Starting phenix.real_space_refine on Thu Aug 6 14:36:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8evi_28630/08_2026/8evi_28630.cif Found real_map, /net/cci-nas-00/data/ceres_data/8evi_28630/08_2026/8evi_28630.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8evi_28630/08_2026/8evi_28630.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8evi_28630/08_2026/8evi_28630.map" model { file = "/net/cci-nas-00/data/ceres_data/8evi_28630/08_2026/8evi_28630.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8evi_28630/08_2026/8evi_28630.cif" } resolution = 2.64 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= 0.004 sd= 0.120 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 P 285 5.49 5 S 37 5.16 5 C 9296 2.51 5 N 2927 2.21 5 O 3612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16157 Number of models: 1 Model: "" Number of chains: 13 Chain: "J" Number of atoms: 2931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2931 Classifications: {'DNA': 143} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 142} Chain: "I" Number of atoms: 2929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2929 Classifications: {'DNA': 143} Link IDs: {'rna3p': 142} Chain breaks: 1 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 819 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1769 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "N" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1769 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "O" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 748 Classifications: {'peptide': 89} Link IDs: {'TRANS': 88} Time building chain proxies: 3.31, per 1000 atoms: 0.20 Number of scatterers: 16157 At special positions: 0 Unit cell: (140.448, 130.944, 141.504, 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 37 16.00 P 285 15.00 O 3612 8.00 N 2927 7.00 C 9296 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 76 " - pdb=" SG CYS O 220 " distance=2.03 Simple disulfide: pdb=" SG CYS M 44 " - pdb=" SG CYS M 118 " distance=2.03 Simple disulfide: pdb=" SG CYS M 181 " - pdb=" SG CYS M 246 " distance=2.03 Simple disulfide: pdb=" SG CYS N 44 " - pdb=" SG CYS N 118 " distance=2.03 Simple disulfide: pdb=" SG CYS N 181 " - pdb=" SG CYS N 246 " distance=2.03 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: 1.26 Conformation dependent library (CDL) restraints added in 489.0 milliseconds 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2422 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 24 sheets defined 47.6% alpha, 19.2% beta 138 base pairs and 264 stacking pairs defined. Time for finding SS restraints: 2.22 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.035A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.748A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.513A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.742A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.518A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.780A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.422A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.775A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 50 through 52 No H-bonds generated for 'chain 'M' and resid 50 through 52' Processing helix chain 'M' and resid 84 through 87 Processing helix chain 'M' and resid 109 through 113 removed outlier: 3.868A pdb=" N SER M 113 " --> pdb=" O SER M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 237 through 241 removed outlier: 3.539A pdb=" N THR M 241 " --> pdb=" O SER M 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 52 No H-bonds generated for 'chain 'N' and resid 50 through 52' Processing helix chain 'N' and resid 109 through 113 removed outlier: 3.751A pdb=" N SER N 113 " --> pdb=" O SER N 110 " (cutoff:3.500A) Processing helix chain 'N' and resid 237 through 241 removed outlier: 4.008A pdb=" N THR N 241 " --> pdb=" O SER N 238 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 185 removed outlier: 4.062A pdb=" N GLN O 176 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU O 182 " --> pdb=" O LEU O 178 " (cutoff:3.500A) Processing helix chain 'O' and resid 207 through 220 Processing helix chain 'O' and resid 226 through 241 removed outlier: 3.783A pdb=" N ALA O 233 " --> pdb=" O LYS O 229 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU O 234 " --> pdb=" O MET O 230 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG O 235 " --> pdb=" O ALA O 231 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN O 236 " --> pdb=" O ARG O 232 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR O 237 " --> pdb=" O ALA O 233 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY O 238 " --> pdb=" O LEU O 234 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS O 239 " --> pdb=" O ARG O 235 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR O 240 " --> pdb=" O ASN O 236 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.064A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.625A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.160A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.182A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'M' and resid 25 through 26 Processing sheet with id=AB2, first strand: chain 'M' and resid 32 through 34 removed outlier: 3.608A pdb=" N GLU M 32 " --> pdb=" O SER M 137 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LYS M 60 " --> pdb=" O TRP M 69 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N TRP M 69 " --> pdb=" O LYS M 60 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR M 62 " --> pdb=" O LEU M 67 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N LEU M 67 " --> pdb=" O THR M 62 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 32 through 34 removed outlier: 3.608A pdb=" N GLU M 32 " --> pdb=" O SER M 137 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR M 131 " --> pdb=" O ARG M 120 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N SER M 122 " --> pdb=" O LEU M 129 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU M 129 " --> pdb=" O SER M 122 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 40 through 43 Processing sheet with id=AB5, first strand: chain 'M' and resid 168 through 171 removed outlier: 6.515A pdb=" N MET M 169 " --> pdb=" O GLU M 263 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU M 191 " --> pdb=" O TYR M 207 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N TYR M 207 " --> pdb=" O LEU M 191 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TRP M 193 " --> pdb=" O LEU M 205 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 168 through 171 removed outlier: 6.515A pdb=" N MET M 169 " --> pdb=" O GLU M 263 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR M 255 " --> pdb=" O GLN M 248 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 177 through 180 removed outlier: 3.795A pdb=" N ASP M 228 " --> pdb=" O SER M 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 25 through 26 Processing sheet with id=AB9, first strand: chain 'N' and resid 32 through 34 removed outlier: 6.500A pdb=" N ILE N 56 " --> pdb=" O TYR N 72 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TYR N 72 " --> pdb=" O ILE N 56 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TRP N 58 " --> pdb=" O ILE N 70 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 32 through 34 removed outlier: 3.854A pdb=" N TYR N 131 " --> pdb=" O ARG N 120 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N SER N 122 " --> pdb=" O LEU N 129 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LEU N 129 " --> pdb=" O SER N 122 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 40 through 43 Processing sheet with id=AC3, first strand: chain 'N' and resid 162 through 164 removed outlier: 3.829A pdb=" N VAL N 177 " --> pdb=" O ILE N 233 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE N 229 " --> pdb=" O CYS N 181 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP N 228 " --> pdb=" O SER N 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 168 through 171 removed outlier: 6.307A pdb=" N MET N 169 " --> pdb=" O GLU N 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'N' and resid 211 through 212 removed outlier: 6.454A pdb=" N TRP N 193 " --> pdb=" O LEU N 205 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N TYR N 207 " --> pdb=" O LEU N 191 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU N 191 " --> pdb=" O TYR N 207 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'O' and resid 191 through 195 removed outlier: 4.150A pdb=" N VAL O 194 " --> pdb=" O THR O 200 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N THR O 200 " --> pdb=" O VAL O 194 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN O 253 " --> pdb=" O LYS O 244 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS O 244 " --> pdb=" O GLN O 253 " (cutoff:3.500A) 567 hydrogen bonds defined for protein. 1587 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 342 hydrogen bonds 684 hydrogen bond angles 0 basepair planarities 138 basepair parallelities 264 stacking parallelities Total time for adding SS restraints: 3.70 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1917 1.30 - 1.43: 5964 1.43 - 1.56: 8539 1.56 - 1.69: 568 1.69 - 1.82: 60 Bond restraints: 17048 Sorted by residual: bond pdb=" C HIS D 46 " pdb=" O HIS D 46 " ideal model delta sigma weight residual 1.238 1.174 0.064 1.08e-02 8.57e+03 3.53e+01 bond pdb=" C GLN E 125 " pdb=" O GLN E 125 " ideal model delta sigma weight residual 1.237 1.169 0.068 1.19e-02 7.06e+03 3.26e+01 bond pdb=" C ARG B 92 " pdb=" O ARG B 92 " ideal model delta sigma weight residual 1.236 1.169 0.067 1.29e-02 6.01e+03 2.69e+01 bond pdb=" CA ARG B 92 " pdb=" C ARG B 92 " ideal model delta sigma weight residual 1.522 1.458 0.065 1.40e-02 5.10e+03 2.14e+01 bond pdb=" C ARG B 92 " pdb=" N GLN B 93 " ideal model delta sigma weight residual 1.334 1.275 0.058 1.30e-02 5.92e+03 2.00e+01 ... (remaining 17043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.24: 24233 7.24 - 14.49: 6 14.49 - 21.73: 0 21.73 - 28.98: 0 28.98 - 36.22: 1 Bond angle restraints: 24240 Sorted by residual: angle pdb=" C LYS O 249 " pdb=" CA LYS O 249 " pdb=" CB LYS O 249 " ideal model delta sigma weight residual 109.80 73.58 36.22 1.23e+00 6.61e-01 8.67e+02 angle pdb=" N LEU O 250 " pdb=" CA LEU O 250 " pdb=" C LEU O 250 " ideal model delta sigma weight residual 111.74 122.51 -10.77 1.35e+00 5.49e-01 6.37e+01 angle pdb=" N LEU O 250 " pdb=" CA LEU O 250 " pdb=" CB LEU O 250 " ideal model delta sigma weight residual 112.13 120.06 -7.93 1.51e+00 4.39e-01 2.75e+01 angle pdb=" C3' DA I 146 " pdb=" O3' DA I 146 " pdb=" P DT I 147 " ideal model delta sigma weight residual 119.70 125.31 -5.61 1.20e+00 6.94e-01 2.19e+01 angle pdb=" O4' DG J 84 " pdb=" C4' DG J 84 " pdb=" C3' DG J 84 " ideal model delta sigma weight residual 106.00 103.30 2.70 6.00e-01 2.78e+00 2.03e+01 ... (remaining 24235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.16: 7847 33.16 - 66.32: 1678 66.32 - 99.48: 38 99.48 - 132.64: 0 132.64 - 165.81: 2 Dihedral angle restraints: 9565 sinusoidal: 5787 harmonic: 3778 Sorted by residual: dihedral pdb=" C LYS O 249 " pdb=" N LYS O 249 " pdb=" CA LYS O 249 " pdb=" CB LYS O 249 " ideal model delta harmonic sigma weight residual -122.60 -80.24 -42.36 0 2.50e+00 1.60e-01 2.87e+02 dihedral pdb=" N LEU O 250 " pdb=" C LEU O 250 " pdb=" CA LEU O 250 " pdb=" CB LEU O 250 " ideal model delta harmonic sigma weight residual 122.80 151.21 -28.41 0 2.50e+00 1.60e-01 1.29e+02 dihedral pdb=" C LEU O 250 " pdb=" N LEU O 250 " pdb=" CA LEU O 250 " pdb=" CB LEU O 250 " ideal model delta harmonic sigma weight residual -122.60 -148.65 26.05 0 2.50e+00 1.60e-01 1.09e+02 ... (remaining 9562 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.243: 2718 0.243 - 0.487: 2 0.487 - 0.730: 0 0.730 - 0.973: 0 0.973 - 1.216: 1 Chirality restraints: 2721 Sorted by residual: chirality pdb=" CA LEU O 250 " pdb=" N LEU O 250 " pdb=" C LEU O 250 " pdb=" CB LEU O 250 " both_signs ideal model delta sigma weight residual False 2.51 1.29 1.22 2.00e-01 2.50e+01 3.70e+01 chirality pdb=" CA LYS O 249 " pdb=" N LYS O 249 " pdb=" C LYS O 249 " pdb=" CB LYS O 249 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CA GLN E 125 " pdb=" N GLN E 125 " pdb=" C GLN E 125 " pdb=" CB GLN E 125 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 2718 not shown) Planarity restraints: 2062 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT I 147 " -0.033 2.00e-02 2.50e+03 1.65e-02 6.84e+00 pdb=" N1 DT I 147 " 0.022 2.00e-02 2.50e+03 pdb=" C2 DT I 147 " -0.001 2.00e-02 2.50e+03 pdb=" O2 DT I 147 " 0.024 2.00e-02 2.50e+03 pdb=" N3 DT I 147 " -0.016 2.00e-02 2.50e+03 pdb=" C4 DT I 147 " -0.011 2.00e-02 2.50e+03 pdb=" O4 DT I 147 " -0.007 2.00e-02 2.50e+03 pdb=" C5 DT I 147 " 0.006 2.00e-02 2.50e+03 pdb=" C7 DT I 147 " 0.008 2.00e-02 2.50e+03 pdb=" C6 DT I 147 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 91 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.81e+00 pdb=" C LYS B 91 " 0.045 2.00e-02 2.50e+03 pdb=" O LYS B 91 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG B 92 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 24 " 0.009 2.00e-02 2.50e+03 1.87e-02 3.49e+00 pdb=" CG ASP B 24 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASP B 24 " 0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP B 24 " 0.011 2.00e-02 2.50e+03 ... (remaining 2059 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 180 2.62 - 3.19: 12967 3.19 - 3.76: 28525 3.76 - 4.33: 39717 4.33 - 4.90: 58056 Nonbonded interactions: 139445 Sorted by model distance: nonbonded pdb=" O LYS O 249 " pdb=" CB LYS O 249 " model vdw 2.045 2.752 nonbonded pdb=" N4 DC J 15 " pdb=" O6 DG I 148 " model vdw 2.132 3.120 nonbonded pdb=" OG1 THR O 240 " pdb=" OE1 GLU O 242 " model vdw 2.164 3.040 nonbonded pdb=" NH2 ARG N 120 " pdb=" OD2 ASP N 130 " model vdw 2.199 3.120 nonbonded pdb=" NE2 GLN C 104 " pdb=" OE2 GLU E 94 " model vdw 2.208 3.120 ... (remaining 139440 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 133) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 12 through 75 or resid 77 through 118)) selection = (chain 'G' and (resid 12 through 75 or resid 77 through 118)) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'M' selection = chain 'N' } 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 17.400 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 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:8.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 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 : 0.006 0.068 17053 Z= 0.503 Angle : 0.802 36.222 24250 Z= 0.651 Chirality : 0.052 1.216 2721 Planarity : 0.004 0.037 2062 Dihedral : 26.592 165.806 7128 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.09 % Allowed : 25.27 % Favored : 74.64 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.24), residues: 1275 helix: 2.21 (0.22), residues: 570 sheet: 0.25 (0.35), residues: 236 loop : -0.40 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG M 176 TYR 0.028 0.001 TYR O 175 PHE 0.025 0.002 PHE O 254 TRP 0.015 0.001 TRP O 193 HIS 0.004 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.50 (17048) covalent geometry : angle 0.80130 / 0.65 (24240) SS BOND : bond 0.00268 / 0.22 ( 5) SS BOND : angle 1.33082 / 2.64 ( 10) hydrogen bonds : bond 0.13329 / 15.03 ( 892) hydrogen bonds : angle 4.84404 / 6.05 ( 2271) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 205 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8528 (mtt) cc_final: 0.8185 (mtt) REVERT: C 36 LYS cc_start: 0.8677 (mmmm) cc_final: 0.8405 (mtpp) REVERT: C 42 ARG cc_start: 0.7903 (mtp85) cc_final: 0.7614 (mtp85) REVERT: D 82 LYS cc_start: 0.8566 (mtmm) cc_final: 0.8252 (mtmm) REVERT: D 113 LYS cc_start: 0.7665 (ttmt) cc_final: 0.7311 (ttpt) REVERT: E 64 LYS cc_start: 0.8323 (mttm) cc_final: 0.8115 (mttm) REVERT: G 73 ASN cc_start: 0.8401 (t0) cc_final: 0.7776 (t0) REVERT: G 91 GLU cc_start: 0.7964 (tt0) cc_final: 0.7641 (tt0) REVERT: H 34 TYR cc_start: 0.8495 (m-80) cc_final: 0.8252 (m-80) REVERT: H 60 ASN cc_start: 0.7991 (t0) cc_final: 0.7773 (t0) REVERT: H 68 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6942 (mt-10) REVERT: H 82 LYS cc_start: 0.8270 (mttp) cc_final: 0.8008 (mtmm) REVERT: M 261 LYS cc_start: 0.8517 (mtpp) cc_final: 0.7384 (tptt) REVERT: M 263 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7155 (mp0) REVERT: N 25 GLN cc_start: 0.7806 (mm-40) cc_final: 0.7496 (mm-40) REVERT: N 102 TYR cc_start: 0.8262 (m-80) cc_final: 0.7988 (m-80) REVERT: N 111 GLU cc_start: 0.8429 (pp20) cc_final: 0.8081 (pp20) REVERT: N 112 ASP cc_start: 0.8336 (m-30) cc_final: 0.7761 (m-30) REVERT: N 169 MET cc_start: 0.7898 (ptp) cc_final: 0.7598 (pmm) REVERT: N 180 THR cc_start: 0.8952 (m) cc_final: 0.8696 (p) REVERT: N 219 ARG cc_start: 0.8173 (mtm110) cc_final: 0.7532 (ptm160) REVERT: N 261 LYS cc_start: 0.8461 (mtpm) cc_final: 0.8253 (ttmt) REVERT: N 263 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7288 (tm-30) REVERT: O 187 MET cc_start: 0.3326 (ttt) cc_final: 0.3030 (ttp) REVERT: O 225 MET cc_start: 0.4728 (ptm) cc_final: 0.3922 (ppp) outliers start: 1 outliers final: 0 residues processed: 206 average time/residue: 0.7262 time to fit residues: 161.3018 Evaluate side-chains 165 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 30.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 76 GLN E 125 GLN G 110 ASN H 64 ASN M 27 GLN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 253 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.165251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.115099 restraints weight = 16497.623| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.55 r_work: 0.3291 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.0874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17053 Z= 0.150 Angle : 0.654 10.668 24250 Z= 0.374 Chirality : 0.045 0.261 2721 Planarity : 0.004 0.034 2062 Dihedral : 28.973 168.875 4605 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.97 % Allowed : 23.01 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.42 (0.24), residues: 1275 helix: 2.37 (0.22), residues: 575 sheet: 0.54 (0.37), residues: 196 loop : -0.59 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 214 TYR 0.014 0.001 TYR O 175 PHE 0.012 0.001 PHE O 254 TRP 0.011 0.001 TRP O 215 HIS 0.003 0.001 HIS O 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.15 (17048) covalent geometry : angle 0.65409 / 0.37 (24240) SS BOND : bond 0.00336 / 0.36 ( 5) SS BOND : angle 1.18027 / 2.36 ( 10) hydrogen bonds : bond 0.04842 / 5.18 ( 892) hydrogen bonds : angle 3.87228 / 5.01 ( 2271) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 160 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8407 (tttt) cc_final: 0.7452 (mptt) REVERT: A 94 GLU cc_start: 0.7900 (tp30) cc_final: 0.7639 (mm-30) REVERT: C 36 LYS cc_start: 0.8794 (mmmm) cc_final: 0.8575 (mtpp) REVERT: C 42 ARG cc_start: 0.7890 (mtp85) cc_final: 0.7423 (mtp85) REVERT: D 82 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8074 (mttm) REVERT: D 113 LYS cc_start: 0.7466 (ttmt) cc_final: 0.7026 (ttpp) REVERT: E 64 LYS cc_start: 0.8221 (mttm) cc_final: 0.8021 (mttm) REVERT: F 91 LYS cc_start: 0.8374 (tttm) cc_final: 0.8073 (tptt) REVERT: G 73 ASN cc_start: 0.7983 (t0) cc_final: 0.7454 (t0) REVERT: G 89 ASN cc_start: 0.8868 (m-40) cc_final: 0.8617 (m110) REVERT: G 91 GLU cc_start: 0.8012 (tt0) cc_final: 0.7775 (tt0) REVERT: H 34 TYR cc_start: 0.8516 (m-80) cc_final: 0.8283 (m-80) REVERT: H 68 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7162 (mt-10) REVERT: H 82 LYS cc_start: 0.8218 (mttp) cc_final: 0.7912 (mtmm) REVERT: M 95 ASP cc_start: 0.7918 (t0) cc_final: 0.7716 (t0) REVERT: M 261 LYS cc_start: 0.8521 (mtpp) cc_final: 0.7303 (tptt) REVERT: M 263 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7265 (mp0) REVERT: N 25 GLN cc_start: 0.7662 (mm-40) cc_final: 0.7371 (mm-40) REVERT: N 111 GLU cc_start: 0.8421 (pp20) cc_final: 0.8210 (pp20) REVERT: N 112 ASP cc_start: 0.7824 (m-30) cc_final: 0.7208 (m-30) REVERT: N 162 MET cc_start: 0.8893 (mmp) cc_final: 0.8565 (mmp) REVERT: N 261 LYS cc_start: 0.8429 (mtpm) cc_final: 0.8071 (ttmt) REVERT: O 187 MET cc_start: 0.3704 (ttt) cc_final: 0.3325 (ttt) REVERT: O 225 MET cc_start: 0.5254 (ptm) cc_final: 0.4460 (ppp) REVERT: O 253 GLN cc_start: 0.5569 (OUTLIER) cc_final: 0.3559 (mt0) outliers start: 44 outliers final: 11 residues processed: 188 average time/residue: 0.6669 time to fit residues: 135.8533 Evaluate side-chains 167 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain O residue 226 THR Chi-restraints excluded: chain O residue 253 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 11 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 131 optimal weight: 8.9990 chunk 54 optimal weight: 0.0370 chunk 79 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 overall best weight: 3.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN C 104 GLN E 76 GLN G 110 ASN H 60 ASN M 27 GLN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 253 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.159181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.108488 restraints weight = 16780.882| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.56 r_work: 0.3198 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 17053 Z= 0.287 Angle : 0.735 9.649 24250 Z= 0.406 Chirality : 0.051 0.290 2721 Planarity : 0.005 0.037 2062 Dihedral : 29.184 165.198 4605 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.33 % Allowed : 22.20 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.23), residues: 1275 helix: 1.72 (0.21), residues: 571 sheet: 0.51 (0.36), residues: 196 loop : -0.78 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 214 TYR 0.015 0.002 TYR N 72 PHE 0.026 0.002 PHE O 254 TRP 0.014 0.002 TRP O 193 HIS 0.005 0.002 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00640 / 0.29 (17048) covalent geometry : angle 0.73440 / 0.41 (24240) SS BOND : bond 0.00371 / 0.44 ( 5) SS BOND : angle 1.46142 / 2.90 ( 10) hydrogen bonds : bond 0.05938 / 6.42 ( 892) hydrogen bonds : angle 3.86619 / 4.95 ( 2271) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 151 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 36 LYS cc_start: 0.8740 (mmmm) cc_final: 0.8471 (mmmt) REVERT: C 42 ARG cc_start: 0.7949 (mtp85) cc_final: 0.7302 (mtp85) REVERT: D 60 ASN cc_start: 0.8217 (OUTLIER) cc_final: 0.7674 (m-40) REVERT: D 90 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7988 (mp0) REVERT: D 113 LYS cc_start: 0.7648 (ttmt) cc_final: 0.7192 (ttpt) REVERT: E 40 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.6879 (ttt-90) REVERT: E 90 MET cc_start: 0.7993 (mmm) cc_final: 0.6999 (mtp) REVERT: G 73 ASN cc_start: 0.8021 (t0) cc_final: 0.7461 (t0) REVERT: G 89 ASN cc_start: 0.8822 (m-40) cc_final: 0.8612 (m110) REVERT: G 95 LYS cc_start: 0.8349 (tttp) cc_final: 0.7921 (ttmt) REVERT: H 68 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7179 (mt-10) REVERT: H 82 LYS cc_start: 0.8097 (mttp) cc_final: 0.7872 (mtmm) REVERT: M 95 ASP cc_start: 0.7968 (t0) cc_final: 0.7763 (t0) REVERT: M 175 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7714 (mm-30) REVERT: M 235 ASN cc_start: 0.7863 (OUTLIER) cc_final: 0.6966 (m110) REVERT: M 261 LYS cc_start: 0.8538 (mtpp) cc_final: 0.7672 (mtpp) REVERT: M 263 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7445 (mp0) REVERT: N 23 GLU cc_start: 0.5585 (OUTLIER) cc_final: 0.5207 (tp30) REVERT: N 25 GLN cc_start: 0.7698 (mm-40) cc_final: 0.7402 (mm-40) REVERT: N 111 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8220 (pp20) REVERT: N 162 MET cc_start: 0.8975 (mmp) cc_final: 0.8549 (mmp) REVERT: N 261 LYS cc_start: 0.8361 (mtpm) cc_final: 0.8018 (ttpt) REVERT: O 225 MET cc_start: 0.5462 (ptm) cc_final: 0.4495 (ppp) outliers start: 48 outliers final: 19 residues processed: 181 average time/residue: 0.6974 time to fit residues: 136.6080 Evaluate side-chains 173 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 138 VAL Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain N residue 23 GLU Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain N residue 228 ASP Chi-restraints excluded: chain N residue 255 THR Chi-restraints excluded: chain O residue 226 THR Chi-restraints excluded: chain O residue 232 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 93 optimal weight: 0.0770 chunk 56 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 138 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 chunk 136 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 130 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN E 76 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN H 60 ASN M 25 GLN M 27 GLN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 253 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.162647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.112448 restraints weight = 16586.030| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.55 r_work: 0.3251 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17053 Z= 0.139 Angle : 0.664 8.737 24250 Z= 0.372 Chirality : 0.047 0.262 2721 Planarity : 0.004 0.035 2062 Dihedral : 29.177 168.109 4605 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.24 % Allowed : 23.19 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.24), residues: 1275 helix: 2.09 (0.22), residues: 573 sheet: 0.56 (0.37), residues: 196 loop : -0.70 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 176 TYR 0.014 0.001 TYR H 34 PHE 0.011 0.001 PHE F 61 TRP 0.012 0.001 TRP O 193 HIS 0.003 0.001 HIS M 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.14 (17048) covalent geometry : angle 0.66351 / 0.37 (24240) SS BOND : bond 0.00414 / 0.46 ( 5) SS BOND : angle 1.10854 / 2.22 ( 10) hydrogen bonds : bond 0.04658 / 4.97 ( 892) hydrogen bonds : angle 3.67533 / 4.74 ( 2271) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 154 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 GLU cc_start: 0.7168 (mp0) cc_final: 0.6966 (mp0) REVERT: B 74 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7661 (mt-10) REVERT: C 36 LYS cc_start: 0.8794 (mmmm) cc_final: 0.8520 (mmmt) REVERT: C 42 ARG cc_start: 0.7852 (mtp85) cc_final: 0.7325 (mtp85) REVERT: D 36 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.8099 (pt) REVERT: D 60 ASN cc_start: 0.8013 (OUTLIER) cc_final: 0.7538 (m-40) REVERT: D 82 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8073 (mttm) REVERT: D 90 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.8002 (mp0) REVERT: D 113 LYS cc_start: 0.7476 (ttmt) cc_final: 0.6980 (ttpt) REVERT: E 40 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.6951 (ttt-90) REVERT: E 131 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.6974 (mtp85) REVERT: G 73 ASN cc_start: 0.7932 (t0) cc_final: 0.7339 (t0) REVERT: G 84 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7348 (tm-30) REVERT: G 89 ASN cc_start: 0.8800 (m-40) cc_final: 0.8594 (m110) REVERT: G 95 LYS cc_start: 0.8331 (tttp) cc_final: 0.7907 (ttmt) REVERT: H 68 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.7100 (mt-10) REVERT: H 82 LYS cc_start: 0.8085 (mttp) cc_final: 0.7880 (mtmm) REVERT: M 111 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7742 (pp20) REVERT: M 175 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7638 (mm-30) REVERT: M 235 ASN cc_start: 0.7930 (OUTLIER) cc_final: 0.7017 (m110) REVERT: M 261 LYS cc_start: 0.8459 (mtpp) cc_final: 0.7557 (mtpp) REVERT: M 263 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7332 (mp0) REVERT: N 25 GLN cc_start: 0.7672 (mm-40) cc_final: 0.7389 (mm-40) REVERT: N 33 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7280 (mm) REVERT: N 95 ASP cc_start: 0.7712 (t70) cc_final: 0.7494 (t70) REVERT: N 162 MET cc_start: 0.8883 (mmp) cc_final: 0.8558 (mmp) REVERT: N 169 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.7508 (ptp) REVERT: N 261 LYS cc_start: 0.8385 (mtpm) cc_final: 0.7953 (ttpt) REVERT: O 211 LEU cc_start: 0.4374 (OUTLIER) cc_final: 0.4158 (tm) REVERT: O 225 MET cc_start: 0.5465 (ptm) cc_final: 0.4553 (ppp) outliers start: 47 outliers final: 16 residues processed: 182 average time/residue: 0.6735 time to fit residues: 132.9471 Evaluate side-chains 184 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain N residue 191 LEU Chi-restraints excluded: chain N residue 228 ASP Chi-restraints excluded: chain O residue 211 LEU Chi-restraints excluded: chain O residue 226 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 31 optimal weight: 0.7980 chunk 113 optimal weight: 20.0000 chunk 73 optimal weight: 0.1980 chunk 22 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 chunk 146 optimal weight: 20.0000 chunk 57 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 55 optimal weight: 0.0000 chunk 27 optimal weight: 40.0000 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN H 60 ASN M 25 GLN M 27 GLN N 61 GLN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.163205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.112835 restraints weight = 16726.274| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.56 r_work: 0.3258 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17053 Z= 0.146 Angle : 0.629 8.814 24250 Z= 0.357 Chirality : 0.044 0.284 2721 Planarity : 0.004 0.034 2062 Dihedral : 29.117 168.165 4605 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.88 % Allowed : 24.19 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.27 (0.24), residues: 1275 helix: 2.21 (0.22), residues: 573 sheet: 0.61 (0.37), residues: 196 loop : -0.66 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 96 TYR 0.012 0.001 TYR M 72 PHE 0.012 0.001 PHE O 254 TRP 0.012 0.001 TRP O 193 HIS 0.004 0.001 HIS M 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.15 (17048) covalent geometry : angle 0.62841 / 0.36 (24240) SS BOND : bond 0.00272 / 0.30 ( 5) SS BOND : angle 1.01001 / 2.02 ( 10) hydrogen bonds : bond 0.04499 / 4.79 ( 892) hydrogen bonds : angle 3.53528 / 4.58 ( 2271) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 159 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.7901 (tp30) cc_final: 0.7649 (mm-30) REVERT: B 74 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7709 (mt-10) REVERT: C 36 LYS cc_start: 0.8827 (mmmm) cc_final: 0.8514 (mmmt) REVERT: C 42 ARG cc_start: 0.7841 (mtp85) cc_final: 0.7317 (mtp85) REVERT: D 36 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.8108 (pt) REVERT: D 60 ASN cc_start: 0.8001 (OUTLIER) cc_final: 0.7564 (m-40) REVERT: D 82 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7945 (mttm) REVERT: D 90 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7954 (mp0) REVERT: D 113 LYS cc_start: 0.7421 (ttmt) cc_final: 0.6956 (ttpt) REVERT: E 40 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.6912 (ttt-90) REVERT: E 90 MET cc_start: 0.7935 (mmm) cc_final: 0.6946 (mtp) REVERT: F 92 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7365 (ptm160) REVERT: G 73 ASN cc_start: 0.7940 (t0) cc_final: 0.7367 (t0) REVERT: G 89 ASN cc_start: 0.8783 (m-40) cc_final: 0.8570 (m110) REVERT: H 68 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7155 (mt-10) REVERT: H 82 LYS cc_start: 0.8066 (mttp) cc_final: 0.7837 (mtmm) REVERT: M 38 THR cc_start: 0.7760 (p) cc_final: 0.7508 (t) REVERT: M 111 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7802 (pp20) REVERT: M 175 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7640 (mm-30) REVERT: M 235 ASN cc_start: 0.7917 (OUTLIER) cc_final: 0.7009 (m110) REVERT: M 261 LYS cc_start: 0.8542 (mtpp) cc_final: 0.7687 (mtpp) REVERT: M 263 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7327 (mp0) REVERT: N 25 GLN cc_start: 0.7679 (mm-40) cc_final: 0.7398 (mm-40) REVERT: N 33 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7198 (mm) REVERT: N 95 ASP cc_start: 0.7778 (t70) cc_final: 0.7520 (t70) REVERT: N 162 MET cc_start: 0.8896 (mmp) cc_final: 0.8638 (mmp) REVERT: N 175 GLU cc_start: 0.7622 (pm20) cc_final: 0.7290 (pm20) REVERT: N 261 LYS cc_start: 0.8427 (mtpm) cc_final: 0.8024 (ttpt) outliers start: 43 outliers final: 16 residues processed: 187 average time/residue: 0.6904 time to fit residues: 139.2352 Evaluate side-chains 181 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain N residue 191 LEU Chi-restraints excluded: chain N residue 228 ASP Chi-restraints excluded: chain O residue 226 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 54 optimal weight: 2.9990 chunk 134 optimal weight: 0.0870 chunk 42 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 19 optimal weight: 10.9990 chunk 104 optimal weight: 0.0370 chunk 118 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 overall best weight: 1.2240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN E 76 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN H 60 ASN M 25 GLN M 27 GLN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 253 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.163628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.113531 restraints weight = 16648.751| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.55 r_work: 0.3268 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17053 Z= 0.148 Angle : 0.629 8.499 24250 Z= 0.355 Chirality : 0.044 0.284 2721 Planarity : 0.004 0.034 2062 Dihedral : 29.113 168.288 4605 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.33 % Allowed : 24.19 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.24), residues: 1275 helix: 2.26 (0.22), residues: 573 sheet: 0.67 (0.37), residues: 196 loop : -0.63 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 96 TYR 0.013 0.001 TYR O 175 PHE 0.009 0.001 PHE F 61 TRP 0.012 0.001 TRP O 193 HIS 0.004 0.001 HIS M 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.15 (17048) covalent geometry : angle 0.62881 / 0.36 (24240) SS BOND : bond 0.00324 / 0.32 ( 5) SS BOND : angle 1.05307 / 2.10 ( 10) hydrogen bonds : bond 0.04382 / 4.66 ( 892) hydrogen bonds : angle 3.45369 / 4.47 ( 2271) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 158 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.7904 (tp30) cc_final: 0.7644 (mm-30) REVERT: B 74 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7763 (mt-10) REVERT: C 36 LYS cc_start: 0.8823 (mmmm) cc_final: 0.8512 (mmmt) REVERT: C 42 ARG cc_start: 0.7835 (mtp85) cc_final: 0.7321 (mtp85) REVERT: D 36 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8103 (pt) REVERT: D 60 ASN cc_start: 0.7998 (OUTLIER) cc_final: 0.7583 (m-40) REVERT: D 82 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7884 (mttm) REVERT: D 90 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7914 (mp0) REVERT: D 113 LYS cc_start: 0.7481 (ttmt) cc_final: 0.6987 (ttpt) REVERT: E 40 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.6917 (ttt-90) REVERT: E 90 MET cc_start: 0.7962 (mmm) cc_final: 0.6947 (mtp) REVERT: E 122 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7746 (ptmt) REVERT: F 92 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7350 (ptm160) REVERT: G 73 ASN cc_start: 0.7953 (t0) cc_final: 0.7357 (t0) REVERT: G 84 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7367 (tm-30) REVERT: H 34 TYR cc_start: 0.8652 (m-80) cc_final: 0.8393 (m-80) REVERT: H 68 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.7149 (mt-10) REVERT: H 82 LYS cc_start: 0.8067 (mttp) cc_final: 0.7838 (mtmm) REVERT: M 25 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7836 (tt0) REVERT: M 38 THR cc_start: 0.7756 (OUTLIER) cc_final: 0.7461 (t) REVERT: M 134 GLN cc_start: 0.8450 (pt0) cc_final: 0.8044 (mp10) REVERT: M 175 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7647 (mm-30) REVERT: M 235 ASN cc_start: 0.7905 (OUTLIER) cc_final: 0.6998 (m110) REVERT: M 261 LYS cc_start: 0.8550 (mtpp) cc_final: 0.8052 (mtpp) REVERT: N 25 GLN cc_start: 0.7702 (mm-40) cc_final: 0.7415 (mm-40) REVERT: N 95 ASP cc_start: 0.7792 (t70) cc_final: 0.7477 (t70) REVERT: N 103 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7685 (ttp) REVERT: N 162 MET cc_start: 0.8897 (mmp) cc_final: 0.8687 (mmp) REVERT: N 169 MET cc_start: 0.7781 (ptm) cc_final: 0.7456 (ptp) REVERT: N 175 GLU cc_start: 0.7558 (pm20) cc_final: 0.7241 (pm20) REVERT: N 261 LYS cc_start: 0.8435 (mtpm) cc_final: 0.8031 (ttpt) outliers start: 48 outliers final: 17 residues processed: 187 average time/residue: 0.6923 time to fit residues: 140.1027 Evaluate side-chains 186 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain M residue 25 GLN Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain N residue 191 LEU Chi-restraints excluded: chain O residue 226 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 77 optimal weight: 4.9990 chunk 72 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 151 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 11 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 15 optimal weight: 40.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN E 76 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN H 60 ASN M 25 GLN M 27 GLN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.164760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.114824 restraints weight = 16593.012| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.55 r_work: 0.3286 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17053 Z= 0.133 Angle : 0.615 8.483 24250 Z= 0.348 Chirality : 0.043 0.283 2721 Planarity : 0.004 0.034 2062 Dihedral : 29.072 168.794 4605 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.06 % Allowed : 24.19 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.24), residues: 1275 helix: 2.36 (0.22), residues: 573 sheet: 0.70 (0.37), residues: 196 loop : -0.59 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 96 TYR 0.012 0.001 TYR M 72 PHE 0.010 0.001 PHE O 254 TRP 0.012 0.001 TRP O 193 HIS 0.004 0.001 HIS M 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.13 (17048) covalent geometry : angle 0.61441 / 0.35 (24240) SS BOND : bond 0.00249 / 0.26 ( 5) SS BOND : angle 0.95253 / 1.91 ( 10) hydrogen bonds : bond 0.04196 / 4.46 ( 892) hydrogen bonds : angle 3.38590 / 4.40 ( 2271) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 158 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.7909 (tp30) cc_final: 0.7662 (mm-30) REVERT: A 120 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7352 (mtt) REVERT: B 74 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7783 (mt-10) REVERT: C 36 LYS cc_start: 0.8793 (mmmm) cc_final: 0.8507 (mmmt) REVERT: C 42 ARG cc_start: 0.7823 (mtp85) cc_final: 0.7324 (mtp85) REVERT: D 60 ASN cc_start: 0.7965 (OUTLIER) cc_final: 0.7574 (m-40) REVERT: D 82 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7905 (mttm) REVERT: D 90 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7931 (mp0) REVERT: D 113 LYS cc_start: 0.7464 (ttmt) cc_final: 0.6973 (ttpt) REVERT: E 40 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.6907 (ttt-90) REVERT: E 90 MET cc_start: 0.7897 (mmm) cc_final: 0.6870 (mtp) REVERT: E 122 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7802 (ptmm) REVERT: E 131 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7860 (mtt180) REVERT: G 73 ASN cc_start: 0.7932 (t0) cc_final: 0.7482 (t0) REVERT: G 84 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7401 (tm-30) REVERT: H 34 TYR cc_start: 0.8637 (m-80) cc_final: 0.8365 (m-80) REVERT: H 68 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.7143 (mt-10) REVERT: H 82 LYS cc_start: 0.8065 (mttp) cc_final: 0.7824 (mtmm) REVERT: M 25 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7602 (tm-30) REVERT: M 38 THR cc_start: 0.7813 (OUTLIER) cc_final: 0.7515 (t) REVERT: M 134 GLN cc_start: 0.8452 (pt0) cc_final: 0.8056 (mp10) REVERT: M 175 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7676 (mm-30) REVERT: M 235 ASN cc_start: 0.7895 (OUTLIER) cc_final: 0.6989 (m110) REVERT: M 261 LYS cc_start: 0.8544 (mtpp) cc_final: 0.8053 (mtpp) REVERT: N 25 GLN cc_start: 0.7698 (mm-40) cc_final: 0.7415 (mm-40) REVERT: N 95 ASP cc_start: 0.7799 (t70) cc_final: 0.7486 (t70) REVERT: N 103 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7657 (ttp) REVERT: N 108 LEU cc_start: 0.8190 (mp) cc_final: 0.7928 (mp) REVERT: N 169 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.7493 (ptp) REVERT: N 175 GLU cc_start: 0.7478 (pm20) cc_final: 0.7199 (pm20) REVERT: N 177 VAL cc_start: 0.8857 (OUTLIER) cc_final: 0.8616 (m) REVERT: N 219 ARG cc_start: 0.8187 (mtm110) cc_final: 0.7940 (ptm-80) REVERT: N 261 LYS cc_start: 0.8445 (mtpm) cc_final: 0.8039 (ttpt) REVERT: O 249 LYS cc_start: 0.6225 (OUTLIER) cc_final: 0.6022 (tppt) outliers start: 45 outliers final: 17 residues processed: 188 average time/residue: 0.6978 time to fit residues: 141.9014 Evaluate side-chains 187 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain M residue 25 GLN Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 177 VAL Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain N residue 191 LEU Chi-restraints excluded: chain O residue 226 THR Chi-restraints excluded: chain O residue 249 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 46 optimal weight: 0.0870 chunk 60 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 chunk 0 optimal weight: 50.0000 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN E 76 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN H 60 ASN M 25 GLN M 27 GLN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 253 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.159629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.107450 restraints weight = 16575.037| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.60 r_work: 0.3145 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17053 Z= 0.198 Angle : 0.649 8.414 24250 Z= 0.363 Chirality : 0.046 0.291 2721 Planarity : 0.004 0.034 2062 Dihedral : 29.140 167.256 4605 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.15 % Allowed : 24.10 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.24), residues: 1275 helix: 2.12 (0.22), residues: 573 sheet: 0.70 (0.37), residues: 196 loop : -0.66 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 96 TYR 0.015 0.002 TYR B 88 PHE 0.011 0.002 PHE O 254 TRP 0.013 0.001 TRP O 193 HIS 0.005 0.001 HIS M 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.20 (17048) covalent geometry : angle 0.64877 / 0.36 (24240) SS BOND : bond 0.00303 / 0.35 ( 5) SS BOND : angle 1.11028 / 2.21 ( 10) hydrogen bonds : bond 0.04764 / 5.09 ( 892) hydrogen bonds : angle 3.49177 / 4.51 ( 2271) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 157 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7598 (mt-10) REVERT: C 36 LYS cc_start: 0.8582 (mmmm) cc_final: 0.8314 (mmmt) REVERT: C 42 ARG cc_start: 0.7549 (mtp85) cc_final: 0.6866 (mtp85) REVERT: D 36 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7974 (pt) REVERT: D 60 ASN cc_start: 0.7811 (OUTLIER) cc_final: 0.7365 (m-40) REVERT: D 82 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7770 (mttm) REVERT: D 90 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7841 (mp0) REVERT: D 113 LYS cc_start: 0.7419 (ttmt) cc_final: 0.6969 (ttpt) REVERT: E 40 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.6745 (ttt-90) REVERT: E 90 MET cc_start: 0.7757 (mmm) cc_final: 0.6729 (mtp) REVERT: E 122 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7435 (ptmt) REVERT: E 131 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7032 (mtp85) REVERT: G 73 ASN cc_start: 0.7757 (t0) cc_final: 0.7281 (t0) REVERT: G 84 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7109 (tm-30) REVERT: H 34 TYR cc_start: 0.8519 (m-80) cc_final: 0.8177 (m-80) REVERT: H 68 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6952 (mt-10) REVERT: H 82 LYS cc_start: 0.7875 (mttp) cc_final: 0.7608 (mtmm) REVERT: M 25 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7652 (tm-30) REVERT: M 38 THR cc_start: 0.7636 (OUTLIER) cc_final: 0.7349 (t) REVERT: M 134 GLN cc_start: 0.8344 (pt0) cc_final: 0.8046 (pt0) REVERT: M 175 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7677 (mm-30) REVERT: M 235 ASN cc_start: 0.7863 (OUTLIER) cc_final: 0.6966 (m110) REVERT: M 261 LYS cc_start: 0.8423 (mtpp) cc_final: 0.8102 (mtpp) REVERT: N 25 GLN cc_start: 0.7547 (mm-40) cc_final: 0.7238 (mm-40) REVERT: N 95 ASP cc_start: 0.7604 (t70) cc_final: 0.7225 (t70) REVERT: N 103 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7647 (ttp) REVERT: N 108 LEU cc_start: 0.8039 (mp) cc_final: 0.7790 (mp) REVERT: N 162 MET cc_start: 0.8937 (mmp) cc_final: 0.8698 (mmp) REVERT: N 169 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7507 (ptp) REVERT: N 175 GLU cc_start: 0.7540 (pm20) cc_final: 0.7201 (pm20) REVERT: N 261 LYS cc_start: 0.8265 (mtpm) cc_final: 0.7863 (ttpt) REVERT: O 249 LYS cc_start: 0.6284 (OUTLIER) cc_final: 0.6083 (tppt) REVERT: O 250 LEU cc_start: 0.5219 (OUTLIER) cc_final: 0.4951 (tp) outliers start: 46 outliers final: 17 residues processed: 187 average time/residue: 0.7034 time to fit residues: 142.2876 Evaluate side-chains 189 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain M residue 25 GLN Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain N residue 191 LEU Chi-restraints excluded: chain O residue 226 THR Chi-restraints excluded: chain O residue 249 LYS Chi-restraints excluded: chain O residue 250 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 126 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 23 optimal weight: 10.0000 chunk 1 optimal weight: 40.0000 chunk 26 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN C 104 GLN E 76 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN H 60 ASN M 25 GLN M 27 GLN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.161312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.109293 restraints weight = 16604.105| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.60 r_work: 0.3173 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17053 Z= 0.144 Angle : 0.632 8.106 24250 Z= 0.355 Chirality : 0.044 0.281 2721 Planarity : 0.004 0.033 2062 Dihedral : 29.136 168.500 4605 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.98 % Allowed : 24.91 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.24), residues: 1275 helix: 2.20 (0.22), residues: 575 sheet: 0.71 (0.37), residues: 196 loop : -0.61 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 219 TYR 0.020 0.001 TYR B 88 PHE 0.010 0.001 PHE O 254 TRP 0.013 0.001 TRP O 193 HIS 0.004 0.001 HIS M 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 (17048) covalent geometry : angle 0.63152 / 0.35 (24240) SS BOND : bond 0.00261 / 0.29 ( 5) SS BOND : angle 1.00870 / 2.03 ( 10) hydrogen bonds : bond 0.04353 / 4.64 ( 892) hydrogen bonds : angle 3.43380 / 4.44 ( 2271) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.7765 (tp30) cc_final: 0.7519 (mm-30) REVERT: A 133 GLU cc_start: 0.7340 (mt-10) cc_final: 0.7036 (mt-10) REVERT: B 74 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7624 (mt-10) REVERT: C 36 LYS cc_start: 0.8669 (mmmm) cc_final: 0.8356 (mmmt) REVERT: C 42 ARG cc_start: 0.7592 (mtp85) cc_final: 0.7020 (mtp85) REVERT: D 60 ASN cc_start: 0.7730 (OUTLIER) cc_final: 0.7303 (m-40) REVERT: D 82 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7765 (mttm) REVERT: D 90 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7793 (mp0) REVERT: D 113 LYS cc_start: 0.7363 (ttmt) cc_final: 0.6879 (ttpt) REVERT: E 40 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.6853 (ttt-90) REVERT: E 90 MET cc_start: 0.7674 (mmm) cc_final: 0.6626 (mtp) REVERT: E 122 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7523 (ptmm) REVERT: E 131 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7721 (mtt180) REVERT: G 73 ASN cc_start: 0.7718 (t0) cc_final: 0.7241 (t0) REVERT: H 34 TYR cc_start: 0.8563 (m-80) cc_final: 0.8244 (m-80) REVERT: H 68 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6929 (mt-10) REVERT: H 82 LYS cc_start: 0.7873 (mttp) cc_final: 0.7606 (mtmm) REVERT: M 27 GLN cc_start: 0.7418 (mm-40) cc_final: 0.6922 (mm110) REVERT: M 38 THR cc_start: 0.7719 (OUTLIER) cc_final: 0.7402 (t) REVERT: M 134 GLN cc_start: 0.8326 (pt0) cc_final: 0.8046 (pt0) REVERT: M 175 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7653 (mm-30) REVERT: M 235 ASN cc_start: 0.7844 (OUTLIER) cc_final: 0.6939 (m110) REVERT: M 261 LYS cc_start: 0.8424 (mtpp) cc_final: 0.7962 (mtpp) REVERT: N 25 GLN cc_start: 0.7538 (mm-40) cc_final: 0.7232 (mm-40) REVERT: N 95 ASP cc_start: 0.7656 (t70) cc_final: 0.7301 (t70) REVERT: N 103 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7640 (ttp) REVERT: N 108 LEU cc_start: 0.8033 (mp) cc_final: 0.7760 (mp) REVERT: N 162 MET cc_start: 0.8884 (mmp) cc_final: 0.8593 (mmp) REVERT: N 169 MET cc_start: 0.7762 (ptm) cc_final: 0.7537 (ptp) REVERT: N 175 GLU cc_start: 0.7481 (pm20) cc_final: 0.7148 (pm20) REVERT: N 261 LYS cc_start: 0.8257 (mtpm) cc_final: 0.7856 (ttpt) outliers start: 33 outliers final: 16 residues processed: 178 average time/residue: 0.6922 time to fit residues: 133.0927 Evaluate side-chains 180 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain N residue 191 LEU Chi-restraints excluded: chain O residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 101 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 135 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 113 optimal weight: 20.0000 chunk 81 optimal weight: 0.9990 chunk 143 optimal weight: 0.9990 chunk 115 optimal weight: 0.4980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN C 104 GLN E 76 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN H 60 ASN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.161539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.109551 restraints weight = 16584.044| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.60 r_work: 0.3177 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17053 Z= 0.137 Angle : 0.627 8.146 24250 Z= 0.354 Chirality : 0.044 0.280 2721 Planarity : 0.004 0.039 2062 Dihedral : 29.126 168.447 4605 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.71 % Allowed : 25.09 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.24), residues: 1275 helix: 2.23 (0.22), residues: 575 sheet: 0.71 (0.37), residues: 196 loop : -0.60 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 219 TYR 0.027 0.001 TYR B 88 PHE 0.010 0.001 PHE O 254 TRP 0.012 0.001 TRP O 193 HIS 0.004 0.001 HIS M 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.14 (17048) covalent geometry : angle 0.62707 / 0.35 (24240) SS BOND : bond 0.00246 / 0.28 ( 5) SS BOND : angle 0.97120 / 1.95 ( 10) hydrogen bonds : bond 0.04292 / 4.57 ( 892) hydrogen bonds : angle 3.42369 / 4.44 ( 2271) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.7751 (tp30) cc_final: 0.7507 (mm-30) REVERT: B 74 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7619 (mt-10) REVERT: C 36 LYS cc_start: 0.8666 (mmmm) cc_final: 0.8354 (mmmt) REVERT: C 42 ARG cc_start: 0.7588 (mtp85) cc_final: 0.7017 (mtp85) REVERT: D 60 ASN cc_start: 0.7710 (OUTLIER) cc_final: 0.7289 (m-40) REVERT: D 82 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7764 (mttm) REVERT: D 90 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7760 (mp0) REVERT: D 113 LYS cc_start: 0.7360 (ttmt) cc_final: 0.6876 (ttpt) REVERT: E 40 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.6846 (ttt-90) REVERT: E 90 MET cc_start: 0.7670 (mmm) cc_final: 0.6622 (mtp) REVERT: E 122 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7531 (ptmm) REVERT: E 131 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7721 (mtt180) REVERT: G 73 ASN cc_start: 0.7718 (t0) cc_final: 0.7240 (t0) REVERT: H 34 TYR cc_start: 0.8562 (m-80) cc_final: 0.8240 (m-80) REVERT: H 68 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6926 (mt-10) REVERT: H 82 LYS cc_start: 0.7873 (mttp) cc_final: 0.7605 (mtmm) REVERT: M 27 GLN cc_start: 0.7462 (mm-40) cc_final: 0.6944 (mm110) REVERT: M 38 THR cc_start: 0.7730 (OUTLIER) cc_final: 0.7421 (t) REVERT: M 175 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7659 (mm-30) REVERT: M 235 ASN cc_start: 0.7858 (OUTLIER) cc_final: 0.6956 (m110) REVERT: M 261 LYS cc_start: 0.8447 (mtpp) cc_final: 0.7982 (mtpp) REVERT: N 25 GLN cc_start: 0.7536 (mm-40) cc_final: 0.7231 (mm-40) REVERT: N 95 ASP cc_start: 0.7662 (t70) cc_final: 0.7282 (t70) REVERT: N 103 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.7634 (ttp) REVERT: N 108 LEU cc_start: 0.8075 (mp) cc_final: 0.7805 (mp) REVERT: N 162 MET cc_start: 0.8884 (mmp) cc_final: 0.8592 (mmp) REVERT: N 169 MET cc_start: 0.7811 (ptm) cc_final: 0.7546 (ptp) REVERT: N 175 GLU cc_start: 0.7397 (pm20) cc_final: 0.7096 (pm20) REVERT: N 261 LYS cc_start: 0.8289 (mtpm) cc_final: 0.7883 (ttpt) outliers start: 30 outliers final: 16 residues processed: 178 average time/residue: 0.7208 time to fit residues: 138.2283 Evaluate side-chains 181 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain N residue 191 LEU Chi-restraints excluded: chain O residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 44 optimal weight: 0.8980 chunk 135 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 151 optimal weight: 30.0000 chunk 24 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 78 optimal weight: 0.0030 chunk 95 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 75 optimal weight: 0.7980 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN E 76 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN H 60 ASN ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.161778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.109815 restraints weight = 16568.287| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.60 r_work: 0.3180 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17053 Z= 0.145 Angle : 0.633 12.232 24250 Z= 0.354 Chirality : 0.043 0.285 2721 Planarity : 0.004 0.033 2062 Dihedral : 29.109 168.549 4605 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.80 % Allowed : 25.09 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.24), residues: 1275 helix: 2.26 (0.22), residues: 573 sheet: 0.70 (0.37), residues: 196 loop : -0.58 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 96 TYR 0.013 0.001 TYR D 37 PHE 0.009 0.001 PHE F 61 TRP 0.013 0.001 TRP O 193 HIS 0.004 0.001 HIS M 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.15 (17048) covalent geometry : angle 0.63251 / 0.35 (24240) SS BOND : bond 0.00235 / 0.25 ( 5) SS BOND : angle 0.95601 / 1.92 ( 10) hydrogen bonds : bond 0.04288 / 4.55 ( 892) hydrogen bonds : angle 3.39853 / 4.42 ( 2271) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6041.29 seconds wall clock time: 103 minutes 8.39 seconds (6188.39 seconds total)