Starting phenix.real_space_refine on Sat Oct 31 15:07:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pn8_71746/10_2026/9pn8_71746_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pn8_71746/10_2026/9pn8_71746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pn8_71746/10_2026/9pn8_71746_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pn8_71746/10_2026/9pn8_71746_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pn8_71746/10_2026/9pn8_71746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pn8_71746/10_2026/9pn8_71746.map" } resolution = 2.96 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= 0.048 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 S 90 5.16 5 C 13626 2.51 5 N 3780 2.21 5 O 4131 1.98 5 H 21537 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 43164 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 851 Classifications: {'peptide': 58} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "B" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 851 Classifications: {'peptide': 58} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "C" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 851 Classifications: {'peptide': 58} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "D" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 851 Classifications: {'peptide': 58} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "E" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 851 Classifications: {'peptide': 58} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "F" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 851 Classifications: {'peptide': 58} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "G" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 851 Classifications: {'peptide': 58} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "H" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 851 Classifications: {'peptide': 58} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "I" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 851 Classifications: {'peptide': 58} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "J" Number of atoms: 3945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 3945 Classifications: {'peptide': 253} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 240} Chain: "K" Number of atoms: 3945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 3945 Classifications: {'peptide': 253} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 240} Chain: "L" Number of atoms: 3945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 3945 Classifications: {'peptide': 253} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 240} Chain: "M" Number of atoms: 3945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 3945 Classifications: {'peptide': 253} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 240} Chain: "N" Number of atoms: 3945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 3945 Classifications: {'peptide': 253} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 240} Chain: "O" Number of atoms: 3945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 3945 Classifications: {'peptide': 253} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 240} Chain: "P" Number of atoms: 3945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 3945 Classifications: {'peptide': 253} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 240} Chain: "Q" Number of atoms: 3945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 3945 Classifications: {'peptide': 253} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 240} Chain: "R" Number of atoms: 3945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 3945 Classifications: {'peptide': 253} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 240} Time building chain proxies: 7.03, per 1000 atoms: 0.16 Number of scatterers: 43164 At special positions: 0 Unit cell: (133.44, 132.606, 125.934, 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) S 90 16.00 O 4131 8.00 N 3780 7.00 C 13626 6.00 H 21537 1.00 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: 4.18 Conformation dependent library (CDL) restraints added in 1.7 seconds 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5166 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 1 sheets defined 38.8% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 17 through 41 removed outlier: 4.445A pdb=" N PHE A 21 " --> pdb=" O ASN A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 57 Processing helix chain 'B' and resid 17 through 41 removed outlier: 4.619A pdb=" N PHE B 21 " --> pdb=" O ASN B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 58 removed outlier: 3.973A pdb=" N CYS B 58 " --> pdb=" O VAL B 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 41 removed outlier: 4.463A pdb=" N PHE C 21 " --> pdb=" O ASN C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 58 removed outlier: 4.018A pdb=" N CYS C 58 " --> pdb=" O VAL C 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 41 removed outlier: 4.414A pdb=" N PHE D 21 " --> pdb=" O ASN D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 57 Processing helix chain 'E' and resid 17 through 41 removed outlier: 4.406A pdb=" N PHE E 21 " --> pdb=" O ASN E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 58 removed outlier: 4.052A pdb=" N CYS E 58 " --> pdb=" O VAL E 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 41 removed outlier: 4.599A pdb=" N PHE F 21 " --> pdb=" O ASN F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 57 Processing helix chain 'G' and resid 17 through 41 removed outlier: 4.471A pdb=" N PHE G 21 " --> pdb=" O ASN G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 56 Processing helix chain 'H' and resid 17 through 41 removed outlier: 4.445A pdb=" N PHE H 21 " --> pdb=" O ASN H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 57 Processing helix chain 'I' and resid 17 through 41 removed outlier: 4.439A pdb=" N PHE I 21 " --> pdb=" O ASN I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 57 Processing helix chain 'J' and resid 18 through 26 removed outlier: 3.694A pdb=" N HIS J 26 " --> pdb=" O LYS J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 75 Processing helix chain 'J' and resid 85 through 102 removed outlier: 3.866A pdb=" N ASN J 102 " --> pdb=" O ALA J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 197 No H-bonds generated for 'chain 'J' and resid 195 through 197' Processing helix chain 'J' and resid 211 through 234 Processing helix chain 'J' and resid 241 through 246 removed outlier: 3.804A pdb=" N GLN J 246 " --> pdb=" O ALA J 243 " (cutoff:3.500A) Processing helix chain 'J' and resid 247 through 256 Processing helix chain 'K' and resid 18 through 26 removed outlier: 3.724A pdb=" N HIS K 26 " --> pdb=" O LYS K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 75 Processing helix chain 'K' and resid 85 through 102 removed outlier: 3.599A pdb=" N ASN K 102 " --> pdb=" O ALA K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 211 through 234 Processing helix chain 'K' and resid 241 through 246 removed outlier: 3.849A pdb=" N GLN K 246 " --> pdb=" O ALA K 243 " (cutoff:3.500A) Processing helix chain 'K' and resid 247 through 256 Processing helix chain 'L' and resid 18 through 26 removed outlier: 3.703A pdb=" N HIS L 26 " --> pdb=" O LYS L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 75 Processing helix chain 'L' and resid 85 through 101 Processing helix chain 'L' and resid 211 through 234 Processing helix chain 'L' and resid 241 through 246 removed outlier: 3.520A pdb=" N ARG L 245 " --> pdb=" O LYS L 242 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLN L 246 " --> pdb=" O ALA L 243 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 256 Processing helix chain 'M' and resid 18 through 26 removed outlier: 3.751A pdb=" N HIS M 26 " --> pdb=" O LYS M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 75 Processing helix chain 'M' and resid 85 through 101 Processing helix chain 'M' and resid 211 through 234 Processing helix chain 'M' and resid 241 through 246 removed outlier: 3.842A pdb=" N GLN M 246 " --> pdb=" O ALA M 243 " (cutoff:3.500A) Processing helix chain 'M' and resid 247 through 256 Processing helix chain 'N' and resid 18 through 26 removed outlier: 3.674A pdb=" N HIS N 26 " --> pdb=" O LYS N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 75 Processing helix chain 'N' and resid 85 through 101 Processing helix chain 'N' and resid 211 through 234 Processing helix chain 'N' and resid 241 through 246 removed outlier: 3.858A pdb=" N GLN N 246 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 247 through 256 Processing helix chain 'O' and resid 18 through 26 removed outlier: 3.725A pdb=" N HIS O 26 " --> pdb=" O LYS O 22 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 75 Processing helix chain 'O' and resid 85 through 101 Processing helix chain 'O' and resid 195 through 197 No H-bonds generated for 'chain 'O' and resid 195 through 197' Processing helix chain 'O' and resid 211 through 234 Processing helix chain 'O' and resid 241 through 246 removed outlier: 3.878A pdb=" N GLN O 246 " --> pdb=" O ALA O 243 " (cutoff:3.500A) Processing helix chain 'O' and resid 247 through 256 Processing helix chain 'P' and resid 18 through 26 removed outlier: 3.679A pdb=" N HIS P 26 " --> pdb=" O LYS P 22 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 75 removed outlier: 3.504A pdb=" N SER P 75 " --> pdb=" O ALA P 71 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 101 Processing helix chain 'P' and resid 211 through 234 Processing helix chain 'P' and resid 241 through 246 removed outlier: 3.857A pdb=" N GLN P 246 " --> pdb=" O ALA P 243 " (cutoff:3.500A) Processing helix chain 'P' and resid 247 through 256 Processing helix chain 'Q' and resid 18 through 26 removed outlier: 3.718A pdb=" N HIS Q 26 " --> pdb=" O LYS Q 22 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 75 Processing helix chain 'Q' and resid 85 through 102 removed outlier: 3.614A pdb=" N ASN Q 102 " --> pdb=" O ALA Q 98 " (cutoff:3.500A) Processing helix chain 'Q' and resid 211 through 234 Processing helix chain 'Q' and resid 241 through 246 removed outlier: 3.862A pdb=" N GLN Q 246 " --> pdb=" O ALA Q 243 " (cutoff:3.500A) Processing helix chain 'Q' and resid 247 through 256 Processing helix chain 'R' and resid 18 through 26 removed outlier: 3.609A pdb=" N HIS R 26 " --> pdb=" O LYS R 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 75 Processing helix chain 'R' and resid 85 through 101 Processing helix chain 'R' and resid 195 through 197 No H-bonds generated for 'chain 'R' and resid 195 through 197' Processing helix chain 'R' and resid 211 through 234 Processing helix chain 'R' and resid 241 through 246 removed outlier: 3.839A pdb=" N GLN R 246 " --> pdb=" O ALA R 243 " (cutoff:3.500A) Processing helix chain 'R' and resid 247 through 256 Processing sheet with id=AA1, first strand: chain 'J' and resid 13 through 14 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 13 through 14 current: chain 'J' and resid 146 through 165 removed outlier: 3.575A pdb=" N SER J 173 " --> pdb=" O VAL J 163 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN J 165 " --> pdb=" O ILE J 171 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE J 171 " --> pdb=" O ASN J 165 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 198 through 209 current: chain 'K' and resid 146 through 165 removed outlier: 3.576A pdb=" N SER K 173 " --> pdb=" O VAL K 163 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASN K 165 " --> pdb=" O ILE K 171 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE K 171 " --> pdb=" O ASN K 165 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 198 through 209 current: chain 'L' and resid 146 through 165 removed outlier: 3.554A pdb=" N SER L 173 " --> pdb=" O VAL L 163 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASN L 165 " --> pdb=" O ILE L 171 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE L 171 " --> pdb=" O ASN L 165 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 200 through 209 current: chain 'M' and resid 146 through 165 removed outlier: 3.529A pdb=" N SER M 173 " --> pdb=" O VAL M 163 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN M 165 " --> pdb=" O ILE M 171 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE M 171 " --> pdb=" O ASN M 165 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 198 through 209 current: chain 'N' and resid 146 through 165 removed outlier: 3.565A pdb=" N SER N 173 " --> pdb=" O VAL N 163 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASN N 165 " --> pdb=" O ILE N 171 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ILE N 171 " --> pdb=" O ASN N 165 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 198 through 209 current: chain 'O' and resid 146 through 165 removed outlier: 3.541A pdb=" N SER O 173 " --> pdb=" O VAL O 163 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASN O 165 " --> pdb=" O ILE O 171 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE O 171 " --> pdb=" O ASN O 165 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 198 through 209 current: chain 'P' and resid 146 through 165 removed outlier: 3.557A pdb=" N SER P 173 " --> pdb=" O VAL P 163 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ASN P 165 " --> pdb=" O ILE P 171 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE P 171 " --> pdb=" O ASN P 165 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 198 through 209 current: chain 'Q' and resid 146 through 165 removed outlier: 3.536A pdb=" N SER Q 173 " --> pdb=" O VAL Q 163 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASN Q 165 " --> pdb=" O ILE Q 171 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE Q 171 " --> pdb=" O ASN Q 165 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 198 through 209 current: chain 'R' and resid 146 through 165 removed outlier: 3.561A pdb=" N SER R 173 " --> pdb=" O VAL R 163 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASN R 165 " --> pdb=" O ILE R 171 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE R 171 " --> pdb=" O ASN R 165 " (cutoff:3.500A) 1021 hydrogen bonds defined for protein. 2985 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: 11.20 Time building geometry restraints manager: 5.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 21510 1.03 - 1.23: 60 1.23 - 1.42: 9138 1.42 - 1.62: 12690 1.62 - 1.81: 153 Bond restraints: 43551 Sorted by residual: bond pdb=" N ALA R 10 " pdb=" CA ALA R 10 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.18e+00 bond pdb=" N ALA K 10 " pdb=" CA ALA K 10 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.15e+00 bond pdb=" N ALA P 10 " pdb=" CA ALA P 10 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.08e+00 bond pdb=" N ALA M 10 " pdb=" CA ALA M 10 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.07e+00 bond pdb=" N ALA L 10 " pdb=" CA ALA L 10 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 ... (remaining 43546 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.95: 72462 0.95 - 1.91: 5683 1.91 - 2.86: 263 2.86 - 3.82: 130 3.82 - 4.77: 14 Bond angle restraints: 78552 Sorted by residual: angle pdb=" N GLY M 129 " pdb=" CA GLY M 129 " pdb=" C GLY M 129 " ideal model delta sigma weight residual 110.38 115.15 -4.77 1.48e+00 4.57e-01 1.04e+01 angle pdb=" N TYR O 196 " pdb=" CA TYR O 196 " pdb=" CB TYR O 196 " ideal model delta sigma weight residual 114.17 110.90 3.27 1.14e+00 7.69e-01 8.25e+00 angle pdb=" CB GLN D 56 " pdb=" CG GLN D 56 " pdb=" CD GLN D 56 " ideal model delta sigma weight residual 112.60 116.87 -4.27 1.70e+00 3.46e-01 6.30e+00 angle pdb=" N TYR P 196 " pdb=" CA TYR P 196 " pdb=" CB TYR P 196 " ideal model delta sigma weight residual 113.65 110.49 3.16 1.47e+00 4.63e-01 4.63e+00 angle pdb=" N TYR J 196 " pdb=" CA TYR J 196 " pdb=" CB TYR J 196 " ideal model delta sigma weight residual 113.65 110.67 2.98 1.47e+00 4.63e-01 4.12e+00 ... (remaining 78547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 18372 17.28 - 34.55: 1397 34.55 - 51.83: 506 51.83 - 69.11: 237 69.11 - 86.38: 35 Dihedral angle restraints: 20547 sinusoidal: 11349 harmonic: 9198 Sorted by residual: dihedral pdb=" CA ASP L 74 " pdb=" C ASP L 74 " pdb=" N SER L 75 " pdb=" CA SER L 75 " ideal model delta harmonic sigma weight residual 180.00 160.48 19.52 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA ASP P 74 " pdb=" C ASP P 74 " pdb=" N SER P 75 " pdb=" CA SER P 75 " ideal model delta harmonic sigma weight residual 180.00 161.93 18.07 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA ASP O 195 " pdb=" C ASP O 195 " pdb=" N TYR O 196 " pdb=" CA TYR O 196 " ideal model delta harmonic sigma weight residual 180.00 162.51 17.49 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 20544 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2015 0.027 - 0.054: 881 0.054 - 0.081: 215 0.081 - 0.108: 157 0.108 - 0.136: 125 Chirality restraints: 3393 Sorted by residual: chirality pdb=" CA ILE M 79 " pdb=" N ILE M 79 " pdb=" C ILE M 79 " pdb=" CB ILE M 79 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA ILE O 79 " pdb=" N ILE O 79 " pdb=" C ILE O 79 " pdb=" CB ILE O 79 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CA ILE J 79 " pdb=" N ILE J 79 " pdb=" C ILE J 79 " pdb=" CB ILE J 79 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 ... (remaining 3390 not shown) Planarity restraints: 6606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN D 56 " -0.008 2.00e-02 2.50e+03 1.66e-02 4.13e+00 pdb=" CD GLN D 56 " 0.035 2.00e-02 2.50e+03 pdb=" OE1 GLN D 56 " -0.017 2.00e-02 2.50e+03 pdb=" NE2 GLN D 56 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN D 56 " -0.009 2.00e-02 2.50e+03 pdb="HE22 GLN D 56 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 15 " 0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO A 16 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 16 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 16 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP L 74 " 0.006 2.00e-02 2.50e+03 1.12e-02 1.26e+00 pdb=" CG ASP L 74 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASP L 74 " 0.007 2.00e-02 2.50e+03 pdb=" OD2 ASP L 74 " 0.007 2.00e-02 2.50e+03 ... (remaining 6603 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.35: 13716 2.35 - 2.91: 98619 2.91 - 3.47: 111817 3.47 - 4.04: 155791 4.04 - 4.60: 238334 Nonbonded interactions: 618277 Sorted by model distance: nonbonded pdb=" HA GLN D 56 " pdb="HE21 GLN D 56 " model vdw 1.783 2.270 nonbonded pdb=" HG3 ARG I 8 " pdb="HH11 ARG I 8 " model vdw 1.885 2.270 nonbonded pdb=" HG3 ARG B 8 " pdb="HH11 ARG B 8 " model vdw 1.894 2.270 nonbonded pdb=" HG3 ARG A 8 " pdb="HH11 ARG A 8 " model vdw 1.905 2.270 nonbonded pdb=" HG3 ARG H 8 " pdb="HH11 ARG H 8 " model vdw 1.914 2.270 ... (remaining 618272 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.090 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: 0.100 Extract box with map and model: 0.620 Check model and map are aligned: 0.160 Set scattering table: 0.120 Process input model: 41.660 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5924 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 : 0.004 0.034 22014 Z= 0.170 Angle : 0.514 4.771 29898 Z= 0.294 Chirality : 0.041 0.136 3393 Planarity : 0.003 0.038 3951 Dihedral : 14.782 86.384 8091 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.34 % Allowed : 11.97 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 are not related in a simple way. whole: 2.06 (0.16), residues: 2763 helix: 3.15 (0.16), residues: 981 sheet: 0.29 (0.20), residues: 693 loop : 0.52 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 8 TYR 0.013 0.001 TYR J 196 PHE 0.006 0.001 PHE I 7 TRP 0.004 0.001 TRP F 39 HIS 0.001 0.000 HIS J 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (22014) covalent geometry : angle 0.51421 / 0.29 (29898) hydrogen bonds : bond 0.16980 / 11.32 ( 1021) hydrogen bonds : angle 6.16449 / 4.54 ( 2985) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 477 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 GLN cc_start: 0.8163 (mt0) cc_final: 0.7923 (mt0) REVERT: D 29 GLN cc_start: 0.6720 (OUTLIER) cc_final: 0.6410 (mp-120) REVERT: E 7 PHE cc_start: 0.4943 (m-80) cc_final: 0.4550 (m-80) REVERT: I 6 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.7101 (mt0) REVERT: I 9 ASN cc_start: 0.6437 (t0) cc_final: 0.6154 (t0) REVERT: J 67 MET cc_start: 0.5912 (mtt) cc_final: 0.5604 (mtt) REVERT: J 185 GLU cc_start: 0.8177 (tt0) cc_final: 0.7957 (tt0) REVERT: K 23 ASP cc_start: 0.7462 (m-30) cc_final: 0.7073 (m-30) REVERT: K 185 GLU cc_start: 0.8470 (tt0) cc_final: 0.7633 (tt0) REVERT: L 131 GLU cc_start: 0.6848 (mt-10) cc_final: 0.6597 (mt-10) REVERT: M 11 ARG cc_start: 0.7060 (ptp-110) cc_final: 0.6771 (mtm110) REVERT: M 124 GLU cc_start: 0.5618 (mm-30) cc_final: 0.5114 (mm-30) REVERT: N 42 GLN cc_start: 0.6853 (mm-40) cc_final: 0.6586 (tp40) REVERT: N 44 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6798 (mt-10) REVERT: N 217 MET cc_start: 0.6360 (tpt) cc_final: 0.5961 (tpp) REVERT: O 20 SER cc_start: 0.7777 (m) cc_final: 0.7572 (p) REVERT: O 22 LYS cc_start: 0.6566 (ttmm) cc_final: 0.6204 (mppt) REVERT: O 131 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7189 (mt-10) REVERT: O 240 GLN cc_start: 0.7973 (tt0) cc_final: 0.7742 (tp40) REVERT: P 175 VAL cc_start: 0.8036 (m) cc_final: 0.7792 (p) REVERT: P 229 ASN cc_start: 0.7100 (t0) cc_final: 0.6876 (t0) REVERT: Q 222 THR cc_start: 0.7585 (m) cc_final: 0.7170 (t) REVERT: R 185 GLU cc_start: 0.6717 (tt0) cc_final: 0.5390 (tm-30) REVERT: R 186 VAL cc_start: 0.6694 (t) cc_final: 0.6428 (t) outliers start: 8 outliers final: 5 residues processed: 480 average time/residue: 0.9129 time to fit residues: 526.0687 Evaluate side-chains 304 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 297 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain L residue 229 ASN Chi-restraints excluded: chain N residue 242 LYS Chi-restraints excluded: chain O residue 238 ASP Chi-restraints excluded: chain Q residue 43 ASP Chi-restraints excluded: chain R residue 149 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 111] chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 ASN B 27 GLN C 37 GLN D 29 GLN ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 11 ASN J 88 ASN J 109 ASN L 102 ASN L 109 ASN M 109 ASN M 153 GLN M 229 ASN N 120 ASN N 153 GLN O 109 ASN O 165 ASN P 62 GLN P 209 ASN R 42 GLN R 197 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.177063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.144848 restraints weight = 79095.839| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.03 r_work: 0.3563 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 22014 Z= 0.206 Angle : 0.739 10.598 29898 Z= 0.389 Chirality : 0.048 0.198 3393 Planarity : 0.005 0.055 3951 Dihedral : 5.396 54.914 3051 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.99 % Allowed : 16.11 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 are not related in a simple way. whole: 1.02 (0.16), residues: 2763 helix: 1.47 (0.15), residues: 1044 sheet: 0.50 (0.20), residues: 675 loop : 0.12 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 17 TYR 0.018 0.002 TYR P 253 PHE 0.032 0.002 PHE F 21 TRP 0.026 0.002 TRP L 77 HIS 0.014 0.003 HIS M 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 (22014) covalent geometry : angle 0.73911 / 0.39 (29898) hydrogen bonds : bond 0.04147 / 2.72 ( 1021) hydrogen bonds : angle 4.60973 / 3.40 ( 2985) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 482 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 ASN cc_start: 0.8101 (m110) cc_final: 0.7749 (m110) REVERT: C 15 ASN cc_start: 0.8501 (t0) cc_final: 0.8221 (t0) REVERT: D 15 ASN cc_start: 0.8554 (t0) cc_final: 0.8345 (t0) REVERT: G 6 GLN cc_start: 0.8033 (mt0) cc_final: 0.7727 (mt0) REVERT: J 67 MET cc_start: 0.8677 (mtt) cc_final: 0.8337 (mtt) REVERT: K 97 ARG cc_start: 0.6026 (tpp-160) cc_final: 0.5647 (mtt180) REVERT: K 185 GLU cc_start: 0.8691 (tt0) cc_final: 0.8346 (pp20) REVERT: L 15 MET cc_start: 0.7328 (OUTLIER) cc_final: 0.6321 (tmm) REVERT: L 204 VAL cc_start: 0.8997 (OUTLIER) cc_final: 0.8741 (m) REVERT: M 15 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.6785 (tmm) REVERT: N 44 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8381 (mt-10) REVERT: O 11 ARG cc_start: 0.7359 (ptp-110) cc_final: 0.7132 (mtm-85) REVERT: O 22 LYS cc_start: 0.8456 (ttmm) cc_final: 0.8138 (tppt) REVERT: Q 11 ARG cc_start: 0.7219 (ptp90) cc_final: 0.6914 (mtm-85) REVERT: Q 113 LEU cc_start: 0.4406 (OUTLIER) cc_final: 0.3756 (mt) REVERT: Q 175 VAL cc_start: 0.8422 (m) cc_final: 0.8028 (p) REVERT: Q 185 GLU cc_start: 0.7819 (tt0) cc_final: 0.7510 (tm-30) REVERT: R 89 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8213 (tm) REVERT: R 164 VAL cc_start: 0.7959 (OUTLIER) cc_final: 0.7615 (p) REVERT: R 175 VAL cc_start: 0.7880 (m) cc_final: 0.7648 (p) REVERT: R 185 GLU cc_start: 0.8281 (tt0) cc_final: 0.7843 (pp20) outliers start: 70 outliers final: 16 residues processed: 523 average time/residue: 0.9986 time to fit residues: 616.0540 Evaluate side-chains 351 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 329 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain E residue 56 GLN Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain L residue 15 MET Chi-restraints excluded: chain L residue 120 ASN Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain M residue 15 MET Chi-restraints excluded: chain M residue 134 VAL Chi-restraints excluded: chain N residue 37 SER Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 207 THR Chi-restraints excluded: chain P residue 37 SER Chi-restraints excluded: chain P residue 185 GLU Chi-restraints excluded: chain P residue 217 MET Chi-restraints excluded: chain Q residue 113 LEU Chi-restraints excluded: chain Q residue 230 ASP Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 89 LEU Chi-restraints excluded: chain R residue 164 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: [142, 28, 266, 242, 56, 25, 55, 3, 175, 240, 209] chunk 142 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 266 optimal weight: 1.9990 chunk 242 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 240 optimal weight: 0.9990 chunk 209 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN E 30 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 9 ASN ** G 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 ASN H 17 ASN J 19 GLN J 42 GLN J 102 ASN K 156 GLN L 40 ASN L 229 ASN M 102 ASN M 156 GLN M 229 ASN N 19 GLN N 55 ASN N 160 ASN P 209 ASN Q 62 GLN Q 197 GLN Q 209 ASN R 40 ASN R 55 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.132123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.097517 restraints weight = 77553.468| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.00 r_work: 0.2938 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.8074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 22014 Z= 0.243 Angle : 0.704 8.323 29898 Z= 0.373 Chirality : 0.048 0.333 3393 Planarity : 0.006 0.113 3951 Dihedral : 4.867 26.773 3033 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.23 % Allowed : 19.23 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 are not related in a simple way. whole: 1.03 (0.16), residues: 2763 helix: 1.79 (0.16), residues: 1044 sheet: 0.40 (0.20), residues: 648 loop : -0.15 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 254 TYR 0.054 0.002 TYR J 196 PHE 0.024 0.002 PHE M 78 TRP 0.012 0.001 TRP L 237 HIS 0.004 0.001 HIS J 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.24 (22014) covalent geometry : angle 0.70403 / 0.37 (29898) hydrogen bonds : bond 0.06572 / 4.27 ( 1021) hydrogen bonds : angle 4.65781 / 3.44 ( 2985) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 363 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 8 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8362 (mtt180) REVERT: D 15 ASN cc_start: 0.8965 (t0) cc_final: 0.8620 (t0) REVERT: G 6 GLN cc_start: 0.8718 (mt0) cc_final: 0.8372 (mt0) REVERT: H 6 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8405 (mt0) REVERT: J 11 ARG cc_start: 0.8507 (mpp-170) cc_final: 0.8165 (mtm110) REVERT: J 22 LYS cc_start: 0.8372 (ttmm) cc_final: 0.7898 (mttm) REVERT: J 241 ASN cc_start: 0.7019 (m-40) cc_final: 0.6575 (t0) REVERT: K 22 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8065 (mttp) REVERT: K 185 GLU cc_start: 0.8805 (tt0) cc_final: 0.8588 (tt0) REVERT: K 197 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8353 (pm20) REVERT: L 122 MET cc_start: 0.8904 (ptm) cc_final: 0.8685 (ptt) REVERT: M 135 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8522 (ttpt) REVERT: N 44 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8577 (mt-10) REVERT: N 242 LYS cc_start: 0.7727 (mttp) cc_final: 0.7516 (mmtm) REVERT: O 22 LYS cc_start: 0.8543 (ttmm) cc_final: 0.8035 (tppt) REVERT: O 230 ASP cc_start: 0.8820 (t70) cc_final: 0.8459 (t70) REVERT: O 256 MET cc_start: 0.8526 (mtp) cc_final: 0.8263 (mtp) REVERT: P 11 ARG cc_start: 0.8452 (ttp80) cc_final: 0.7812 (mtm-85) REVERT: Q 11 ARG cc_start: 0.8334 (ptp90) cc_final: 0.7936 (mtm-85) REVERT: Q 44 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8680 (mt-10) REVERT: Q 113 LEU cc_start: 0.5304 (OUTLIER) cc_final: 0.5104 (pt) REVERT: Q 175 VAL cc_start: 0.8994 (m) cc_final: 0.8747 (p) REVERT: Q 185 GLU cc_start: 0.8623 (tt0) cc_final: 0.8254 (pp20) REVERT: Q 234 ARG cc_start: 0.8185 (ttm170) cc_final: 0.7976 (ptp90) REVERT: R 22 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7796 (mppt) REVERT: R 23 ASP cc_start: 0.8860 (m-30) cc_final: 0.8613 (m-30) REVERT: R 185 GLU cc_start: 0.8809 (tt0) cc_final: 0.8588 (tt0) outliers start: 99 outliers final: 21 residues processed: 421 average time/residue: 1.2155 time to fit residues: 588.9077 Evaluate side-chains 305 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 277 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain K residue 22 LYS Chi-restraints excluded: chain K residue 149 ASP Chi-restraints excluded: chain K residue 197 GLN Chi-restraints excluded: chain L residue 183 SER Chi-restraints excluded: chain M residue 81 LEU Chi-restraints excluded: chain M residue 135 LYS Chi-restraints excluded: chain M residue 150 THR Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain N residue 183 SER Chi-restraints excluded: chain O residue 180 THR Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain Q residue 113 LEU Chi-restraints excluded: chain Q residue 124 GLU Chi-restraints excluded: chain Q residue 132 SER Chi-restraints excluded: chain Q residue 149 ASP Chi-restraints excluded: chain Q residue 173 SER Chi-restraints excluded: chain Q residue 207 THR Chi-restraints excluded: chain Q residue 239 LEU Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain R residue 180 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: [54, 215, 243, 213, 92, 143, 175, 125, 33, 176, 85] chunk 54 optimal weight: 0.8980 chunk 215 optimal weight: 0.6980 chunk 243 optimal weight: 0.2980 chunk 213 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 175 optimal weight: 0.6980 chunk 125 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 85 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 GLN D 27 GLN ** D 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 ASN K 42 GLN K 62 GLN K 229 ASN L 40 ASN L 109 ASN M 156 GLN M 246 GLN Q 209 ASN R 156 GLN R 229 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.130361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.096266 restraints weight = 77649.345| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.98 r_work: 0.2912 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.8492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22014 Z= 0.118 Angle : 0.508 5.774 29898 Z= 0.270 Chirality : 0.042 0.156 3393 Planarity : 0.004 0.051 3951 Dihedral : 4.386 22.200 3033 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.31 % Allowed : 20.56 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 are not related in a simple way. whole: 1.57 (0.16), residues: 2763 helix: 2.19 (0.16), residues: 1044 sheet: 0.83 (0.20), residues: 675 loop : 0.08 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 234 TYR 0.009 0.001 TYR P 253 PHE 0.013 0.001 PHE C 51 TRP 0.005 0.001 TRP B 39 HIS 0.004 0.001 HIS P 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (22014) covalent geometry : angle 0.50833 / 0.27 (29898) hydrogen bonds : bond 0.04040 / 2.61 ( 1021) hydrogen bonds : angle 4.20190 / 3.11 ( 2985) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 299 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 8 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8245 (mtt180) REVERT: C 15 ASN cc_start: 0.8729 (t0) cc_final: 0.8501 (t0) REVERT: C 29 GLN cc_start: 0.7875 (OUTLIER) cc_final: 0.7338 (mp10) REVERT: D 15 ASN cc_start: 0.8884 (t0) cc_final: 0.8614 (t0) REVERT: G 6 GLN cc_start: 0.8724 (mt0) cc_final: 0.8395 (mt0) REVERT: H 37 GLN cc_start: 0.6275 (mm-40) cc_final: 0.5761 (mm110) REVERT: J 22 LYS cc_start: 0.8389 (ttmm) cc_final: 0.7905 (mttm) REVERT: J 241 ASN cc_start: 0.7058 (m-40) cc_final: 0.6566 (t0) REVERT: K 185 GLU cc_start: 0.8808 (tt0) cc_final: 0.8548 (tt0) REVERT: K 236 LEU cc_start: 0.8463 (tt) cc_final: 0.8232 (mt) REVERT: M 44 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8570 (mt-10) REVERT: M 135 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8455 (tttt) REVERT: M 256 MET cc_start: 0.6755 (mtt) cc_final: 0.6540 (mtp) REVERT: N 74 ASP cc_start: 0.8137 (p0) cc_final: 0.7775 (m-30) REVERT: N 242 LYS cc_start: 0.7591 (mttp) cc_final: 0.7325 (mmtm) REVERT: O 11 ARG cc_start: 0.8206 (mtm110) cc_final: 0.7906 (mtm-85) REVERT: O 22 LYS cc_start: 0.8600 (ttmm) cc_final: 0.8360 (ttmm) REVERT: O 97 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7781 (mtt180) REVERT: P 11 ARG cc_start: 0.8398 (ttp80) cc_final: 0.7896 (mtm-85) REVERT: Q 11 ARG cc_start: 0.8333 (ptp90) cc_final: 0.7938 (mtm-85) REVERT: Q 42 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8219 (mm110) REVERT: Q 113 LEU cc_start: 0.5377 (OUTLIER) cc_final: 0.5160 (pt) REVERT: Q 185 GLU cc_start: 0.8646 (tt0) cc_final: 0.8153 (pp20) REVERT: Q 234 ARG cc_start: 0.8172 (ttm170) cc_final: 0.7918 (ptp-170) REVERT: R 22 LYS cc_start: 0.8189 (tppp) cc_final: 0.7799 (mppt) REVERT: R 185 GLU cc_start: 0.8732 (tt0) cc_final: 0.8508 (tt0) outliers start: 54 outliers final: 17 residues processed: 338 average time/residue: 1.2025 time to fit residues: 469.1321 Evaluate side-chains 305 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 283 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain M residue 135 LYS Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain N residue 183 SER Chi-restraints excluded: chain N residue 207 THR Chi-restraints excluded: chain O residue 97 ARG Chi-restraints excluded: chain O residue 180 THR Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain P residue 217 MET Chi-restraints excluded: chain Q residue 113 LEU Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 132 SER Chi-restraints excluded: chain R residue 37 SER Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 234 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: [264, 177, 169, 241, 16, 139, 38, 166, 17, 165, 197] chunk 264 optimal weight: 0.3980 chunk 177 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 241 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 chunk 197 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 ASN D 27 GLN F 17 ASN J 42 GLN J 62 GLN K 42 GLN K 229 ASN L 160 ASN M 40 ASN M 42 GLN M 55 ASN M 156 GLN M 160 ASN O 160 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.119787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.087674 restraints weight = 77772.700| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 1.76 r_work: 0.2751 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.9222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 22014 Z= 0.171 Angle : 0.536 5.566 29898 Z= 0.287 Chirality : 0.043 0.151 3393 Planarity : 0.004 0.074 3951 Dihedral : 4.358 22.595 3033 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.56 % Allowed : 19.53 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 are not related in a simple way. whole: 1.61 (0.16), residues: 2763 helix: 2.25 (0.16), residues: 1053 sheet: 1.01 (0.20), residues: 666 loop : -0.07 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 234 TYR 0.015 0.001 TYR J 253 PHE 0.009 0.001 PHE D 51 TRP 0.007 0.001 TRP O 237 HIS 0.004 0.001 HIS P 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (22014) covalent geometry : angle 0.53609 / 0.29 (29898) hydrogen bonds : bond 0.04201 / 2.70 ( 1021) hydrogen bonds : angle 4.13369 / 3.06 ( 2985) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 308 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.7122 (mpp-170) REVERT: C 8 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8171 (mtt180) REVERT: C 33 ILE cc_start: 0.7541 (mm) cc_final: 0.7336 (mp) REVERT: D 15 ASN cc_start: 0.8899 (t0) cc_final: 0.8655 (t0) REVERT: E 15 ASN cc_start: 0.8735 (t0) cc_final: 0.8398 (t0) REVERT: G 6 GLN cc_start: 0.8721 (mt0) cc_final: 0.8331 (mt0) REVERT: G 37 GLN cc_start: 0.6430 (OUTLIER) cc_final: 0.6193 (tm-30) REVERT: H 37 GLN cc_start: 0.6418 (mm-40) cc_final: 0.5943 (mt0) REVERT: J 22 LYS cc_start: 0.8354 (ttmm) cc_final: 0.7843 (mttm) REVERT: J 241 ASN cc_start: 0.7338 (m-40) cc_final: 0.6709 (t0) REVERT: K 22 LYS cc_start: 0.8296 (tppp) cc_final: 0.7876 (ttmm) REVERT: K 185 GLU cc_start: 0.8756 (tt0) cc_final: 0.8486 (tt0) REVERT: M 44 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8495 (mt-10) REVERT: M 135 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8377 (ttpt) REVERT: M 149 ASP cc_start: 0.8781 (p0) cc_final: 0.8484 (p0) REVERT: M 180 THR cc_start: 0.9189 (OUTLIER) cc_final: 0.8944 (t) REVERT: M 256 MET cc_start: 0.7176 (mtt) cc_final: 0.6821 (mtp) REVERT: N 11 ARG cc_start: 0.8555 (mtm-85) cc_final: 0.7938 (mtm-85) REVERT: N 22 LYS cc_start: 0.8153 (ttmm) cc_final: 0.7617 (mtmt) REVERT: N 256 MET cc_start: 0.8019 (mtp) cc_final: 0.7677 (mtp) REVERT: O 11 ARG cc_start: 0.8219 (mtm110) cc_final: 0.7824 (mtm-85) REVERT: O 22 LYS cc_start: 0.8403 (ttmm) cc_final: 0.8146 (ttmm) REVERT: O 97 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7704 (mtt180) REVERT: P 11 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7704 (mtm-85) REVERT: P 22 LYS cc_start: 0.8294 (mppt) cc_final: 0.8053 (mppt) REVERT: Q 11 ARG cc_start: 0.8358 (ptp90) cc_final: 0.7948 (mtm-85) REVERT: Q 42 GLN cc_start: 0.8670 (mm-40) cc_final: 0.8217 (mm110) REVERT: Q 79 ILE cc_start: 0.8971 (tt) cc_final: 0.8764 (tt) REVERT: Q 113 LEU cc_start: 0.5566 (OUTLIER) cc_final: 0.5295 (pt) REVERT: R 22 LYS cc_start: 0.8175 (tppp) cc_final: 0.7677 (mmmt) REVERT: R 124 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7958 (pt0) REVERT: R 154 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8980 (tp) REVERT: R 185 GLU cc_start: 0.8665 (tt0) cc_final: 0.8412 (tt0) REVERT: R 230 ASP cc_start: 0.8568 (t70) cc_final: 0.8252 (t0) REVERT: R 234 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7189 (ptt180) outliers start: 60 outliers final: 21 residues processed: 350 average time/residue: 1.2353 time to fit residues: 498.5891 Evaluate side-chains 311 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 279 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ARG Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain G residue 37 GLN Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain M residue 22 LYS Chi-restraints excluded: chain M residue 135 LYS Chi-restraints excluded: chain M residue 156 GLN Chi-restraints excluded: chain M residue 180 THR Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain N residue 207 THR Chi-restraints excluded: chain O residue 97 ARG Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain O residue 173 SER Chi-restraints excluded: chain O residue 180 THR Chi-restraints excluded: chain O residue 207 THR Chi-restraints excluded: chain P residue 11 ARG Chi-restraints excluded: chain P residue 37 SER Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain P residue 217 MET Chi-restraints excluded: chain Q residue 113 LEU Chi-restraints excluded: chain Q residue 124 GLU Chi-restraints excluded: chain Q residue 132 SER Chi-restraints excluded: chain R residue 37 SER Chi-restraints excluded: chain R residue 124 GLU Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 234 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: [259, 248, 5, 87, 104, 86, 6, 136, 11, 252, 70] chunk 259 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 136 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 252 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 GLN K 42 GLN K 229 ASN L 62 GLN L 229 ASN M 40 ASN O 62 GLN R 55 ASN R 62 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.118574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.086847 restraints weight = 77577.716| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 1.75 r_work: 0.2733 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.9522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 22014 Z= 0.137 Angle : 0.495 7.751 29898 Z= 0.263 Chirality : 0.042 0.146 3393 Planarity : 0.004 0.077 3951 Dihedral : 4.226 21.518 3033 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.26 % Allowed : 20.26 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 are not related in a simple way. whole: 1.79 (0.16), residues: 2763 helix: 2.47 (0.16), residues: 1044 sheet: 1.11 (0.20), residues: 666 loop : -0.05 (0.20), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG K 234 TYR 0.012 0.001 TYR K 253 PHE 0.011 0.001 PHE E 51 TRP 0.004 0.001 TRP B 39 HIS 0.002 0.001 HIS P 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (22014) covalent geometry : angle 0.49527 / 0.26 (29898) hydrogen bonds : bond 0.03845 / 2.48 ( 1021) hydrogen bonds : angle 4.07134 / 3.01 ( 2985) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 294 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.7176 (mpp-170) REVERT: C 8 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8376 (mtt180) REVERT: E 15 ASN cc_start: 0.8605 (t0) cc_final: 0.8348 (t0) REVERT: G 6 GLN cc_start: 0.8768 (mt0) cc_final: 0.8402 (mt0) REVERT: H 37 GLN cc_start: 0.6382 (mm-40) cc_final: 0.5965 (mt0) REVERT: J 22 LYS cc_start: 0.8396 (ttmm) cc_final: 0.7877 (mttm) REVERT: J 149 ASP cc_start: 0.8881 (p0) cc_final: 0.8666 (p0) REVERT: J 241 ASN cc_start: 0.7336 (m-40) cc_final: 0.6835 (t0) REVERT: K 22 LYS cc_start: 0.8256 (tppp) cc_final: 0.7852 (ttmm) REVERT: K 185 GLU cc_start: 0.8751 (tt0) cc_final: 0.8486 (tt0) REVERT: L 11 ARG cc_start: 0.8326 (mtm110) cc_final: 0.7954 (mtm-85) REVERT: L 74 ASP cc_start: 0.8185 (p0) cc_final: 0.7813 (m-30) REVERT: M 44 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8476 (mt-10) REVERT: M 74 ASP cc_start: 0.8075 (p0) cc_final: 0.7702 (m-30) REVERT: M 97 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7025 (mtp180) REVERT: M 135 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8269 (tttt) REVERT: M 256 MET cc_start: 0.7446 (mtt) cc_final: 0.7055 (mtp) REVERT: N 11 ARG cc_start: 0.8519 (mtm-85) cc_final: 0.7953 (mtm-85) REVERT: N 22 LYS cc_start: 0.8149 (ttmm) cc_final: 0.7626 (mtmt) REVERT: N 122 MET cc_start: 0.9122 (ptm) cc_final: 0.8892 (ptp) REVERT: N 256 MET cc_start: 0.8089 (mtp) cc_final: 0.7738 (mtp) REVERT: O 11 ARG cc_start: 0.8210 (mtm110) cc_final: 0.7412 (mmp-170) REVERT: O 22 LYS cc_start: 0.8377 (ttmm) cc_final: 0.8127 (ttmm) REVERT: O 44 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8521 (mt-10) REVERT: O 97 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7727 (mtt180) REVERT: P 11 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7724 (mtm-85) REVERT: P 42 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8114 (mm110) REVERT: Q 11 ARG cc_start: 0.8393 (ptp90) cc_final: 0.7966 (mtm-85) REVERT: Q 42 GLN cc_start: 0.8656 (mm-40) cc_final: 0.8207 (mm110) REVERT: Q 79 ILE cc_start: 0.9005 (tt) cc_final: 0.8797 (tt) REVERT: Q 113 LEU cc_start: 0.5696 (OUTLIER) cc_final: 0.5427 (pt) REVERT: R 22 LYS cc_start: 0.8191 (tppp) cc_final: 0.7659 (mmmt) REVERT: R 124 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7921 (pt0) REVERT: R 185 GLU cc_start: 0.8658 (tt0) cc_final: 0.8404 (tt0) REVERT: R 230 ASP cc_start: 0.8606 (t70) cc_final: 0.8213 (t0) outliers start: 53 outliers final: 26 residues processed: 329 average time/residue: 1.1944 time to fit residues: 453.2218 Evaluate side-chains 310 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 276 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ARG Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 15 ASN Chi-restraints excluded: chain H residue 15 ASN Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain K residue 217 MET Chi-restraints excluded: chain M residue 97 ARG Chi-restraints excluded: chain M residue 135 LYS Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain N residue 183 SER Chi-restraints excluded: chain N residue 207 THR Chi-restraints excluded: chain O residue 97 ARG Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain O residue 180 THR Chi-restraints excluded: chain O residue 207 THR Chi-restraints excluded: chain O residue 238 ASP Chi-restraints excluded: chain P residue 11 ARG Chi-restraints excluded: chain P residue 37 SER Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain P residue 217 MET Chi-restraints excluded: chain Q residue 113 LEU Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 124 GLU Chi-restraints excluded: chain R residue 37 SER Chi-restraints excluded: chain R residue 124 GLU Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 173 SER Chi-restraints excluded: chain R residue 180 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: [237, 235, 242, 203, 146, 108, 218, 86, 69, 76, 153] chunk 237 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 218 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 153 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 ASN E 56 GLN F 17 ASN J 42 GLN J 120 ASN J 160 ASN K 42 GLN K 229 ASN L 229 ASN M 42 GLN N 62 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.117017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.085650 restraints weight = 77396.122| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 1.73 r_work: 0.2737 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.9763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22014 Z= 0.131 Angle : 0.487 5.273 29898 Z= 0.259 Chirality : 0.042 0.177 3393 Planarity : 0.004 0.097 3951 Dihedral : 4.154 20.850 3033 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.18 % Allowed : 19.79 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 are not related in a simple way. whole: 1.83 (0.16), residues: 2763 helix: 2.52 (0.16), residues: 1044 sheet: 1.16 (0.20), residues: 666 loop : -0.06 (0.20), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG J 234 TYR 0.010 0.001 TYR M 253 PHE 0.007 0.001 PHE D 51 TRP 0.006 0.001 TRP O 237 HIS 0.002 0.000 HIS P 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (22014) covalent geometry : angle 0.48682 / 0.26 (29898) hydrogen bonds : bond 0.03802 / 2.45 ( 1021) hydrogen bonds : angle 4.00193 / 2.96 ( 2985) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 295 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.7128 (mpp-170) REVERT: A 37 GLN cc_start: 0.7294 (mt0) cc_final: 0.6288 (tm-30) REVERT: C 8 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8348 (mtt180) REVERT: E 15 ASN cc_start: 0.8581 (t0) cc_final: 0.8343 (t0) REVERT: G 6 GLN cc_start: 0.8757 (mt0) cc_final: 0.8400 (mt0) REVERT: H 37 GLN cc_start: 0.6537 (mm-40) cc_final: 0.6201 (mt0) REVERT: J 22 LYS cc_start: 0.8420 (ttmm) cc_final: 0.7927 (mttm) REVERT: J 194 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7701 (mp) REVERT: J 241 ASN cc_start: 0.7479 (m-40) cc_final: 0.6994 (t0) REVERT: J 246 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8183 (mp10) REVERT: K 22 LYS cc_start: 0.8259 (tppp) cc_final: 0.7862 (ttmm) REVERT: K 185 GLU cc_start: 0.8746 (tt0) cc_final: 0.8498 (tt0) REVERT: L 11 ARG cc_start: 0.8363 (mtm110) cc_final: 0.8001 (mtm-85) REVERT: L 22 LYS cc_start: 0.8372 (ttmm) cc_final: 0.8104 (mtpm) REVERT: L 74 ASP cc_start: 0.8121 (p0) cc_final: 0.7818 (m-30) REVERT: L 242 LYS cc_start: 0.7867 (mttp) cc_final: 0.7135 (mmmt) REVERT: M 44 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8487 (mt-10) REVERT: M 74 ASP cc_start: 0.8025 (p0) cc_final: 0.7687 (m-30) REVERT: M 97 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7750 (mtt-85) REVERT: M 256 MET cc_start: 0.7594 (mtt) cc_final: 0.7339 (mtp) REVERT: N 11 ARG cc_start: 0.8529 (mtm-85) cc_final: 0.7953 (mtm-85) REVERT: N 22 LYS cc_start: 0.8228 (ttmm) cc_final: 0.7709 (mtmt) REVERT: O 11 ARG cc_start: 0.8259 (mtm110) cc_final: 0.7515 (mmp-170) REVERT: O 22 LYS cc_start: 0.8388 (ttmm) cc_final: 0.8163 (ttmm) REVERT: O 44 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8596 (mt-10) REVERT: O 97 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7791 (mtt180) REVERT: P 11 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7790 (mtm-85) REVERT: P 42 GLN cc_start: 0.8647 (mm-40) cc_final: 0.8158 (mm110) REVERT: Q 11 ARG cc_start: 0.8447 (ptp90) cc_final: 0.7988 (mtm-85) REVERT: Q 42 GLN cc_start: 0.8678 (mm-40) cc_final: 0.8239 (mm110) REVERT: Q 79 ILE cc_start: 0.9009 (tt) cc_final: 0.8797 (tt) REVERT: Q 113 LEU cc_start: 0.5809 (OUTLIER) cc_final: 0.5581 (pt) REVERT: R 22 LYS cc_start: 0.8229 (tppp) cc_final: 0.7716 (mmmt) REVERT: R 124 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7951 (pt0) REVERT: R 185 GLU cc_start: 0.8667 (tt0) cc_final: 0.8413 (tt0) REVERT: R 230 ASP cc_start: 0.8596 (t70) cc_final: 0.8222 (t0) outliers start: 51 outliers final: 24 residues processed: 330 average time/residue: 1.1929 time to fit residues: 453.5119 Evaluate side-chains 319 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 286 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ARG Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 194 ILE Chi-restraints excluded: chain J residue 246 GLN Chi-restraints excluded: chain K residue 217 MET Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain M residue 97 ARG Chi-restraints excluded: chain M residue 180 THR Chi-restraints excluded: chain M residue 197 GLN Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain N residue 207 THR Chi-restraints excluded: chain O residue 97 ARG Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain O residue 173 SER Chi-restraints excluded: chain O residue 180 THR Chi-restraints excluded: chain O residue 207 THR Chi-restraints excluded: chain O residue 238 ASP Chi-restraints excluded: chain P residue 11 ARG Chi-restraints excluded: chain P residue 37 SER Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain P residue 217 MET Chi-restraints excluded: chain Q residue 113 LEU Chi-restraints excluded: chain Q residue 124 GLU Chi-restraints excluded: chain R residue 37 SER Chi-restraints excluded: chain R residue 124 GLU Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 173 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: [172, 244, 95, 238, 219, 82, 43, 69, 196, 143, 129] chunk 172 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 238 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 chunk 196 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 129 optimal weight: 0.2980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 37 GLN D 56 GLN E 56 GLN J 42 GLN K 42 GLN K 229 ASN L 40 ASN L 229 ASN M 42 GLN M 62 GLN P 160 ASN Q 246 GLN R 55 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.114150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.083213 restraints weight = 78211.998| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 1.72 r_work: 0.2697 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2560 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 1.0076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22014 Z= 0.165 Angle : 0.517 5.955 29898 Z= 0.274 Chirality : 0.043 0.242 3393 Planarity : 0.004 0.097 3951 Dihedral : 4.295 22.173 3033 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.26 % Allowed : 19.79 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 are not related in a simple way. whole: 1.78 (0.16), residues: 2763 helix: 2.48 (0.16), residues: 1044 sheet: 1.15 (0.20), residues: 666 loop : -0.10 (0.20), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG J 234 TYR 0.012 0.001 TYR M 253 PHE 0.013 0.001 PHE A 51 TRP 0.005 0.001 TRP O 237 HIS 0.002 0.000 HIS P 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (22014) covalent geometry : angle 0.51720 / 0.27 (29898) hydrogen bonds : bond 0.04075 / 2.64 ( 1021) hydrogen bonds : angle 4.06544 / 3.01 ( 2985) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 299 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.7149 (mpp-170) REVERT: A 37 GLN cc_start: 0.7423 (mt0) cc_final: 0.6934 (mt0) REVERT: C 8 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8411 (mtt180) REVERT: G 6 GLN cc_start: 0.8763 (mt0) cc_final: 0.8370 (mt0) REVERT: H 37 GLN cc_start: 0.6671 (mm-40) cc_final: 0.6427 (mt0) REVERT: J 194 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7671 (mp) REVERT: J 196 TYR cc_start: 0.7725 (m-80) cc_final: 0.7498 (m-10) REVERT: J 241 ASN cc_start: 0.7463 (m-40) cc_final: 0.7060 (t0) REVERT: J 246 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8243 (mp10) REVERT: K 22 LYS cc_start: 0.8317 (tppp) cc_final: 0.7774 (ttmm) REVERT: K 25 THR cc_start: 0.9042 (m) cc_final: 0.8789 (p) REVERT: K 185 GLU cc_start: 0.8743 (tt0) cc_final: 0.8487 (tt0) REVERT: L 11 ARG cc_start: 0.8368 (mtm110) cc_final: 0.7983 (mtm-85) REVERT: L 22 LYS cc_start: 0.8446 (ttmm) cc_final: 0.8151 (mtpm) REVERT: L 74 ASP cc_start: 0.8144 (p0) cc_final: 0.7797 (m-30) REVERT: L 242 LYS cc_start: 0.8149 (mttp) cc_final: 0.7450 (mmmt) REVERT: M 44 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8524 (mt-10) REVERT: M 97 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7210 (mtp180) REVERT: N 11 ARG cc_start: 0.8537 (mtm-85) cc_final: 0.7945 (mtm-85) REVERT: O 11 ARG cc_start: 0.8284 (mtm110) cc_final: 0.7520 (mmp-170) REVERT: O 22 LYS cc_start: 0.8383 (ttmm) cc_final: 0.8168 (ttmm) REVERT: O 44 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8602 (mt-10) REVERT: O 97 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7743 (mtt180) REVERT: P 11 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7800 (mtm-85) REVERT: P 42 GLN cc_start: 0.8644 (mm-40) cc_final: 0.8153 (mm110) REVERT: Q 11 ARG cc_start: 0.8464 (ptp90) cc_final: 0.7945 (mtm-85) REVERT: Q 42 GLN cc_start: 0.8687 (mm-40) cc_final: 0.8255 (mm-40) REVERT: Q 79 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8808 (tt) REVERT: Q 113 LEU cc_start: 0.5818 (OUTLIER) cc_final: 0.5594 (pt) REVERT: R 22 LYS cc_start: 0.8240 (tppp) cc_final: 0.7733 (mmmt) REVERT: R 44 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8238 (mt-10) REVERT: R 124 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8032 (pt0) REVERT: R 185 GLU cc_start: 0.8699 (tt0) cc_final: 0.8413 (tt0) REVERT: R 234 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7356 (ptt180) outliers start: 53 outliers final: 29 residues processed: 332 average time/residue: 1.2227 time to fit residues: 467.7225 Evaluate side-chains 322 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 281 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ARG Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain F residue 15 ASN Chi-restraints excluded: chain H residue 15 ASN Chi-restraints excluded: chain I residue 46 ARG Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 194 ILE Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 246 GLN Chi-restraints excluded: chain K residue 217 MET Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain M residue 97 ARG Chi-restraints excluded: chain M residue 180 THR Chi-restraints excluded: chain M residue 197 GLN Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain N residue 207 THR Chi-restraints excluded: chain O residue 97 ARG Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain O residue 180 THR Chi-restraints excluded: chain O residue 207 THR Chi-restraints excluded: chain P residue 11 ARG Chi-restraints excluded: chain P residue 37 SER Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain P residue 217 MET Chi-restraints excluded: chain P residue 239 LEU Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 113 LEU Chi-restraints excluded: chain Q residue 124 GLU Chi-restraints excluded: chain R residue 37 SER Chi-restraints excluded: chain R residue 44 GLU Chi-restraints excluded: chain R residue 124 GLU Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 173 SER Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain R residue 234 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: [21, 7, 196, 165, 29, 57, 130, 60, 89, 39, 231] chunk 21 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 196 optimal weight: 0.9990 chunk 165 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 39 optimal weight: 10.0000 chunk 231 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 56 GLN K 42 GLN K 229 ASN M 40 ASN M 42 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.113603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.083316 restraints weight = 77642.268| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 1.65 r_work: 0.2676 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2544 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 moved from start: 1.0277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22014 Z= 0.153 Angle : 0.507 5.801 29898 Z= 0.270 Chirality : 0.042 0.147 3393 Planarity : 0.004 0.095 3951 Dihedral : 4.292 25.996 3033 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.05 % Allowed : 20.26 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 are not related in a simple way. whole: 1.79 (0.16), residues: 2763 helix: 2.51 (0.16), residues: 1044 sheet: 1.01 (0.20), residues: 684 loop : -0.03 (0.20), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG J 234 TYR 0.017 0.001 TYR K 196 PHE 0.014 0.001 PHE A 51 TRP 0.008 0.001 TRP O 237 HIS 0.002 0.000 HIS P 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.15 (22014) covalent geometry : angle 0.50741 / 0.27 (29898) hydrogen bonds : bond 0.03972 / 2.57 ( 1021) hydrogen bonds : angle 4.04819 / 3.00 ( 2985) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 286 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.7323 (mpp-170) REVERT: A 37 GLN cc_start: 0.7502 (mt0) cc_final: 0.7033 (mt0) REVERT: C 8 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8541 (mtt180) REVERT: G 6 GLN cc_start: 0.8791 (mt0) cc_final: 0.8453 (mt0) REVERT: J 15 MET cc_start: 0.8753 (ttt) cc_final: 0.8470 (ttt) REVERT: J 123 VAL cc_start: 0.9126 (OUTLIER) cc_final: 0.8892 (t) REVERT: J 196 TYR cc_start: 0.7815 (m-80) cc_final: 0.7463 (m-10) REVERT: J 241 ASN cc_start: 0.7596 (m-40) cc_final: 0.7284 (t0) REVERT: K 22 LYS cc_start: 0.8570 (tppp) cc_final: 0.8306 (ttmm) REVERT: K 241 ASN cc_start: 0.8055 (m-40) cc_final: 0.7354 (t0) REVERT: L 11 ARG cc_start: 0.8436 (mtm110) cc_final: 0.8149 (mtm-85) REVERT: L 74 ASP cc_start: 0.8222 (p0) cc_final: 0.7861 (m-30) REVERT: L 242 LYS cc_start: 0.8137 (mttp) cc_final: 0.7620 (mmmt) REVERT: M 44 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8487 (mt-10) REVERT: M 74 ASP cc_start: 0.8192 (p0) cc_final: 0.7819 (m-30) REVERT: M 97 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.8045 (mtt-85) REVERT: N 11 ARG cc_start: 0.8574 (mtm-85) cc_final: 0.8126 (mtm-85) REVERT: N 22 LYS cc_start: 0.8507 (ttmm) cc_final: 0.8034 (mtmt) REVERT: O 11 ARG cc_start: 0.8309 (mtm110) cc_final: 0.7829 (mmp-170) REVERT: O 44 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8624 (mt-10) REVERT: O 97 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7919 (mtt180) REVERT: P 11 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7952 (mtm-85) REVERT: P 42 GLN cc_start: 0.8683 (mm-40) cc_final: 0.8288 (mm110) REVERT: Q 11 ARG cc_start: 0.8545 (ptp90) cc_final: 0.8145 (mtm-85) REVERT: Q 42 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8376 (mm-40) REVERT: Q 79 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8856 (tt) REVERT: Q 113 LEU cc_start: 0.6162 (OUTLIER) cc_final: 0.5916 (pt) REVERT: R 22 LYS cc_start: 0.8500 (tppp) cc_final: 0.8028 (mmmt) REVERT: R 234 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7402 (ptt180) outliers start: 48 outliers final: 29 residues processed: 316 average time/residue: 1.2433 time to fit residues: 452.2698 Evaluate side-chains 319 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 281 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ARG Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain F residue 15 ASN Chi-restraints excluded: chain H residue 15 ASN Chi-restraints excluded: chain I residue 46 ARG Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain K residue 217 MET Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 159 VAL Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain M residue 97 ARG Chi-restraints excluded: chain M residue 180 THR Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain N residue 207 THR Chi-restraints excluded: chain O residue 97 ARG Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain O residue 173 SER Chi-restraints excluded: chain O residue 180 THR Chi-restraints excluded: chain O residue 207 THR Chi-restraints excluded: chain P residue 11 ARG Chi-restraints excluded: chain P residue 37 SER Chi-restraints excluded: chain P residue 124 GLU Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain P residue 217 MET Chi-restraints excluded: chain P residue 239 LEU Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 113 LEU Chi-restraints excluded: chain Q residue 124 GLU Chi-restraints excluded: chain R residue 37 SER Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 173 SER Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain R residue 234 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: [106, 132, 105, 196, 267, 102, 13, 140, 171, 215, 244] chunk 106 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 196 optimal weight: 0.9990 chunk 267 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 140 optimal weight: 0.2980 chunk 171 optimal weight: 0.9980 chunk 215 optimal weight: 0.5980 chunk 244 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 42 GLN ** J 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 42 GLN K 229 ASN L 197 GLN M 42 GLN Q 114 GLN R 114 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.116308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.084434 restraints weight = 77730.209| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 1.90 r_work: 0.2727 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 1.0338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 22014 Z= 0.108 Angle : 0.485 7.674 29898 Z= 0.257 Chirality : 0.042 0.144 3393 Planarity : 0.004 0.109 3951 Dihedral : 4.161 28.663 3033 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.62 % Allowed : 20.81 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 are not related in a simple way. whole: 1.90 (0.16), residues: 2763 helix: 2.59 (0.16), residues: 1044 sheet: 1.07 (0.20), residues: 684 loop : 0.06 (0.20), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG K 234 TYR 0.015 0.001 TYR M 196 PHE 0.012 0.001 PHE A 51 TRP 0.005 0.001 TRP K 237 HIS 0.001 0.000 HIS P 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (22014) covalent geometry : angle 0.48456 / 0.26 (29898) hydrogen bonds : bond 0.03600 / 2.34 ( 1021) hydrogen bonds : angle 3.99133 / 2.95 ( 2985) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5526 Ramachandran restraints generated. 2763 Oldfield, 0 Emsley, 2763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 292 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.7290 (mpp-170) REVERT: A 37 GLN cc_start: 0.7473 (mt0) cc_final: 0.6969 (mt0) REVERT: C 8 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.8547 (mtt180) REVERT: G 6 GLN cc_start: 0.8818 (mt0) cc_final: 0.8456 (mt0) REVERT: J 15 MET cc_start: 0.8828 (ttt) cc_final: 0.8554 (ttt) REVERT: J 123 VAL cc_start: 0.9086 (OUTLIER) cc_final: 0.8882 (t) REVERT: J 196 TYR cc_start: 0.7555 (m-80) cc_final: 0.7227 (m-10) REVERT: J 241 ASN cc_start: 0.7584 (m-40) cc_final: 0.7270 (t0) REVERT: K 22 LYS cc_start: 0.8337 (tppp) cc_final: 0.7916 (mttp) REVERT: K 241 ASN cc_start: 0.8098 (m-40) cc_final: 0.7367 (t0) REVERT: L 11 ARG cc_start: 0.8477 (mtm110) cc_final: 0.8043 (mtm-85) REVERT: L 74 ASP cc_start: 0.8108 (p0) cc_final: 0.7824 (m-30) REVERT: L 242 LYS cc_start: 0.8224 (mttp) cc_final: 0.8017 (mmtm) REVERT: M 44 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8594 (mt-10) REVERT: M 74 ASP cc_start: 0.7961 (p0) cc_final: 0.7749 (m-30) REVERT: M 97 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7941 (mtt-85) REVERT: M 242 LYS cc_start: 0.7906 (mppt) cc_final: 0.7534 (mmtm) REVERT: N 11 ARG cc_start: 0.8578 (mtm-85) cc_final: 0.8065 (mtm-85) REVERT: N 22 LYS cc_start: 0.8396 (ttmm) cc_final: 0.7900 (mtmt) REVERT: O 11 ARG cc_start: 0.8324 (mtm110) cc_final: 0.7787 (mmp-170) REVERT: O 44 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8645 (mt-10) REVERT: O 97 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7887 (mtt180) REVERT: P 11 ARG cc_start: 0.8319 (ttp80) cc_final: 0.7915 (mtm-85) REVERT: P 42 GLN cc_start: 0.8664 (mm-40) cc_final: 0.8253 (mm110) REVERT: Q 11 ARG cc_start: 0.8564 (ptp90) cc_final: 0.8093 (mtm-85) REVERT: Q 42 GLN cc_start: 0.8684 (mm-40) cc_final: 0.8313 (mm110) REVERT: Q 113 LEU cc_start: 0.6204 (OUTLIER) cc_final: 0.5956 (pt) REVERT: R 22 LYS cc_start: 0.8465 (tppp) cc_final: 0.7949 (mtpp) REVERT: R 42 GLN cc_start: 0.8698 (mm-40) cc_final: 0.8458 (mm-40) REVERT: R 230 ASP cc_start: 0.8723 (t70) cc_final: 0.8342 (t0) outliers start: 38 outliers final: 21 residues processed: 318 average time/residue: 1.2094 time to fit residues: 442.9425 Evaluate side-chains 307 residues out of total 2340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 280 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ARG Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain F residue 15 ASN Chi-restraints excluded: chain H residue 15 ASN Chi-restraints excluded: chain I residue 46 ARG Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain K residue 217 MET Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain M residue 97 ARG Chi-restraints excluded: chain M residue 204 VAL Chi-restraints excluded: chain O residue 97 ARG Chi-restraints excluded: chain O residue 180 THR Chi-restraints excluded: chain O residue 207 THR Chi-restraints excluded: chain O residue 238 ASP Chi-restraints excluded: chain P residue 37 SER Chi-restraints excluded: chain P residue 124 GLU Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain P residue 217 MET Chi-restraints excluded: chain Q residue 113 LEU Chi-restraints excluded: chain Q residue 124 GLU Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 173 SER Chi-restraints excluded: chain R residue 180 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: [225, 60, 79, 72, 206, 139, 53, 243, 127, 152, 70] chunk 225 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 chunk 206 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 243 optimal weight: 0.1980 chunk 127 optimal weight: 0.6980 chunk 152 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 42 GLN ** J 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 42 GLN K 229 ASN L 197 GLN M 42 GLN N 246 GLN Q 114 GLN R 55 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.115836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.083966 restraints weight = 78351.912| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 1.91 r_work: 0.2719 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9025 moved from start: 1.0368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22014 Z= 0.122 Angle : 0.494 6.400 29898 Z= 0.261 Chirality : 0.042 0.142 3393 Planarity : 0.004 0.072 3951 Dihedral : 4.139 26.649 3033 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.37 % Allowed : 21.07 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 are not related in a simple way. whole: 1.90 (0.16), residues: 2763 helix: 2.61 (0.16), residues: 1044 sheet: 0.91 (0.20), residues: 702 loop : 0.14 (0.21), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG R 234 TYR 0.020 0.001 TYR M 196 PHE 0.012 0.001 PHE A 51 TRP 0.004 0.001 TRP B 39 HIS 0.001 0.000 HIS P 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 (22014) covalent geometry : angle 0.49370 / 0.26 (29898) hydrogen bonds : bond 0.03644 / 2.36 ( 1021) hydrogen bonds : angle 3.97622 / 2.94 ( 2985) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13041.95 seconds wall clock time: 221 minutes 3.44 seconds (13263.44 seconds total)