERT: H 95 LEU cc_start: 0.9173 (mt) cc_final: 0.8707 (pp) REVERT: J 14 GLN cc_start: 0.8641 (tp40) cc_final: 0.8090 (tp40) REVERT: J 137 GLN cc_start: 0.8463 (pt0) cc_final: 0.7829 (tt0) REVERT: K 115 THR cc_start: 0.7253 (m) cc_final: 0.6981 (m) REVERT: N 22 ILE cc_start: 0.9104 (mt) cc_final: 0.8827 (mm) REVERT: N 86 MET cc_start: 0.7600 (tmm) cc_final: 0.7397 (tmm) REVERT: P 90 ASP cc_start: 0.8965 (m-30) cc_final: 0.8753 (m-30) REVERT: P 149 TYR cc_start: 0.8407 (t80) cc_final: 0.8048 (t80) REVERT: T 22 ILE cc_start: 0.9472 (pt) cc_final: 0.9262 (pt) REVERT: T 86 MET cc_start: 0.7980 (mtm) cc_final: 0.7348 (mtm) REVERT: T 90 ASP cc_start: 0.8974 (m-30) cc_final: 0.8756 (m-30) REVERT: U 86 MET cc_start: 0.8494 (mtm) cc_final: 0.8001 (mtt) REVERT: U 114 ILE cc_start: 0.7782 (mm) cc_final: 0.7423 (mm) REVERT: U 143 LYS cc_start: 0.8806 (tttt) cc_final: 0.8581 (tptm) REVERT: V 86 MET cc_start: 0.7920 (mtm) cc_final: 0.7535 (mtt) outliers start: 6 outliers final: 4 residues processed: 508 average time/residue: 0.1886 time to fit residues: 156.9486 Evaluate side-chains 328 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 324 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 227 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 65 optimal weight: 20.0000 chunk 235 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 335 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 133 optimal weight: 20.0000 chunk 240 optimal weight: 20.0000 chunk 156 optimal weight: 20.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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 G 156 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 HIS 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** ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 118 ASN V 129 HIS V 137 GLN ** 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 = 0.3249 r_free = 0.3249 target = 0.059040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.051423 restraints weight = 184635.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.052669 restraints weight = 120828.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.053567 restraints weight = 87129.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.054244 restraints weight = 67263.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.054758 restraints weight = 54596.383| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 31867 Z= 0.198 Angle : 0.597 8.162 43071 Z= 0.333 Chirality : 0.037 0.169 4895 Planarity : 0.003 0.034 5626 Dihedral : 4.157 23.632 4193 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.07 % Favored : 96.77 % Rotamer: Outliers : 0.15 % Allowed : 4.55 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.29 (0.13), residues: 3810 helix: 2.44 (0.08), residues: 3066 sheet: None (None), residues: 0 loop : -2.71 (0.20), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 78 TYR 0.029 0.002 TYR Q 71 PHE 0.039 0.002 PHE A 120 TRP 0.023 0.002 TRP G 37 HIS 0.009 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00437 (31867) covalent geometry : angle 0.59749 (43071) hydrogen bonds : bond 0.06258 ( 2606) hydrogen bonds : angle 3.85541 ( 7818) *********************** 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 492 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 487 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8736 (ttt) cc_final: 0.8476 (ttm) REVERT: A 66 ASP cc_start: 0.8622 (t70) cc_final: 0.8335 (t0) REVERT: C 70 ASN cc_start: 0.8525 (t0) cc_final: 0.8208 (t0) REVERT: C 119 VAL cc_start: 0.9111 (m) cc_final: 0.8872 (p) REVERT: D 95 LEU cc_start: 0.9015 (mt) cc_final: 0.8763 (pp) REVERT: F 56 GLU cc_start: 0.8843 (tp30) cc_final: 0.8243 (mm-30) REVERT: F 99 ASP cc_start: 0.8554 (t0) cc_final: 0.8288 (t0) REVERT: F 108 MET cc_start: 0.8252 (ptp) cc_final: 0.7765 (ptp) REVERT: H 61 ARG cc_start: 0.8455 (tpt170) cc_final: 0.8083 (tpm170) REVERT: H 86 MET cc_start: 0.8019 (ptp) cc_final: 0.7523 (ptp) REVERT: H 95 LEU cc_start: 0.9232 (mt) cc_final: 0.8754 (pp) REVERT: J 14 GLN cc_start: 0.8565 (tp40) cc_final: 0.8083 (tp40) REVERT: K 86 MET cc_start: 0.7575 (ptp) cc_final: 0.7162 (ptp) REVERT: K 115 THR cc_start: 0.7369 (m) cc_final: 0.7129 (m) REVERT: M 95 LEU cc_start: 0.9030 (mt) cc_final: 0.8461 (mt) REVERT: N 1 MET cc_start: 0.7655 (tmm) cc_final: 0.7330 (tmm) REVERT: N 22 ILE cc_start: 0.9076 (mt) cc_final: 0.8745 (mm) REVERT: P 52 MET cc_start: 0.7039 (ttm) cc_final: 0.6776 (ttm) REVERT: P 128 GLU cc_start: 0.9010 (tp30) cc_final: 0.8804 (mm-30) REVERT: P 149 TYR cc_start: 0.8473 (t80) cc_final: 0.8142 (t80) REVERT: T 86 MET cc_start: 0.8031 (mtm) cc_final: 0.7474 (mtt) REVERT: T 90 ASP cc_start: 0.9009 (m-30) cc_final: 0.8744 (m-30) REVERT: U 86 MET cc_start: 0.8477 (mtm) cc_final: 0.7988 (mtt) REVERT: U 114 ILE cc_start: 0.8056 (mm) cc_final: 0.7705 (mm) REVERT: U 143 LYS cc_start: 0.8838 (tttt) cc_final: 0.8580 (tptm) REVERT: V 86 MET cc_start: 0.7994 (mtm) cc_final: 0.7437 (mtt) REVERT: X 23 ASN cc_start: 0.8671 (t0) cc_final: 0.8431 (t0) REVERT: X 94 GLU cc_start: 0.8742 (mp0) cc_final: 0.8510 (mp0) outliers start: 5 outliers final: 3 residues processed: 491 average time/residue: 0.1792 time to fit residues: 142.9891 Evaluate side-chains 323 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 320 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 348 optimal weight: 0.9980 chunk 5 optimal weight: 20.0000 chunk 217 optimal weight: 8.9990 chunk 134 optimal weight: 20.0000 chunk 264 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 358 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 329 optimal weight: 10.0000 chunk 362 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 GLN D 28 HIS ** F 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN G 137 GLN ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 137 GLN ** K 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 112 HIS ** N 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 HIS O 156 GLN P 23 ASN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 23 ASN U 118 ASN ** X 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 130 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.060134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.052493 restraints weight = 181966.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.053765 restraints weight = 118793.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.054650 restraints weight = 85292.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.055364 restraints weight = 66065.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.055884 restraints weight = 53308.032| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31867 Z= 0.149 Angle : 0.556 8.375 43071 Z= 0.305 Chirality : 0.036 0.141 4895 Planarity : 0.003 0.035 5626 Dihedral : 4.058 22.783 4193 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.91 % Favored : 96.93 % Rotamer: Outliers : 0.18 % Allowed : 2.78 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.51 (0.13), residues: 3810 helix: 2.60 (0.08), residues: 3070 sheet: None (None), residues: 0 loop : -2.69 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG X 53 TYR 0.024 0.001 TYR Q 71 PHE 0.034 0.001 PHE L 120 TRP 0.034 0.002 TRP A 37 HIS 0.011 0.001 HIS M 112 Details of bonding type rmsd covalent geometry : bond 0.00318 (31867) covalent geometry : angle 0.55558 (43071) hydrogen bonds : bond 0.05927 ( 2606) hydrogen bonds : angle 3.65102 ( 7818) *********************** 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 510 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 504 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8773 (ttt) cc_final: 0.8504 (ttm) REVERT: A 66 ASP cc_start: 0.8605 (t70) cc_final: 0.8344 (t0) REVERT: B 128 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7808 (mt-10) REVERT: C 70 ASN cc_start: 0.8498 (t0) cc_final: 0.8177 (t0) REVERT: C 119 VAL cc_start: 0.9108 (m) cc_final: 0.8847 (p) REVERT: D 95 LEU cc_start: 0.9047 (mt) cc_final: 0.8832 (pp) REVERT: F 56 GLU cc_start: 0.8848 (tp30) cc_final: 0.8237 (mm-30) REVERT: F 99 ASP cc_start: 0.8561 (t0) cc_final: 0.8299 (t0) REVERT: G 123 ILE cc_start: 0.8573 (mm) cc_final: 0.8328 (mm) REVERT: H 61 ARG cc_start: 0.8351 (tpt170) cc_final: 0.8080 (tpm170) REVERT: H 86 MET cc_start: 0.8029 (ptp) cc_final: 0.7494 (ptp) REVERT: H 95 LEU cc_start: 0.9203 (mt) cc_final: 0.8708 (pp) REVERT: K 108 MET cc_start: 0.8679 (tmm) cc_final: 0.8460 (tmm) REVERT: K 115 THR cc_start: 0.7206 (m) cc_final: 0.7002 (m) REVERT: M 95 LEU cc_start: 0.8957 (mt) cc_final: 0.8396 (mt) REVERT: P 52 MET cc_start: 0.7037 (ttm) cc_final: 0.6800 (ttm) REVERT: P 149 TYR cc_start: 0.8484 (t80) cc_final: 0.8076 (t80) REVERT: P 154 ILE cc_start: 0.9244 (mm) cc_final: 0.8991 (mt) REVERT: S 52 MET cc_start: 0.8171 (ttt) cc_final: 0.7946 (ttp) REVERT: T 86 MET cc_start: 0.8063 (mtm) cc_final: 0.7596 (mtt) REVERT: T 90 ASP cc_start: 0.9023 (m-30) cc_final: 0.8809 (m-30) REVERT: U 86 MET cc_start: 0.8392 (mtm) cc_final: 0.7825 (mtt) REVERT: U 114 ILE cc_start: 0.8036 (mm) cc_final: 0.7648 (mm) REVERT: U 143 LYS cc_start: 0.8802 (tttt) cc_final: 0.8593 (tptm) REVERT: V 86 MET cc_start: 0.7970 (mtm) cc_final: 0.7240 (mtt) REVERT: W 150 LEU cc_start: 0.9377 (mt) cc_final: 0.9154 (tt) REVERT: X 23 ASN cc_start: 0.8765 (t0) cc_final: 0.8528 (t0) outliers start: 6 outliers final: 3 residues processed: 508 average time/residue: 0.1882 time to fit residues: 156.5456 Evaluate side-chains 332 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 329 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 34 optimal weight: 20.0000 chunk 325 optimal weight: 40.0000 chunk 329 optimal weight: 7.9990 chunk 188 optimal weight: 5.9990 chunk 195 optimal weight: 4.9990 chunk 270 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 322 optimal weight: 8.9990 chunk 173 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- 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** C 129 HIS D 28 HIS E 32 GLN H 24 GLN J 137 GLN ** K 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 28 HIS ** N 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 23 ASN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 28 HIS ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 HIS U 118 ASN ** 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 = 0.3269 r_free = 0.3269 target = 0.059931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.052162 restraints weight = 183244.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.053445 restraints weight = 120053.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.054371 restraints weight = 86598.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.055017 restraints weight = 66654.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.055537 restraints weight = 54329.233| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 31867 Z= 0.162 Angle : 0.573 8.289 43071 Z= 0.318 Chirality : 0.036 0.142 4895 Planarity : 0.003 0.033 5626 Dihedral : 4.038 22.535 4193 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.04 % Favored : 96.80 % Rotamer: Outliers : 0.15 % Allowed : 2.48 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.43 (0.13), residues: 3810 helix: 2.53 (0.08), residues: 3070 sheet: None (None), residues: 0 loop : -2.66 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG U 109 TYR 0.021 0.002 TYR K 25 PHE 0.039 0.001 PHE A 120 TRP 0.015 0.001 TRP A 37 HIS 0.010 0.001 HIS O 28 Details of bonding type rmsd covalent geometry : bond 0.00352 (31867) covalent geometry : angle 0.57324 (43071) hydrogen bonds : bond 0.05895 ( 2606) hydrogen bonds : angle 3.71740 ( 7818) *********************** 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 484 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 479 time to evaluate : 1.102 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. 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: 0.8753 (ttt) cc_final: 0.8483 (ttm) REVERT: A 66 ASP cc_start: 0.8704 (t70) cc_final: 0.8445 (t0) REVERT: B 18 GLU cc_start: 0.8027 (tt0) cc_final: 0.7150 (tm-30) REVERT: B 128 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7837 (mt-10) REVERT: C 70 ASN cc_start: 0.8501 (t0) cc_final: 0.8197 (t0) REVERT: C 119 VAL cc_start: 0.9144 (m) cc_final: 0.8902 (p) REVERT: F 99 ASP cc_start: 0.8571 (t0) cc_final: 0.8303 (t0) REVERT: G 123 ILE cc_start: 0.8661 (mm) cc_final: 0.8415 (mm) REVERT: H 24 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8565 (mm-40) REVERT: H 86 MET cc_start: 0.8080 (ptp) cc_final: 0.7515 (ptp) REVERT: H 95 LEU cc_start: 0.9223 (mt) cc_final: 0.8734 (pp) REVERT: I 52 MET cc_start: 0.7505 (ttm) cc_final: 0.7281 (ttm) REVERT: J 114 ILE cc_start: 0.6570 (mp) cc_final: 0.6275 (mp) REVERT: K 25 TYR cc_start: 0.8400 (m-80) cc_final: 0.8186 (m-80) REVERT: K 86 MET cc_start: 0.7573 (ptp) cc_final: 0.7186 (ptp) REVERT: K 115 THR cc_start: 0.7264 (m) cc_final: 0.7022 (m) REVERT: M 95 LEU cc_start: 0.8926 (mt) cc_final: 0.8469 (mt) REVERT: M 132 ASP cc_start: 0.8568 (t0) cc_final: 0.8300 (t0) REVERT: N 1 MET cc_start: 0.7387 (tmm) cc_final: 0.7017 (tmm) REVERT: P 154 ILE cc_start: 0.9288 (mm) cc_final: 0.9033 (mt) REVERT: T 86 MET cc_start: 0.8101 (mtm) cc_final: 0.7587 (mtt) REVERT: T 90 ASP cc_start: 0.9032 (m-30) cc_final: 0.8763 (m-30) REVERT: U 86 MET cc_start: 0.8393 (mtm) cc_final: 0.7781 (mtt) REVERT: U 114 ILE cc_start: 0.8102 (mm) cc_final: 0.7764 (mm) REVERT: U 143 LYS cc_start: 0.8799 (tttt) cc_final: 0.8587 (tptm) REVERT: W 1 MET cc_start: 0.8193 (pmm) cc_final: 0.7730 (pmm) REVERT: W 150 LEU cc_start: 0.9406 (mt) cc_final: 0.9151 (tt) REVERT: X 23 ASN cc_start: 0.8770 (t0) cc_final: 0.8523 (t0) outliers start: 5 outliers final: 4 residues processed: 483 average time/residue: 0.1788 time to fit residues: 142.6697 Evaluate side-chains 333 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 328 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 69 optimal weight: 20.0000 chunk 340 optimal weight: 5.9990 chunk 167 optimal weight: 10.0000 chunk 190 optimal weight: 0.0470 chunk 127 optimal weight: 6.9990 chunk 39 optimal weight: 30.0000 chunk 35 optimal weight: 20.0000 chunk 136 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 329 optimal weight: 6.9990 chunk 80 optimal weight: 40.0000 overall best weight: 4.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN D 28 HIS ** F 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN H 24 GLN ** N 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 72 GLN P 23 ASN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 130 HIS ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 HIS U 118 ASN X 23 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.060143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.052382 restraints weight = 185487.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.053614 restraints weight = 121119.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.054566 restraints weight = 87826.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.055245 restraints weight = 67632.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.055730 restraints weight = 54772.532| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31867 Z= 0.153 Angle : 0.570 9.880 43071 Z= 0.314 Chirality : 0.036 0.159 4895 Planarity : 0.003 0.031 5626 Dihedral : 4.010 21.392 4193 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.73 % Favored : 97.11 % Rotamer: Outliers : 0.09 % Allowed : 1.79 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.49 (0.13), residues: 3810 helix: 2.56 (0.08), residues: 3072 sheet: None (None), residues: 0 loop : -2.59 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG X 53 TYR 0.030 0.001 TYR Q 71 PHE 0.032 0.001 PHE W 120 TRP 0.013 0.001 TRP G 37 HIS 0.010 0.001 HIS R 28 Details of bonding type rmsd covalent geometry : bond 0.00329 (31867) covalent geometry : angle 0.57031 (43071) hydrogen bonds : bond 0.05766 ( 2606) hydrogen bonds : angle 3.70344 ( 7818) *********************** 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 483 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 480 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP L 160 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP Q 160 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8761 (ttt) cc_final: 0.8491 (ttm) REVERT: A 66 ASP cc_start: 0.8698 (t70) cc_final: 0.8452 (t0) REVERT: B 18 GLU cc_start: 0.7818 (tt0) cc_final: 0.7310 (tm-30) REVERT: B 128 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7889 (mt-10) REVERT: C 70 ASN cc_start: 0.8470 (t0) cc_final: 0.8178 (t0) REVERT: C 119 VAL cc_start: 0.9154 (m) cc_final: 0.8910 (p) REVERT: F 99 ASP cc_start: 0.8605 (t0) cc_final: 0.8335 (t0) REVERT: F 108 MET cc_start: 0.8356 (ptp) cc_final: 0.7867 (ptp) REVERT: G 123 ILE cc_start: 0.8692 (mm) cc_final: 0.8423 (mm) REVERT: H 86 MET cc_start: 0.8094 (ptp) cc_final: 0.7510 (ptp) REVERT: H 95 LEU cc_start: 0.9228 (mt) cc_final: 0.8748 (pp) REVERT: H 108 MET cc_start: 0.7872 (mtm) cc_final: 0.7628 (mtp) REVERT: I 52 MET cc_start: 0.7620 (ttm) cc_final: 0.7374 (ttm) REVERT: K 115 THR cc_start: 0.7093 (m) cc_final: 0.6865 (m) REVERT: M 95 LEU cc_start: 0.8909 (mt) cc_final: 0.8441 (mt) REVERT: M 132 ASP cc_start: 0.8573 (t0) cc_final: 0.8296 (t0) REVERT: N 1 MET cc_start: 0.7306 (tmm) cc_final: 0.7082 (tmm) REVERT: O 52 MET cc_start: 0.6392 (ttm) cc_final: 0.6029 (ttm) REVERT: P 154 ILE cc_start: 0.9278 (mm) cc_final: 0.8974 (mt) REVERT: R 153 VAL cc_start: 0.6411 (m) cc_final: 0.6129 (t) REVERT: T 86 MET cc_start: 0.8090 (mtm) cc_final: 0.7569 (mtt) REVERT: T 90 ASP cc_start: 0.9015 (m-30) cc_final: 0.8755 (m-30) REVERT: T 126 ASP cc_start: 0.8596 (t70) cc_final: 0.8393 (t70) REVERT: U 86 MET cc_start: 0.8404 (mtm) cc_final: 0.7937 (mtt) REVERT: U 90 ASP cc_start: 0.8570 (m-30) cc_final: 0.8211 (m-30) REVERT: U 114 ILE cc_start: 0.8141 (mm) cc_final: 0.7787 (mm) REVERT: U 139 ASP cc_start: 0.7974 (m-30) cc_final: 0.7711 (m-30) REVERT: W 1 MET cc_start: 0.8157 (pmm) cc_final: 0.7716 (pmm) REVERT: W 150 LEU cc_start: 0.9418 (mt) cc_final: 0.9147 (tt) outliers start: 3 outliers final: 2 residues processed: 483 average time/residue: 0.1825 time to fit residues: 145.2152 Evaluate side-chains 327 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 325 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 339 optimal weight: 8.9990 chunk 378 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 327 optimal weight: 20.0000 chunk 175 optimal weight: 20.0000 chunk 133 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 chunk 317 optimal weight: 5.9990 chunk 144 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 28 HIS ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 GLN E 32 GLN M 118 ASN ** N 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 156 GLN P 14 GLN P 23 ASN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 HIS U 118 ASN W 130 HIS X 23 ASN X 156 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.058907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.051114 restraints weight = 184145.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.052325 restraints weight = 121735.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.053249 restraints weight = 89374.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.053977 restraints weight = 69122.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.054490 restraints weight = 55562.470| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 31867 Z= 0.193 Angle : 0.628 10.202 43071 Z= 0.346 Chirality : 0.038 0.188 4895 Planarity : 0.003 0.045 5626 Dihedral : 4.115 21.983 4193 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.23 % Favored : 96.61 % Rotamer: Outliers : 0.06 % Allowed : 1.38 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.31 (0.13), residues: 3810 helix: 2.43 (0.08), residues: 3071 sheet: None (None), residues: 0 loop : -2.62 (0.20), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG U 109 TYR 0.021 0.002 TYR Q 71 PHE 0.041 0.002 PHE I 10 TRP 0.013 0.001 TRP G 37 HIS 0.016 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00426 (31867) covalent geometry : angle 0.62800 (43071) hydrogen bonds : bond 0.06125 ( 2606) hydrogen bonds : angle 3.89997 ( 7818) *********************** 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 462 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 460 time to evaluate : 0.962 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: 0.8750 (ttt) cc_final: 0.8490 (ttm) REVERT: A 66 ASP cc_start: 0.8782 (t70) cc_final: 0.8534 (t0) REVERT: B 128 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7888 (mt-10) REVERT: C 70 ASN cc_start: 0.8502 (t0) cc_final: 0.8223 (t0) REVERT: D 52 MET cc_start: 0.7833 (ttt) cc_final: 0.7589 (ttt) REVERT: F 108 MET cc_start: 0.8333 (ptp) cc_final: 0.7797 (ptp) REVERT: G 123 ILE cc_start: 0.8831 (mm) cc_final: 0.8570 (mm) REVERT: H 61 ARG cc_start: 0.8322 (tpt170) cc_final: 0.7935 (tpm170) REVERT: H 86 MET cc_start: 0.8069 (ptp) cc_final: 0.7432 (ptp) REVERT: I 52 MET cc_start: 0.7943 (ttm) cc_final: 0.7578 (ttm) REVERT: K 108 MET cc_start: 0.8530 (tmm) cc_final: 0.8173 (tmm) REVERT: K 115 THR cc_start: 0.7245 (m) cc_final: 0.7032 (m) REVERT: M 95 LEU cc_start: 0.8903 (mt) cc_final: 0.8413 (mt) REVERT: M 108 MET cc_start: 0.7908 (tmm) cc_final: 0.7331 (ttp) REVERT: M 132 ASP cc_start: 0.8592 (t0) cc_final: 0.8321 (t0) REVERT: N 43 TYR cc_start: 0.6103 (m-80) cc_final: 0.5875 (m-10) REVERT: O 52 MET cc_start: 0.6503 (ttm) cc_final: 0.6100 (ttm) REVERT: O 86 MET cc_start: 0.8314 (mtp) cc_final: 0.7734 (ttm) REVERT: P 154 ILE cc_start: 0.9326 (mm) cc_final: 0.9104 (mm) REVERT: R 153 VAL cc_start: 0.6679 (m) cc_final: 0.6460 (t) REVERT: T 86 MET cc_start: 0.8116 (mtm) cc_final: 0.7708 (mtt) REVERT: T 90 ASP cc_start: 0.9004 (m-30) cc_final: 0.8710 (m-30) REVERT: U 86 MET cc_start: 0.8431 (mtm) cc_final: 0.7901 (mtt) REVERT: U 90 ASP cc_start: 0.8627 (m-30) cc_final: 0.8237 (m-30) REVERT: W 1 MET cc_start: 0.8109 (pmm) cc_final: 0.7698 (pmm) REVERT: W 150 LEU cc_start: 0.9456 (mt) cc_final: 0.9140 (tt) outliers start: 2 outliers final: 2 residues processed: 462 average time/residue: 0.1586 time to fit residues: 121.4264 Evaluate side-chains 306 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 304 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 348 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 29 optimal weight: 20.0000 chunk 138 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 347 optimal weight: 6.9990 chunk 175 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 HIS ** D 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN ** N 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 72 GLN O 156 GLN P 23 ASN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 HIS S 76 HIS V 129 HIS W 130 HIS X 23 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.059253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.051526 restraints weight = 184496.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.052804 restraints weight = 121263.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.053665 restraints weight = 87817.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.054359 restraints weight = 68291.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.054905 restraints weight = 55667.827| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 31867 Z= 0.174 Angle : 0.619 9.281 43071 Z= 0.342 Chirality : 0.037 0.179 4895 Planarity : 0.003 0.037 5626 Dihedral : 4.116 21.382 4193 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.15 % Favored : 96.69 % Rotamer: Outliers : 0.06 % Allowed : 1.11 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.30 (0.13), residues: 3810 helix: 2.42 (0.09), residues: 3078 sheet: None (None), residues: 0 loop : -2.66 (0.20), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG V 100 TYR 0.021 0.002 TYR B 133 PHE 0.033 0.002 PHE P 10 TRP 0.029 0.002 TRP F 37 HIS 0.012 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00379 (31867) covalent geometry : angle 0.61886 (43071) hydrogen bonds : bond 0.06104 ( 2606) hydrogen bonds : angle 3.87757 ( 7818) *********************** 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 458 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 456 time to evaluate : 1.284 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: 0.8851 (ttt) cc_final: 0.8582 (ttm) REVERT: A 66 ASP cc_start: 0.8757 (t70) cc_final: 0.8541 (t0) REVERT: B 52 MET cc_start: 0.7081 (ttt) cc_final: 0.6798 (ttt) REVERT: B 128 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7937 (mt-10) REVERT: C 70 ASN cc_start: 0.8401 (t0) cc_final: 0.8092 (t0) REVERT: D 52 MET cc_start: 0.7846 (ttt) cc_final: 0.7633 (ttt) REVERT: F 108 MET cc_start: 0.8334 (ptp) cc_final: 0.7720 (ptp) REVERT: G 123 ILE cc_start: 0.8880 (mm) cc_final: 0.8626 (mm) REVERT: H 61 ARG cc_start: 0.8325 (tpt170) cc_final: 0.7909 (tpm170) REVERT: H 86 MET cc_start: 0.8067 (ptp) cc_final: 0.7467 (ptp) REVERT: H 95 LEU cc_start: 0.9115 (mt) cc_final: 0.8711 (pp) REVERT: I 52 MET cc_start: 0.8054 (ttm) cc_final: 0.7747 (ttm) REVERT: K 108 MET cc_start: 0.8666 (tmm) cc_final: 0.8084 (tmm) REVERT: K 115 THR cc_start: 0.7223 (m) cc_final: 0.7017 (m) REVERT: L 111 LYS cc_start: 0.8681 (tppt) cc_final: 0.8372 (ttmt) REVERT: L 123 ILE cc_start: 0.8945 (pt) cc_final: 0.8553 (tt) REVERT: M 95 LEU cc_start: 0.8928 (mt) cc_final: 0.8439 (mt) REVERT: M 108 MET cc_start: 0.7837 (tmm) cc_final: 0.7454 (ttp) REVERT: M 132 ASP cc_start: 0.8594 (t0) cc_final: 0.8312 (t0) REVERT: O 52 MET cc_start: 0.6509 (ttm) cc_final: 0.6027 (ttm) REVERT: O 86 MET cc_start: 0.8310 (mtp) cc_final: 0.7801 (ttm) REVERT: P 154 ILE cc_start: 0.9338 (mm) cc_final: 0.9107 (mm) REVERT: T 86 MET cc_start: 0.8118 (mtm) cc_final: 0.7727 (mtt) REVERT: T 90 ASP cc_start: 0.9001 (m-30) cc_final: 0.8711 (m-30) REVERT: U 86 MET cc_start: 0.8402 (mtm) cc_final: 0.7874 (mtt) REVERT: U 90 ASP cc_start: 0.8593 (m-30) cc_final: 0.8199 (m-30) REVERT: U 114 ILE cc_start: 0.8145 (mm) cc_final: 0.7804 (mm) REVERT: W 1 MET cc_start: 0.8109 (pmm) cc_final: 0.7734 (pmm) REVERT: W 150 LEU cc_start: 0.9447 (mt) cc_final: 0.9142 (tt) outliers start: 2 outliers final: 2 residues processed: 458 average time/residue: 0.1688 time to fit residues: 127.5490 Evaluate side-chains 306 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 304 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 155 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 282 optimal weight: 5.9990 chunk 255 optimal weight: 5.9990 chunk 79 optimal weight: 0.3980 chunk 143 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 249 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 205 optimal weight: 5.9990 overall best weight: 4.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 HIS C 129 HIS D 28 HIS ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 HIS E 32 GLN G 12 ASN P 23 ASN ** P 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 HIS W 130 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.059592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.051835 restraints weight = 182666.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.053062 restraints weight = 120568.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.053980 restraints weight = 88018.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.054691 restraints weight = 68256.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.055230 restraints weight = 54931.120| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31867 Z= 0.162 Angle : 0.617 10.063 43071 Z= 0.338 Chirality : 0.037 0.176 4895 Planarity : 0.003 0.034 5626 Dihedral : 4.092 21.505 4193 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.28 % Favored : 96.56 % Rotamer: Outliers : 0.06 % Allowed : 0.57 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.35 (0.13), residues: 3810 helix: 2.46 (0.09), residues: 3074 sheet: None (None), residues: 0 loop : -2.66 (0.20), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG X 53 TYR 0.020 0.002 TYR J 133 PHE 0.031 0.002 PHE P 120 TRP 0.026 0.002 TRP F 37 HIS 0.012 0.001 HIS X 28 Details of bonding type rmsd covalent geometry : bond 0.00351 (31867) covalent geometry : angle 0.61684 (43071) hydrogen bonds : bond 0.05894 ( 2606) hydrogen bonds : angle 3.83173 ( 7818) ********************** 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 455 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 453 time to evaluate : 1.148 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 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: 0.8887 (ttt) cc_final: 0.8597 (ttm) REVERT: A 60 ASP cc_start: 0.8268 (m-30) cc_final: 0.8046 (m-30) REVERT: A 66 ASP cc_start: 0.8737 (t70) cc_final: 0.8528 (t0) REVERT: B 128 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7936 (mt-10) REVERT: C 70 ASN cc_start: 0.8391 (t0) cc_final: 0.8101 (t0) REVERT: D 52 MET cc_start: 0.7866 (ttt) cc_final: 0.7597 (ttt) REVERT: F 108 MET cc_start: 0.8235 (ptp) cc_final: 0.7871 (ptp) REVERT: E 52 MET cc_start: 0.8002 (mtp) cc_final: 0.7736 (mtp) REVERT: G 123 ILE cc_start: 0.8839 (mm) cc_final: 0.8575 (mm) REVERT: H 2 GLN cc_start: 0.7834 (mm110) cc_final: 0.7076 (pm20) REVERT: H 86 MET cc_start: 0.7972 (ptp) cc_final: 0.7489 (ptp) REVERT: H 95 LEU cc_start: 0.9085 (mt) cc_final: 0.8715 (pp) REVERT: I 52 MET cc_start: 0.8034 (ttm) cc_final: 0.7704 (ttm) REVERT: K 86 MET cc_start: 0.7780 (ptp) cc_final: 0.7255 (ptp) REVERT: K 108 MET cc_start: 0.8667 (tmm) cc_final: 0.8336 (tmm) REVERT: K 115 THR cc_start: 0.7253 (m) cc_final: 0.7022 (m) REVERT: M 66 ASP cc_start: 0.8198 (t0) cc_final: 0.7851 (t0) REVERT: M 95 LEU cc_start: 0.8926 (mt) cc_final: 0.8454 (mt) REVERT: M 108 MET cc_start: 0.7658 (tmm) cc_final: 0.7322 (ttp) REVERT: M 132 ASP cc_start: 0.8604 (t0) cc_final: 0.8333 (t0) REVERT: O 52 MET cc_start: 0.6500 (ttm) cc_final: 0.6012 (ttm) REVERT: O 86 MET cc_start: 0.8299 (mtp) cc_final: 0.7800 (ttm) REVERT: P 154 ILE cc_start: 0.9349 (mm) cc_final: 0.9113 (mm) REVERT: T 86 MET cc_start: 0.8063 (mtm) cc_final: 0.7698 (mtt) REVERT: T 90 ASP cc_start: 0.9039 (m-30) cc_final: 0.8755 (m-30) REVERT: U 86 MET cc_start: 0.8439 (mtm) cc_final: 0.7922 (mtt) REVERT: U 90 ASP cc_start: 0.8599 (m-30) cc_final: 0.8219 (m-30) REVERT: V 108 MET cc_start: 0.8236 (ptp) cc_final: 0.7771 (ptp) REVERT: W 1 MET cc_start: 0.8167 (pmm) cc_final: 0.7750 (pmm) REVERT: W 150 LEU cc_start: 0.9433 (mt) cc_final: 0.9136 (tt) outliers start: 2 outliers final: 2 residues processed: 455 average time/residue: 0.1680 time to fit residues: 125.2413 Evaluate side-chains 313 residues out of total 3426 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 311 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 381 random chunks: chunk 151 optimal weight: 8.9990 chunk 305 optimal weight: 5.9990 chunk 302 optimal weight: 0.9990 chunk 200 optimal weight: 7.9990 chunk 220 optimal weight: 1.9990 chunk 360 optimal weight: 8.9990 chunk 299 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 chunk 288 optimal weight: 9.9990 chunk 154 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 HIS ** D 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN H 54 HIS L 28 HIS N 14 GLN O 130 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 V 129 HIS W 130 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.060505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.052752 restraints weight = 182884.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.054016 restraints weight = 120386.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.054916 restraints weight = 87055.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.055630 restraints weight = 67716.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.056174 restraints weight = 54459.796| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31867 Z= 0.147 Angle : 0.609 10.315 43071 Z= 0.332 Chirality : 0.036 0.166 4895 Planarity : 0.003 0.034 5626 Dihedral : 4.046 21.744 4193 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.96 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.40 (0.13), residues: 3810 helix: 2.52 (0.09), residues: 3070 sheet: None (None), residues: 0 loop : -2.73 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG X 53 TYR 0.018 0.001 TYR K 25 PHE 0.033 0.001 PHE W 120 TRP 0.020 0.002 TRP F 37 HIS 0.009 0.001 HIS X 28 Details of bonding type rmsd covalent geometry : bond 0.00314 (31867) covalent geometry : angle 0.60885 (43071) hydrogen bonds : bond 0.05620 ( 2606) hydrogen bonds : angle 3.75646 ( 7818) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4253.75 seconds wall clock time: 74 minutes 56.40 seconds (4496.40 seconds total)