Starting phenix.real_space_refine on Fri Mar 6 03:28:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7svu_25453/03_2026/7svu_25453.cif Found real_map, /net/cci-nas-00/data/ceres_data/7svu_25453/03_2026/7svu_25453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7svu_25453/03_2026/7svu_25453.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7svu_25453/03_2026/7svu_25453.map" model { file = "/net/cci-nas-00/data/ceres_data/7svu_25453/03_2026/7svu_25453.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7svu_25453/03_2026/7svu_25453.cif" } resolution = 3.5 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= 0.176 sd= 0.689 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: 6 Type Number sf(0) Gaussians P 89 5.49 5 Mg 11 5.21 5 S 116 5.16 5 C 17459 2.51 5 N 5051 2.21 5 O 5289 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28015 Number of models: 1 Model: "" Number of chains: 35 Chain: "1" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 560 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "2" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 588 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain breaks: 1 Chain: "A" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "a" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "B" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "b" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "C" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "c" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "D" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "d" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "E" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "e" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "F" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "f" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "G" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "H" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "h" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "I" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "J" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "j" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "K" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "k" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "X" Number of atoms: 1314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1314 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 13, 'TRANS': 151} Chain: "Y" Number of atoms: 1314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1314 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 13, 'TRANS': 151} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.23, per 1000 atoms: 0.22 Number of scatterers: 28015 At special positions: 0 Unit cell: (136.99, 142.31, 168.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 116 16.00 P 89 15.00 Mg 11 11.99 O 5289 8.00 N 5051 7.00 C 17459 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM 484 O5' DT 1 25 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 1.0 seconds 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6156 Finding SS restraints... Secondary structure from input PDB file: 181 helices and 22 sheets defined 59.9% alpha, 6.0% beta 22 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 3.27 Creating SS restraints... Processing helix chain 'A' and resid 19 through 29 Processing helix chain 'A' and resid 36 through 53 Processing helix chain 'A' and resid 65 through 75 Processing helix chain 'A' and resid 101 through 113 removed outlier: 3.874A pdb=" N PHE A 106 " --> pdb=" O PRO A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 134 Processing helix chain 'A' and resid 145 through 149 Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 153 through 164 Processing helix chain 'A' and resid 173 through 181 removed outlier: 4.012A pdb=" N ASP A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 190 removed outlier: 3.954A pdb=" N ARG A 189 " --> pdb=" O GLN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 215 Processing helix chain 'A' and resid 226 through 238 removed outlier: 4.355A pdb=" N ILE A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 258 removed outlier: 3.657A pdb=" N ARG A 258 " --> pdb=" O ARG A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 273 Processing helix chain 'a' and resid 575 through 581 removed outlier: 3.931A pdb=" N ARG a 579 " --> pdb=" O TYR a 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 29 Processing helix chain 'B' and resid 36 through 53 Processing helix chain 'B' and resid 65 through 75 Processing helix chain 'B' and resid 101 through 113 removed outlier: 3.874A pdb=" N PHE B 106 " --> pdb=" O PRO B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 134 Processing helix chain 'B' and resid 145 through 149 Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 153 through 164 Processing helix chain 'B' and resid 173 through 181 removed outlier: 4.013A pdb=" N ASP B 177 " --> pdb=" O THR B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 190 removed outlier: 3.955A pdb=" N ARG B 189 " --> pdb=" O GLN B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 215 Processing helix chain 'B' and resid 226 through 238 removed outlier: 4.356A pdb=" N ILE B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 258 removed outlier: 3.657A pdb=" N ARG B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'b' and resid 575 through 581 removed outlier: 3.930A pdb=" N ARG b 579 " --> pdb=" O TYR b 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 29 Processing helix chain 'C' and resid 36 through 53 Processing helix chain 'C' and resid 65 through 75 Processing helix chain 'C' and resid 101 through 113 removed outlier: 3.874A pdb=" N PHE C 106 " --> pdb=" O PRO C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 134 Processing helix chain 'C' and resid 145 through 149 Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 153 through 164 Processing helix chain 'C' and resid 173 through 181 removed outlier: 4.011A pdb=" N ASP C 177 " --> pdb=" O THR C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 190 removed outlier: 3.954A pdb=" N ARG C 189 " --> pdb=" O GLN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 215 Processing helix chain 'C' and resid 226 through 238 removed outlier: 4.355A pdb=" N ILE C 232 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 258 removed outlier: 3.656A pdb=" N ARG C 258 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 273 Processing helix chain 'c' and resid 575 through 581 removed outlier: 3.930A pdb=" N ARG c 579 " --> pdb=" O TYR c 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 29 Processing helix chain 'D' and resid 36 through 53 Processing helix chain 'D' and resid 65 through 75 Processing helix chain 'D' and resid 101 through 113 removed outlier: 3.874A pdb=" N PHE D 106 " --> pdb=" O PRO D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 134 Processing helix chain 'D' and resid 145 through 149 Processing helix chain 'D' and resid 150 through 152 No H-bonds generated for 'chain 'D' and resid 150 through 152' Processing helix chain 'D' and resid 153 through 164 Processing helix chain 'D' and resid 173 through 181 removed outlier: 4.013A pdb=" N ASP D 177 " --> pdb=" O THR D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 190 removed outlier: 3.955A pdb=" N ARG D 189 " --> pdb=" O GLN D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 215 Processing helix chain 'D' and resid 226 through 238 removed outlier: 4.356A pdb=" N ILE D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 258 removed outlier: 3.657A pdb=" N ARG D 258 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 273 Processing helix chain 'd' and resid 575 through 581 removed outlier: 3.931A pdb=" N ARG d 579 " --> pdb=" O TYR d 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 29 Processing helix chain 'E' and resid 36 through 53 Processing helix chain 'E' and resid 65 through 75 Processing helix chain 'E' and resid 101 through 113 removed outlier: 3.873A pdb=" N PHE E 106 " --> pdb=" O PRO E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 134 Processing helix chain 'E' and resid 145 through 149 Processing helix chain 'E' and resid 150 through 152 No H-bonds generated for 'chain 'E' and resid 150 through 152' Processing helix chain 'E' and resid 153 through 164 Processing helix chain 'E' and resid 173 through 181 removed outlier: 4.011A pdb=" N ASP E 177 " --> pdb=" O THR E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 190 removed outlier: 3.954A pdb=" N ARG E 189 " --> pdb=" O GLN E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 215 Processing helix chain 'E' and resid 226 through 238 removed outlier: 4.355A pdb=" N ILE E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 258 removed outlier: 3.657A pdb=" N ARG E 258 " --> pdb=" O ARG E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 273 Processing helix chain 'e' and resid 575 through 581 removed outlier: 3.931A pdb=" N ARG e 579 " --> pdb=" O TYR e 575 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 29 Processing helix chain 'F' and resid 36 through 53 Processing helix chain 'F' and resid 65 through 75 Processing helix chain 'F' and resid 101 through 113 removed outlier: 3.874A pdb=" N PHE F 106 " --> pdb=" O PRO F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 134 Processing helix chain 'F' and resid 145 through 149 Processing helix chain 'F' and resid 150 through 152 No H-bonds generated for 'chain 'F' and resid 150 through 152' Processing helix chain 'F' and resid 153 through 164 Processing helix chain 'F' and resid 173 through 181 removed outlier: 4.013A pdb=" N ASP F 177 " --> pdb=" O THR F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 190 removed outlier: 3.954A pdb=" N ARG F 189 " --> pdb=" O GLN F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 215 Processing helix chain 'F' and resid 226 through 238 removed outlier: 4.356A pdb=" N ILE F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 258 removed outlier: 3.657A pdb=" N ARG F 258 " --> pdb=" O ARG F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 273 Processing helix chain 'f' and resid 575 through 581 removed outlier: 3.930A pdb=" N ARG f 579 " --> pdb=" O TYR f 575 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 29 Processing helix chain 'G' and resid 36 through 53 Processing helix chain 'G' and resid 65 through 75 Processing helix chain 'G' and resid 101 through 112 removed outlier: 4.070A pdb=" N PHE G 106 " --> pdb=" O PRO G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 134 Processing helix chain 'G' and resid 145 through 149 Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 153 through 164 Processing helix chain 'G' and resid 173 through 181 removed outlier: 4.085A pdb=" N ASP G 177 " --> pdb=" O THR G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 190 removed outlier: 3.555A pdb=" N GLU G 188 " --> pdb=" O GLU G 184 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG G 189 " --> pdb=" O GLN G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 215 Processing helix chain 'G' and resid 226 through 238 removed outlier: 3.979A pdb=" N ILE G 232 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 258 Processing helix chain 'G' and resid 264 through 273 Processing helix chain 'H' and resid 20 through 29 Processing helix chain 'H' and resid 36 through 53 removed outlier: 3.725A pdb=" N THR H 41 " --> pdb=" O GLN H 37 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU H 42 " --> pdb=" O GLN H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 75 Processing helix chain 'H' and resid 101 through 113 removed outlier: 4.025A pdb=" N PHE H 106 " --> pdb=" O PRO H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 134 Processing helix chain 'H' and resid 145 through 149 Processing helix chain 'H' and resid 150 through 152 No H-bonds generated for 'chain 'H' and resid 150 through 152' Processing helix chain 'H' and resid 153 through 164 Processing helix chain 'H' and resid 173 through 181 removed outlier: 4.067A pdb=" N ASP H 177 " --> pdb=" O THR H 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 190 removed outlier: 3.572A pdb=" N GLU H 188 " --> pdb=" O GLU H 184 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG H 189 " --> pdb=" O GLN H 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 200 through 215 Processing helix chain 'H' and resid 226 through 238 removed outlier: 4.260A pdb=" N ILE H 232 " --> pdb=" O GLU H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 258 removed outlier: 3.591A pdb=" N ARG H 258 " --> pdb=" O ARG H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 264 through 273 Processing helix chain 'h' and resid 576 through 581 Processing helix chain 'I' and resid 20 through 29 Processing helix chain 'I' and resid 36 through 53 Processing helix chain 'I' and resid 65 through 75 Processing helix chain 'I' and resid 101 through 112 removed outlier: 4.069A pdb=" N PHE I 106 " --> pdb=" O PRO I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 134 Processing helix chain 'I' and resid 145 through 149 Processing helix chain 'I' and resid 150 through 152 No H-bonds generated for 'chain 'I' and resid 150 through 152' Processing helix chain 'I' and resid 153 through 164 Processing helix chain 'I' and resid 173 through 181 removed outlier: 4.085A pdb=" N ASP I 177 " --> pdb=" O THR I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 190 removed outlier: 3.554A pdb=" N GLU I 188 " --> pdb=" O GLU I 184 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG I 189 " --> pdb=" O GLN I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 200 through 215 Processing helix chain 'I' and resid 226 through 238 removed outlier: 3.980A pdb=" N ILE I 232 " --> pdb=" O GLU I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 240 through 258 Processing helix chain 'I' and resid 264 through 273 Processing helix chain 'J' and resid 20 through 29 Processing helix chain 'J' and resid 36 through 53 removed outlier: 3.726A pdb=" N THR J 41 " --> pdb=" O GLN J 37 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU J 42 " --> pdb=" O GLN J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 75 Processing helix chain 'J' and resid 101 through 113 removed outlier: 4.025A pdb=" N PHE J 106 " --> pdb=" O PRO J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 134 Processing helix chain 'J' and resid 145 through 149 Processing helix chain 'J' and resid 150 through 152 No H-bonds generated for 'chain 'J' and resid 150 through 152' Processing helix chain 'J' and resid 153 through 164 Processing helix chain 'J' and resid 173 through 181 removed outlier: 4.066A pdb=" N ASP J 177 " --> pdb=" O THR J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 190 removed outlier: 3.573A pdb=" N GLU J 188 " --> pdb=" O GLU J 184 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG J 189 " --> pdb=" O GLN J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 200 through 215 Processing helix chain 'J' and resid 226 through 238 removed outlier: 4.259A pdb=" N ILE J 232 " --> pdb=" O GLU J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 240 through 258 removed outlier: 3.590A pdb=" N ARG J 258 " --> pdb=" O ARG J 254 " (cutoff:3.500A) Processing helix chain 'J' and resid 264 through 273 Processing helix chain 'j' and resid 576 through 581 Processing helix chain 'K' and resid 20 through 29 Processing helix chain 'K' and resid 36 through 53 removed outlier: 3.726A pdb=" N THR K 41 " --> pdb=" O GLN K 37 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU K 42 " --> pdb=" O GLN K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 65 through 75 Processing helix chain 'K' and resid 101 through 113 removed outlier: 4.025A pdb=" N PHE K 106 " --> pdb=" O PRO K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 134 Processing helix chain 'K' and resid 145 through 149 Processing helix chain 'K' and resid 150 through 152 No H-bonds generated for 'chain 'K' and resid 150 through 152' Processing helix chain 'K' and resid 153 through 164 Processing helix chain 'K' and resid 173 through 181 removed outlier: 4.067A pdb=" N ASP K 177 " --> pdb=" O THR K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 190 removed outlier: 3.573A pdb=" N GLU K 188 " --> pdb=" O GLU K 184 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG K 189 " --> pdb=" O GLN K 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 200 through 215 Processing helix chain 'K' and resid 226 through 238 removed outlier: 4.259A pdb=" N ILE K 232 " --> pdb=" O GLU K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 240 through 258 removed outlier: 3.591A pdb=" N ARG K 258 " --> pdb=" O ARG K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 264 through 273 Processing helix chain 'k' and resid 576 through 581 Processing helix chain 'X' and resid 21 through 33 Processing helix chain 'X' and resid 36 through 45 Processing helix chain 'X' and resid 47 through 53 removed outlier: 4.403A pdb=" N VAL X 50 " --> pdb=" O GLY X 47 " (cutoff:3.500A) Processing helix chain 'X' and resid 65 through 75 removed outlier: 3.983A pdb=" N ALA X 71 " --> pdb=" O LEU X 67 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER X 72 " --> pdb=" O GLU X 68 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL X 73 " --> pdb=" O ALA X 69 " (cutoff:3.500A) Processing helix chain 'X' and resid 77 through 83 Processing helix chain 'X' and resid 100 through 104 Processing helix chain 'X' and resid 111 through 116 Processing helix chain 'X' and resid 142 through 146 Processing helix chain 'X' and resid 158 through 164 removed outlier: 4.017A pdb=" N LYS X 163 " --> pdb=" O GLU X 160 " (cutoff:3.500A) Processing helix chain 'Y' and resid 21 through 33 Processing helix chain 'Y' and resid 36 through 45 Processing helix chain 'Y' and resid 47 through 53 removed outlier: 4.404A pdb=" N VAL Y 50 " --> pdb=" O GLY Y 47 " (cutoff:3.500A) Processing helix chain 'Y' and resid 65 through 75 removed outlier: 3.982A pdb=" N ALA Y 71 " --> pdb=" O LEU Y 67 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER Y 72 " --> pdb=" O GLU Y 68 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL Y 73 " --> pdb=" O ALA Y 69 " (cutoff:3.500A) Processing helix chain 'Y' and resid 77 through 83 Processing helix chain 'Y' and resid 100 through 104 Processing helix chain 'Y' and resid 111 through 116 Processing helix chain 'Y' and resid 142 through 146 Processing helix chain 'Y' and resid 158 through 164 removed outlier: 4.018A pdb=" N LYS Y 163 " --> pdb=" O GLU Y 160 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 33 Processing sheet with id=AA2, first strand: chain 'A' and resid 91 through 94 removed outlier: 6.597A pdb=" N LEU A 141 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL A 171 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE A 143 " --> pdb=" O VAL A 171 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 32 through 33 Processing sheet with id=AA4, first strand: chain 'B' and resid 91 through 94 removed outlier: 6.597A pdb=" N LEU B 141 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL B 171 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE B 143 " --> pdb=" O VAL B 171 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=AA6, first strand: chain 'C' and resid 91 through 94 removed outlier: 6.597A pdb=" N LEU C 141 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL C 171 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE C 143 " --> pdb=" O VAL C 171 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 32 through 33 Processing sheet with id=AA8, first strand: chain 'D' and resid 91 through 94 removed outlier: 6.597A pdb=" N LEU D 141 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL D 171 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE D 143 " --> pdb=" O VAL D 171 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 32 through 33 Processing sheet with id=AB1, first strand: chain 'E' and resid 91 through 94 removed outlier: 6.597A pdb=" N LEU E 141 " --> pdb=" O VAL E 169 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL E 171 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE E 143 " --> pdb=" O VAL E 171 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 32 through 33 Processing sheet with id=AB3, first strand: chain 'F' and resid 91 through 94 removed outlier: 6.598A pdb=" N LEU F 141 " --> pdb=" O VAL F 169 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL F 171 " --> pdb=" O LEU F 141 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE F 143 " --> pdb=" O VAL F 171 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 91 through 94 removed outlier: 6.750A pdb=" N VAL G 92 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU G 141 " --> pdb=" O VAL G 169 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL G 171 " --> pdb=" O LEU G 141 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE G 143 " --> pdb=" O VAL G 171 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 32 through 33 Processing sheet with id=AB6, first strand: chain 'H' and resid 91 through 94 removed outlier: 6.765A pdb=" N VAL H 92 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU H 141 " --> pdb=" O VAL H 169 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL H 171 " --> pdb=" O LEU H 141 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE H 143 " --> pdb=" O VAL H 171 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 91 through 94 removed outlier: 6.751A pdb=" N VAL I 92 " --> pdb=" O ILE I 142 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU I 141 " --> pdb=" O VAL I 169 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL I 171 " --> pdb=" O LEU I 141 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE I 143 " --> pdb=" O VAL I 171 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 32 through 33 Processing sheet with id=AB9, first strand: chain 'J' and resid 91 through 94 removed outlier: 6.765A pdb=" N VAL J 92 " --> pdb=" O ILE J 142 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU J 141 " --> pdb=" O VAL J 169 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL J 171 " --> pdb=" O LEU J 141 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE J 143 " --> pdb=" O VAL J 171 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 32 through 33 Processing sheet with id=AC2, first strand: chain 'K' and resid 91 through 94 removed outlier: 6.765A pdb=" N VAL K 92 " --> pdb=" O ILE K 142 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU K 141 " --> pdb=" O VAL K 169 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL K 171 " --> pdb=" O LEU K 141 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE K 143 " --> pdb=" O VAL K 171 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'X' and resid 121 through 122 Processing sheet with id=AC4, first strand: chain 'Y' and resid 121 through 122 1301 hydrogen bonds defined for protein. 3693 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 44 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 4.68 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 4484 1.29 - 1.42: 7161 1.42 - 1.55: 16626 1.55 - 1.69: 168 1.69 - 1.82: 170 Bond restraints: 28609 Sorted by residual: bond pdb=" C5 ATP J 302 " pdb=" N7 ATP J 302 " ideal model delta sigma weight residual 1.387 1.286 0.101 1.00e-02 1.00e+04 1.02e+02 bond pdb=" C4 ATP J 302 " pdb=" N9 ATP J 302 " ideal model delta sigma weight residual 1.374 1.278 0.096 1.00e-02 1.00e+04 9.19e+01 bond pdb=" C4 ATP A 302 " pdb=" C5 ATP A 302 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.04e+01 bond pdb=" C4 ATP D 302 " pdb=" C5 ATP D 302 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.95e+01 bond pdb=" C4 ATP G 302 " pdb=" C5 ATP G 302 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.93e+01 ... (remaining 28604 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.40: 37852 5.40 - 10.79: 875 10.79 - 16.19: 44 16.19 - 21.58: 24 21.58 - 26.98: 2 Bond angle restraints: 38797 Sorted by residual: angle pdb=" PA ATP J 302 " pdb=" O3A ATP J 302 " pdb=" PB ATP J 302 " ideal model delta sigma weight residual 136.83 109.85 26.98 1.00e+00 1.00e+00 7.28e+02 angle pdb=" PB ATP J 302 " pdb=" O3B ATP J 302 " pdb=" PG ATP J 302 " ideal model delta sigma weight residual 139.87 113.39 26.48 1.00e+00 1.00e+00 7.01e+02 angle pdb=" PB ATP B 302 " pdb=" O3B ATP B 302 " pdb=" PG ATP B 302 " ideal model delta sigma weight residual 139.87 120.44 19.43 1.00e+00 1.00e+00 3.78e+02 angle pdb=" PB ATP C 302 " pdb=" O3B ATP C 302 " pdb=" PG ATP C 302 " ideal model delta sigma weight residual 139.87 120.46 19.41 1.00e+00 1.00e+00 3.77e+02 angle pdb=" PB ATP A 302 " pdb=" O3B ATP A 302 " pdb=" PG ATP A 302 " ideal model delta sigma weight residual 139.87 120.47 19.40 1.00e+00 1.00e+00 3.76e+02 ... (remaining 38792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.98: 16977 29.98 - 59.95: 665 59.95 - 89.93: 93 89.93 - 119.90: 1 119.90 - 149.88: 4 Dihedral angle restraints: 17740 sinusoidal: 8222 harmonic: 9518 Sorted by residual: dihedral pdb=" N ARG J 116 " pdb=" C ARG J 116 " pdb=" CA ARG J 116 " pdb=" CB ARG J 116 " ideal model delta harmonic sigma weight residual 122.80 138.90 -16.10 0 2.50e+00 1.60e-01 4.15e+01 dihedral pdb=" C TYR j 582 " pdb=" N TYR j 582 " pdb=" CA TYR j 582 " pdb=" CB TYR j 582 " ideal model delta harmonic sigma weight residual -122.60 -137.36 14.76 0 2.50e+00 1.60e-01 3.48e+01 dihedral pdb=" C TYR k 582 " pdb=" N TYR k 582 " pdb=" CA TYR k 582 " pdb=" CB TYR k 582 " ideal model delta harmonic sigma weight residual -122.60 -137.33 14.73 0 2.50e+00 1.60e-01 3.47e+01 ... (remaining 17737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 3637 0.134 - 0.267: 536 0.267 - 0.401: 83 0.401 - 0.534: 14 0.534 - 0.668: 12 Chirality restraints: 4282 Sorted by residual: chirality pdb=" CA TYR j 582 " pdb=" N TYR j 582 " pdb=" C TYR j 582 " pdb=" CB TYR j 582 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" CA TYR k 582 " pdb=" N TYR k 582 " pdb=" C TYR k 582 " pdb=" CB TYR k 582 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" CA TYR e 582 " pdb=" N TYR e 582 " pdb=" C TYR e 582 " pdb=" CB TYR e 582 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.11e+01 ... (remaining 4279 not shown) Planarity restraints: 4690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 255 " -0.030 2.00e-02 2.50e+03 5.94e-02 3.52e+01 pdb=" C SER A 255 " 0.103 2.00e-02 2.50e+03 pdb=" O SER A 255 " -0.037 2.00e-02 2.50e+03 pdb=" N LEU A 256 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 255 " -0.030 2.00e-02 2.50e+03 5.93e-02 3.52e+01 pdb=" C SER F 255 " 0.103 2.00e-02 2.50e+03 pdb=" O SER F 255 " -0.037 2.00e-02 2.50e+03 pdb=" N LEU F 256 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 255 " 0.030 2.00e-02 2.50e+03 5.93e-02 3.52e+01 pdb=" C SER D 255 " -0.103 2.00e-02 2.50e+03 pdb=" O SER D 255 " 0.037 2.00e-02 2.50e+03 pdb=" N LEU D 256 " 0.036 2.00e-02 2.50e+03 ... (remaining 4687 not shown) Histogram of nonbonded interaction distances: 0.87 - 1.68: 30 1.68 - 2.48: 279 2.48 - 3.29: 32569 3.29 - 4.09: 66214 4.09 - 4.90: 117354 Warning: very small nonbonded interaction distances. Nonbonded interactions: 216446 Sorted by model distance: nonbonded pdb=" CZ ARG F 116 " pdb=" OE2 GLU K 184 " model vdw 0.871 3.270 nonbonded pdb=" NH2 ARG B 85 " pdb=" C LYS I 273 " model vdw 0.897 3.350 nonbonded pdb=" NH2 ARG F 116 " pdb=" OE2 GLU K 184 " model vdw 0.949 3.120 nonbonded pdb=" NH2 ARG A 85 " pdb=" C LYS H 273 " model vdw 0.964 3.350 nonbonded pdb=" CG1 VAL I 220 " pdb=" O LYS I 261 " model vdw 0.974 3.460 ... (remaining 216441 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'X' selection = chain 'Y' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'h' selection = chain 'j' selection = chain 'k' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 26.010 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.090 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 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 : 0.023 0.993 28617 Z= 1.867 Angle : 1.915 26.975 38797 Z= 1.453 Chirality : 0.108 0.668 4282 Planarity : 0.011 0.076 4690 Dihedral : 15.097 149.877 11584 Min Nonbonded Distance : 0.871 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.28 % Favored : 97.56 % Rotamer: Outliers : 0.42 % Allowed : 2.80 % Favored : 96.78 % Cbeta Deviations : 0.39 % 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: -0.41 (0.14), residues: 3239 helix: -0.71 (0.11), residues: 1810 sheet: 2.49 (0.30), residues: 253 loop : 0.13 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Y 155 TYR 0.026 0.002 TYR G 112 PHE 0.027 0.001 PHE F 125 TRP 0.013 0.002 TRP Y 10 HIS 0.004 0.000 HIS Y 152 Details of bonding type rmsd covalent geometry : bond 0.01954 (28609) covalent geometry : angle 1.91536 (38797) hydrogen bonds : bond 0.26080 ( 1345) hydrogen bonds : angle 7.78225 ( 3781) Misc. bond : bond 0.71833 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1515 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 1503 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 LYS cc_start: 0.7247 (mttt) cc_final: 0.6317 (mtpp) REVERT: A 183 ASP cc_start: 0.7583 (t0) cc_final: 0.7348 (t70) REVERT: B 42 LEU cc_start: 0.8379 (tp) cc_final: 0.8071 (tt) REVERT: B 53 ARG cc_start: 0.8234 (mmt-90) cc_final: 0.6921 (mmt90) REVERT: B 104 ASP cc_start: 0.8384 (m-30) cc_final: 0.8056 (m-30) REVERT: B 132 VAL cc_start: 0.8763 (m) cc_final: 0.8376 (t) REVERT: C 36 LEU cc_start: 0.8563 (mt) cc_final: 0.8338 (mp) REVERT: C 78 LYS cc_start: 0.7228 (mttt) cc_final: 0.6360 (mtpp) REVERT: C 113 LEU cc_start: 0.9077 (mt) cc_final: 0.8865 (mp) REVERT: C 125 PHE cc_start: 0.8777 (m-10) cc_final: 0.8524 (m-80) REVERT: C 130 ILE cc_start: 0.9291 (mm) cc_final: 0.9076 (mt) REVERT: C 136 CYS cc_start: 0.6789 (t) cc_final: 0.6405 (t) REVERT: C 145 GLU cc_start: 0.7343 (mt-10) cc_final: 0.7112 (mt-10) REVERT: D 25 ILE cc_start: 0.6918 (mm) cc_final: 0.6685 (mm) REVERT: D 73 TYR cc_start: 0.8844 (t80) cc_final: 0.8556 (t80) REVERT: D 78 LYS cc_start: 0.8027 (mttt) cc_final: 0.7531 (mmmm) REVERT: D 132 VAL cc_start: 0.8744 (m) cc_final: 0.8373 (p) REVERT: E 33 ILE cc_start: 0.8898 (mt) cc_final: 0.8494 (mt) REVERT: E 47 ASP cc_start: 0.5398 (t70) cc_final: 0.5087 (t70) REVERT: E 53 ARG cc_start: 0.8154 (mmt-90) cc_final: 0.7894 (mpt180) REVERT: E 78 LYS cc_start: 0.7479 (mttt) cc_final: 0.6753 (mtpp) REVERT: E 89 VAL cc_start: 0.7578 (t) cc_final: 0.7291 (m) REVERT: E 93 TYR cc_start: 0.8633 (t80) cc_final: 0.8019 (t80) REVERT: E 144 ASP cc_start: 0.8459 (t0) cc_final: 0.8093 (t0) REVERT: E 159 ASP cc_start: 0.7352 (t70) cc_final: 0.6983 (t0) REVERT: E 163 ASP cc_start: 0.6178 (t70) cc_final: 0.5820 (t0) REVERT: F 34 VAL cc_start: 0.8419 (t) cc_final: 0.7988 (m) REVERT: F 41 THR cc_start: 0.8352 (m) cc_final: 0.8139 (m) REVERT: F 42 LEU cc_start: 0.8462 (tp) cc_final: 0.8217 (tt) REVERT: F 49 LYS cc_start: 0.8693 (mmtt) cc_final: 0.8442 (mmmm) REVERT: G 115 TYR cc_start: 0.7959 (t80) cc_final: 0.6410 (t80) REVERT: G 153 THR cc_start: 0.8722 (p) cc_final: 0.8505 (t) REVERT: G 180 ILE cc_start: 0.9060 (mt) cc_final: 0.8857 (mm) REVERT: G 268 LEU cc_start: 0.8967 (tp) cc_final: 0.8521 (tt) REVERT: G 269 GLN cc_start: 0.7805 (mt0) cc_final: 0.7546 (mt0) REVERT: G 275 TYR cc_start: 0.6406 (m-80) cc_final: 0.5998 (m-80) REVERT: H 64 THR cc_start: 0.8349 (p) cc_final: 0.8146 (p) REVERT: H 89 VAL cc_start: 0.8633 (t) cc_final: 0.8328 (m) REVERT: H 132 VAL cc_start: 0.8755 (m) cc_final: 0.8470 (t) REVERT: H 184 GLU cc_start: 0.6849 (mt-10) cc_final: 0.6373 (mt-10) REVERT: H 232 ILE cc_start: 0.8302 (mt) cc_final: 0.8089 (mt) REVERT: h 573 TRP cc_start: 0.7670 (m-90) cc_final: 0.7468 (m-90) REVERT: I 25 ILE cc_start: 0.7916 (mm) cc_final: 0.7689 (mm) REVERT: I 33 ILE cc_start: 0.8870 (mt) cc_final: 0.8650 (mm) REVERT: I 44 ASP cc_start: 0.7698 (m-30) cc_final: 0.7491 (m-30) REVERT: I 64 THR cc_start: 0.8336 (p) cc_final: 0.8133 (p) REVERT: I 240 TYR cc_start: 0.8569 (m-80) cc_final: 0.8334 (m-80) REVERT: I 268 LEU cc_start: 0.8837 (tp) cc_final: 0.8577 (tp) REVERT: J 29 LYS cc_start: 0.8469 (ttpt) cc_final: 0.8221 (ttpp) REVERT: J 47 ASP cc_start: 0.7743 (t70) cc_final: 0.7482 (t0) REVERT: J 91 VAL cc_start: 0.8841 (t) cc_final: 0.8632 (p) REVERT: J 104 ASP cc_start: 0.7781 (m-30) cc_final: 0.7558 (m-30) REVERT: J 124 ASP cc_start: 0.7962 (m-30) cc_final: 0.7405 (m-30) REVERT: J 129 THR cc_start: 0.8665 (m) cc_final: 0.8405 (t) REVERT: J 211 TRP cc_start: 0.8211 (t-100) cc_final: 0.7840 (t-100) REVERT: J 220 VAL cc_start: 0.8367 (OUTLIER) cc_final: 0.8040 (t) REVERT: J 235 SER cc_start: 0.8846 (t) cc_final: 0.8585 (p) REVERT: J 246 GLU cc_start: 0.6675 (tt0) cc_final: 0.6372 (tt0) REVERT: J 268 LEU cc_start: 0.8813 (tp) cc_final: 0.8541 (tt) REVERT: K 58 VAL cc_start: 0.9306 (t) cc_final: 0.9104 (p) REVERT: K 91 VAL cc_start: 0.8304 (t) cc_final: 0.7998 (m) REVERT: K 121 THR cc_start: 0.7298 (t) cc_final: 0.6825 (t) REVERT: K 145 GLU cc_start: 0.7354 (mt-10) cc_final: 0.7120 (mt-10) REVERT: K 164 LEU cc_start: 0.7717 (mt) cc_final: 0.7424 (mt) REVERT: K 220 VAL cc_start: 0.5870 (OUTLIER) cc_final: 0.5622 (t) REVERT: X 35 LEU cc_start: 0.8484 (pt) cc_final: 0.8069 (pp) REVERT: Y 13 LEU cc_start: 0.8212 (mm) cc_final: 0.7919 (mm) REVERT: Y 25 PHE cc_start: 0.7999 (t80) cc_final: 0.7506 (t80) outliers start: 12 outliers final: 7 residues processed: 1513 average time/residue: 0.2053 time to fit residues: 461.0183 Evaluate side-chains 1136 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 1127 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 119 LYS Chi-restraints excluded: chain I residue 220 VAL Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 220 VAL Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 224 LEU Chi-restraints excluded: chain Y residue 158 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.3980 chunk 261 optimal weight: 0.0970 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN D 81 GLN D 269 GLN F 43 HIS f 577 GLN G 38 GLN G 98 GLN ** H 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 206 ASN J 38 GLN J 80 GLN J 185 GLN K 38 GLN X 34 HIS X 57 HIS X 94 HIS Y 137 GLN Y 165 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.124054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.104908 restraints weight = 56502.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.107943 restraints weight = 25157.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.109836 restraints weight = 13989.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.111020 restraints weight = 9215.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.111730 restraints weight = 7014.912| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28617 Z= 0.157 Angle : 0.711 11.024 38797 Z= 0.383 Chirality : 0.046 0.257 4282 Planarity : 0.006 0.095 4690 Dihedral : 16.033 154.714 4713 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.64 % Allowed : 16.46 % Favored : 79.89 % 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: 1.21 (0.15), residues: 3239 helix: 1.08 (0.12), residues: 1838 sheet: 2.54 (0.33), residues: 253 loop : 0.10 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 85 TYR 0.017 0.001 TYR B 112 PHE 0.024 0.002 PHE F 125 TRP 0.022 0.002 TRP X 114 HIS 0.007 0.001 HIS X 57 Details of bonding type rmsd covalent geometry : bond 0.00331 (28609) covalent geometry : angle 0.71089 (38797) hydrogen bonds : bond 0.05050 ( 1345) hydrogen bonds : angle 4.80407 ( 3781) Misc. bond : bond 0.00478 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1306 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 1202 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.8475 (m-30) cc_final: 0.8158 (m-30) REVERT: A 124 ASP cc_start: 0.8112 (m-30) cc_final: 0.7828 (m-30) REVERT: A 144 ASP cc_start: 0.7674 (m-30) cc_final: 0.7421 (m-30) REVERT: A 188 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7794 (mm-30) REVERT: A 247 ILE cc_start: 0.7546 (mm) cc_final: 0.7096 (mm) REVERT: B 31 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8323 (mmmt) REVERT: B 62 SER cc_start: 0.7350 (p) cc_final: 0.6499 (p) REVERT: B 73 TYR cc_start: 0.8847 (t80) cc_final: 0.8402 (t80) REVERT: B 110 THR cc_start: 0.8678 (m) cc_final: 0.8429 (m) REVERT: B 125 PHE cc_start: 0.8869 (m-80) cc_final: 0.8606 (m-80) REVERT: B 140 MET cc_start: 0.8336 (ttm) cc_final: 0.7950 (ttp) REVERT: B 183 ASP cc_start: 0.7298 (t0) cc_final: 0.6966 (t0) REVERT: B 275 TYR cc_start: 0.6237 (m-80) cc_final: 0.5681 (m-80) REVERT: C 24 GLU cc_start: 0.8447 (mm-30) cc_final: 0.7963 (mm-30) REVERT: C 40 LYS cc_start: 0.8459 (tttt) cc_final: 0.7939 (ttpt) REVERT: C 47 ASP cc_start: 0.8108 (t70) cc_final: 0.7724 (t0) REVERT: C 125 PHE cc_start: 0.8858 (m-10) cc_final: 0.8499 (m-80) REVERT: C 129 THR cc_start: 0.8491 (OUTLIER) cc_final: 0.7822 (p) REVERT: C 136 CYS cc_start: 0.7046 (t) cc_final: 0.6781 (t) REVERT: C 183 ASP cc_start: 0.7408 (t0) cc_final: 0.7112 (t0) REVERT: C 204 PHE cc_start: 0.7585 (t80) cc_final: 0.7109 (t80) REVERT: C 206 ASN cc_start: 0.8672 (m-40) cc_final: 0.8450 (m110) REVERT: C 210 MET cc_start: 0.8081 (mtp) cc_final: 0.7878 (mtp) REVERT: C 230 LEU cc_start: 0.8563 (mt) cc_final: 0.8325 (mp) REVERT: C 260 LEU cc_start: 0.7504 (mm) cc_final: 0.7232 (mp) REVERT: c 575 TYR cc_start: 0.8509 (t80) cc_final: 0.7917 (t80) REVERT: D 25 ILE cc_start: 0.7650 (mm) cc_final: 0.7303 (mm) REVERT: D 61 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7208 (mm-30) REVERT: D 73 TYR cc_start: 0.8890 (t80) cc_final: 0.8664 (t80) REVERT: D 89 VAL cc_start: 0.8749 (t) cc_final: 0.8389 (m) REVERT: D 111 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7454 (mt-10) REVERT: D 144 ASP cc_start: 0.8549 (t0) cc_final: 0.7944 (m-30) REVERT: D 177 ASP cc_start: 0.8385 (m-30) cc_final: 0.8158 (m-30) REVERT: D 182 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7402 (mpp80) REVERT: d 581 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6636 (tm-30) REVERT: E 89 VAL cc_start: 0.7906 (t) cc_final: 0.7535 (m) REVERT: E 92 VAL cc_start: 0.8944 (m) cc_final: 0.8677 (p) REVERT: E 93 TYR cc_start: 0.8873 (t80) cc_final: 0.8658 (t80) REVERT: E 144 ASP cc_start: 0.8790 (t0) cc_final: 0.8349 (t0) REVERT: E 159 ASP cc_start: 0.7631 (t70) cc_final: 0.7307 (t0) REVERT: E 163 ASP cc_start: 0.7035 (t70) cc_final: 0.6573 (t0) REVERT: E 186 VAL cc_start: 0.8216 (m) cc_final: 0.7966 (p) REVERT: F 34 VAL cc_start: 0.8903 (t) cc_final: 0.8624 (m) REVERT: F 49 LYS cc_start: 0.8886 (mmtt) cc_final: 0.8429 (mmmm) REVERT: F 88 THR cc_start: 0.8316 (m) cc_final: 0.7644 (t) REVERT: F 140 MET cc_start: 0.7293 (OUTLIER) cc_final: 0.6929 (ttp) REVERT: F 145 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7247 (mt-10) REVERT: F 164 LEU cc_start: 0.8495 (mt) cc_final: 0.8023 (mp) REVERT: F 173 THR cc_start: 0.8870 (t) cc_final: 0.8615 (p) REVERT: F 187 LEU cc_start: 0.8677 (tt) cc_final: 0.8388 (tp) REVERT: F 240 TYR cc_start: 0.7952 (m-80) cc_final: 0.7729 (m-80) REVERT: G 73 TYR cc_start: 0.8817 (t80) cc_final: 0.8506 (t80) REVERT: G 108 LYS cc_start: 0.8398 (tttm) cc_final: 0.8029 (tttm) REVERT: G 116 ARG cc_start: 0.7876 (mtm180) cc_final: 0.7658 (mtp180) REVERT: G 127 ASP cc_start: 0.8004 (t70) cc_final: 0.7568 (t0) REVERT: G 268 LEU cc_start: 0.8879 (tp) cc_final: 0.8372 (tt) REVERT: H 89 VAL cc_start: 0.8678 (t) cc_final: 0.8249 (m) REVERT: H 105 LEU cc_start: 0.8793 (tp) cc_final: 0.8573 (tp) REVERT: H 110 THR cc_start: 0.8608 (m) cc_final: 0.8224 (p) REVERT: H 188 GLU cc_start: 0.8153 (mp0) cc_final: 0.7390 (mp0) REVERT: H 245 ASP cc_start: 0.8286 (t0) cc_final: 0.7901 (t0) REVERT: H 247 ILE cc_start: 0.8668 (mm) cc_final: 0.8467 (mm) REVERT: H 269 GLN cc_start: 0.8424 (mt0) cc_final: 0.8114 (mt0) REVERT: I 25 ILE cc_start: 0.8274 (mm) cc_final: 0.7871 (mm) REVERT: I 33 ILE cc_start: 0.9092 (mt) cc_final: 0.8858 (mm) REVERT: I 64 THR cc_start: 0.8147 (p) cc_final: 0.7877 (p) REVERT: I 115 TYR cc_start: 0.8689 (t80) cc_final: 0.8430 (t80) REVERT: I 144 ASP cc_start: 0.8586 (t0) cc_final: 0.8303 (t70) REVERT: I 162 GLU cc_start: 0.6823 (mt-10) cc_final: 0.6066 (mt-10) REVERT: I 231 ARG cc_start: 0.8032 (ttm170) cc_final: 0.7774 (ttm-80) REVERT: I 245 ASP cc_start: 0.8130 (t70) cc_final: 0.7725 (t0) REVERT: I 269 GLN cc_start: 0.8494 (mt0) cc_final: 0.8116 (mt0) REVERT: I 271 VAL cc_start: 0.8708 (t) cc_final: 0.8476 (p) REVERT: J 28 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7733 (mm) REVERT: J 29 LYS cc_start: 0.8634 (ttpt) cc_final: 0.8239 (ttpp) REVERT: J 111 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7074 (mt-10) REVERT: J 229 MET cc_start: 0.6444 (mmt) cc_final: 0.6228 (mmt) REVERT: J 246 GLU cc_start: 0.7548 (tt0) cc_final: 0.7273 (tt0) REVERT: J 268 LEU cc_start: 0.8980 (tp) cc_final: 0.8731 (tp) REVERT: J 275 TYR cc_start: 0.7313 (m-80) cc_final: 0.6834 (m-80) REVERT: K 73 TYR cc_start: 0.8759 (t80) cc_final: 0.8540 (t80) REVERT: K 164 LEU cc_start: 0.8006 (mt) cc_final: 0.7765 (mt) REVERT: K 215 VAL cc_start: 0.8730 (t) cc_final: 0.8327 (m) REVERT: K 269 GLN cc_start: 0.8862 (tp40) cc_final: 0.8071 (tp40) REVERT: X 11 LEU cc_start: 0.8550 (pp) cc_final: 0.8342 (pp) REVERT: X 35 LEU cc_start: 0.8343 (pt) cc_final: 0.8039 (pp) REVERT: X 80 ARG cc_start: 0.7887 (tpt170) cc_final: 0.7487 (tpm170) REVERT: X 142 MET cc_start: 0.7572 (mmt) cc_final: 0.7144 (mmt) REVERT: Y 10 TRP cc_start: 0.8980 (p-90) cc_final: 0.8738 (p-90) REVERT: Y 22 LEU cc_start: 0.8138 (tt) cc_final: 0.7705 (tp) REVERT: Y 29 PHE cc_start: 0.8850 (t80) cc_final: 0.8612 (t80) REVERT: Y 40 LEU cc_start: 0.8537 (tp) cc_final: 0.8283 (tp) REVERT: Y 84 MET cc_start: 0.7770 (mtt) cc_final: 0.7444 (mtt) REVERT: Y 95 GLU cc_start: 0.7914 (tp30) cc_final: 0.7694 (tp30) REVERT: Y 137 GLN cc_start: 0.7444 (mm-40) cc_final: 0.6986 (mp10) REVERT: Y 156 MET cc_start: 0.6660 (mtm) cc_final: 0.6310 (mtm) REVERT: Y 164 LEU cc_start: 0.9094 (mm) cc_final: 0.8842 (mm) outliers start: 104 outliers final: 57 residues processed: 1237 average time/residue: 0.1870 time to fit residues: 357.3383 Evaluate side-chains 1120 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 1057 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 TRP Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain d residue 581 GLU Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 100 CYS Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain e residue 572 VAL Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain f residue 573 TRP Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 163 ASP Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 235 SER Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 119 LYS Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 136 CYS Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 226 SER Chi-restraints excluded: chain H residue 255 SER Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 163 ASP Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 255 SER Chi-restraints excluded: chain K residue 20 TRP Chi-restraints excluded: chain K residue 163 ASP Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 200 SER Chi-restraints excluded: chain K residue 213 GLN Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 154 CYS Chi-restraints excluded: chain Y residue 158 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 101 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 266 optimal weight: 0.9990 chunk 236 optimal weight: 0.7980 chunk 200 optimal weight: 0.9980 chunk 181 optimal weight: 3.9990 chunk 293 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 265 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 HIS G 38 GLN H 185 GLN ** H 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 80 GLN I 213 GLN J 38 GLN K 38 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.121598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.102756 restraints weight = 56689.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.105838 restraints weight = 25050.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.107738 restraints weight = 13754.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.108941 restraints weight = 8961.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.109701 restraints weight = 6753.105| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28617 Z= 0.141 Angle : 0.621 9.972 38797 Z= 0.333 Chirality : 0.043 0.294 4282 Planarity : 0.005 0.065 4690 Dihedral : 15.927 154.047 4703 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.10 % Allowed : 19.75 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.53 (0.15), residues: 3239 helix: 1.47 (0.12), residues: 1837 sheet: 2.41 (0.31), residues: 253 loop : 0.05 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 85 TYR 0.017 0.001 TYR K 93 PHE 0.020 0.001 PHE I 204 TRP 0.031 0.002 TRP Y 114 HIS 0.005 0.001 HIS K 43 Details of bonding type rmsd covalent geometry : bond 0.00304 (28609) covalent geometry : angle 0.62063 (38797) hydrogen bonds : bond 0.04604 ( 1345) hydrogen bonds : angle 4.57961 ( 3781) Misc. bond : bond 0.00140 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1240 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 1123 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.8448 (m-30) cc_final: 0.8136 (m-30) REVERT: A 124 ASP cc_start: 0.8140 (m-30) cc_final: 0.7816 (m-30) REVERT: A 144 ASP cc_start: 0.7814 (m-30) cc_final: 0.7462 (m-30) REVERT: A 159 ASP cc_start: 0.7882 (t0) cc_final: 0.7640 (t0) REVERT: A 246 GLU cc_start: 0.6772 (tp30) cc_final: 0.6021 (tm-30) REVERT: a 573 TRP cc_start: 0.8023 (m-90) cc_final: 0.7452 (m-10) REVERT: B 31 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8314 (mmmt) REVERT: B 62 SER cc_start: 0.6953 (p) cc_final: 0.6634 (p) REVERT: B 73 TYR cc_start: 0.8876 (t80) cc_final: 0.8538 (t80) REVERT: B 140 MET cc_start: 0.8288 (ttm) cc_final: 0.7952 (ttp) REVERT: B 183 ASP cc_start: 0.7254 (t0) cc_final: 0.6936 (t0) REVERT: B 249 ARG cc_start: 0.8510 (ttm-80) cc_final: 0.8215 (ttm-80) REVERT: C 40 LYS cc_start: 0.8519 (tttt) cc_final: 0.8199 (ttpt) REVERT: C 47 ASP cc_start: 0.8023 (t70) cc_final: 0.7601 (t0) REVERT: C 129 THR cc_start: 0.8479 (OUTLIER) cc_final: 0.8251 (m) REVERT: C 136 CYS cc_start: 0.7148 (t) cc_final: 0.6795 (t) REVERT: C 162 GLU cc_start: 0.7095 (mt-10) cc_final: 0.6620 (mt-10) REVERT: C 183 ASP cc_start: 0.7534 (t0) cc_final: 0.7231 (t0) REVERT: C 210 MET cc_start: 0.8067 (mtp) cc_final: 0.7723 (ttm) REVERT: C 230 LEU cc_start: 0.8582 (mt) cc_final: 0.8339 (mp) REVERT: C 260 LEU cc_start: 0.7572 (mm) cc_final: 0.7320 (mp) REVERT: c 575 TYR cc_start: 0.8509 (t80) cc_final: 0.8076 (t80) REVERT: D 25 ILE cc_start: 0.7657 (mm) cc_final: 0.7333 (mm) REVERT: D 61 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7396 (mt-10) REVERT: D 89 VAL cc_start: 0.8788 (t) cc_final: 0.8471 (m) REVERT: D 111 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7504 (mt-10) REVERT: D 144 ASP cc_start: 0.8534 (t0) cc_final: 0.8084 (m-30) REVERT: D 182 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7489 (mpp80) REVERT: E 89 VAL cc_start: 0.8095 (t) cc_final: 0.7734 (m) REVERT: E 92 VAL cc_start: 0.9104 (m) cc_final: 0.8886 (p) REVERT: E 159 ASP cc_start: 0.7682 (t70) cc_final: 0.7365 (t0) REVERT: E 163 ASP cc_start: 0.7282 (t70) cc_final: 0.6969 (t0) REVERT: E 186 VAL cc_start: 0.8597 (m) cc_final: 0.8351 (p) REVERT: F 34 VAL cc_start: 0.8906 (t) cc_final: 0.8643 (m) REVERT: F 41 THR cc_start: 0.8695 (m) cc_final: 0.8241 (p) REVERT: F 42 LEU cc_start: 0.8264 (tp) cc_final: 0.8009 (tp) REVERT: F 49 LYS cc_start: 0.8929 (mmtt) cc_final: 0.8633 (mmmm) REVERT: F 88 THR cc_start: 0.8379 (m) cc_final: 0.7705 (t) REVERT: F 140 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.7140 (ttp) REVERT: F 144 ASP cc_start: 0.8532 (t70) cc_final: 0.7826 (t0) REVERT: F 187 LEU cc_start: 0.8910 (tt) cc_final: 0.8669 (tp) REVERT: G 73 TYR cc_start: 0.8828 (t80) cc_final: 0.8529 (t80) REVERT: G 108 LYS cc_start: 0.8384 (tttm) cc_final: 0.8160 (tttm) REVERT: G 116 ARG cc_start: 0.7902 (mtm180) cc_final: 0.7597 (mtp180) REVERT: G 127 ASP cc_start: 0.8180 (t70) cc_final: 0.7715 (t0) REVERT: G 129 THR cc_start: 0.8654 (m) cc_final: 0.8266 (p) REVERT: G 183 ASP cc_start: 0.7535 (t0) cc_final: 0.7291 (t0) REVERT: G 184 GLU cc_start: 0.8005 (mp0) cc_final: 0.7654 (mp0) REVERT: G 263 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8111 (mt) REVERT: G 268 LEU cc_start: 0.8770 (tp) cc_final: 0.8371 (tt) REVERT: H 89 VAL cc_start: 0.8842 (t) cc_final: 0.8540 (m) REVERT: H 145 GLU cc_start: 0.8233 (pt0) cc_final: 0.6681 (pt0) REVERT: H 184 GLU cc_start: 0.7632 (mp0) cc_final: 0.7048 (mp0) REVERT: H 188 GLU cc_start: 0.8347 (mp0) cc_final: 0.7628 (mp0) REVERT: H 202 GLU cc_start: 0.6853 (mp0) cc_final: 0.6212 (mp0) REVERT: H 214 MET cc_start: 0.7649 (mmm) cc_final: 0.7440 (mmm) REVERT: H 269 GLN cc_start: 0.8320 (mt0) cc_final: 0.7944 (mt0) REVERT: I 33 ILE cc_start: 0.9129 (mt) cc_final: 0.8895 (mm) REVERT: I 42 LEU cc_start: 0.8829 (tp) cc_final: 0.8587 (tp) REVERT: I 46 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8445 (mp) REVERT: I 54 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8153 (mtpp) REVERT: I 62 SER cc_start: 0.7988 (p) cc_final: 0.7597 (p) REVERT: I 64 THR cc_start: 0.8015 (p) cc_final: 0.7781 (p) REVERT: I 128 ARG cc_start: 0.8583 (ttm170) cc_final: 0.8059 (mtp180) REVERT: I 131 GLU cc_start: 0.7468 (tt0) cc_final: 0.7263 (mt-10) REVERT: I 162 GLU cc_start: 0.7078 (mt-10) cc_final: 0.6518 (mt-10) REVERT: I 229 MET cc_start: 0.7731 (mmt) cc_final: 0.7348 (mmp) REVERT: I 230 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8248 (mm) REVERT: I 232 ILE cc_start: 0.8698 (mm) cc_final: 0.8448 (tt) REVERT: I 245 ASP cc_start: 0.8265 (t70) cc_final: 0.7987 (t0) REVERT: I 269 GLN cc_start: 0.8466 (mt0) cc_final: 0.8047 (mt0) REVERT: I 271 VAL cc_start: 0.8667 (t) cc_final: 0.8424 (p) REVERT: J 28 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.7917 (mm) REVERT: J 145 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7916 (mt-10) REVERT: J 230 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.7740 (tp) REVERT: J 234 THR cc_start: 0.8512 (t) cc_final: 0.8034 (p) REVERT: J 246 GLU cc_start: 0.7303 (tt0) cc_final: 0.7102 (tt0) REVERT: J 275 TYR cc_start: 0.6980 (m-80) cc_final: 0.6200 (m-80) REVERT: j 570 ILE cc_start: 0.7566 (OUTLIER) cc_final: 0.7173 (tp) REVERT: K 91 VAL cc_start: 0.8765 (t) cc_final: 0.8470 (m) REVERT: K 164 LEU cc_start: 0.8136 (mt) cc_final: 0.7868 (mt) REVERT: K 215 VAL cc_start: 0.8671 (t) cc_final: 0.8282 (m) REVERT: K 269 GLN cc_start: 0.8828 (tp40) cc_final: 0.8010 (tp-100) REVERT: K 270 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7297 (tm-30) REVERT: K 271 VAL cc_start: 0.8883 (t) cc_final: 0.8427 (p) REVERT: X 11 LEU cc_start: 0.8658 (pp) cc_final: 0.8335 (pp) REVERT: X 35 LEU cc_start: 0.8443 (pt) cc_final: 0.8112 (pp) REVERT: X 79 GLN cc_start: 0.8404 (mp10) cc_final: 0.8180 (pm20) REVERT: X 80 ARG cc_start: 0.7792 (tpt170) cc_final: 0.7422 (tpm170) REVERT: Y 10 TRP cc_start: 0.9031 (p-90) cc_final: 0.8700 (p-90) REVERT: Y 12 PHE cc_start: 0.8657 (m-80) cc_final: 0.8446 (m-80) REVERT: Y 22 LEU cc_start: 0.8249 (tt) cc_final: 0.7881 (tp) REVERT: Y 25 PHE cc_start: 0.8709 (t80) cc_final: 0.8037 (t80) REVERT: Y 31 ARG cc_start: 0.8885 (ttm-80) cc_final: 0.8550 (ttm-80) REVERT: Y 64 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7872 (mm-40) REVERT: Y 79 GLN cc_start: 0.8792 (mp10) cc_final: 0.8474 (mp10) REVERT: Y 84 MET cc_start: 0.7812 (mtt) cc_final: 0.7570 (mtt) REVERT: Y 104 TYR cc_start: 0.6569 (m-10) cc_final: 0.6363 (m-10) REVERT: Y 124 ARG cc_start: 0.7456 (tpt90) cc_final: 0.7230 (tpt90) REVERT: Y 137 GLN cc_start: 0.7527 (mm-40) cc_final: 0.6895 (mp10) outliers start: 117 outliers final: 64 residues processed: 1165 average time/residue: 0.1835 time to fit residues: 332.0399 Evaluate side-chains 1137 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 1060 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 TRP Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain b residue 572 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 136 CYS Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 255 SER Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 54 LYS Chi-restraints excluded: chain I residue 181 LYS Chi-restraints excluded: chain I residue 213 GLN Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 253 ILE Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 31 LYS Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 225 LYS Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain j residue 570 ILE Chi-restraints excluded: chain K residue 20 TRP Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 180 ILE Chi-restraints excluded: chain K residue 200 SER Chi-restraints excluded: chain K residue 213 GLN Chi-restraints excluded: chain K residue 226 SER Chi-restraints excluded: chain K residue 270 GLU Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 43 LEU Chi-restraints excluded: chain Y residue 64 GLN Chi-restraints excluded: chain Y residue 154 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 2 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 214 optimal weight: 2.9990 chunk 200 optimal weight: 7.9990 chunk 174 optimal weight: 6.9990 chunk 191 optimal weight: 3.9990 chunk 289 optimal weight: 10.0000 chunk 307 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 235 optimal weight: 2.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN B 81 GLN C 38 GLN C 81 GLN D 80 GLN D 81 GLN D 98 GLN E 213 GLN ** f 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 206 ASN I 223 ASN J 38 GLN K 38 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.113638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.095162 restraints weight = 56179.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.098140 restraints weight = 24570.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.099978 restraints weight = 13398.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.101134 restraints weight = 8709.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.101866 restraints weight = 6554.489| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.5407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 28617 Z= 0.229 Angle : 0.677 11.815 38797 Z= 0.366 Chirality : 0.046 0.198 4282 Planarity : 0.005 0.053 4690 Dihedral : 15.832 152.687 4696 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 5.53 % Allowed : 20.21 % Favored : 74.26 % 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: 1.25 (0.15), residues: 3239 helix: 1.25 (0.12), residues: 1849 sheet: 2.19 (0.30), residues: 253 loop : -0.08 (0.19), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG C 85 TYR 0.018 0.002 TYR G 115 PHE 0.026 0.002 PHE B 204 TRP 0.033 0.002 TRP F 20 HIS 0.010 0.002 HIS E 77 Details of bonding type rmsd covalent geometry : bond 0.00513 (28609) covalent geometry : angle 0.67733 (38797) hydrogen bonds : bond 0.06015 ( 1345) hydrogen bonds : angle 4.66679 ( 3781) Misc. bond : bond 0.00843 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1264 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 1106 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASP cc_start: 0.8366 (m-30) cc_final: 0.8059 (m-30) REVERT: A 124 ASP cc_start: 0.8076 (m-30) cc_final: 0.7726 (m-30) REVERT: A 144 ASP cc_start: 0.7941 (m-30) cc_final: 0.7622 (m-30) REVERT: A 159 ASP cc_start: 0.7954 (t0) cc_final: 0.7688 (t0) REVERT: A 163 ASP cc_start: 0.7568 (m-30) cc_final: 0.7314 (m-30) REVERT: A 232 ILE cc_start: 0.7406 (mt) cc_final: 0.7118 (tp) REVERT: A 246 GLU cc_start: 0.6913 (tp30) cc_final: 0.6172 (tm-30) REVERT: a 573 TRP cc_start: 0.8149 (m-90) cc_final: 0.7093 (m-10) REVERT: B 62 SER cc_start: 0.7615 (p) cc_final: 0.7334 (p) REVERT: B 104 ASP cc_start: 0.8611 (m-30) cc_final: 0.8327 (m-30) REVERT: B 183 ASP cc_start: 0.7557 (t0) cc_final: 0.7296 (t0) REVERT: B 213 GLN cc_start: 0.8275 (tp-100) cc_final: 0.7872 (tp-100) REVERT: B 245 ASP cc_start: 0.8088 (t0) cc_final: 0.7831 (t0) REVERT: B 250 GLU cc_start: 0.8359 (tp30) cc_final: 0.7709 (tt0) REVERT: C 24 GLU cc_start: 0.8486 (mm-30) cc_final: 0.7917 (mm-30) REVERT: C 40 LYS cc_start: 0.8800 (tttt) cc_final: 0.8230 (ttpt) REVERT: C 111 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7217 (tm-30) REVERT: C 129 THR cc_start: 0.8643 (OUTLIER) cc_final: 0.8378 (m) REVERT: C 136 CYS cc_start: 0.7268 (t) cc_final: 0.6929 (t) REVERT: C 183 ASP cc_start: 0.7490 (t0) cc_final: 0.7203 (t0) REVERT: C 210 MET cc_start: 0.8072 (mtp) cc_final: 0.7760 (ttm) REVERT: C 230 LEU cc_start: 0.8728 (mt) cc_final: 0.8446 (mp) REVERT: C 260 LEU cc_start: 0.7986 (mm) cc_final: 0.7747 (mp) REVERT: D 25 ILE cc_start: 0.7793 (mm) cc_final: 0.7476 (mm) REVERT: D 75 TYR cc_start: 0.8960 (m-80) cc_final: 0.8740 (m-10) REVERT: D 89 VAL cc_start: 0.8892 (t) cc_final: 0.8542 (m) REVERT: D 111 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7628 (mm-30) REVERT: D 144 ASP cc_start: 0.8587 (t0) cc_final: 0.8024 (m-30) REVERT: D 182 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7960 (mpp80) REVERT: D 209 GLU cc_start: 0.7752 (tp30) cc_final: 0.7415 (tp30) REVERT: D 229 MET cc_start: 0.8072 (mmm) cc_final: 0.7655 (mmm) REVERT: D 230 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8104 (tp) REVERT: E 46 LEU cc_start: 0.8552 (mt) cc_final: 0.8107 (mp) REVERT: E 89 VAL cc_start: 0.8635 (t) cc_final: 0.8183 (m) REVERT: E 152 GLU cc_start: 0.7867 (mp0) cc_final: 0.7643 (mp0) REVERT: E 163 ASP cc_start: 0.7726 (t70) cc_final: 0.7416 (t0) REVERT: E 164 LEU cc_start: 0.8537 (mt) cc_final: 0.8241 (mm) REVERT: E 177 ASP cc_start: 0.8168 (m-30) cc_final: 0.7788 (m-30) REVERT: E 186 VAL cc_start: 0.8883 (m) cc_final: 0.8641 (p) REVERT: E 203 ASP cc_start: 0.7377 (m-30) cc_final: 0.7146 (m-30) REVERT: E 233 LEU cc_start: 0.7712 (mm) cc_final: 0.7470 (mm) REVERT: F 34 VAL cc_start: 0.8984 (t) cc_final: 0.8729 (m) REVERT: F 41 THR cc_start: 0.8905 (m) cc_final: 0.8496 (p) REVERT: F 88 THR cc_start: 0.8573 (m) cc_final: 0.8073 (t) REVERT: F 92 VAL cc_start: 0.8229 (t) cc_final: 0.8022 (p) REVERT: F 111 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7466 (mt-10) REVERT: F 140 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7539 (ttp) REVERT: F 144 ASP cc_start: 0.8563 (t70) cc_final: 0.7939 (t0) REVERT: F 145 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7570 (mp0) REVERT: F 148 ARG cc_start: 0.8489 (mtt180) cc_final: 0.8270 (mtp180) REVERT: F 187 LEU cc_start: 0.9028 (tt) cc_final: 0.8815 (tp) REVERT: G 38 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7682 (mt0) REVERT: G 49 LYS cc_start: 0.9111 (mmtt) cc_final: 0.8518 (mmmm) REVERT: G 92 VAL cc_start: 0.9123 (t) cc_final: 0.8849 (p) REVERT: G 108 LYS cc_start: 0.8495 (tttm) cc_final: 0.8234 (tttm) REVERT: G 129 THR cc_start: 0.8882 (m) cc_final: 0.8565 (p) REVERT: G 268 LEU cc_start: 0.8811 (tp) cc_final: 0.8382 (tt) REVERT: G 274 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7788 (mt-10) REVERT: H 89 VAL cc_start: 0.8978 (t) cc_final: 0.8697 (m) REVERT: H 184 GLU cc_start: 0.7707 (mp0) cc_final: 0.7231 (mp0) REVERT: H 188 GLU cc_start: 0.8410 (mp0) cc_final: 0.7711 (mp0) REVERT: H 202 GLU cc_start: 0.7538 (mp0) cc_final: 0.7231 (mp0) REVERT: H 215 VAL cc_start: 0.8537 (t) cc_final: 0.8336 (m) REVERT: H 269 GLN cc_start: 0.8265 (mt0) cc_final: 0.7939 (mt0) REVERT: I 24 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7768 (mm-30) REVERT: I 33 ILE cc_start: 0.9165 (mt) cc_final: 0.8918 (mm) REVERT: I 42 LEU cc_start: 0.8936 (tp) cc_final: 0.8685 (tp) REVERT: I 46 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8587 (mp) REVERT: I 64 THR cc_start: 0.8135 (p) cc_final: 0.7886 (p) REVERT: I 128 ARG cc_start: 0.8663 (ttm170) cc_final: 0.8265 (mtm180) REVERT: I 144 ASP cc_start: 0.8717 (t70) cc_final: 0.8275 (t70) REVERT: I 159 ASP cc_start: 0.7804 (OUTLIER) cc_final: 0.7549 (m-30) REVERT: I 213 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7584 (mt0) REVERT: I 229 MET cc_start: 0.7805 (mmt) cc_final: 0.7502 (mmt) REVERT: I 232 ILE cc_start: 0.8660 (mm) cc_final: 0.8443 (tt) REVERT: I 245 ASP cc_start: 0.8397 (t70) cc_final: 0.8118 (t0) REVERT: I 269 GLN cc_start: 0.8602 (mt0) cc_final: 0.8236 (mt0) REVERT: J 28 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8037 (mm) REVERT: J 29 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7736 (tptp) REVERT: J 116 ARG cc_start: 0.6437 (ptp-170) cc_final: 0.6156 (ptp-170) REVERT: J 145 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7829 (mt-10) REVERT: J 180 ILE cc_start: 0.8589 (mt) cc_final: 0.8277 (mm) REVERT: J 205 LYS cc_start: 0.9100 (tptt) cc_final: 0.8860 (tptp) REVERT: J 234 THR cc_start: 0.8375 (t) cc_final: 0.7951 (p) REVERT: J 246 GLU cc_start: 0.7452 (tt0) cc_final: 0.7144 (tt0) REVERT: j 570 ILE cc_start: 0.7511 (OUTLIER) cc_final: 0.6713 (tp) REVERT: j 581 GLU cc_start: 0.7965 (tp30) cc_final: 0.7706 (tp30) REVERT: K 91 VAL cc_start: 0.8829 (t) cc_final: 0.8518 (m) REVERT: K 164 LEU cc_start: 0.8421 (mt) cc_final: 0.8134 (mt) REVERT: K 215 VAL cc_start: 0.8754 (t) cc_final: 0.8328 (m) REVERT: K 245 ASP cc_start: 0.8687 (t70) cc_final: 0.8487 (t70) REVERT: K 269 GLN cc_start: 0.8903 (tp40) cc_final: 0.8308 (tp-100) REVERT: K 270 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7426 (tm-30) REVERT: K 271 VAL cc_start: 0.8915 (t) cc_final: 0.8409 (p) REVERT: X 10 TRP cc_start: 0.8181 (p-90) cc_final: 0.7481 (p-90) REVERT: X 11 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8390 (pp) REVERT: X 80 ARG cc_start: 0.7750 (tpt170) cc_final: 0.7454 (tpm170) REVERT: X 146 TRP cc_start: 0.6331 (m100) cc_final: 0.5788 (m100) REVERT: X 153 ARG cc_start: 0.6736 (mmm160) cc_final: 0.6523 (mmm160) REVERT: Y 22 LEU cc_start: 0.8359 (tt) cc_final: 0.7996 (tp) REVERT: Y 25 PHE cc_start: 0.8774 (t80) cc_final: 0.8224 (t80) REVERT: Y 53 TRP cc_start: 0.8982 (m-10) cc_final: 0.8667 (m100) REVERT: Y 64 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7957 (mm-40) REVERT: Y 79 GLN cc_start: 0.8789 (mp10) cc_final: 0.8453 (mp10) REVERT: Y 120 TRP cc_start: 0.7302 (p-90) cc_final: 0.7073 (p-90) REVERT: Y 137 GLN cc_start: 0.7645 (mm-40) cc_final: 0.7251 (mm-40) REVERT: Y 142 MET cc_start: 0.7088 (tpp) cc_final: 0.6773 (tpp) outliers start: 158 outliers final: 102 residues processed: 1167 average time/residue: 0.1804 time to fit residues: 325.4675 Evaluate side-chains 1172 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 1058 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain a residue 572 VAL Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain b residue 572 VAL Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain e residue 572 VAL Chi-restraints excluded: chain F residue 27 ARG Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 152 GLU Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain G residue 20 TRP Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 136 CYS Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 255 SER Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 166 ILE Chi-restraints excluded: chain I residue 184 GLU Chi-restraints excluded: chain I residue 213 GLN Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 29 LYS Chi-restraints excluded: chain J residue 31 LYS Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 225 LYS Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain J residue 247 ILE Chi-restraints excluded: chain J residue 255 SER Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 268 LEU Chi-restraints excluded: chain j residue 570 ILE Chi-restraints excluded: chain j residue 578 LEU Chi-restraints excluded: chain K residue 20 TRP Chi-restraints excluded: chain K residue 32 SER Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain K residue 163 ASP Chi-restraints excluded: chain K residue 180 ILE Chi-restraints excluded: chain K residue 200 SER Chi-restraints excluded: chain K residue 213 GLN Chi-restraints excluded: chain K residue 226 SER Chi-restraints excluded: chain k residue 572 VAL Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain X residue 11 LEU Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 64 GLN Chi-restraints excluded: chain Y residue 154 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 136 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 293 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 289 optimal weight: 5.9990 chunk 110 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 223 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 298 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN D 81 GLN D 98 GLN G 80 GLN I 206 ASN I 213 GLN J 38 GLN K 38 GLN ** k 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.116203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.097733 restraints weight = 55964.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.100736 restraints weight = 24515.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.102611 restraints weight = 13389.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.103792 restraints weight = 8665.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.104513 restraints weight = 6493.778| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.5700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28617 Z= 0.137 Angle : 0.631 19.040 38797 Z= 0.333 Chirality : 0.043 0.260 4282 Planarity : 0.005 0.161 4690 Dihedral : 15.525 151.208 4696 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.38 % Allowed : 22.87 % Favored : 72.75 % 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: 1.43 (0.15), residues: 3239 helix: 1.49 (0.12), residues: 1831 sheet: 2.12 (0.31), residues: 253 loop : -0.10 (0.19), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG B 85 TYR 0.016 0.001 TYR J 93 PHE 0.025 0.001 PHE I 204 TRP 0.031 0.002 TRP Y 114 HIS 0.004 0.001 HIS X 125 Details of bonding type rmsd covalent geometry : bond 0.00303 (28609) covalent geometry : angle 0.63093 (38797) hydrogen bonds : bond 0.04458 ( 1345) hydrogen bonds : angle 4.54455 ( 3781) Misc. bond : bond 0.00565 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1231 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 1106 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASP cc_start: 0.8374 (m-30) cc_final: 0.8062 (m-30) REVERT: A 124 ASP cc_start: 0.8051 (m-30) cc_final: 0.7730 (m-30) REVERT: A 144 ASP cc_start: 0.7971 (m-30) cc_final: 0.7554 (m-30) REVERT: A 159 ASP cc_start: 0.7894 (t0) cc_final: 0.7603 (t0) REVERT: A 163 ASP cc_start: 0.7553 (m-30) cc_final: 0.7274 (m-30) REVERT: A 232 ILE cc_start: 0.7359 (mt) cc_final: 0.7150 (tp) REVERT: A 246 GLU cc_start: 0.6904 (tp30) cc_final: 0.6197 (tm-30) REVERT: A 262 LYS cc_start: 0.7066 (OUTLIER) cc_final: 0.6741 (pttt) REVERT: A 274 GLU cc_start: 0.6412 (OUTLIER) cc_final: 0.5892 (mt-10) REVERT: a 573 TRP cc_start: 0.8173 (m-90) cc_final: 0.7479 (m-10) REVERT: B 66 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7873 (pttp) REVERT: B 68 VAL cc_start: 0.9034 (p) cc_final: 0.8784 (m) REVERT: B 73 TYR cc_start: 0.8902 (t80) cc_final: 0.8557 (t80) REVERT: B 104 ASP cc_start: 0.8564 (m-30) cc_final: 0.8276 (m-30) REVERT: B 183 ASP cc_start: 0.7409 (t0) cc_final: 0.7131 (t0) REVERT: B 213 GLN cc_start: 0.8265 (tp-100) cc_final: 0.7976 (tp-100) REVERT: B 245 ASP cc_start: 0.8034 (t0) cc_final: 0.7555 (t0) REVERT: B 269 GLN cc_start: 0.7721 (mt0) cc_final: 0.7279 (mt0) REVERT: C 40 LYS cc_start: 0.8758 (tttt) cc_final: 0.8222 (ttpt) REVERT: C 111 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7098 (tm-30) REVERT: C 129 THR cc_start: 0.8530 (OUTLIER) cc_final: 0.8279 (m) REVERT: C 136 CYS cc_start: 0.7248 (t) cc_final: 0.6914 (t) REVERT: C 162 GLU cc_start: 0.6785 (mt-10) cc_final: 0.6505 (mt-10) REVERT: C 183 ASP cc_start: 0.7343 (t0) cc_final: 0.7017 (t0) REVERT: C 203 ASP cc_start: 0.7608 (t0) cc_final: 0.7402 (t0) REVERT: C 210 MET cc_start: 0.8048 (mtp) cc_final: 0.7790 (ttm) REVERT: C 225 LYS cc_start: 0.8668 (pttt) cc_final: 0.8145 (ptmm) REVERT: C 230 LEU cc_start: 0.8674 (mt) cc_final: 0.8374 (mp) REVERT: C 260 LEU cc_start: 0.7912 (mm) cc_final: 0.7706 (mp) REVERT: D 25 ILE cc_start: 0.7731 (mm) cc_final: 0.7397 (mm) REVERT: D 61 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7622 (mt-10) REVERT: D 89 VAL cc_start: 0.8834 (t) cc_final: 0.8583 (m) REVERT: D 111 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7475 (mt-10) REVERT: D 139 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7228 (mm-30) REVERT: D 144 ASP cc_start: 0.8562 (t0) cc_final: 0.8133 (m-30) REVERT: D 145 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7939 (mt-10) REVERT: D 182 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7721 (mpp80) REVERT: D 228 GLU cc_start: 0.7388 (pm20) cc_final: 0.7173 (pt0) REVERT: D 229 MET cc_start: 0.8124 (mmm) cc_final: 0.7622 (mmm) REVERT: E 49 LYS cc_start: 0.8304 (mmtt) cc_final: 0.7906 (mmtm) REVERT: E 53 ARG cc_start: 0.8831 (mmt-90) cc_final: 0.8609 (mpt180) REVERT: E 87 PRO cc_start: 0.8547 (Cg_exo) cc_final: 0.8293 (Cg_endo) REVERT: E 89 VAL cc_start: 0.8663 (t) cc_final: 0.8303 (m) REVERT: E 163 ASP cc_start: 0.7792 (t70) cc_final: 0.7511 (t70) REVERT: E 164 LEU cc_start: 0.8462 (mt) cc_final: 0.7914 (mm) REVERT: E 177 ASP cc_start: 0.8094 (m-30) cc_final: 0.7687 (m-30) REVERT: E 186 VAL cc_start: 0.8961 (m) cc_final: 0.8703 (p) REVERT: E 203 ASP cc_start: 0.7326 (m-30) cc_final: 0.7055 (m-30) REVERT: F 41 THR cc_start: 0.8895 (m) cc_final: 0.8493 (p) REVERT: F 66 LYS cc_start: 0.8859 (mtmm) cc_final: 0.7805 (mtmm) REVERT: F 88 THR cc_start: 0.8603 (m) cc_final: 0.8088 (t) REVERT: F 111 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7265 (mt-10) REVERT: F 140 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7491 (ttp) REVERT: F 144 ASP cc_start: 0.8523 (t70) cc_final: 0.7910 (t0) REVERT: F 145 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7578 (mp0) REVERT: F 148 ARG cc_start: 0.8651 (mtt180) cc_final: 0.8404 (mtp180) REVERT: F 187 LEU cc_start: 0.8946 (tt) cc_final: 0.8743 (tp) REVERT: F 246 GLU cc_start: 0.7679 (tt0) cc_final: 0.7115 (tt0) REVERT: F 274 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7496 (mt-10) REVERT: G 38 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7522 (mt0) REVERT: G 49 LYS cc_start: 0.9071 (mmtt) cc_final: 0.8507 (mmmm) REVERT: G 92 VAL cc_start: 0.9098 (t) cc_final: 0.8794 (p) REVERT: G 108 LYS cc_start: 0.8417 (tttm) cc_final: 0.8138 (tttm) REVERT: G 129 THR cc_start: 0.8894 (m) cc_final: 0.8559 (p) REVERT: G 238 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7888 (mt-10) REVERT: G 268 LEU cc_start: 0.8781 (tp) cc_final: 0.8343 (tt) REVERT: G 274 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7726 (mt-10) REVERT: H 89 VAL cc_start: 0.8984 (t) cc_final: 0.8708 (m) REVERT: H 209 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8109 (pp20) REVERT: H 245 ASP cc_start: 0.8398 (t0) cc_final: 0.7717 (t0) REVERT: H 269 GLN cc_start: 0.8295 (mt0) cc_final: 0.7981 (mt0) REVERT: I 33 ILE cc_start: 0.9143 (mt) cc_final: 0.8906 (mm) REVERT: I 42 LEU cc_start: 0.8917 (tp) cc_final: 0.8606 (tp) REVERT: I 46 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8470 (mp) REVERT: I 54 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8091 (mtpp) REVERT: I 64 THR cc_start: 0.8122 (p) cc_final: 0.7891 (p) REVERT: I 114 LYS cc_start: 0.8812 (mtpp) cc_final: 0.8464 (mtpp) REVERT: I 128 ARG cc_start: 0.8577 (ttm170) cc_final: 0.8135 (mtm180) REVERT: I 144 ASP cc_start: 0.8670 (t70) cc_final: 0.8252 (t70) REVERT: I 229 MET cc_start: 0.7769 (mmt) cc_final: 0.7410 (mmp) REVERT: I 230 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8361 (mm) REVERT: I 232 ILE cc_start: 0.8695 (mm) cc_final: 0.8473 (tt) REVERT: I 245 ASP cc_start: 0.8318 (t70) cc_final: 0.8071 (t0) REVERT: I 269 GLN cc_start: 0.8571 (mt0) cc_final: 0.8289 (mt0) REVERT: J 28 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.7878 (mm) REVERT: J 29 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7877 (tptt) REVERT: J 61 GLU cc_start: 0.7213 (mt-10) cc_final: 0.7012 (mt-10) REVERT: J 145 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7856 (mt-10) REVERT: J 180 ILE cc_start: 0.8518 (mt) cc_final: 0.8168 (mm) REVERT: J 230 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7724 (tp) REVERT: J 234 THR cc_start: 0.8448 (t) cc_final: 0.8048 (p) REVERT: J 246 GLU cc_start: 0.7517 (tt0) cc_final: 0.7148 (tt0) REVERT: j 578 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7340 (mt) REVERT: K 91 VAL cc_start: 0.8811 (t) cc_final: 0.8506 (m) REVERT: K 131 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7818 (mm-30) REVERT: K 164 LEU cc_start: 0.8452 (mt) cc_final: 0.8150 (mt) REVERT: K 250 GLU cc_start: 0.8208 (tp30) cc_final: 0.7933 (tp30) REVERT: K 269 GLN cc_start: 0.8854 (tp40) cc_final: 0.8372 (tp-100) REVERT: K 270 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7344 (tm-30) REVERT: K 271 VAL cc_start: 0.8833 (t) cc_final: 0.8340 (p) REVERT: X 10 TRP cc_start: 0.8043 (p-90) cc_final: 0.7425 (p-90) REVERT: X 146 TRP cc_start: 0.6279 (m100) cc_final: 0.5848 (m100) REVERT: X 153 ARG cc_start: 0.6879 (mmm160) cc_final: 0.6670 (mmm160) REVERT: Y 22 LEU cc_start: 0.8228 (tt) cc_final: 0.7882 (tp) REVERT: Y 40 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8437 (mp) REVERT: Y 53 TRP cc_start: 0.9017 (m-10) cc_final: 0.8544 (m-10) REVERT: Y 64 GLN cc_start: 0.8189 (mm-40) cc_final: 0.7705 (mm-40) REVERT: Y 79 GLN cc_start: 0.8826 (mp10) cc_final: 0.8559 (mp10) REVERT: Y 84 MET cc_start: 0.7842 (mtt) cc_final: 0.7607 (mtt) REVERT: Y 137 GLN cc_start: 0.7632 (mm-40) cc_final: 0.7215 (mm-40) outliers start: 125 outliers final: 83 residues processed: 1160 average time/residue: 0.1764 time to fit residues: 318.0253 Evaluate side-chains 1167 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 1069 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 TRP Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain a residue 572 VAL Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain b residue 572 VAL Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain e residue 572 VAL Chi-restraints excluded: chain F residue 27 ARG Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 152 GLU Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 250 GLU Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 209 GLU Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 255 SER Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 54 LYS Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 181 LYS Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 29 LYS Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 220 VAL Chi-restraints excluded: chain J residue 225 LYS Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 255 SER Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 268 LEU Chi-restraints excluded: chain j residue 578 LEU Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain K residue 159 ASP Chi-restraints excluded: chain K residue 166 ILE Chi-restraints excluded: chain K residue 180 ILE Chi-restraints excluded: chain K residue 200 SER Chi-restraints excluded: chain K residue 226 SER Chi-restraints excluded: chain K residue 246 GLU Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain Y residue 40 LEU Chi-restraints excluded: chain Y residue 43 LEU Chi-restraints excluded: chain Y residue 112 ILE Chi-restraints excluded: chain Y residue 154 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 232 optimal weight: 0.9980 chunk 228 optimal weight: 0.5980 chunk 106 optimal weight: 0.0470 chunk 118 optimal weight: 0.5980 chunk 196 optimal weight: 0.4980 chunk 30 optimal weight: 0.5980 chunk 302 optimal weight: 10.0000 chunk 179 optimal weight: 4.9990 chunk 301 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 GLN B 185 GLN C 38 GLN D 98 GLN H 98 GLN I 81 GLN J 38 GLN K 38 GLN k 577 GLN ** Y 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.117563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.099088 restraints weight = 55782.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.102121 restraints weight = 24423.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.103972 restraints weight = 13277.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.105148 restraints weight = 8607.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.105874 restraints weight = 6437.846| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.5911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28617 Z= 0.124 Angle : 0.622 14.928 38797 Z= 0.328 Chirality : 0.042 0.271 4282 Planarity : 0.004 0.077 4690 Dihedral : 15.352 151.083 4696 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.06 % Allowed : 23.68 % Favored : 72.26 % 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: 1.54 (0.15), residues: 3239 helix: 1.57 (0.12), residues: 1831 sheet: 2.11 (0.30), residues: 253 loop : -0.04 (0.19), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 85 TYR 0.017 0.001 TYR J 93 PHE 0.017 0.001 PHE E 204 TRP 0.028 0.002 TRP Y 114 HIS 0.003 0.000 HIS F 43 Details of bonding type rmsd covalent geometry : bond 0.00266 (28609) covalent geometry : angle 0.62153 (38797) hydrogen bonds : bond 0.03960 ( 1345) hydrogen bonds : angle 4.49135 ( 3781) Misc. bond : bond 0.00582 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1221 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 1105 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASP cc_start: 0.8413 (m-30) cc_final: 0.8199 (m-30) REVERT: A 124 ASP cc_start: 0.8031 (m-30) cc_final: 0.7723 (m-30) REVERT: A 144 ASP cc_start: 0.7991 (m-30) cc_final: 0.7553 (m-30) REVERT: A 183 ASP cc_start: 0.7490 (t0) cc_final: 0.7250 (t70) REVERT: A 228 GLU cc_start: 0.7289 (pm20) cc_final: 0.7047 (pm20) REVERT: A 246 GLU cc_start: 0.6833 (tp30) cc_final: 0.6209 (tm-30) REVERT: A 274 GLU cc_start: 0.6472 (OUTLIER) cc_final: 0.5962 (mt-10) REVERT: a 573 TRP cc_start: 0.8147 (m-90) cc_final: 0.7363 (m-10) REVERT: B 66 LYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7857 (pttp) REVERT: B 68 VAL cc_start: 0.8991 (p) cc_final: 0.8738 (m) REVERT: B 104 ASP cc_start: 0.8551 (m-30) cc_final: 0.8275 (m-30) REVERT: B 140 MET cc_start: 0.8219 (ttm) cc_final: 0.7888 (ttp) REVERT: B 183 ASP cc_start: 0.7312 (t0) cc_final: 0.7017 (t0) REVERT: B 213 GLN cc_start: 0.8316 (tp-100) cc_final: 0.8005 (tp-100) REVERT: B 245 ASP cc_start: 0.8041 (t0) cc_final: 0.7652 (t0) REVERT: C 24 GLU cc_start: 0.8400 (mm-30) cc_final: 0.7793 (mm-30) REVERT: C 111 GLU cc_start: 0.7518 (tm-30) cc_final: 0.6898 (tm-30) REVERT: C 113 LEU cc_start: 0.8740 (mt) cc_final: 0.8518 (mp) REVERT: C 129 THR cc_start: 0.8527 (OUTLIER) cc_final: 0.8267 (m) REVERT: C 136 CYS cc_start: 0.7034 (t) cc_final: 0.6704 (t) REVERT: C 162 GLU cc_start: 0.6812 (mt-10) cc_final: 0.6500 (mt-10) REVERT: C 183 ASP cc_start: 0.7278 (t0) cc_final: 0.7018 (t0) REVERT: C 210 MET cc_start: 0.8003 (mtp) cc_final: 0.7605 (mtp) REVERT: C 241 ILE cc_start: 0.8447 (tt) cc_final: 0.8240 (mm) REVERT: C 260 LEU cc_start: 0.7789 (mm) cc_final: 0.7577 (mp) REVERT: D 25 ILE cc_start: 0.7652 (mm) cc_final: 0.7320 (mm) REVERT: D 61 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7199 (mm-30) REVERT: D 89 VAL cc_start: 0.8843 (t) cc_final: 0.8605 (m) REVERT: D 111 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7474 (mt-10) REVERT: D 139 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7200 (mm-30) REVERT: D 144 ASP cc_start: 0.8534 (t0) cc_final: 0.8132 (m-30) REVERT: D 182 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7671 (mpp80) REVERT: D 228 GLU cc_start: 0.7329 (pm20) cc_final: 0.7089 (pt0) REVERT: E 49 LYS cc_start: 0.8293 (mmtt) cc_final: 0.7864 (mmtm) REVERT: E 89 VAL cc_start: 0.8725 (t) cc_final: 0.8367 (m) REVERT: E 163 ASP cc_start: 0.7769 (t70) cc_final: 0.7414 (t70) REVERT: E 164 LEU cc_start: 0.8317 (mt) cc_final: 0.7738 (mm) REVERT: E 177 ASP cc_start: 0.8064 (m-30) cc_final: 0.7681 (m-30) REVERT: E 186 VAL cc_start: 0.8896 (m) cc_final: 0.8656 (p) REVERT: E 203 ASP cc_start: 0.7290 (m-30) cc_final: 0.7067 (m-30) REVERT: F 41 THR cc_start: 0.8920 (m) cc_final: 0.8492 (p) REVERT: F 66 LYS cc_start: 0.8871 (mtmm) cc_final: 0.7958 (mtmm) REVERT: F 88 THR cc_start: 0.8579 (m) cc_final: 0.8073 (t) REVERT: F 111 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7093 (mt-10) REVERT: F 140 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7444 (ttp) REVERT: F 144 ASP cc_start: 0.8519 (t70) cc_final: 0.7808 (t0) REVERT: F 145 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7461 (mp0) REVERT: F 148 ARG cc_start: 0.8648 (mtt180) cc_final: 0.8418 (mtp180) REVERT: F 238 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7724 (tm-30) REVERT: F 246 GLU cc_start: 0.7563 (tt0) cc_final: 0.7306 (tt0) REVERT: F 274 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7362 (mt-10) REVERT: G 38 GLN cc_start: 0.8018 (mm-40) cc_final: 0.7465 (mt0) REVERT: G 49 LYS cc_start: 0.9077 (mmtt) cc_final: 0.8501 (mmmm) REVERT: G 54 LYS cc_start: 0.8897 (mtmt) cc_final: 0.8686 (mttt) REVERT: G 92 VAL cc_start: 0.9077 (t) cc_final: 0.8746 (p) REVERT: G 108 LYS cc_start: 0.8399 (tttm) cc_final: 0.8179 (tttm) REVERT: G 117 VAL cc_start: 0.8179 (p) cc_final: 0.7783 (t) REVERT: G 128 ARG cc_start: 0.8465 (mtp180) cc_final: 0.8218 (ttp-170) REVERT: G 129 THR cc_start: 0.8910 (m) cc_final: 0.8532 (p) REVERT: G 238 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7808 (mt-10) REVERT: G 268 LEU cc_start: 0.8747 (tp) cc_final: 0.8281 (tt) REVERT: G 274 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7719 (mt-10) REVERT: H 89 VAL cc_start: 0.8958 (t) cc_final: 0.8677 (m) REVERT: H 108 LYS cc_start: 0.8590 (ttmt) cc_final: 0.8314 (ttmm) REVERT: H 144 ASP cc_start: 0.9013 (t0) cc_final: 0.8714 (t70) REVERT: H 245 ASP cc_start: 0.8317 (t0) cc_final: 0.7632 (t0) REVERT: H 269 GLN cc_start: 0.8312 (mt0) cc_final: 0.8006 (mt0) REVERT: I 33 ILE cc_start: 0.9154 (mt) cc_final: 0.8928 (mm) REVERT: I 42 LEU cc_start: 0.8871 (tp) cc_final: 0.8604 (tp) REVERT: I 46 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8385 (mp) REVERT: I 64 THR cc_start: 0.8100 (p) cc_final: 0.7876 (p) REVERT: I 114 LYS cc_start: 0.8798 (mtpp) cc_final: 0.8435 (mtpp) REVERT: I 128 ARG cc_start: 0.8546 (ttm170) cc_final: 0.8108 (mtm180) REVERT: I 144 ASP cc_start: 0.8653 (t70) cc_final: 0.8225 (t70) REVERT: I 209 GLU cc_start: 0.7653 (tp30) cc_final: 0.7249 (tp30) REVERT: I 225 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7470 (mtmm) REVERT: I 229 MET cc_start: 0.7789 (mmt) cc_final: 0.7413 (mmp) REVERT: I 230 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8335 (mm) REVERT: I 245 ASP cc_start: 0.8287 (t70) cc_final: 0.8048 (t0) REVERT: I 269 GLN cc_start: 0.8487 (mt0) cc_final: 0.8199 (mt0) REVERT: J 28 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7719 (mm) REVERT: J 61 GLU cc_start: 0.7241 (mt-10) cc_final: 0.7020 (mt-10) REVERT: J 71 ASP cc_start: 0.8155 (t70) cc_final: 0.7781 (t0) REVERT: J 75 TYR cc_start: 0.7978 (m-10) cc_final: 0.7751 (m-10) REVERT: J 128 ARG cc_start: 0.8219 (mmt180) cc_final: 0.7820 (mmp80) REVERT: J 145 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7833 (mt-10) REVERT: J 234 THR cc_start: 0.8418 (t) cc_final: 0.8021 (p) REVERT: J 246 GLU cc_start: 0.7498 (tt0) cc_final: 0.7131 (tt0) REVERT: K 91 VAL cc_start: 0.8798 (t) cc_final: 0.8476 (m) REVERT: K 131 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7841 (mm-30) REVERT: K 164 LEU cc_start: 0.8300 (mt) cc_final: 0.7988 (mt) REVERT: K 250 GLU cc_start: 0.8157 (tp30) cc_final: 0.7805 (tp30) REVERT: K 268 LEU cc_start: 0.8831 (tt) cc_final: 0.8577 (tp) REVERT: K 269 GLN cc_start: 0.8768 (tp40) cc_final: 0.8309 (tp-100) REVERT: K 270 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7312 (tm-30) REVERT: K 271 VAL cc_start: 0.8717 (t) cc_final: 0.8251 (p) REVERT: X 142 MET cc_start: 0.7172 (tpp) cc_final: 0.6947 (tpp) REVERT: X 146 TRP cc_start: 0.6382 (m100) cc_final: 0.6063 (m100) REVERT: Y 12 PHE cc_start: 0.8718 (m-80) cc_final: 0.8516 (m-80) REVERT: Y 22 LEU cc_start: 0.8189 (tt) cc_final: 0.7843 (tp) REVERT: Y 64 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7653 (mm-40) REVERT: Y 84 MET cc_start: 0.7841 (mtt) cc_final: 0.7546 (mtt) REVERT: Y 137 GLN cc_start: 0.7616 (mm-40) cc_final: 0.7182 (mm-40) outliers start: 116 outliers final: 85 residues processed: 1146 average time/residue: 0.1794 time to fit residues: 318.9329 Evaluate side-chains 1171 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 1076 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain a residue 572 VAL Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain b residue 572 VAL Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain e residue 572 VAL Chi-restraints excluded: chain F residue 27 ARG Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 152 GLU Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 184 GLU Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 250 GLU Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 255 SER Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 152 GLU Chi-restraints excluded: chain I residue 213 GLN Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 225 LYS Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 31 LYS Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 225 LYS Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 255 SER Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 268 LEU Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain K residue 140 MET Chi-restraints excluded: chain K residue 159 ASP Chi-restraints excluded: chain K residue 166 ILE Chi-restraints excluded: chain K residue 180 ILE Chi-restraints excluded: chain K residue 200 SER Chi-restraints excluded: chain K residue 226 SER Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 246 GLU Chi-restraints excluded: chain X residue 75 GLU Chi-restraints excluded: chain Y residue 64 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 301 optimal weight: 0.0970 chunk 87 optimal weight: 1.9990 chunk 115 optimal weight: 0.1980 chunk 281 optimal weight: 0.9990 chunk 151 optimal weight: 5.9990 chunk 266 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 GLN B 206 ASN C 38 GLN D 98 GLN ** f 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 GLN H 223 ASN K 38 GLN ** Y 125 HIS ** 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 = 0.3653 r_free = 0.3653 target = 0.117583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.099096 restraints weight = 55772.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.102089 restraints weight = 24444.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.103956 restraints weight = 13328.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.105125 restraints weight = 8626.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.105844 restraints weight = 6472.879| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.6102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 28617 Z= 0.128 Angle : 0.627 11.179 38797 Z= 0.332 Chirality : 0.042 0.242 4282 Planarity : 0.006 0.241 4690 Dihedral : 15.245 151.148 4696 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.89 % Allowed : 24.45 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.58 (0.15), residues: 3239 helix: 1.60 (0.12), residues: 1831 sheet: 2.10 (0.30), residues: 253 loop : -0.01 (0.19), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.001 ARG B 85 TYR 0.020 0.001 TYR G 115 PHE 0.034 0.001 PHE E 204 TRP 0.028 0.001 TRP Y 114 HIS 0.004 0.001 HIS C 77 Details of bonding type rmsd covalent geometry : bond 0.00284 (28609) covalent geometry : angle 0.62665 (38797) hydrogen bonds : bond 0.03895 ( 1345) hydrogen bonds : angle 4.48951 ( 3781) Misc. bond : bond 0.00556 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1213 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 1102 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASP cc_start: 0.8372 (m-30) cc_final: 0.8148 (m-30) REVERT: A 76 ARG cc_start: 0.8360 (tpp80) cc_final: 0.8092 (tpt-90) REVERT: A 124 ASP cc_start: 0.8013 (m-30) cc_final: 0.7715 (m-30) REVERT: A 144 ASP cc_start: 0.7995 (m-30) cc_final: 0.7635 (m-30) REVERT: A 183 ASP cc_start: 0.7493 (t0) cc_final: 0.7203 (t70) REVERT: A 246 GLU cc_start: 0.6888 (tp30) cc_final: 0.6196 (tm-30) REVERT: A 274 GLU cc_start: 0.6472 (OUTLIER) cc_final: 0.5963 (mt-10) REVERT: a 570 ILE cc_start: 0.8109 (mm) cc_final: 0.7857 (mm) REVERT: a 573 TRP cc_start: 0.8107 (m-90) cc_final: 0.7259 (m-10) REVERT: B 42 LEU cc_start: 0.8666 (tp) cc_final: 0.8356 (tt) REVERT: B 66 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7853 (pttp) REVERT: B 68 VAL cc_start: 0.8983 (p) cc_final: 0.8729 (m) REVERT: B 104 ASP cc_start: 0.8559 (m-30) cc_final: 0.8275 (m-30) REVERT: B 213 GLN cc_start: 0.8478 (tp-100) cc_final: 0.8108 (tp-100) REVERT: B 245 ASP cc_start: 0.8140 (t0) cc_final: 0.7713 (t0) REVERT: B 273 LYS cc_start: 0.8794 (tppp) cc_final: 0.8513 (ttmm) REVERT: C 111 GLU cc_start: 0.7499 (tm-30) cc_final: 0.6908 (tm-30) REVERT: C 129 THR cc_start: 0.8532 (OUTLIER) cc_final: 0.8276 (m) REVERT: C 136 CYS cc_start: 0.6820 (t) cc_final: 0.6468 (t) REVERT: C 176 LEU cc_start: 0.8886 (tp) cc_final: 0.8685 (tt) REVERT: C 183 ASP cc_start: 0.7387 (t0) cc_final: 0.7151 (t0) REVERT: C 210 MET cc_start: 0.7972 (mtp) cc_final: 0.7587 (mtp) REVERT: C 218 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7761 (mm) REVERT: C 225 LYS cc_start: 0.8661 (pttt) cc_final: 0.8175 (ptmm) REVERT: C 260 LEU cc_start: 0.7773 (mm) cc_final: 0.7568 (mp) REVERT: D 25 ILE cc_start: 0.7568 (mm) cc_final: 0.7245 (mm) REVERT: D 54 LYS cc_start: 0.8400 (ttpt) cc_final: 0.7952 (mtmt) REVERT: D 61 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7225 (mm-30) REVERT: D 89 VAL cc_start: 0.8846 (t) cc_final: 0.8598 (m) REVERT: D 111 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7480 (mt-10) REVERT: D 139 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7206 (mm-30) REVERT: D 144 ASP cc_start: 0.8512 (t0) cc_final: 0.8183 (m-30) REVERT: D 145 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7824 (mp0) REVERT: D 182 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7662 (mpp80) REVERT: D 206 ASN cc_start: 0.9228 (m-40) cc_final: 0.8991 (m110) REVERT: D 228 GLU cc_start: 0.7322 (pm20) cc_final: 0.7037 (pt0) REVERT: D 229 MET cc_start: 0.8102 (mmm) cc_final: 0.7546 (mmm) REVERT: D 270 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7894 (tt0) REVERT: E 49 LYS cc_start: 0.8328 (mmtt) cc_final: 0.7872 (mmtm) REVERT: E 89 VAL cc_start: 0.8757 (t) cc_final: 0.8424 (m) REVERT: E 163 ASP cc_start: 0.7780 (t70) cc_final: 0.7335 (t0) REVERT: E 164 LEU cc_start: 0.8188 (mt) cc_final: 0.7758 (mm) REVERT: E 177 ASP cc_start: 0.8036 (m-30) cc_final: 0.7656 (m-30) REVERT: E 186 VAL cc_start: 0.8905 (m) cc_final: 0.8620 (p) REVERT: E 203 ASP cc_start: 0.7268 (m-30) cc_final: 0.7025 (m-30) REVERT: E 250 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7732 (mm-30) REVERT: F 41 THR cc_start: 0.8872 (m) cc_final: 0.8528 (p) REVERT: F 66 LYS cc_start: 0.8794 (mtmm) cc_final: 0.7847 (mtmm) REVERT: F 88 THR cc_start: 0.8583 (m) cc_final: 0.8084 (t) REVERT: F 111 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7049 (mt-10) REVERT: F 140 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.7430 (ttp) REVERT: F 144 ASP cc_start: 0.8505 (t70) cc_final: 0.7728 (t0) REVERT: F 145 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7452 (mp0) REVERT: F 274 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7353 (mt-10) REVERT: G 28 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8129 (mm) REVERT: G 38 GLN cc_start: 0.8028 (mm-40) cc_final: 0.7440 (mt0) REVERT: G 49 LYS cc_start: 0.9091 (mmtt) cc_final: 0.8503 (mmmm) REVERT: G 54 LYS cc_start: 0.8920 (mtmt) cc_final: 0.8664 (mttt) REVERT: G 92 VAL cc_start: 0.9052 (t) cc_final: 0.8711 (p) REVERT: G 108 LYS cc_start: 0.8402 (tttm) cc_final: 0.8160 (tttm) REVERT: G 117 VAL cc_start: 0.8178 (p) cc_final: 0.7806 (t) REVERT: G 128 ARG cc_start: 0.8444 (mtp180) cc_final: 0.8225 (ttp-170) REVERT: G 129 THR cc_start: 0.8886 (m) cc_final: 0.8570 (p) REVERT: G 153 THR cc_start: 0.8847 (p) cc_final: 0.8586 (t) REVERT: G 238 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7731 (mt-10) REVERT: G 268 LEU cc_start: 0.8715 (tp) cc_final: 0.8253 (tt) REVERT: G 274 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7555 (mt-10) REVERT: H 89 VAL cc_start: 0.8951 (t) cc_final: 0.8673 (m) REVERT: H 108 LYS cc_start: 0.8569 (ttmt) cc_final: 0.8303 (ttmm) REVERT: H 144 ASP cc_start: 0.8913 (t0) cc_final: 0.8197 (t70) REVERT: H 145 GLU cc_start: 0.8110 (pm20) cc_final: 0.7338 (pm20) REVERT: H 265 LYS cc_start: 0.7054 (tttt) cc_final: 0.6731 (tttp) REVERT: H 269 GLN cc_start: 0.8243 (mt0) cc_final: 0.7964 (mt0) REVERT: I 42 LEU cc_start: 0.8876 (tp) cc_final: 0.8598 (tp) REVERT: I 46 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8386 (mp) REVERT: I 64 THR cc_start: 0.8088 (p) cc_final: 0.7867 (p) REVERT: I 114 LYS cc_start: 0.8794 (mtpp) cc_final: 0.8472 (mtpp) REVERT: I 128 ARG cc_start: 0.8552 (ttm170) cc_final: 0.8100 (mtm180) REVERT: I 144 ASP cc_start: 0.8620 (t70) cc_final: 0.8245 (t70) REVERT: I 209 GLU cc_start: 0.7513 (tp30) cc_final: 0.7108 (tp30) REVERT: I 225 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7506 (mtmm) REVERT: I 229 MET cc_start: 0.7752 (mmt) cc_final: 0.7435 (mmm) REVERT: I 230 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8365 (mm) REVERT: I 245 ASP cc_start: 0.8281 (t70) cc_final: 0.8056 (t0) REVERT: J 28 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7667 (mm) REVERT: J 61 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6969 (mt-10) REVERT: J 71 ASP cc_start: 0.8117 (t70) cc_final: 0.7646 (t0) REVERT: J 75 TYR cc_start: 0.8013 (m-10) cc_final: 0.7725 (m-10) REVERT: J 128 ARG cc_start: 0.8170 (mmt180) cc_final: 0.7796 (mmp80) REVERT: J 145 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7825 (mt-10) REVERT: J 205 LYS cc_start: 0.8970 (tptt) cc_final: 0.8465 (tptp) REVERT: J 230 LEU cc_start: 0.8382 (mt) cc_final: 0.7746 (tp) REVERT: J 234 THR cc_start: 0.8406 (t) cc_final: 0.8052 (p) REVERT: J 246 GLU cc_start: 0.7286 (tt0) cc_final: 0.7024 (tt0) REVERT: K 25 ILE cc_start: 0.8384 (mm) cc_final: 0.8150 (mm) REVERT: K 75 TYR cc_start: 0.7830 (m-10) cc_final: 0.7584 (m-10) REVERT: K 91 VAL cc_start: 0.8811 (t) cc_final: 0.8495 (m) REVERT: K 131 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7799 (mm-30) REVERT: K 164 LEU cc_start: 0.8392 (mt) cc_final: 0.8103 (mt) REVERT: K 184 GLU cc_start: 0.8119 (pm20) cc_final: 0.7776 (pp20) REVERT: K 250 GLU cc_start: 0.8198 (tp30) cc_final: 0.7851 (tp30) REVERT: K 269 GLN cc_start: 0.8749 (tp40) cc_final: 0.8273 (tp-100) REVERT: K 270 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7376 (tm-30) REVERT: K 271 VAL cc_start: 0.8821 (t) cc_final: 0.8358 (p) REVERT: X 10 TRP cc_start: 0.7919 (p-90) cc_final: 0.7489 (p-90) REVERT: X 84 MET cc_start: 0.7761 (mtt) cc_final: 0.7122 (ttt) REVERT: X 142 MET cc_start: 0.7154 (tpp) cc_final: 0.6852 (tpp) REVERT: Y 12 PHE cc_start: 0.8725 (m-80) cc_final: 0.8516 (m-80) REVERT: Y 22 LEU cc_start: 0.8171 (tt) cc_final: 0.7828 (tp) REVERT: Y 40 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8458 (mp) REVERT: Y 64 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7595 (mm-40) REVERT: Y 79 GLN cc_start: 0.8749 (mp10) cc_final: 0.8501 (mp10) REVERT: Y 83 GLN cc_start: 0.8606 (mt0) cc_final: 0.8250 (mt0) REVERT: Y 84 MET cc_start: 0.7831 (mtt) cc_final: 0.7597 (mtt) REVERT: Y 137 GLN cc_start: 0.7648 (mm-40) cc_final: 0.7192 (mm-40) outliers start: 111 outliers final: 77 residues processed: 1145 average time/residue: 0.1721 time to fit residues: 305.8994 Evaluate side-chains 1154 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 1063 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain a residue 572 VAL Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain b residue 572 VAL Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain e residue 572 VAL Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 152 GLU Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 184 GLU Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 250 GLU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 255 SER Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 152 GLU Chi-restraints excluded: chain I residue 213 GLN Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 225 LYS Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain J residue 255 SER Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 268 LEU Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain K residue 127 ASP Chi-restraints excluded: chain K residue 140 MET Chi-restraints excluded: chain K residue 159 ASP Chi-restraints excluded: chain K residue 226 SER Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 246 GLU Chi-restraints excluded: chain K residue 248 LEU Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain X residue 104 TYR Chi-restraints excluded: chain Y residue 40 LEU Chi-restraints excluded: chain Y residue 64 GLN Chi-restraints excluded: chain Y residue 154 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 137 optimal weight: 0.9980 chunk 249 optimal weight: 0.8980 chunk 169 optimal weight: 5.9990 chunk 172 optimal weight: 0.9980 chunk 234 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 180 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 GLN B 185 GLN C 38 GLN C 98 GLN D 98 GLN ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 GLN J 38 GLN K 38 GLN ** Y 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.116353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.097829 restraints weight = 56024.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.100839 restraints weight = 24675.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.102710 restraints weight = 13485.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.103899 restraints weight = 8734.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.104672 restraints weight = 6523.505| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.6243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 28617 Z= 0.142 Angle : 0.645 14.693 38797 Z= 0.340 Chirality : 0.043 0.202 4282 Planarity : 0.005 0.194 4690 Dihedral : 15.169 150.985 4696 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.10 % Allowed : 25.01 % Favored : 70.89 % 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: 1.52 (0.15), residues: 3239 helix: 1.58 (0.12), residues: 1831 sheet: 2.06 (0.30), residues: 253 loop : -0.07 (0.19), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG C 85 TYR 0.020 0.001 TYR A 73 PHE 0.014 0.001 PHE X 140 TRP 0.029 0.002 TRP Y 114 HIS 0.003 0.001 HIS E 77 Details of bonding type rmsd covalent geometry : bond 0.00321 (28609) covalent geometry : angle 0.64459 (38797) hydrogen bonds : bond 0.04173 ( 1345) hydrogen bonds : angle 4.52439 ( 3781) Misc. bond : bond 0.00485 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1220 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 1103 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.8002 (m-30) cc_final: 0.7755 (m-30) REVERT: A 144 ASP cc_start: 0.7978 (m-30) cc_final: 0.7658 (m-30) REVERT: A 159 ASP cc_start: 0.7838 (t0) cc_final: 0.7555 (t0) REVERT: A 228 GLU cc_start: 0.7265 (pm20) cc_final: 0.6799 (pm20) REVERT: A 246 GLU cc_start: 0.6916 (tp30) cc_final: 0.6249 (tm-30) REVERT: A 274 GLU cc_start: 0.6489 (OUTLIER) cc_final: 0.5971 (mt-10) REVERT: a 570 ILE cc_start: 0.8066 (mm) cc_final: 0.7815 (mm) REVERT: a 573 TRP cc_start: 0.8106 (m-90) cc_final: 0.7305 (m-10) REVERT: B 66 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7684 (pttp) REVERT: B 68 VAL cc_start: 0.8990 (p) cc_final: 0.8727 (m) REVERT: B 73 TYR cc_start: 0.8892 (t80) cc_final: 0.8620 (t80) REVERT: B 104 ASP cc_start: 0.8548 (m-30) cc_final: 0.8262 (m-30) REVERT: B 183 ASP cc_start: 0.7311 (t0) cc_final: 0.7035 (t0) REVERT: B 213 GLN cc_start: 0.8478 (tp-100) cc_final: 0.8019 (tp-100) REVERT: B 273 LYS cc_start: 0.8822 (tppp) cc_final: 0.8523 (ttmm) REVERT: b 571 GLU cc_start: 0.7907 (pt0) cc_final: 0.7653 (pt0) REVERT: C 24 GLU cc_start: 0.8420 (mm-30) cc_final: 0.7819 (mm-30) REVERT: C 78 LYS cc_start: 0.8155 (mmmt) cc_final: 0.7699 (tptt) REVERT: C 111 GLU cc_start: 0.7507 (tm-30) cc_final: 0.6919 (tm-30) REVERT: C 129 THR cc_start: 0.8533 (OUTLIER) cc_final: 0.8259 (m) REVERT: C 176 LEU cc_start: 0.8884 (tp) cc_final: 0.8680 (tt) REVERT: C 183 ASP cc_start: 0.7152 (t0) cc_final: 0.6924 (t0) REVERT: C 210 MET cc_start: 0.7987 (mtp) cc_final: 0.7605 (mtp) REVERT: C 218 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7522 (mm) REVERT: D 25 ILE cc_start: 0.7637 (mm) cc_final: 0.7319 (mm) REVERT: D 61 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7041 (mm-30) REVERT: D 89 VAL cc_start: 0.8869 (t) cc_final: 0.8603 (m) REVERT: D 111 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7503 (mt-10) REVERT: D 144 ASP cc_start: 0.8528 (t0) cc_final: 0.8232 (m-30) REVERT: D 182 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7728 (mpp80) REVERT: D 206 ASN cc_start: 0.9237 (m-40) cc_final: 0.8995 (m110) REVERT: D 229 MET cc_start: 0.8095 (mmm) cc_final: 0.7627 (mmm) REVERT: D 245 ASP cc_start: 0.8489 (t70) cc_final: 0.8265 (t70) REVERT: D 270 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7928 (tt0) REVERT: E 49 LYS cc_start: 0.8339 (mmtt) cc_final: 0.7911 (mmtm) REVERT: E 54 LYS cc_start: 0.8223 (ttmm) cc_final: 0.7823 (tttt) REVERT: E 89 VAL cc_start: 0.8823 (t) cc_final: 0.8487 (m) REVERT: E 163 ASP cc_start: 0.7847 (t70) cc_final: 0.7336 (t0) REVERT: E 164 LEU cc_start: 0.8327 (mt) cc_final: 0.7950 (mm) REVERT: E 177 ASP cc_start: 0.8053 (m-30) cc_final: 0.7688 (m-30) REVERT: E 186 VAL cc_start: 0.8946 (m) cc_final: 0.8665 (p) REVERT: E 203 ASP cc_start: 0.7267 (m-30) cc_final: 0.7056 (m-30) REVERT: E 204 PHE cc_start: 0.8260 (t80) cc_final: 0.8033 (t80) REVERT: E 206 ASN cc_start: 0.8672 (m-40) cc_final: 0.8422 (m110) REVERT: E 250 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7793 (mt-10) REVERT: F 41 THR cc_start: 0.8918 (m) cc_final: 0.8555 (p) REVERT: F 66 LYS cc_start: 0.8815 (mtmm) cc_final: 0.7898 (mtmm) REVERT: F 88 THR cc_start: 0.8591 (m) cc_final: 0.8092 (t) REVERT: F 111 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7068 (mt-10) REVERT: F 140 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7503 (ttp) REVERT: F 180 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8195 (tp) REVERT: F 274 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7371 (mt-10) REVERT: G 38 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7445 (mt0) REVERT: G 49 LYS cc_start: 0.9087 (mmtt) cc_final: 0.8508 (mmmm) REVERT: G 54 LYS cc_start: 0.8968 (mtmt) cc_final: 0.8752 (mttt) REVERT: G 92 VAL cc_start: 0.9056 (t) cc_final: 0.8715 (p) REVERT: G 108 LYS cc_start: 0.8395 (tttm) cc_final: 0.8147 (tttm) REVERT: G 117 VAL cc_start: 0.8294 (p) cc_final: 0.8026 (t) REVERT: G 128 ARG cc_start: 0.8375 (mtp180) cc_final: 0.8147 (ttp-170) REVERT: G 129 THR cc_start: 0.8922 (m) cc_final: 0.8605 (p) REVERT: G 153 THR cc_start: 0.8817 (p) cc_final: 0.8586 (t) REVERT: G 238 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7709 (mt-10) REVERT: G 268 LEU cc_start: 0.8716 (tp) cc_final: 0.8236 (tt) REVERT: H 89 VAL cc_start: 0.8850 (t) cc_final: 0.8549 (m) REVERT: H 108 LYS cc_start: 0.8564 (ttmt) cc_final: 0.8294 (ttmm) REVERT: H 144 ASP cc_start: 0.8882 (t0) cc_final: 0.8494 (t70) REVERT: H 245 ASP cc_start: 0.8352 (t0) cc_final: 0.7760 (t0) REVERT: H 269 GLN cc_start: 0.8243 (mt0) cc_final: 0.7878 (mt0) REVERT: I 25 ILE cc_start: 0.8597 (mm) cc_final: 0.8220 (mm) REVERT: I 38 GLN cc_start: 0.8429 (mm-40) cc_final: 0.8227 (tp40) REVERT: I 42 LEU cc_start: 0.8889 (tp) cc_final: 0.8619 (tp) REVERT: I 46 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8368 (mp) REVERT: I 64 THR cc_start: 0.8105 (p) cc_final: 0.7865 (p) REVERT: I 128 ARG cc_start: 0.8622 (ttm170) cc_final: 0.8153 (mtm180) REVERT: I 144 ASP cc_start: 0.8669 (t70) cc_final: 0.8252 (t70) REVERT: I 209 GLU cc_start: 0.7519 (tp30) cc_final: 0.7094 (tp30) REVERT: I 218 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8453 (mm) REVERT: I 225 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7468 (mtmm) REVERT: I 229 MET cc_start: 0.7786 (mmt) cc_final: 0.7470 (mmm) REVERT: I 230 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8263 (mm) REVERT: I 245 ASP cc_start: 0.8256 (t70) cc_final: 0.8027 (t0) REVERT: J 28 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7604 (mm) REVERT: J 71 ASP cc_start: 0.8126 (t70) cc_final: 0.7604 (t0) REVERT: J 128 ARG cc_start: 0.8089 (mmt180) cc_final: 0.7708 (mmp80) REVERT: J 204 PHE cc_start: 0.8267 (t80) cc_final: 0.8016 (t80) REVERT: J 230 LEU cc_start: 0.8445 (mt) cc_final: 0.7730 (tp) REVERT: J 234 THR cc_start: 0.8413 (t) cc_final: 0.8084 (p) REVERT: J 246 GLU cc_start: 0.7269 (tt0) cc_final: 0.6979 (tt0) REVERT: K 75 TYR cc_start: 0.7880 (m-10) cc_final: 0.7474 (m-10) REVERT: K 91 VAL cc_start: 0.8818 (t) cc_final: 0.8508 (m) REVERT: K 131 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7833 (mm-30) REVERT: K 143 ILE cc_start: 0.9144 (mt) cc_final: 0.8900 (mp) REVERT: K 164 LEU cc_start: 0.8445 (mt) cc_final: 0.8148 (mt) REVERT: K 250 GLU cc_start: 0.8175 (tp30) cc_final: 0.7756 (tp30) REVERT: K 269 GLN cc_start: 0.8754 (tp40) cc_final: 0.8254 (tp-100) REVERT: K 270 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7402 (tm-30) REVERT: K 271 VAL cc_start: 0.8781 (t) cc_final: 0.8313 (p) REVERT: X 10 TRP cc_start: 0.7879 (p-90) cc_final: 0.7555 (p-90) REVERT: X 84 MET cc_start: 0.7738 (mtt) cc_final: 0.7071 (ttt) REVERT: X 92 MET cc_start: 0.6333 (tmm) cc_final: 0.5792 (tpt) REVERT: Y 22 LEU cc_start: 0.8207 (tt) cc_final: 0.7873 (tp) REVERT: Y 28 ARG cc_start: 0.8733 (mmm-85) cc_final: 0.8265 (ttp80) REVERT: Y 64 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7664 (mm-40) REVERT: Y 84 MET cc_start: 0.7810 (mtt) cc_final: 0.7565 (mtt) REVERT: Y 137 GLN cc_start: 0.7730 (mm-40) cc_final: 0.7292 (mm-40) outliers start: 117 outliers final: 84 residues processed: 1150 average time/residue: 0.1744 time to fit residues: 313.6283 Evaluate side-chains 1181 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 1083 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain a residue 572 VAL Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain b residue 572 VAL Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain e residue 572 VAL Chi-restraints excluded: chain F residue 27 ARG Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 152 GLU Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain G residue 184 GLU Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 250 GLU Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 255 SER Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 213 GLN Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 225 LYS Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 269 GLN Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 220 VAL Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 255 SER Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 268 LEU Chi-restraints excluded: chain j residue 578 LEU Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain K residue 140 MET Chi-restraints excluded: chain K residue 226 SER Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 246 GLU Chi-restraints excluded: chain K residue 248 LEU Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain X residue 75 GLU Chi-restraints excluded: chain X residue 104 TYR Chi-restraints excluded: chain Y residue 35 LEU Chi-restraints excluded: chain Y residue 64 GLN Chi-restraints excluded: chain Y residue 154 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 250 optimal weight: 0.8980 chunk 229 optimal weight: 0.9990 chunk 270 optimal weight: 0.8980 chunk 203 optimal weight: 0.9990 chunk 166 optimal weight: 6.9990 chunk 152 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 228 optimal weight: 0.0010 chunk 109 optimal weight: 5.9990 chunk 252 optimal weight: 0.9980 chunk 303 optimal weight: 4.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 GLN B 185 GLN C 38 GLN D 98 GLN D 213 GLN ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 GLN H 223 ASN I 206 ASN J 38 GLN K 38 GLN ** k 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.116721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.098347 restraints weight = 55919.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.101385 restraints weight = 24651.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.103237 restraints weight = 13416.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.104424 restraints weight = 8672.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.105187 restraints weight = 6458.903| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.6393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 28617 Z= 0.136 Angle : 0.660 13.075 38797 Z= 0.347 Chirality : 0.043 0.182 4282 Planarity : 0.005 0.171 4690 Dihedral : 15.099 150.620 4696 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.92 % Allowed : 25.67 % Favored : 70.40 % 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: 1.52 (0.15), residues: 3239 helix: 1.58 (0.12), residues: 1831 sheet: 2.03 (0.30), residues: 253 loop : -0.07 (0.19), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG C 85 TYR 0.021 0.001 TYR K 93 PHE 0.024 0.001 PHE G 204 TRP 0.027 0.001 TRP F 20 HIS 0.003 0.000 HIS F 43 Details of bonding type rmsd covalent geometry : bond 0.00308 (28609) covalent geometry : angle 0.65995 (38797) hydrogen bonds : bond 0.03963 ( 1345) hydrogen bonds : angle 4.50537 ( 3781) Misc. bond : bond 0.00461 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1222 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 1110 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.7976 (m-30) cc_final: 0.7728 (m-30) REVERT: A 144 ASP cc_start: 0.7978 (m-30) cc_final: 0.7630 (m-30) REVERT: A 174 ASP cc_start: 0.7435 (t0) cc_final: 0.7016 (t0) REVERT: A 246 GLU cc_start: 0.6890 (tp30) cc_final: 0.6316 (tm-30) REVERT: A 270 GLU cc_start: 0.8324 (pt0) cc_final: 0.7877 (pt0) REVERT: A 274 GLU cc_start: 0.6477 (OUTLIER) cc_final: 0.5931 (mt-10) REVERT: a 570 ILE cc_start: 0.8117 (mm) cc_final: 0.7870 (mm) REVERT: a 573 TRP cc_start: 0.8100 (m-90) cc_final: 0.7310 (m-10) REVERT: B 42 LEU cc_start: 0.8668 (tp) cc_final: 0.8385 (tt) REVERT: B 66 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7696 (pttp) REVERT: B 68 VAL cc_start: 0.8972 (p) cc_final: 0.8724 (m) REVERT: B 104 ASP cc_start: 0.8537 (m-30) cc_final: 0.8256 (m-30) REVERT: B 183 ASP cc_start: 0.7283 (t0) cc_final: 0.7016 (t0) REVERT: B 250 GLU cc_start: 0.8358 (tp30) cc_final: 0.8102 (tp30) REVERT: b 571 GLU cc_start: 0.7954 (pt0) cc_final: 0.7713 (pt0) REVERT: C 24 GLU cc_start: 0.8403 (mm-30) cc_final: 0.7814 (mm-30) REVERT: C 111 GLU cc_start: 0.7494 (tm-30) cc_final: 0.6888 (tm-30) REVERT: C 129 THR cc_start: 0.8529 (OUTLIER) cc_final: 0.8263 (m) REVERT: C 176 LEU cc_start: 0.8884 (tp) cc_final: 0.8672 (tt) REVERT: C 183 ASP cc_start: 0.7140 (t0) cc_final: 0.6918 (t0) REVERT: C 210 MET cc_start: 0.8010 (mtp) cc_final: 0.7618 (mtp) REVERT: C 218 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7630 (mm) REVERT: c 581 GLU cc_start: 0.8433 (tm-30) cc_final: 0.8120 (tm-30) REVERT: D 25 ILE cc_start: 0.7471 (mm) cc_final: 0.7120 (mm) REVERT: D 61 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7022 (mm-30) REVERT: D 89 VAL cc_start: 0.8871 (t) cc_final: 0.8610 (m) REVERT: D 111 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7597 (mt-10) REVERT: D 144 ASP cc_start: 0.8530 (t0) cc_final: 0.8239 (m-30) REVERT: D 182 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7715 (mpp80) REVERT: D 206 ASN cc_start: 0.9211 (m-40) cc_final: 0.8979 (m110) REVERT: D 229 MET cc_start: 0.8069 (mmm) cc_final: 0.7552 (mmm) REVERT: D 270 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7941 (tt0) REVERT: E 49 LYS cc_start: 0.8358 (mmtt) cc_final: 0.8013 (mmtm) REVERT: E 89 VAL cc_start: 0.8835 (t) cc_final: 0.8508 (m) REVERT: E 163 ASP cc_start: 0.7813 (t70) cc_final: 0.7297 (t0) REVERT: E 164 LEU cc_start: 0.8265 (mt) cc_final: 0.7869 (mm) REVERT: E 177 ASP cc_start: 0.8043 (m-30) cc_final: 0.7673 (m-30) REVERT: E 186 VAL cc_start: 0.9003 (m) cc_final: 0.8715 (p) REVERT: E 203 ASP cc_start: 0.7206 (m-30) cc_final: 0.6959 (m-30) REVERT: F 41 THR cc_start: 0.8934 (m) cc_final: 0.8571 (p) REVERT: F 66 LYS cc_start: 0.8761 (mtmm) cc_final: 0.8008 (mtmm) REVERT: F 88 THR cc_start: 0.8564 (m) cc_final: 0.8073 (t) REVERT: F 111 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7031 (mt-10) REVERT: F 140 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7547 (ttp) REVERT: F 148 ARG cc_start: 0.8663 (mtt180) cc_final: 0.8302 (mtt180) REVERT: F 180 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8254 (tp) REVERT: F 211 TRP cc_start: 0.7541 (t60) cc_final: 0.7256 (t60) REVERT: F 274 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7451 (mt-10) REVERT: G 24 GLU cc_start: 0.7266 (mm-30) cc_final: 0.6376 (mm-30) REVERT: G 38 GLN cc_start: 0.8009 (mm-40) cc_final: 0.7415 (mt0) REVERT: G 49 LYS cc_start: 0.9113 (mmtt) cc_final: 0.8520 (mmmm) REVERT: G 54 LYS cc_start: 0.8946 (mtmt) cc_final: 0.8737 (mttt) REVERT: G 92 VAL cc_start: 0.9060 (t) cc_final: 0.8729 (p) REVERT: G 108 LYS cc_start: 0.8399 (tttm) cc_final: 0.8151 (tttm) REVERT: G 129 THR cc_start: 0.8911 (m) cc_final: 0.8587 (p) REVERT: G 153 THR cc_start: 0.8789 (p) cc_final: 0.8538 (t) REVERT: G 238 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7696 (mt-10) REVERT: G 268 LEU cc_start: 0.8705 (tp) cc_final: 0.8255 (tt) REVERT: G 273 LYS cc_start: 0.8402 (mmtt) cc_final: 0.8128 (mptt) REVERT: H 89 VAL cc_start: 0.8875 (t) cc_final: 0.8567 (m) REVERT: H 108 LYS cc_start: 0.8543 (ttmt) cc_final: 0.8282 (ttmm) REVERT: H 145 GLU cc_start: 0.8141 (pm20) cc_final: 0.7861 (pm20) REVERT: H 245 ASP cc_start: 0.8357 (t0) cc_final: 0.7718 (t0) REVERT: H 265 LYS cc_start: 0.7098 (tttt) cc_final: 0.6721 (tttp) REVERT: H 269 GLN cc_start: 0.8267 (mt0) cc_final: 0.7943 (mt0) REVERT: I 25 ILE cc_start: 0.8540 (mm) cc_final: 0.8170 (mm) REVERT: I 38 GLN cc_start: 0.8413 (mm-40) cc_final: 0.8195 (tp40) REVERT: I 42 LEU cc_start: 0.8891 (tp) cc_final: 0.8627 (tp) REVERT: I 46 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8343 (mp) REVERT: I 64 THR cc_start: 0.8097 (p) cc_final: 0.7842 (p) REVERT: I 114 LYS cc_start: 0.8818 (mtpp) cc_final: 0.8609 (mtmt) REVERT: I 128 ARG cc_start: 0.8619 (ttm170) cc_final: 0.8145 (mtm180) REVERT: I 144 ASP cc_start: 0.8646 (t70) cc_final: 0.8244 (t70) REVERT: I 209 GLU cc_start: 0.7550 (tp30) cc_final: 0.7159 (tp30) REVERT: I 218 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8437 (mm) REVERT: I 225 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7511 (mtmm) REVERT: I 229 MET cc_start: 0.7700 (mmt) cc_final: 0.7455 (mmm) REVERT: I 245 ASP cc_start: 0.8201 (t70) cc_final: 0.7970 (t0) REVERT: J 28 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7544 (mm) REVERT: J 71 ASP cc_start: 0.8059 (t70) cc_final: 0.7706 (t0) REVERT: J 128 ARG cc_start: 0.8110 (mmt180) cc_final: 0.7741 (mmp80) REVERT: J 204 PHE cc_start: 0.8237 (t80) cc_final: 0.7992 (t80) REVERT: J 205 LYS cc_start: 0.8895 (tptt) cc_final: 0.8502 (tptp) REVERT: J 230 LEU cc_start: 0.8421 (mt) cc_final: 0.7784 (tp) REVERT: J 234 THR cc_start: 0.8404 (t) cc_final: 0.8161 (p) REVERT: J 246 GLU cc_start: 0.7242 (tt0) cc_final: 0.7003 (tt0) REVERT: K 75 TYR cc_start: 0.7848 (m-10) cc_final: 0.7420 (m-10) REVERT: K 91 VAL cc_start: 0.8811 (t) cc_final: 0.8494 (m) REVERT: K 143 ILE cc_start: 0.9139 (mt) cc_final: 0.8893 (mp) REVERT: K 164 LEU cc_start: 0.8472 (mt) cc_final: 0.8212 (mt) REVERT: K 202 GLU cc_start: 0.7841 (pm20) cc_final: 0.7062 (pm20) REVERT: K 233 LEU cc_start: 0.8492 (tp) cc_final: 0.8239 (tt) REVERT: K 269 GLN cc_start: 0.8751 (tp40) cc_final: 0.8252 (tp-100) REVERT: K 270 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7374 (tm-30) REVERT: K 271 VAL cc_start: 0.8772 (t) cc_final: 0.8332 (p) REVERT: k 574 ASP cc_start: 0.7610 (t0) cc_final: 0.7264 (t0) REVERT: X 10 TRP cc_start: 0.7796 (p-90) cc_final: 0.7471 (p-90) REVERT: X 84 MET cc_start: 0.7794 (mtt) cc_final: 0.7091 (ttt) REVERT: Y 22 LEU cc_start: 0.8199 (tt) cc_final: 0.7884 (tp) REVERT: Y 28 ARG cc_start: 0.8738 (mmm-85) cc_final: 0.8277 (ttp80) REVERT: Y 30 ARG cc_start: 0.8552 (mtp180) cc_final: 0.7709 (mmm-85) REVERT: Y 64 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7559 (mm-40) REVERT: Y 137 GLN cc_start: 0.7734 (mm-40) cc_final: 0.7279 (mm-40) outliers start: 112 outliers final: 77 residues processed: 1156 average time/residue: 0.1794 time to fit residues: 324.5850 Evaluate side-chains 1186 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 1096 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain a residue 572 VAL Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain b residue 572 VAL Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain e residue 572 VAL Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 152 GLU Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain G residue 184 GLU Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 250 GLU Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 255 SER Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 152 GLU Chi-restraints excluded: chain I residue 213 GLN Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 225 LYS Chi-restraints excluded: chain I residue 269 GLN Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 220 VAL Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 255 SER Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 268 LEU Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain K residue 140 MET Chi-restraints excluded: chain K residue 226 SER Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 246 GLU Chi-restraints excluded: chain K residue 248 LEU Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain X residue 104 TYR Chi-restraints excluded: chain Y residue 64 GLN Chi-restraints excluded: chain Y residue 112 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 161 optimal weight: 0.9990 chunk 128 optimal weight: 0.6980 chunk 246 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 283 optimal weight: 0.8980 chunk 307 optimal weight: 2.9990 chunk 272 optimal weight: 0.0170 chunk 203 optimal weight: 2.9990 chunk 303 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 GLN B 185 GLN B 206 ASN C 38 GLN ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 GLN H 38 GLN I 206 ASN J 38 GLN K 38 GLN ** Y 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.116850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.098516 restraints weight = 55486.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.101534 restraints weight = 24520.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.103409 restraints weight = 13415.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.104589 restraints weight = 8659.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.105341 restraints weight = 6446.769| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.6512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28617 Z= 0.135 Angle : 0.677 15.119 38797 Z= 0.352 Chirality : 0.043 0.195 4282 Planarity : 0.005 0.154 4690 Dihedral : 15.024 150.431 4696 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.36 % Allowed : 26.90 % Favored : 69.74 % 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: 1.50 (0.15), residues: 3239 helix: 1.56 (0.12), residues: 1831 sheet: 2.02 (0.30), residues: 253 loop : -0.08 (0.19), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG C 85 TYR 0.021 0.001 TYR A 73 PHE 0.020 0.001 PHE E 204 TRP 0.026 0.001 TRP F 20 HIS 0.003 0.000 HIS F 43 Details of bonding type rmsd covalent geometry : bond 0.00308 (28609) covalent geometry : angle 0.67661 (38797) hydrogen bonds : bond 0.03916 ( 1345) hydrogen bonds : angle 4.49906 ( 3781) Misc. bond : bond 0.00374 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1207 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 1111 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.7949 (m-30) cc_final: 0.7711 (m-30) REVERT: A 144 ASP cc_start: 0.7990 (m-30) cc_final: 0.7651 (m-30) REVERT: A 159 ASP cc_start: 0.7810 (t0) cc_final: 0.7536 (t0) REVERT: A 174 ASP cc_start: 0.7447 (t0) cc_final: 0.7042 (t0) REVERT: A 228 GLU cc_start: 0.7704 (pm20) cc_final: 0.7463 (pm20) REVERT: A 246 GLU cc_start: 0.6896 (tp30) cc_final: 0.6316 (tm-30) REVERT: A 270 GLU cc_start: 0.8450 (pt0) cc_final: 0.7970 (pt0) REVERT: A 274 GLU cc_start: 0.6387 (OUTLIER) cc_final: 0.5832 (mt-10) REVERT: a 570 ILE cc_start: 0.8126 (mm) cc_final: 0.7855 (mm) REVERT: a 573 TRP cc_start: 0.8140 (m-90) cc_final: 0.7325 (m-10) REVERT: B 42 LEU cc_start: 0.8661 (tp) cc_final: 0.8406 (tt) REVERT: B 66 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7774 (ptpt) REVERT: B 68 VAL cc_start: 0.8965 (p) cc_final: 0.8716 (m) REVERT: B 104 ASP cc_start: 0.8532 (m-30) cc_final: 0.8258 (m-30) REVERT: B 250 GLU cc_start: 0.8354 (tp30) cc_final: 0.7997 (tt0) REVERT: b 571 GLU cc_start: 0.7963 (pt0) cc_final: 0.7730 (pt0) REVERT: C 24 GLU cc_start: 0.8407 (mm-30) cc_final: 0.7802 (mm-30) REVERT: C 111 GLU cc_start: 0.7498 (tm-30) cc_final: 0.6891 (tm-30) REVERT: C 129 THR cc_start: 0.8532 (OUTLIER) cc_final: 0.8266 (m) REVERT: C 176 LEU cc_start: 0.8886 (tp) cc_final: 0.8676 (tt) REVERT: C 183 ASP cc_start: 0.7329 (t0) cc_final: 0.7112 (t0) REVERT: C 210 MET cc_start: 0.8018 (mtp) cc_final: 0.7616 (mtp) REVERT: C 218 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7516 (mm) REVERT: c 581 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8111 (tm-30) REVERT: D 25 ILE cc_start: 0.7484 (mm) cc_final: 0.7129 (mm) REVERT: D 61 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7165 (mm-30) REVERT: D 89 VAL cc_start: 0.8873 (t) cc_final: 0.8624 (m) REVERT: D 111 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7607 (mt-10) REVERT: D 139 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7183 (mm-30) REVERT: D 144 ASP cc_start: 0.8525 (t0) cc_final: 0.8240 (m-30) REVERT: D 182 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7769 (mpp80) REVERT: D 206 ASN cc_start: 0.9203 (m-40) cc_final: 0.8959 (m110) REVERT: D 229 MET cc_start: 0.8037 (mmm) cc_final: 0.7495 (mmm) REVERT: E 49 LYS cc_start: 0.8371 (mmtt) cc_final: 0.8008 (mmtm) REVERT: E 89 VAL cc_start: 0.8900 (t) cc_final: 0.8567 (m) REVERT: E 139 GLU cc_start: 0.7997 (mp0) cc_final: 0.7760 (mp0) REVERT: E 163 ASP cc_start: 0.7790 (t70) cc_final: 0.7262 (t0) REVERT: E 164 LEU cc_start: 0.8199 (mt) cc_final: 0.7825 (mm) REVERT: E 177 ASP cc_start: 0.8047 (m-30) cc_final: 0.7685 (m-30) REVERT: E 186 VAL cc_start: 0.9042 (m) cc_final: 0.8779 (p) REVERT: E 189 ARG cc_start: 0.7779 (mtm180) cc_final: 0.7286 (mtt180) REVERT: E 203 ASP cc_start: 0.7171 (m-30) cc_final: 0.6941 (m-30) REVERT: F 41 THR cc_start: 0.8952 (m) cc_final: 0.8592 (p) REVERT: F 66 LYS cc_start: 0.8680 (mtmm) cc_final: 0.7923 (mtmm) REVERT: F 88 THR cc_start: 0.8558 (m) cc_final: 0.8084 (t) REVERT: F 111 GLU cc_start: 0.7607 (mt-10) cc_final: 0.6996 (mt-10) REVERT: F 140 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7585 (ttp) REVERT: F 180 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8220 (tp) REVERT: F 240 TYR cc_start: 0.7735 (m-10) cc_final: 0.7197 (m-10) REVERT: F 274 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7463 (mt-10) REVERT: G 24 GLU cc_start: 0.7248 (mm-30) cc_final: 0.6386 (mm-30) REVERT: G 38 GLN cc_start: 0.8001 (mm-40) cc_final: 0.7391 (mt0) REVERT: G 92 VAL cc_start: 0.9054 (t) cc_final: 0.8729 (p) REVERT: G 108 LYS cc_start: 0.8400 (tttm) cc_final: 0.8153 (tttm) REVERT: G 129 THR cc_start: 0.8949 (m) cc_final: 0.8636 (p) REVERT: G 153 THR cc_start: 0.8828 (p) cc_final: 0.8551 (t) REVERT: G 238 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7683 (mt-10) REVERT: G 268 LEU cc_start: 0.8734 (tp) cc_final: 0.8453 (tt) REVERT: H 89 VAL cc_start: 0.8870 (t) cc_final: 0.8485 (m) REVERT: H 108 LYS cc_start: 0.8521 (ttmt) cc_final: 0.8264 (ttmm) REVERT: H 145 GLU cc_start: 0.8142 (pm20) cc_final: 0.7853 (pm20) REVERT: H 245 ASP cc_start: 0.8372 (t0) cc_final: 0.7703 (t0) REVERT: H 265 LYS cc_start: 0.7259 (tttt) cc_final: 0.6999 (ttmm) REVERT: H 269 GLN cc_start: 0.8248 (mt0) cc_final: 0.7886 (mt0) REVERT: I 25 ILE cc_start: 0.8518 (mm) cc_final: 0.8129 (mm) REVERT: I 33 ILE cc_start: 0.9085 (mt) cc_final: 0.8777 (mm) REVERT: I 38 GLN cc_start: 0.8409 (mm-40) cc_final: 0.8179 (tp40) REVERT: I 64 THR cc_start: 0.8101 (p) cc_final: 0.7859 (p) REVERT: I 114 LYS cc_start: 0.8877 (mtpp) cc_final: 0.8618 (mtmt) REVERT: I 128 ARG cc_start: 0.8596 (ttm170) cc_final: 0.8100 (mtm180) REVERT: I 144 ASP cc_start: 0.8665 (t70) cc_final: 0.8235 (t70) REVERT: I 209 GLU cc_start: 0.7542 (tp30) cc_final: 0.7160 (tp30) REVERT: I 218 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8429 (mm) REVERT: I 225 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7476 (mtmm) REVERT: I 229 MET cc_start: 0.7835 (mmt) cc_final: 0.7563 (mmm) REVERT: I 245 ASP cc_start: 0.8164 (t70) cc_final: 0.7842 (t0) REVERT: I 250 GLU cc_start: 0.8088 (tp30) cc_final: 0.7774 (tt0) REVERT: J 28 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7452 (mm) REVERT: J 71 ASP cc_start: 0.8056 (t70) cc_final: 0.7716 (t0) REVERT: J 128 ARG cc_start: 0.8111 (mmt180) cc_final: 0.7742 (mmp80) REVERT: J 204 PHE cc_start: 0.8221 (t80) cc_final: 0.7968 (t80) REVERT: J 205 LYS cc_start: 0.8890 (tptt) cc_final: 0.8480 (tptp) REVERT: J 230 LEU cc_start: 0.8405 (mt) cc_final: 0.7790 (tp) REVERT: J 234 THR cc_start: 0.8561 (t) cc_final: 0.8222 (p) REVERT: J 246 GLU cc_start: 0.7232 (tt0) cc_final: 0.7012 (tt0) REVERT: K 25 ILE cc_start: 0.8396 (mm) cc_final: 0.8173 (mm) REVERT: K 75 TYR cc_start: 0.7837 (m-10) cc_final: 0.7400 (m-10) REVERT: K 91 VAL cc_start: 0.8831 (t) cc_final: 0.8517 (m) REVERT: K 143 ILE cc_start: 0.9106 (mt) cc_final: 0.8870 (mp) REVERT: K 164 LEU cc_start: 0.8468 (mt) cc_final: 0.8223 (mt) REVERT: K 202 GLU cc_start: 0.7830 (pm20) cc_final: 0.7063 (pm20) REVERT: K 233 LEU cc_start: 0.8614 (tp) cc_final: 0.8366 (tt) REVERT: K 270 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7380 (tm-30) REVERT: K 271 VAL cc_start: 0.8786 (t) cc_final: 0.8324 (p) REVERT: X 10 TRP cc_start: 0.7827 (p-90) cc_final: 0.7493 (p-90) REVERT: X 84 MET cc_start: 0.7779 (mtt) cc_final: 0.7089 (ttt) REVERT: Y 22 LEU cc_start: 0.8164 (tt) cc_final: 0.7759 (tp) REVERT: Y 28 ARG cc_start: 0.8753 (mmm-85) cc_final: 0.8290 (ttp80) REVERT: Y 64 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7527 (mm-40) REVERT: Y 84 MET cc_start: 0.7761 (mtt) cc_final: 0.7476 (ttt) REVERT: Y 137 GLN cc_start: 0.7736 (mm-40) cc_final: 0.7329 (mm-40) outliers start: 96 outliers final: 74 residues processed: 1150 average time/residue: 0.1716 time to fit residues: 308.9880 Evaluate side-chains 1180 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 1095 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain a residue 572 VAL Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain b residue 572 VAL Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain e residue 572 VAL Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 152 GLU Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain G residue 184 GLU Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 250 GLU Chi-restraints excluded: chain H residue 38 GLN Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 255 SER Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 29 LYS Chi-restraints excluded: chain I residue 85 ARG Chi-restraints excluded: chain I residue 152 GLU Chi-restraints excluded: chain I residue 213 GLN Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 225 LYS Chi-restraints excluded: chain I residue 269 GLN Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 184 GLU Chi-restraints excluded: chain J residue 220 VAL Chi-restraints excluded: chain J residue 255 SER Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 268 LEU Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain K residue 140 MET Chi-restraints excluded: chain K residue 226 SER Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 246 GLU Chi-restraints excluded: chain K residue 248 LEU Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain X residue 104 TYR Chi-restraints excluded: chain Y residue 64 GLN Chi-restraints excluded: chain Y residue 81 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 302 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 257 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 232 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 185 optimal weight: 0.6980 chunk 316 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 GLN B 185 GLN C 38 GLN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN H 223 ASN I 206 ASN J 38 GLN K 38 GLN Y 83 GLN ** Y 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.116790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.098435 restraints weight = 55834.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.101447 restraints weight = 24581.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.103320 restraints weight = 13431.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.104500 restraints weight = 8668.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.105261 restraints weight = 6456.888| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.6600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 28617 Z= 0.136 Angle : 0.684 15.512 38797 Z= 0.356 Chirality : 0.043 0.203 4282 Planarity : 0.005 0.149 4690 Dihedral : 14.980 150.249 4696 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.19 % Allowed : 27.22 % Favored : 69.60 % 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: 1.48 (0.15), residues: 3239 helix: 1.54 (0.12), residues: 1831 sheet: 2.01 (0.30), residues: 253 loop : -0.09 (0.19), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG C 85 TYR 0.023 0.001 TYR K 93 PHE 0.025 0.001 PHE G 204 TRP 0.033 0.002 TRP Y 114 HIS 0.004 0.000 HIS Y 125 Details of bonding type rmsd covalent geometry : bond 0.00312 (28609) covalent geometry : angle 0.68444 (38797) hydrogen bonds : bond 0.03896 ( 1345) hydrogen bonds : angle 4.51120 ( 3781) Misc. bond : bond 0.00401 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6676.31 seconds wall clock time: 114 minutes 53.32 seconds (6893.32 seconds total)