Starting phenix.real_space_refine on Sun Aug 24 21:18:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h7q_34524/08_2025/8h7q_34524.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h7q_34524/08_2025/8h7q_34524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8h7q_34524/08_2025/8h7q_34524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h7q_34524/08_2025/8h7q_34524.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h7q_34524/08_2025/8h7q_34524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h7q_34524/08_2025/8h7q_34524.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 82 5.49 5 S 68 5.16 5 C 14292 2.51 5 N 3928 2.21 5 O 4514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22884 Number of models: 1 Model: "" Number of chains: 15 Chain: "D" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 753 Classifications: {'RNA': 36} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 8, 'rna3p_pur': 8, 'rna3p_pyr': 15} Link IDs: {'rna2p': 13, 'rna3p': 22} Chain: "L" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 725 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "M" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 231 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "B" Number of atoms: 1992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1992 Classifications: {'peptide': 251} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 236} Chain breaks: 3 Chain: "C" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2366 Classifications: {'peptide': 299} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 283} Chain: "E" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2366 Classifications: {'peptide': 299} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 283} Chain: "F" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2366 Classifications: {'peptide': 299} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 283} Chain: "G" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2366 Classifications: {'peptide': 299} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 283} Chain: "H" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2366 Classifications: {'peptide': 299} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 283} Chain: "I" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2334 Classifications: {'peptide': 295} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 279} Chain breaks: 1 Chain: "J" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 925 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 3, 'TRANS': 107} Chain: "K" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 890 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain: "N" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 883 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 2, 'TRANS': 103} Chain: "O" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 704 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain breaks: 2 Chain: "A" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1617 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 184} Chain breaks: 2 Time building chain proxies: 4.43, per 1000 atoms: 0.19 Number of scatterers: 22884 At special positions: 0 Unit cell: (108.625, 119.625, 206.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 P 82 15.00 O 4514 8.00 N 3928 7.00 C 14292 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 920.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5050 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 25 sheets defined 34.9% alpha, 5.0% beta 13 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'B' and resid 45 through 60 removed outlier: 3.861A pdb=" N MET B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 110 Processing helix chain 'B' and resid 181 through 194 removed outlier: 4.712A pdb=" N ALA B 187 " --> pdb=" O GLU B 183 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN B 190 " --> pdb=" O LYS B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 246 removed outlier: 4.554A pdb=" N LEU B 243 " --> pdb=" O GLU B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 267 removed outlier: 3.680A pdb=" N VAL B 265 " --> pdb=" O GLY B 262 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG B 266 " --> pdb=" O GLU B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 278 removed outlier: 3.670A pdb=" N GLN B 275 " --> pdb=" O GLU B 271 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 299 removed outlier: 3.728A pdb=" N ALA B 292 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP B 293 " --> pdb=" O LYS B 289 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASP B 296 " --> pdb=" O ALA B 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 60 removed outlier: 3.837A pdb=" N MET C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 94 Processing helix chain 'C' and resid 104 through 110 Processing helix chain 'C' and resid 180 through 193 removed outlier: 3.927A pdb=" N TRP C 184 " --> pdb=" O ALA C 180 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA C 187 " --> pdb=" O GLU C 183 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 245 removed outlier: 4.506A pdb=" N LEU C 243 " --> pdb=" O GLU C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 278 removed outlier: 3.677A pdb=" N ALA C 278 " --> pdb=" O ALA C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 299 removed outlier: 3.555A pdb=" N ASP C 296 " --> pdb=" O ALA C 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 60 removed outlier: 3.813A pdb=" N MET E 49 " --> pdb=" O SER E 45 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU E 60 " --> pdb=" O MET E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 110 Processing helix chain 'E' and resid 180 through 194 removed outlier: 4.032A pdb=" N TRP E 184 " --> pdb=" O ALA E 180 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA E 187 " --> pdb=" O GLU E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 242 Processing helix chain 'E' and resid 270 through 278 removed outlier: 3.552A pdb=" N GLN E 275 " --> pdb=" O GLU E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 299 removed outlier: 4.084A pdb=" N ASP E 296 " --> pdb=" O ALA E 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 60 removed outlier: 3.923A pdb=" N MET F 49 " --> pdb=" O SER F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 95 removed outlier: 4.410A pdb=" N GLY F 95 " --> pdb=" O ASP F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 110 Processing helix chain 'F' and resid 181 through 194 removed outlier: 3.765A pdb=" N GLU F 194 " --> pdb=" O GLN F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 240 removed outlier: 4.120A pdb=" N GLU F 239 " --> pdb=" O ASN F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 246 Processing helix chain 'F' and resid 255 through 259 removed outlier: 3.669A pdb=" N PHE F 258 " --> pdb=" O ALA F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 267 Processing helix chain 'F' and resid 270 through 278 removed outlier: 3.854A pdb=" N GLN F 275 " --> pdb=" O GLU F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 299 removed outlier: 3.789A pdb=" N ALA F 295 " --> pdb=" O PHE F 291 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP F 296 " --> pdb=" O ALA F 292 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER F 297 " --> pdb=" O ASP F 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 60 removed outlier: 4.013A pdb=" N MET G 49 " --> pdb=" O SER G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 94 removed outlier: 3.709A pdb=" N LEU G 93 " --> pdb=" O ALA G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 110 removed outlier: 3.649A pdb=" N LYS G 108 " --> pdb=" O ALA G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 194 removed outlier: 3.719A pdb=" N TRP G 184 " --> pdb=" O ALA G 180 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS G 186 " --> pdb=" O PRO G 182 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA G 187 " --> pdb=" O GLU G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 236 through 239 removed outlier: 4.106A pdb=" N GLU G 239 " --> pdb=" O ASN G 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 236 through 239' Processing helix chain 'G' and resid 240 through 247 removed outlier: 4.152A pdb=" N THR G 244 " --> pdb=" O LEU G 240 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR G 246 " --> pdb=" O ARG G 242 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASP G 247 " --> pdb=" O LEU G 243 " (cutoff:3.500A) Processing helix chain 'G' and resid 262 through 267 removed outlier: 3.732A pdb=" N VAL G 265 " --> pdb=" O GLY G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 277 Processing helix chain 'G' and resid 286 through 299 removed outlier: 3.722A pdb=" N ALA G 292 " --> pdb=" O GLU G 288 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP G 293 " --> pdb=" O LYS G 289 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA G 295 " --> pdb=" O PHE G 291 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASP G 296 " --> pdb=" O ALA G 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 60 removed outlier: 3.882A pdb=" N MET H 49 " --> pdb=" O SER H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 94 removed outlier: 3.734A pdb=" N LEU H 93 " --> pdb=" O ALA H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 110 Processing helix chain 'H' and resid 180 through 194 removed outlier: 4.301A pdb=" N TRP H 184 " --> pdb=" O ALA H 180 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA H 187 " --> pdb=" O GLU H 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 237 through 246 removed outlier: 4.093A pdb=" N SER H 241 " --> pdb=" O TRP H 237 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LEU H 243 " --> pdb=" O GLU H 239 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N THR H 244 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR H 246 " --> pdb=" O ARG H 242 " (cutoff:3.500A) Processing helix chain 'H' and resid 263 through 267 Processing helix chain 'H' and resid 270 through 278 removed outlier: 3.683A pdb=" N ALA H 278 " --> pdb=" O ALA H 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 299 removed outlier: 4.001A pdb=" N ASP H 296 " --> pdb=" O ALA H 292 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 60 removed outlier: 4.164A pdb=" N MET I 49 " --> pdb=" O SER I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 104 through 110 Processing helix chain 'I' and resid 180 through 193 removed outlier: 4.220A pdb=" N TRP I 184 " --> pdb=" O ALA I 180 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA I 187 " --> pdb=" O GLU I 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 246 removed outlier: 3.553A pdb=" N THR I 244 " --> pdb=" O LEU I 240 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR I 246 " --> pdb=" O ARG I 242 " (cutoff:3.500A) Processing helix chain 'I' and resid 262 through 267 removed outlier: 3.694A pdb=" N VAL I 265 " --> pdb=" O GLY I 262 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 278 Processing helix chain 'I' and resid 286 through 299 removed outlier: 3.633A pdb=" N PHE I 291 " --> pdb=" O PRO I 287 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA I 292 " --> pdb=" O GLU I 288 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP I 293 " --> pdb=" O LYS I 289 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA I 295 " --> pdb=" O PHE I 291 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASP I 296 " --> pdb=" O ALA I 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 31 Processing helix chain 'J' and resid 34 through 38 Processing helix chain 'J' and resid 41 through 66 removed outlier: 4.496A pdb=" N ARG J 66 " --> pdb=" O ALA J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 80 Processing helix chain 'J' and resid 88 through 99 removed outlier: 3.901A pdb=" N GLN J 98 " --> pdb=" O GLN J 94 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP J 99 " --> pdb=" O LYS J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 113 Processing helix chain 'K' and resid 11 through 31 Processing helix chain 'K' and resid 34 through 38 Processing helix chain 'K' and resid 41 through 65 removed outlier: 3.551A pdb=" N GLU K 45 " --> pdb=" O ASN K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 80 removed outlier: 3.651A pdb=" N SER K 78 " --> pdb=" O ASP K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 95 removed outlier: 4.164A pdb=" N PHE K 92 " --> pdb=" O GLU K 88 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS K 95 " --> pdb=" O ASP K 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 114 removed outlier: 4.927A pdb=" N SER K 105 " --> pdb=" O ASP K 101 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN K 114 " --> pdb=" O ALA K 110 " (cutoff:3.500A) Processing helix chain 'N' and resid 11 through 32 Processing helix chain 'N' and resid 34 through 41 removed outlier: 4.007A pdb=" N ASN N 41 " --> pdb=" O LYS N 37 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 64 Processing helix chain 'N' and resid 68 through 78 removed outlier: 3.746A pdb=" N SER N 78 " --> pdb=" O ASP N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 81 No H-bonds generated for 'chain 'N' and resid 79 through 81' Processing helix chain 'N' and resid 90 through 100 removed outlier: 3.548A pdb=" N LEU N 96 " --> pdb=" O PHE N 92 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE N 97 " --> pdb=" O ALA N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 101 through 114 removed outlier: 3.556A pdb=" N SER N 105 " --> pdb=" O ASP N 101 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN N 114 " --> pdb=" O ALA N 110 " (cutoff:3.500A) Processing helix chain 'O' and resid 12 through 30 removed outlier: 3.664A pdb=" N LYS O 30 " --> pdb=" O LYS O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 64 removed outlier: 3.613A pdb=" N ASN O 57 " --> pdb=" O GLU O 53 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLU O 58 " --> pdb=" O LYS O 54 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ALA O 59 " --> pdb=" O VAL O 55 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE O 60 " --> pdb=" O VAL O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 84 through 98 removed outlier: 3.787A pdb=" N GLU O 88 " --> pdb=" O VAL O 84 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE O 89 " --> pdb=" O ARG O 85 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE O 92 " --> pdb=" O GLU O 88 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ALA O 93 " --> pdb=" O PHE O 89 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU O 96 " --> pdb=" O PHE O 92 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE O 97 " --> pdb=" O ALA O 93 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN O 98 " --> pdb=" O GLN O 94 " (cutoff:3.500A) Processing helix chain 'O' and resid 98 through 114 removed outlier: 3.685A pdb=" N ILE O 103 " --> pdb=" O ASP O 99 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ARG O 104 " --> pdb=" O THR O 100 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER O 105 " --> pdb=" O ASP O 101 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU O 106 " --> pdb=" O GLU O 102 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR O 107 " --> pdb=" O ILE O 103 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA O 110 " --> pdb=" O LEU O 106 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER O 113 " --> pdb=" O LEU O 109 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN O 114 " --> pdb=" O ALA O 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 53 Processing helix chain 'A' and resid 139 through 148 removed outlier: 4.026A pdb=" N GLN A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS A 144 " --> pdb=" O GLU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 Processing sheet with id=AA1, first strand: chain 'B' and resid 5 through 8 Processing sheet with id=AA2, first strand: chain 'B' and resid 43 through 44 removed outlier: 3.695A pdb=" N ILE B 44 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA B 125 " --> pdb=" O ILE B 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 67 through 68 removed outlier: 3.524A pdb=" N THR B 67 " --> pdb=" O GLU B 78 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 5 through 8 Processing sheet with id=AA5, first strand: chain 'C' and resid 15 through 16 Processing sheet with id=AA6, first strand: chain 'C' and resid 28 through 29 Processing sheet with id=AA7, first strand: chain 'C' and resid 67 through 68 removed outlier: 4.463A pdb=" N THR C 67 " --> pdb=" O GLU C 78 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU C 78 " --> pdb=" O THR C 67 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 5 through 8 removed outlier: 4.121A pdb=" N PHE E 171 " --> pdb=" O ALA E 8 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 15 through 16 Processing sheet with id=AB1, first strand: chain 'E' and resid 28 through 29 removed outlier: 3.535A pdb=" N SER E 29 " --> pdb=" O HIS E 159 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 67 through 68 Processing sheet with id=AB3, first strand: chain 'F' and resid 5 through 10 removed outlier: 3.576A pdb=" N ILE F 10 " --> pdb=" O TYR F 169 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR F 169 " --> pdb=" O ILE F 10 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 15 through 16 Processing sheet with id=AB5, first strand: chain 'F' and resid 67 through 68 removed outlier: 3.916A pdb=" N THR F 67 " --> pdb=" O GLU F 78 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU F 78 " --> pdb=" O THR F 67 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'F' and resid 136 through 140 Processing sheet with id=AB7, first strand: chain 'G' and resid 5 through 10 Processing sheet with id=AB8, first strand: chain 'G' and resid 15 through 17 Processing sheet with id=AB9, first strand: chain 'G' and resid 67 through 68 Processing sheet with id=AC1, first strand: chain 'H' and resid 5 through 10 Processing sheet with id=AC2, first strand: chain 'H' and resid 15 through 17 removed outlier: 3.584A pdb=" N ALA H 15 " --> pdb=" O THR H 165 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 43 through 44 removed outlier: 3.841A pdb=" N ILE H 44 " --> pdb=" O ALA H 125 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA H 125 " --> pdb=" O ILE H 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'H' and resid 67 through 68 Processing sheet with id=AC5, first strand: chain 'I' and resid 120 through 121 removed outlier: 3.841A pdb=" N ALA I 172 " --> pdb=" O ARG I 121 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL I 215 " --> pdb=" O THR I 9 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AC7, first strand: chain 'A' and resid 88 through 95 removed outlier: 3.718A pdb=" N GLN A 93 " --> pdb=" O VAL A 121 " (cutoff:3.500A) 597 hydrogen bonds defined for protein. 1674 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 30 hydrogen bonds 60 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 2.89 Time building geometry restraints manager: 2.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7073 1.34 - 1.46: 4469 1.46 - 1.58: 11748 1.58 - 1.70: 162 1.70 - 1.82: 117 Bond restraints: 23569 Sorted by residual: bond pdb=" C CYS C 122 " pdb=" N ASN C 123 " ideal model delta sigma weight residual 1.330 1.375 -0.045 1.22e-02 6.72e+03 1.37e+01 bond pdb=" CA ARG B 116 " pdb=" C ARG B 116 " ideal model delta sigma weight residual 1.524 1.565 -0.042 1.29e-02 6.01e+03 1.04e+01 bond pdb=" C LEU C 253 " pdb=" N PRO C 254 " ideal model delta sigma weight residual 1.333 1.353 -0.020 7.80e-03 1.64e+04 6.46e+00 bond pdb=" CA GLU B 257 " pdb=" C GLU B 257 " ideal model delta sigma weight residual 1.521 1.548 -0.027 1.22e-02 6.72e+03 4.82e+00 bond pdb=" CA VAL H 223 " pdb=" C VAL H 223 " ideal model delta sigma weight residual 1.523 1.551 -0.028 1.27e-02 6.20e+03 4.78e+00 ... (remaining 23564 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 31766 2.85 - 5.69: 435 5.69 - 8.54: 56 8.54 - 11.39: 10 11.39 - 14.24: 8 Bond angle restraints: 32275 Sorted by residual: angle pdb=" N ARG B 116 " pdb=" CA ARG B 116 " pdb=" C ARG B 116 " ideal model delta sigma weight residual 111.36 123.23 -11.87 1.09e+00 8.42e-01 1.19e+02 angle pdb=" N GLY A 159 " pdb=" CA GLY A 159 " pdb=" C GLY A 159 " ideal model delta sigma weight residual 112.73 124.55 -11.82 1.20e+00 6.94e-01 9.70e+01 angle pdb=" N PHE B 258 " pdb=" CA PHE B 258 " pdb=" C PHE B 258 " ideal model delta sigma weight residual 111.54 123.30 -11.76 1.36e+00 5.41e-01 7.48e+01 angle pdb=" N TYR A 158 " pdb=" CA TYR A 158 " pdb=" C TYR A 158 " ideal model delta sigma weight residual 111.36 120.53 -9.17 1.09e+00 8.42e-01 7.08e+01 angle pdb=" N ASN C 19 " pdb=" CA ASN C 19 " pdb=" C ASN C 19 " ideal model delta sigma weight residual 111.74 122.49 -10.75 1.35e+00 5.49e-01 6.34e+01 ... (remaining 32270 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.06: 13676 35.06 - 70.12: 468 70.12 - 105.17: 37 105.17 - 140.23: 2 140.23 - 175.29: 5 Dihedral angle restraints: 14188 sinusoidal: 6383 harmonic: 7805 Sorted by residual: dihedral pdb=" O4' U D 38 " pdb=" C1' U D 38 " pdb=" N1 U D 38 " pdb=" C2 U D 38 " ideal model delta sinusoidal sigma weight residual 200.00 45.93 154.07 1 1.50e+01 4.44e-03 8.10e+01 dihedral pdb=" O4' C D 14 " pdb=" C1' C D 14 " pdb=" N1 C D 14 " pdb=" C2 C D 14 " ideal model delta sinusoidal sigma weight residual 200.00 50.59 149.41 1 1.50e+01 4.44e-03 7.94e+01 dihedral pdb=" O4' U D 41 " pdb=" C1' U D 41 " pdb=" N1 U D 41 " pdb=" C2 U D 41 " ideal model delta sinusoidal sigma weight residual -160.00 -77.75 -82.25 1 1.50e+01 4.44e-03 3.69e+01 ... (remaining 14185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 3318 0.098 - 0.196: 169 0.196 - 0.294: 11 0.294 - 0.392: 7 0.392 - 0.491: 3 Chirality restraints: 3508 Sorted by residual: chirality pdb=" CA VAL I 223 " pdb=" N VAL I 223 " pdb=" C VAL I 223 " pdb=" CB VAL I 223 " both_signs ideal model delta sigma weight residual False 2.44 1.95 0.49 2.00e-01 2.50e+01 6.02e+00 chirality pdb=" CA TRP A 204 " pdb=" N TRP A 204 " pdb=" C TRP A 204 " pdb=" CB TRP A 204 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.54e+00 chirality pdb=" CA ASN C 19 " pdb=" N ASN C 19 " pdb=" C ASN C 19 " pdb=" CB ASN C 19 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.28e+00 ... (remaining 3505 not shown) Planarity restraints: 3927 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 210 " 0.091 5.00e-02 4.00e+02 1.42e-01 3.21e+01 pdb=" N PRO C 211 " -0.245 5.00e-02 4.00e+02 pdb=" CA PRO C 211 " 0.081 5.00e-02 4.00e+02 pdb=" CD PRO C 211 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 219 " -0.082 5.00e-02 4.00e+02 1.27e-01 2.58e+01 pdb=" N PRO A 220 " 0.220 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN E 84 " 0.077 5.00e-02 4.00e+02 1.13e-01 2.03e+01 pdb=" N PRO E 85 " -0.194 5.00e-02 4.00e+02 pdb=" CA PRO E 85 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO E 85 " 0.062 5.00e-02 4.00e+02 ... (remaining 3924 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.13: 25 2.13 - 2.83: 7195 2.83 - 3.52: 32744 3.52 - 4.21: 50573 4.21 - 4.90: 83844 Nonbonded interactions: 174381 Sorted by model distance: nonbonded pdb=" O TRP A 184 " pdb=" CB SER A 221 " model vdw 1.442 3.440 nonbonded pdb=" CD2 LEU A 160 " pdb=" OD1 ASN A 166 " model vdw 1.549 3.460 nonbonded pdb=" CD PRO G 141 " pdb=" O ALA G 156 " model vdw 1.759 3.440 nonbonded pdb=" O CYS A 199 " pdb=" CG2 ILE A 215 " model vdw 1.793 3.460 nonbonded pdb=" O ALA G 191 " pdb=" O GLU G 194 " model vdw 1.798 3.040 ... (remaining 174376 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 'B' and (resid 3 through 248 or resid 253 through 301)) selection = (chain 'I' and (resid 3 through 18 or resid 30 through 133 or resid 163 through \ 198 or resid 207 through 301)) } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = (chain 'J' and resid 10 through 115) selection = (chain 'K' and resid 10 through 115) selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.480 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.352 23571 Z= 0.291 Angle : 0.840 14.237 32275 Z= 0.483 Chirality : 0.049 0.491 3508 Planarity : 0.007 0.142 3927 Dihedral : 17.417 175.288 9138 Min Nonbonded Distance : 1.442 Molprobity Statistics. All-atom Clashscore : 25.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.69 % Favored : 90.16 % Rotamer: Outliers : 0.72 % Allowed : 1.71 % Favored : 97.57 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.36 (0.16), residues: 2612 helix: -0.08 (0.19), residues: 780 sheet: -1.44 (0.30), residues: 250 loop : -2.51 (0.14), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 46 TYR 0.013 0.001 TYR F 226 PHE 0.025 0.001 PHE J 97 TRP 0.053 0.002 TRP C 184 HIS 0.006 0.001 HIS K 31 Details of bonding type rmsd covalent geometry : bond 0.00325 (23569) covalent geometry : angle 0.83955 (32275) hydrogen bonds : bond 0.21958 ( 627) hydrogen bonds : angle 7.68368 ( 1734) Misc. bond : bond 0.24942 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 331 time to evaluate : 0.797 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: B 70 HIS cc_start: 0.8585 (m90) cc_final: 0.8281 (m-70) REVERT: B 184 TRP cc_start: 0.8599 (m100) cc_final: 0.8395 (m100) REVERT: B 223 VAL cc_start: 0.8134 (t) cc_final: 0.6714 (t) REVERT: B 237 TRP cc_start: 0.7076 (t60) cc_final: 0.6196 (t60) REVERT: B 258 PHE cc_start: 0.2968 (t80) cc_final: 0.2737 (t80) REVERT: C 209 PHE cc_start: 0.3923 (OUTLIER) cc_final: 0.3488 (p90) REVERT: C 279 MET cc_start: 0.8097 (mpp) cc_final: 0.7781 (mpp) REVERT: E 10 ILE cc_start: 0.7531 (mp) cc_final: 0.7046 (mm) REVERT: E 97 MET cc_start: 0.4913 (mpp) cc_final: 0.4701 (mpp) REVERT: F 40 LYS cc_start: 0.7632 (mmmt) cc_final: 0.7352 (mmmt) REVERT: F 149 TRP cc_start: 0.4405 (t-100) cc_final: 0.3613 (t-100) REVERT: F 167 PHE cc_start: 0.7922 (p90) cc_final: 0.7008 (p90) REVERT: F 252 ASP cc_start: 0.7352 (m-30) cc_final: 0.6853 (p0) REVERT: G 232 ASP cc_start: 0.8513 (m-30) cc_final: 0.8175 (m-30) REVERT: H 112 ARG cc_start: 0.6998 (pmt-80) cc_final: 0.6655 (pmt-80) REVERT: H 279 MET cc_start: 0.7938 (mpp) cc_final: 0.7706 (mpp) REVERT: I 222 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8522 (tp) REVERT: I 236 ASN cc_start: 0.8055 (m-40) cc_final: 0.7478 (p0) REVERT: K 53 GLU cc_start: 0.8935 (pp20) cc_final: 0.8707 (pp20) REVERT: K 58 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8634 (tm-30) REVERT: N 77 VAL cc_start: 0.8415 (t) cc_final: 0.8172 (t) REVERT: O 58 GLU cc_start: 0.9223 (pp20) cc_final: 0.8987 (pp20) REVERT: A 70 LYS cc_start: 0.7209 (OUTLIER) cc_final: 0.6713 (mmpt) REVERT: A 199 CYS cc_start: 0.8023 (p) cc_final: 0.7811 (t) outliers start: 16 outliers final: 3 residues processed: 344 average time/residue: 0.1420 time to fit residues: 73.5581 Evaluate side-chains 221 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 215 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain G residue 139 GLN Chi-restraints excluded: chain I residue 222 LEU Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 216 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.0770 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.7544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 256 ASN C 286 ASN ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN F 139 GLN F 196 ASN G 51 ASN ** G 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 282 HIS ** H 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 196 ASN ** I 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.081316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.068584 restraints weight = 112212.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.070347 restraints weight = 65766.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.071493 restraints weight = 45510.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.072258 restraints weight = 35252.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.072807 restraints weight = 29392.838| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23571 Z= 0.178 Angle : 0.751 9.649 32275 Z= 0.392 Chirality : 0.044 0.274 3508 Planarity : 0.006 0.100 3927 Dihedral : 16.851 173.394 4005 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.41 % Favored : 89.47 % Rotamer: Outliers : 1.71 % Allowed : 13.59 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.43 (0.16), residues: 2612 helix: -0.28 (0.18), residues: 810 sheet: -1.21 (0.37), residues: 193 loop : -2.53 (0.14), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 46 TYR 0.043 0.002 TYR B 96 PHE 0.018 0.002 PHE I 167 TRP 0.027 0.002 TRP C 184 HIS 0.005 0.001 HIS K 31 Details of bonding type rmsd covalent geometry : bond 0.00393 (23569) covalent geometry : angle 0.75078 (32275) hydrogen bonds : bond 0.05132 ( 627) hydrogen bonds : angle 5.45403 ( 1734) Misc. bond : bond 0.00933 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 247 time to evaluate : 0.810 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: B 70 HIS cc_start: 0.8528 (m90) cc_final: 0.8257 (m-70) REVERT: B 97 MET cc_start: 0.5830 (mpp) cc_final: 0.5499 (mpp) REVERT: B 184 TRP cc_start: 0.8696 (m100) cc_final: 0.8400 (m100) REVERT: B 258 PHE cc_start: 0.3511 (t80) cc_final: 0.3157 (t80) REVERT: B 268 MET cc_start: 0.7298 (mpp) cc_final: 0.6452 (mmp) REVERT: C 209 PHE cc_start: 0.4026 (OUTLIER) cc_final: 0.3675 (p90) REVERT: E 97 MET cc_start: 0.5756 (mpp) cc_final: 0.5449 (mpp) REVERT: F 149 TRP cc_start: 0.4108 (t-100) cc_final: 0.3679 (t-100) REVERT: F 279 MET cc_start: 0.7953 (mpp) cc_final: 0.7595 (mpp) REVERT: H 181 LYS cc_start: 0.5666 (ttmt) cc_final: 0.5461 (ttmt) REVERT: H 282 HIS cc_start: 0.7302 (OUTLIER) cc_final: 0.7080 (m-70) REVERT: I 137 PHE cc_start: 0.7823 (p90) cc_final: 0.7567 (p90) REVERT: I 222 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8256 (tp) REVERT: I 279 MET cc_start: 0.6149 (ttp) cc_final: 0.5946 (tpp) REVERT: J 97 PHE cc_start: 0.8280 (m-10) cc_final: 0.7928 (m-10) REVERT: K 53 GLU cc_start: 0.8915 (pp20) cc_final: 0.8634 (pp20) REVERT: K 58 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8558 (tm-30) REVERT: K 91 ASP cc_start: 0.8879 (p0) cc_final: 0.8655 (p0) REVERT: O 54 LYS cc_start: 0.9408 (tppt) cc_final: 0.9168 (mmtt) REVERT: O 58 GLU cc_start: 0.9017 (pp20) cc_final: 0.8787 (pm20) REVERT: O 98 GLN cc_start: 0.6882 (pm20) cc_final: 0.6422 (pm20) outliers start: 38 outliers final: 20 residues processed: 269 average time/residue: 0.1436 time to fit residues: 58.5916 Evaluate side-chains 224 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 201 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 167 PHE Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain F residue 27 ASN Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain F residue 139 GLN Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 139 GLN Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain H residue 167 PHE Chi-restraints excluded: chain H residue 282 HIS Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain I residue 222 LEU Chi-restraints excluded: chain J residue 61 LEU Chi-restraints excluded: chain J residue 111 LEU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain A residue 83 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 36 optimal weight: 0.8980 chunk 186 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 227 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 237 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 198 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 ASN F 32 GLN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 GLN ** G 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 ASN H 51 ASN ** H 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 98 GLN ** N 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.081889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.069142 restraints weight = 112718.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.070919 restraints weight = 66101.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.072103 restraints weight = 45750.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.072888 restraints weight = 35234.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.073427 restraints weight = 29316.292| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 23571 Z= 0.144 Angle : 0.695 9.869 32275 Z= 0.360 Chirality : 0.042 0.254 3508 Planarity : 0.005 0.086 3927 Dihedral : 16.662 174.648 3997 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.03 % Favored : 89.74 % Rotamer: Outliers : 1.93 % Allowed : 17.41 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.36 (0.16), residues: 2612 helix: -0.19 (0.19), residues: 809 sheet: -1.43 (0.34), residues: 206 loop : -2.47 (0.14), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 242 TYR 0.041 0.001 TYR B 96 PHE 0.023 0.001 PHE A 218 TRP 0.018 0.001 TRP A 184 HIS 0.006 0.001 HIS K 31 Details of bonding type rmsd covalent geometry : bond 0.00314 (23569) covalent geometry : angle 0.69501 (32275) hydrogen bonds : bond 0.04356 ( 627) hydrogen bonds : angle 5.02959 ( 1734) Misc. bond : bond 0.00493 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 233 time to evaluate : 0.602 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: B 56 MET cc_start: 0.8617 (mpp) cc_final: 0.7886 (mpp) REVERT: B 70 HIS cc_start: 0.8515 (m90) cc_final: 0.8232 (m-70) REVERT: B 266 ARG cc_start: 0.8635 (ptt90) cc_final: 0.8311 (ptt90) REVERT: C 55 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8311 (mm-30) REVERT: E 10 ILE cc_start: 0.7759 (mp) cc_final: 0.7037 (mm) REVERT: F 56 MET cc_start: 0.8526 (mtp) cc_final: 0.8320 (mtt) REVERT: F 149 TRP cc_start: 0.4309 (t-100) cc_final: 0.3917 (t-100) REVERT: G 82 TYR cc_start: 0.6921 (t80) cc_final: 0.6498 (t80) REVERT: I 97 MET cc_start: 0.7180 (tmm) cc_final: 0.6932 (tmm) REVERT: I 137 PHE cc_start: 0.7794 (p90) cc_final: 0.7551 (p90) REVERT: I 236 ASN cc_start: 0.7845 (m-40) cc_final: 0.7620 (p0) REVERT: K 53 GLU cc_start: 0.8924 (pp20) cc_final: 0.8606 (pp20) REVERT: K 58 GLU cc_start: 0.8876 (tm-30) cc_final: 0.8599 (tm-30) REVERT: O 54 LYS cc_start: 0.9418 (tppt) cc_final: 0.9107 (mmpt) REVERT: A 135 LEU cc_start: 0.8733 (tp) cc_final: 0.8504 (tt) outliers start: 43 outliers final: 26 residues processed: 258 average time/residue: 0.1560 time to fit residues: 61.5642 Evaluate side-chains 229 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 203 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 167 PHE Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 139 GLN Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 139 GLN Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 111 LEU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain A residue 83 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 37 optimal weight: 9.9990 chunk 202 optimal weight: 9.9990 chunk 69 optimal weight: 0.5980 chunk 161 optimal weight: 0.0020 chunk 116 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 205 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 10 optimal weight: 0.0970 overall best weight: 1.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 32 GLN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 GLN H 32 GLN ** H 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 34 GLN ** O 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.081156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.068380 restraints weight = 112189.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.070098 restraints weight = 66001.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.071283 restraints weight = 45894.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.072060 restraints weight = 35511.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.072592 restraints weight = 29625.813| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 23571 Z= 0.147 Angle : 0.688 10.913 32275 Z= 0.356 Chirality : 0.041 0.259 3508 Planarity : 0.005 0.077 3927 Dihedral : 16.493 174.693 3995 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.83 % Favored : 88.94 % Rotamer: Outliers : 2.61 % Allowed : 19.61 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.30 (0.16), residues: 2612 helix: -0.16 (0.19), residues: 811 sheet: -1.21 (0.36), residues: 192 loop : -2.44 (0.14), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 242 TYR 0.049 0.001 TYR B 96 PHE 0.024 0.001 PHE A 162 TRP 0.018 0.001 TRP I 237 HIS 0.005 0.001 HIS K 31 Details of bonding type rmsd covalent geometry : bond 0.00324 (23569) covalent geometry : angle 0.68791 (32275) hydrogen bonds : bond 0.04257 ( 627) hydrogen bonds : angle 4.88947 ( 1734) Misc. bond : bond 0.00391 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 220 time to evaluate : 0.752 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: B 70 HIS cc_start: 0.8503 (m90) cc_final: 0.8195 (m-70) REVERT: B 266 ARG cc_start: 0.8691 (ptt90) cc_final: 0.8334 (ptt90) REVERT: C 55 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8214 (mm-30) REVERT: E 10 ILE cc_start: 0.7926 (mp) cc_final: 0.7459 (mm) REVERT: E 97 MET cc_start: 0.5652 (mpp) cc_final: 0.5262 (mpp) REVERT: F 56 MET cc_start: 0.8614 (mtp) cc_final: 0.8385 (mtt) REVERT: F 149 TRP cc_start: 0.4763 (t-100) cc_final: 0.4281 (t-100) REVERT: G 82 TYR cc_start: 0.7072 (t80) cc_final: 0.6654 (t80) REVERT: I 97 MET cc_start: 0.7159 (tmm) cc_final: 0.6855 (tmm) REVERT: I 222 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8157 (tm) REVERT: I 236 ASN cc_start: 0.7912 (m-40) cc_final: 0.7676 (p0) REVERT: J 87 ASP cc_start: 0.8199 (p0) cc_final: 0.7788 (m-30) REVERT: J 92 PHE cc_start: 0.7558 (m-80) cc_final: 0.7143 (m-80) REVERT: K 13 GLU cc_start: 0.8563 (mp0) cc_final: 0.8251 (mp0) REVERT: K 53 GLU cc_start: 0.8934 (pp20) cc_final: 0.8670 (pp20) REVERT: K 58 GLU cc_start: 0.8912 (tm-30) cc_final: 0.8640 (tm-30) REVERT: O 54 LYS cc_start: 0.9419 (tppt) cc_final: 0.9099 (mmpt) outliers start: 58 outliers final: 36 residues processed: 260 average time/residue: 0.1517 time to fit residues: 60.2441 Evaluate side-chains 232 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 195 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 167 PHE Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 268 MET Chi-restraints excluded: chain F residue 27 ASN Chi-restraints excluded: chain F residue 139 GLN Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 139 GLN Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 237 TRP Chi-restraints excluded: chain G residue 282 HIS Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain I residue 49 MET Chi-restraints excluded: chain I residue 222 LEU Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 61 LEU Chi-restraints excluded: chain J residue 111 LEU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain O residue 111 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 71 optimal weight: 3.9990 chunk 142 optimal weight: 0.0970 chunk 249 optimal weight: 10.0000 chunk 169 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 chunk 188 optimal weight: 0.9980 chunk 177 optimal weight: 4.9990 chunk 87 optimal weight: 0.4980 chunk 150 optimal weight: 4.9990 chunk 217 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 32 GLN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 GLN ** H 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 272 GLN ** O 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.081706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.068980 restraints weight = 110664.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.070730 restraints weight = 65454.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.071888 restraints weight = 45458.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.072670 restraints weight = 35197.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.073199 restraints weight = 29395.140| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 23571 Z= 0.133 Angle : 0.682 11.375 32275 Z= 0.350 Chirality : 0.041 0.209 3508 Planarity : 0.005 0.073 3927 Dihedral : 16.342 174.879 3994 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.22 % Favored : 89.51 % Rotamer: Outliers : 3.10 % Allowed : 20.38 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.24 (0.16), residues: 2612 helix: -0.09 (0.19), residues: 803 sheet: -1.12 (0.36), residues: 192 loop : -2.42 (0.14), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 242 TYR 0.032 0.001 TYR C 96 PHE 0.011 0.001 PHE G 79 TRP 0.014 0.001 TRP C 184 HIS 0.005 0.001 HIS K 31 Details of bonding type rmsd covalent geometry : bond 0.00291 (23569) covalent geometry : angle 0.68201 (32275) hydrogen bonds : bond 0.03970 ( 627) hydrogen bonds : angle 4.75382 ( 1734) Misc. bond : bond 0.00392 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 215 time to evaluate : 0.817 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: B 70 HIS cc_start: 0.8479 (m90) cc_final: 0.8150 (m-70) REVERT: E 10 ILE cc_start: 0.7926 (mp) cc_final: 0.7542 (mm) REVERT: G 82 TYR cc_start: 0.6923 (t80) cc_final: 0.6570 (t80) REVERT: H 234 GLU cc_start: 0.8230 (pm20) cc_final: 0.7927 (pm20) REVERT: I 97 MET cc_start: 0.7071 (tmm) cc_final: 0.6761 (tmm) REVERT: I 222 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8175 (tm) REVERT: I 279 MET cc_start: 0.6605 (tpp) cc_final: 0.6333 (tpp) REVERT: J 90 VAL cc_start: 0.7685 (OUTLIER) cc_final: 0.7440 (p) REVERT: K 13 GLU cc_start: 0.8550 (mp0) cc_final: 0.8268 (mp0) REVERT: K 53 GLU cc_start: 0.8917 (pp20) cc_final: 0.8711 (pp20) REVERT: K 58 GLU cc_start: 0.8879 (tm-30) cc_final: 0.8601 (tm-30) REVERT: O 54 LYS cc_start: 0.9359 (tppt) cc_final: 0.9042 (mmpt) REVERT: O 58 GLU cc_start: 0.9079 (pp20) cc_final: 0.8810 (pm20) outliers start: 69 outliers final: 38 residues processed: 263 average time/residue: 0.1434 time to fit residues: 58.9673 Evaluate side-chains 237 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 197 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 167 PHE Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain F residue 139 GLN Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 139 GLN Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 282 HIS Chi-restraints excluded: chain H residue 282 HIS Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain I residue 49 MET Chi-restraints excluded: chain I residue 222 LEU Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 111 LEU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain A residue 83 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 227 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 262 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 286 ASN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 GLN ** H 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.080479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.067670 restraints weight = 111921.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.069391 restraints weight = 66273.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.070547 restraints weight = 46131.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.071309 restraints weight = 35897.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.071814 restraints weight = 30072.957| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 23571 Z= 0.157 Angle : 0.701 11.364 32275 Z= 0.362 Chirality : 0.042 0.230 3508 Planarity : 0.005 0.067 3927 Dihedral : 16.236 174.676 3994 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.10 % Favored : 88.67 % Rotamer: Outliers : 3.06 % Allowed : 21.46 % Favored : 75.48 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.22 (0.16), residues: 2612 helix: 0.01 (0.19), residues: 801 sheet: -1.23 (0.35), residues: 198 loop : -2.44 (0.14), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 242 TYR 0.035 0.001 TYR B 96 PHE 0.029 0.002 PHE A 162 TRP 0.024 0.002 TRP F 149 HIS 0.005 0.001 HIS O 83 Details of bonding type rmsd covalent geometry : bond 0.00343 (23569) covalent geometry : angle 0.70147 (32275) hydrogen bonds : bond 0.04093 ( 627) hydrogen bonds : angle 4.81207 ( 1734) Misc. bond : bond 0.00366 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 212 time to evaluate : 0.758 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: B 70 HIS cc_start: 0.8507 (m90) cc_final: 0.8190 (m-70) REVERT: B 96 TYR cc_start: 0.6269 (m-10) cc_final: 0.6064 (m-10) REVERT: E 10 ILE cc_start: 0.8082 (mp) cc_final: 0.7748 (mm) REVERT: E 97 MET cc_start: 0.5922 (mpp) cc_final: 0.5516 (mpp) REVERT: F 139 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8812 (pt0) REVERT: F 149 TRP cc_start: 0.3618 (t-100) cc_final: 0.2935 (t60) REVERT: G 82 TYR cc_start: 0.7018 (t80) cc_final: 0.6654 (t80) REVERT: I 97 MET cc_start: 0.7103 (tmm) cc_final: 0.6732 (tmm) REVERT: I 222 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8178 (tm) REVERT: I 279 MET cc_start: 0.6541 (tpp) cc_final: 0.6200 (tpp) REVERT: J 90 VAL cc_start: 0.7777 (OUTLIER) cc_final: 0.7402 (p) REVERT: K 13 GLU cc_start: 0.8538 (mp0) cc_final: 0.8058 (mp0) REVERT: K 53 GLU cc_start: 0.8927 (pp20) cc_final: 0.8671 (pp20) REVERT: K 58 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8617 (tm-30) REVERT: O 54 LYS cc_start: 0.9343 (tppt) cc_final: 0.9126 (mmtt) REVERT: O 58 GLU cc_start: 0.9103 (pp20) cc_final: 0.8786 (pm20) REVERT: A 135 LEU cc_start: 0.8700 (tp) cc_final: 0.8466 (tt) REVERT: A 222 ASP cc_start: 0.7486 (p0) cc_final: 0.7134 (p0) outliers start: 68 outliers final: 46 residues processed: 260 average time/residue: 0.1561 time to fit residues: 62.3642 Evaluate side-chains 238 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 189 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 167 PHE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 229 TYR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain F residue 27 ASN Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain F residue 139 GLN Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 139 GLN Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 107 MET Chi-restraints excluded: chain H residue 167 PHE Chi-restraints excluded: chain H residue 282 HIS Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain I residue 49 MET Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 165 THR Chi-restraints excluded: chain I residue 222 LEU Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 61 LEU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 111 LEU Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain A residue 83 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 153 optimal weight: 0.9980 chunk 9 optimal weight: 0.0870 chunk 94 optimal weight: 0.7980 chunk 30 optimal weight: 9.9990 chunk 155 optimal weight: 0.1980 chunk 139 optimal weight: 0.9990 chunk 242 optimal weight: 0.3980 chunk 1 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 171 optimal weight: 0.0020 overall best weight: 0.2966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 51 ASN C 62 GLN ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 ASN F 39 GLN ** H 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 272 GLN ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.082532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.069729 restraints weight = 111264.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.071483 restraints weight = 65831.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.072652 restraints weight = 45978.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.073426 restraints weight = 35701.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.073943 restraints weight = 29856.401| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 23571 Z= 0.131 Angle : 0.697 13.051 32275 Z= 0.354 Chirality : 0.041 0.223 3508 Planarity : 0.005 0.065 3927 Dihedral : 16.081 175.042 3994 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.11 % Favored : 89.62 % Rotamer: Outliers : 2.79 % Allowed : 23.03 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.17 (0.16), residues: 2612 helix: -0.04 (0.19), residues: 802 sheet: -1.20 (0.36), residues: 184 loop : -2.35 (0.14), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 242 TYR 0.024 0.001 TYR C 226 PHE 0.032 0.001 PHE H 120 TRP 0.027 0.001 TRP F 259 HIS 0.005 0.001 HIS O 83 Details of bonding type rmsd covalent geometry : bond 0.00285 (23569) covalent geometry : angle 0.69708 (32275) hydrogen bonds : bond 0.03674 ( 627) hydrogen bonds : angle 4.62554 ( 1734) Misc. bond : bond 0.00395 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 231 time to evaluate : 0.830 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: B 70 HIS cc_start: 0.8626 (m90) cc_final: 0.8329 (m-70) REVERT: B 96 TYR cc_start: 0.6148 (m-80) cc_final: 0.5607 (m-10) REVERT: E 10 ILE cc_start: 0.7928 (mp) cc_final: 0.7672 (mm) REVERT: E 97 MET cc_start: 0.5627 (mpp) cc_final: 0.5199 (mpp) REVERT: F 106 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7483 (tm-30) REVERT: F 149 TRP cc_start: 0.3514 (t-100) cc_final: 0.2778 (t60) REVERT: G 82 TYR cc_start: 0.6819 (t80) cc_final: 0.6579 (t80) REVERT: H 112 ARG cc_start: 0.7391 (pmt-80) cc_final: 0.7134 (pmt-80) REVERT: H 234 GLU cc_start: 0.8243 (pm20) cc_final: 0.7954 (pm20) REVERT: H 282 HIS cc_start: 0.6565 (OUTLIER) cc_final: 0.6081 (t-90) REVERT: I 97 MET cc_start: 0.6981 (tmm) cc_final: 0.6641 (tmm) REVERT: I 222 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8155 (tm) REVERT: I 279 MET cc_start: 0.6494 (tpp) cc_final: 0.6185 (tpp) REVERT: J 90 VAL cc_start: 0.7671 (OUTLIER) cc_final: 0.7363 (p) REVERT: J 97 PHE cc_start: 0.8093 (m-80) cc_final: 0.7834 (m-80) REVERT: K 13 GLU cc_start: 0.8511 (mp0) cc_final: 0.8060 (mp0) REVERT: K 53 GLU cc_start: 0.8859 (pp20) cc_final: 0.8605 (pp20) REVERT: K 58 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8613 (tm-30) REVERT: O 54 LYS cc_start: 0.9341 (tppt) cc_final: 0.9120 (mmtt) REVERT: O 58 GLU cc_start: 0.9062 (pp20) cc_final: 0.8840 (pm20) REVERT: A 135 LEU cc_start: 0.8577 (tp) cc_final: 0.8344 (tt) REVERT: A 222 ASP cc_start: 0.7549 (p0) cc_final: 0.7201 (p0) outliers start: 62 outliers final: 36 residues processed: 273 average time/residue: 0.1564 time to fit residues: 65.4428 Evaluate side-chains 243 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 203 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 167 PHE Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain F residue 27 ASN Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 139 GLN Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 107 MET Chi-restraints excluded: chain H residue 282 HIS Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain I residue 49 MET Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 222 LEU Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 111 LEU Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 83 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 127 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 200 optimal weight: 0.0060 chunk 173 optimal weight: 8.9990 chunk 206 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 249 optimal weight: 7.9990 chunk 137 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 27 ASN ** H 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 196 ASN ** O 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.081650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.068856 restraints weight = 111087.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.070588 restraints weight = 65937.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.071739 restraints weight = 46147.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.072532 restraints weight = 35846.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.073076 restraints weight = 29885.127| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 23571 Z= 0.136 Angle : 0.698 12.300 32275 Z= 0.356 Chirality : 0.041 0.239 3508 Planarity : 0.005 0.072 3927 Dihedral : 15.974 174.844 3994 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.53 % Favored : 89.20 % Rotamer: Outliers : 2.70 % Allowed : 23.17 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.16 (0.16), residues: 2612 helix: -0.01 (0.19), residues: 801 sheet: -1.22 (0.36), residues: 184 loop : -2.34 (0.14), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 28 TYR 0.025 0.001 TYR C 226 PHE 0.033 0.001 PHE A 162 TRP 0.056 0.002 TRP F 259 HIS 0.004 0.001 HIS O 83 Details of bonding type rmsd covalent geometry : bond 0.00305 (23569) covalent geometry : angle 0.69779 (32275) hydrogen bonds : bond 0.03732 ( 627) hydrogen bonds : angle 4.57582 ( 1734) Misc. bond : bond 0.00375 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 208 time to evaluate : 0.740 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: B 70 HIS cc_start: 0.8569 (m90) cc_final: 0.8290 (m-70) REVERT: B 96 TYR cc_start: 0.6206 (m-80) cc_final: 0.5698 (m-10) REVERT: B 213 SER cc_start: 0.8626 (p) cc_final: 0.7480 (m) REVERT: E 10 ILE cc_start: 0.7981 (mp) cc_final: 0.7731 (mm) REVERT: E 167 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.7645 (p90) REVERT: F 149 TRP cc_start: 0.3457 (t-100) cc_final: 0.2684 (t60) REVERT: G 82 TYR cc_start: 0.6941 (t80) cc_final: 0.6668 (t80) REVERT: H 49 MET cc_start: 0.8758 (mpp) cc_final: 0.8348 (mtm) REVERT: H 112 ARG cc_start: 0.7464 (pmt-80) cc_final: 0.7262 (pmt-80) REVERT: H 206 TYR cc_start: 0.9101 (OUTLIER) cc_final: 0.8345 (t80) REVERT: H 234 GLU cc_start: 0.8247 (pm20) cc_final: 0.7956 (pm20) REVERT: I 97 MET cc_start: 0.7019 (tmm) cc_final: 0.6661 (tmm) REVERT: I 222 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8148 (tm) REVERT: I 236 ASN cc_start: 0.8112 (m-40) cc_final: 0.7400 (p0) REVERT: J 90 VAL cc_start: 0.7751 (OUTLIER) cc_final: 0.7452 (p) REVERT: K 13 GLU cc_start: 0.8527 (mp0) cc_final: 0.8080 (mp0) REVERT: K 58 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8623 (tm-30) REVERT: O 54 LYS cc_start: 0.9348 (tppt) cc_final: 0.9125 (mmtt) REVERT: O 58 GLU cc_start: 0.9076 (pp20) cc_final: 0.8806 (pm20) REVERT: A 222 ASP cc_start: 0.7390 (p0) cc_final: 0.7084 (p0) outliers start: 60 outliers final: 41 residues processed: 253 average time/residue: 0.1447 time to fit residues: 56.2600 Evaluate side-chains 238 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 193 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 167 PHE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 167 PHE Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 291 PHE Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 139 GLN Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 107 MET Chi-restraints excluded: chain H residue 167 PHE Chi-restraints excluded: chain H residue 206 TYR Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain I residue 49 MET Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 222 LEU Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 111 LEU Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain A residue 83 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 245 optimal weight: 10.0000 chunk 186 optimal weight: 5.9990 chunk 181 optimal weight: 0.8980 chunk 171 optimal weight: 0.0970 chunk 118 optimal weight: 0.3980 chunk 126 optimal weight: 6.9990 chunk 257 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 255 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 overall best weight: 1.0780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.081492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.068658 restraints weight = 111994.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.070391 restraints weight = 66482.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.071530 restraints weight = 46514.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.072315 restraints weight = 36198.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.072837 restraints weight = 30260.906| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 23571 Z= 0.138 Angle : 0.711 12.652 32275 Z= 0.361 Chirality : 0.042 0.244 3508 Planarity : 0.005 0.061 3927 Dihedral : 15.909 174.787 3994 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.76 % Favored : 88.94 % Rotamer: Outliers : 2.38 % Allowed : 23.71 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.16 (0.16), residues: 2612 helix: -0.01 (0.19), residues: 802 sheet: -1.19 (0.35), residues: 198 loop : -2.36 (0.14), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 242 TYR 0.026 0.001 TYR C 226 PHE 0.019 0.001 PHE B 258 TRP 0.054 0.002 TRP F 259 HIS 0.004 0.001 HIS O 83 Details of bonding type rmsd covalent geometry : bond 0.00309 (23569) covalent geometry : angle 0.71143 (32275) hydrogen bonds : bond 0.03730 ( 627) hydrogen bonds : angle 4.54826 ( 1734) Misc. bond : bond 0.00370 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 209 time to evaluate : 0.712 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: B 70 HIS cc_start: 0.8585 (m90) cc_final: 0.8290 (m-70) REVERT: B 96 TYR cc_start: 0.6404 (m-80) cc_final: 0.5756 (m-10) REVERT: B 213 SER cc_start: 0.8598 (p) cc_final: 0.7466 (m) REVERT: E 97 MET cc_start: 0.5552 (mpp) cc_final: 0.5301 (mpp) REVERT: E 167 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.7650 (p90) REVERT: F 149 TRP cc_start: 0.3514 (t-100) cc_final: 0.2735 (t60) REVERT: G 82 TYR cc_start: 0.6968 (t80) cc_final: 0.6703 (t80) REVERT: H 49 MET cc_start: 0.8751 (mpp) cc_final: 0.8361 (mtm) REVERT: H 112 ARG cc_start: 0.7502 (pmt-80) cc_final: 0.7266 (pmt-80) REVERT: H 206 TYR cc_start: 0.9130 (OUTLIER) cc_final: 0.8481 (t80) REVERT: I 97 MET cc_start: 0.7033 (tmm) cc_final: 0.6655 (tmm) REVERT: I 124 MET cc_start: 0.8304 (mmp) cc_final: 0.8052 (mmp) REVERT: I 142 LEU cc_start: 0.7721 (mt) cc_final: 0.7339 (mp) REVERT: I 222 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8207 (tm) REVERT: I 236 ASN cc_start: 0.8162 (m-40) cc_final: 0.7451 (p0) REVERT: J 74 ASP cc_start: 0.8841 (p0) cc_final: 0.8596 (p0) REVERT: J 90 VAL cc_start: 0.7791 (OUTLIER) cc_final: 0.7464 (p) REVERT: K 13 GLU cc_start: 0.8521 (mp0) cc_final: 0.8089 (mp0) REVERT: K 58 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8659 (tm-30) REVERT: O 54 LYS cc_start: 0.9400 (tppt) cc_final: 0.9121 (mmtt) REVERT: A 222 ASP cc_start: 0.7576 (p0) cc_final: 0.7338 (p0) outliers start: 53 outliers final: 42 residues processed: 248 average time/residue: 0.1511 time to fit residues: 58.2612 Evaluate side-chains 242 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 196 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 167 PHE Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain E residue 49 MET Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 167 PHE Chi-restraints excluded: chain E residue 268 MET Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 291 PHE Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 139 GLN Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 107 MET Chi-restraints excluded: chain H residue 167 PHE Chi-restraints excluded: chain H residue 206 TYR Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain I residue 49 MET Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 165 THR Chi-restraints excluded: chain I residue 222 LEU Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 111 LEU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain A residue 83 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 237 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 48 optimal weight: 0.2980 chunk 251 optimal weight: 4.9990 chunk 196 optimal weight: 2.9990 chunk 234 optimal weight: 3.9990 chunk 222 optimal weight: 8.9990 chunk 235 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 GLN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.080048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.067177 restraints weight = 112195.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.068880 restraints weight = 66645.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.070019 restraints weight = 46725.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.070774 restraints weight = 36401.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.071201 restraints weight = 30560.143| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 23571 Z= 0.163 Angle : 0.740 12.644 32275 Z= 0.379 Chirality : 0.042 0.239 3508 Planarity : 0.005 0.059 3927 Dihedral : 15.881 174.699 3994 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.10 % Favored : 88.63 % Rotamer: Outliers : 2.34 % Allowed : 23.53 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.20 (0.16), residues: 2612 helix: -0.03 (0.19), residues: 803 sheet: -1.17 (0.40), residues: 156 loop : -2.38 (0.14), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 242 TYR 0.027 0.001 TYR C 226 PHE 0.041 0.002 PHE A 162 TRP 0.044 0.002 TRP F 259 HIS 0.008 0.001 HIS N 31 Details of bonding type rmsd covalent geometry : bond 0.00365 (23569) covalent geometry : angle 0.74039 (32275) hydrogen bonds : bond 0.04021 ( 627) hydrogen bonds : angle 4.62685 ( 1734) Misc. bond : bond 0.00348 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 199 time to evaluate : 0.853 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: B 70 HIS cc_start: 0.8569 (m90) cc_final: 0.8288 (m-70) REVERT: B 96 TYR cc_start: 0.6667 (m-80) cc_final: 0.6151 (m-10) REVERT: B 213 SER cc_start: 0.8563 (p) cc_final: 0.7387 (m) REVERT: C 242 ARG cc_start: 0.7658 (mmp-170) cc_final: 0.7320 (mmp80) REVERT: E 97 MET cc_start: 0.5709 (mpp) cc_final: 0.5494 (mpp) REVERT: E 167 PHE cc_start: 0.8607 (OUTLIER) cc_final: 0.7775 (p90) REVERT: F 149 TRP cc_start: 0.3600 (t-100) cc_final: 0.2786 (t60) REVERT: G 82 TYR cc_start: 0.7003 (t80) cc_final: 0.6777 (t80) REVERT: G 139 GLN cc_start: 0.6999 (OUTLIER) cc_final: 0.6559 (pm20) REVERT: H 49 MET cc_start: 0.8781 (mpp) cc_final: 0.8389 (mtm) REVERT: H 112 ARG cc_start: 0.7567 (pmt-80) cc_final: 0.7277 (pmt-80) REVERT: H 206 TYR cc_start: 0.9210 (OUTLIER) cc_final: 0.8576 (t80) REVERT: I 97 MET cc_start: 0.7135 (tmm) cc_final: 0.6713 (tmm) REVERT: I 222 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8151 (tm) REVERT: I 236 ASN cc_start: 0.8291 (m-40) cc_final: 0.7535 (p0) REVERT: I 279 MET cc_start: 0.6795 (tpp) cc_final: 0.6566 (tpp) REVERT: J 74 ASP cc_start: 0.8828 (p0) cc_final: 0.8597 (p0) REVERT: K 58 GLU cc_start: 0.8893 (tm-30) cc_final: 0.8641 (tm-30) REVERT: O 54 LYS cc_start: 0.9408 (tppt) cc_final: 0.9132 (mmtt) REVERT: A 222 ASP cc_start: 0.7633 (p0) cc_final: 0.7412 (p0) outliers start: 52 outliers final: 42 residues processed: 235 average time/residue: 0.1546 time to fit residues: 56.3028 Evaluate side-chains 231 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 185 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 167 PHE Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 167 PHE Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 268 MET Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 291 PHE Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 139 GLN Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 158 LEU Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 107 MET Chi-restraints excluded: chain H residue 167 PHE Chi-restraints excluded: chain H residue 206 TYR Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain I residue 49 MET Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 165 THR Chi-restraints excluded: chain I residue 222 LEU Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 111 LEU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain O residue 61 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 203 optimal weight: 0.7980 chunk 163 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 170 optimal weight: 0.9980 chunk 181 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 217 optimal weight: 0.0970 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 196 ASN ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.081358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.068561 restraints weight = 113334.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.070259 restraints weight = 67537.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.071398 restraints weight = 47546.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.072120 restraints weight = 37165.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.072662 restraints weight = 31365.021| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 23571 Z= 0.134 Angle : 0.723 12.219 32275 Z= 0.368 Chirality : 0.042 0.238 3508 Planarity : 0.005 0.059 3927 Dihedral : 15.809 175.117 3994 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.11 % Favored : 89.62 % Rotamer: Outliers : 2.34 % Allowed : 23.89 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.17 (0.16), residues: 2612 helix: -0.02 (0.19), residues: 801 sheet: -1.25 (0.36), residues: 184 loop : -2.35 (0.14), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 112 TYR 0.041 0.001 TYR H 82 PHE 0.016 0.001 PHE H 258 TRP 0.038 0.002 TRP F 259 HIS 0.004 0.001 HIS O 83 Details of bonding type rmsd covalent geometry : bond 0.00299 (23569) covalent geometry : angle 0.72325 (32275) hydrogen bonds : bond 0.03635 ( 627) hydrogen bonds : angle 4.51696 ( 1734) Misc. bond : bond 0.00371 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3200.12 seconds wall clock time: 56 minutes 16.73 seconds (3376.73 seconds total)