Starting phenix.real_space_refine on Fri Aug 7 17:21:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8h7q_34524/08_2026/8h7q_34524.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h7q_34524/08_2026/8h7q_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8h7q_34524/08_2026/8h7q_34524.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8h7q_34524/08_2026/8h7q_34524.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h7q_34524/08_2026/8h7q_34524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h7q_34524/08_2026/8h7q_34524.map" model { file = "/net/cci-nas-00/data/ceres_data/8h7q_34524/08_2026/8h7q_34524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h7q_34524/08_2026/8h7q_34524.cif" } 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-2.2rc3-6140/lib/python3.11/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: {'RNAv2': 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: 4.55, per 1000 atoms: 0.20 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: 1.89 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 2.39 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: 3.38 Time building geometry restraints manager: 2.53 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=" C3' DA L 44 " pdb=" C2' DA L 44 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+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=" C3' DG L 40 " pdb=" C2' DG L 40 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.99e+00 bond pdb=" C3' DT L 36 " pdb=" C2' DT L 36 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.78e+00 ... (remaining 23564 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 31695 2.85 - 5.69: 506 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: 13563 35.06 - 70.12: 452 70.12 - 105.17: 37 105.17 - 140.23: 0 140.23 - 175.29: 2 Dihedral angle restraints: 14054 sinusoidal: 6249 harmonic: 7805 Sorted by residual: dihedral pdb=" C4' A D 26 " pdb=" C3' A D 26 " pdb=" C2' A D 26 " pdb=" C1' A D 26 " ideal model delta sinusoidal sigma weight residual 36.35 -36.07 72.41 1 3.10e+00 1.04e-01 6.97e+02 dihedral pdb=" C4' U D 13 " pdb=" C3' U D 13 " pdb=" C2' U D 13 " pdb=" C1' U D 13 " ideal model delta sinusoidal sigma weight residual 36.34 -35.90 72.24 1 3.10e+00 1.04e-01 6.94e+02 dihedral pdb=" C4' A D 15 " pdb=" C3' A D 15 " pdb=" C2' A D 15 " pdb=" C1' A D 15 " ideal model delta sinusoidal sigma weight residual 36.34 -35.81 72.16 1 3.10e+00 1.04e-01 6.93e+02 ... (remaining 14051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 3254 0.098 - 0.196: 171 0.196 - 0.294: 73 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: 1.630 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 20.750 Find NCS groups from input model: 0.320 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: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 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= 0.327 Angle : 0.880 14.237 32275 Z= 0.519 Chirality : 0.060 0.491 3508 Planarity : 0.007 0.142 3927 Dihedral : 17.028 175.288 9004 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 are 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/Z covalent geometry : bond 0.00355 / 0.23 (23569) covalent geometry : angle 0.87963 / 0.52 (32275) hydrogen bonds : bond 0.21958 / 11.45 ( 627) hydrogen bonds : angle 7.68368 / 6.40 ( 1734) Misc. bond : bond 0.24942 / 12.47 ( 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 : 0.764 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: 0.7921 (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: 0.7810 (t) outliers start: 16 outliers final: 3 residues processed: 344 average time/residue: 0.1616 time to fit residues: 84.4162 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 : 0.765 ------------------------------------------------------------------------------- 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: 4.9990 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... B 102 ASN C 51 ASN C 256 ASN C 286 ASN ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN F 196 ASN G 51 ASN G 196 ASN G 282 HIS H 196 ASN I 19 ASN I 27 ASN ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 94 GLN ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.082165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.069585 restraints weight = 112689.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.071380 restraints weight = 65465.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.072552 restraints weight = 44953.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.073333 restraints weight = 34532.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.073873 restraints weight = 28654.027| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 23571 Z= 0.203 Angle : 1.005 23.458 32275 Z= 0.467 Chirality : 0.074 0.988 3508 Planarity : 0.006 0.081 3927 Dihedral : 14.862 170.989 3871 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.72 % Favored : 89.20 % Rotamer: Outliers : 1.80 % Allowed : 13.05 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.15), residues: 2612 helix: -0.24 (0.19), residues: 799 sheet: -1.35 (0.32), residues: 233 loop : -2.51 (0.14), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 21 TYR 0.042 0.002 TYR B 96 PHE 0.023 0.002 PHE G 209 TRP 0.024 0.002 TRP C 184 HIS 0.005 0.001 HIS K 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.20 (23569) covalent geometry : angle 1.00460 / 0.47 (32275) hydrogen bonds : bond 0.06123 / 3.13 ( 627) hydrogen bonds : angle 5.69455 / 4.57 ( 1734) Misc. bond : bond 0.02109 / 1.05 ( 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 282 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 242 time to evaluate : 0.814 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: 0.8468 (m90) cc_final: 0.8120 (m-70) REVERT: B 97 MET cc_start: 0.5656 (mpp) cc_final: 0.5305 (mpp) REVERT: B 184 TRP cc_start: 0.8757 (m100) cc_final: 0.8433 (m100) REVERT: B 268 MET cc_start: 0.7258 (mpp) cc_final: 0.6354 (mmp) REVERT: C 209 PHE cc_start: 0.3769 (OUTLIER) cc_final: 0.3410 (p90) REVERT: C 279 MET cc_start: 0.8100 (mpp) cc_final: 0.7852 (mpp) REVERT: E 97 MET cc_start: 0.5485 (mpp) cc_final: 0.5246 (mpp) REVERT: F 149 TRP cc_start: 0.3942 (t-100) cc_final: 0.3520 (t-100) REVERT: H 123 ASN cc_start: 0.8028 (t0) cc_final: 0.7801 (t0) REVERT: H 181 LYS cc_start: 0.5643 (ttmt) cc_final: 0.5386 (ttmt) REVERT: I 222 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8212 (tp) REVERT: J 97 PHE cc_start: 0.8243 (m-10) cc_final: 0.7736 (m-10) REVERT: K 13 GLU cc_start: 0.8529 (mp0) cc_final: 0.8309 (mp0) REVERT: K 53 GLU cc_start: 0.8904 (pp20) cc_final: 0.8647 (pp20) REVERT: K 58 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8568 (tm-30) REVERT: O 54 LYS cc_start: 0.9387 (tppt) cc_final: 0.9187 (mmtt) REVERT: O 58 GLU cc_start: 0.8968 (pp20) cc_final: 0.8733 (pm20) REVERT: A 70 LYS cc_start: 0.7007 (mmpt) cc_final: 0.6749 (mmpt) REVERT: A 217 VAL cc_start: 0.1389 (OUTLIER) cc_final: 0.1087 (t) outliers start: 40 outliers final: 21 residues processed: 266 average time/residue: 0.1468 time to fit residues: 60.1824 Evaluate side-chains 228 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 204 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 163 THR 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 E residue 218 LEU Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain F residue 10 ILE Chi-restraints excluded: chain F residue 27 ASN Chi-restraints excluded: chain F residue 32 GLN 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 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 O residue 105 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 218 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 36 optimal weight: 2.9990 chunk 186 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 227 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 chunk 237 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 198 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 51 ASN ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 ASN F 32 GLN ** H 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 98 GLN ** 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 = 0.3780 r_free = 0.3780 target = 0.082087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.069556 restraints weight = 114777.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.071356 restraints weight = 67054.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.072529 restraints weight = 46193.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.073295 restraints weight = 35459.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.073836 restraints weight = 29563.900| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2108 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= 0.165 Angle : 0.829 15.542 32275 Z= 0.405 Chirality : 0.059 0.736 3508 Planarity : 0.005 0.081 3927 Dihedral : 14.963 171.167 3863 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.18 % Favored : 89.70 % Rotamer: Outliers : 2.20 % Allowed : 16.42 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.15), residues: 2612 helix: -0.22 (0.19), residues: 804 sheet: -1.39 (0.34), residues: 208 loop : -2.50 (0.14), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 242 TYR 0.041 0.002 TYR B 96 PHE 0.023 0.002 PHE I 137 TRP 0.017 0.002 TRP C 184 HIS 0.008 0.001 HIS G 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (23569) covalent geometry : angle 0.82898 / 0.40 (32275) hydrogen bonds : bond 0.04875 / 2.49 ( 627) hydrogen bonds : angle 5.26096 / 4.22 ( 1734) Misc. bond : bond 0.01002 / 0.50 ( 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 277 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 228 time to evaluate : 0.875 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: 0.8462 (m90) cc_final: 0.8209 (m-70) REVERT: B 97 MET cc_start: 0.5814 (mpp) cc_final: 0.5569 (mpp) REVERT: B 184 TRP cc_start: 0.8757 (m100) cc_final: 0.8478 (m100) REVERT: B 266 ARG cc_start: 0.8631 (ptt90) cc_final: 0.8297 (ptt90) REVERT: C 198 VAL cc_start: 0.8466 (OUTLIER) cc_final: 0.8236 (p) REVERT: E 10 ILE cc_start: 0.8024 (mp) cc_final: 0.7210 (mm) REVERT: E 97 MET cc_start: 0.5466 (mpp) cc_final: 0.5139 (mpp) REVERT: F 32 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.8275 (mt0) REVERT: F 56 MET cc_start: 0.8507 (mtp) cc_final: 0.8247 (mtt) REVERT: F 149 TRP cc_start: 0.4303 (t-100) cc_final: 0.3818 (t-100) REVERT: G 207 TYR cc_start: 0.8150 (t80) cc_final: 0.7922 (t80) REVERT: G 279 MET cc_start: 0.6854 (OUTLIER) cc_final: 0.5501 (mmm) REVERT: H 123 ASN cc_start: 0.8062 (t0) cc_final: 0.7730 (m-40) REVERT: H 181 LYS cc_start: 0.5607 (ttmt) cc_final: 0.5198 (ttmt) REVERT: I 222 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8328 (tp) REVERT: I 236 ASN cc_start: 0.7816 (m-40) cc_final: 0.7572 (p0) REVERT: K 13 GLU cc_start: 0.8435 (mp0) cc_final: 0.8198 (mp0) REVERT: K 53 GLU cc_start: 0.8917 (pp20) cc_final: 0.8621 (pp20) REVERT: K 58 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8573 (tm-30) REVERT: O 54 LYS cc_start: 0.9402 (tppt) cc_final: 0.9174 (mmtt) REVERT: O 58 GLU cc_start: 0.9006 (pp20) cc_final: 0.8747 (pm20) REVERT: A 70 LYS cc_start: 0.6877 (mmpt) cc_final: 0.6553 (mmpt) REVERT: A 135 LEU cc_start: 0.8893 (tp) cc_final: 0.8212 (pp) outliers start: 49 outliers final: 28 residues processed: 259 average time/residue: 0.1483 time to fit residues: 58.9631 Evaluate side-chains 235 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 203 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 118 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 56 MET Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 242 ARG Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 243 LEU 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 G residue 192 ILE Chi-restraints excluded: chain G residue 279 MET 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 K residue 102 GLU Chi-restraints excluded: chain N residue 45 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: 0.5980 chunk 202 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 161 optimal weight: 0.0870 chunk 116 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 169 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 overall best weight: 1.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 32 GLN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN ** H 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 98 GLN ** 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 = 0.3758 r_free = 0.3758 target = 0.081078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.068586 restraints weight = 115073.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.070301 restraints weight = 67714.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.071452 restraints weight = 47101.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.072214 restraints weight = 36339.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.072703 restraints weight = 30362.093| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 23571 Z= 0.173 Angle : 0.805 12.659 32275 Z= 0.396 Chirality : 0.054 0.566 3508 Planarity : 0.005 0.071 3927 Dihedral : 14.783 171.713 3863 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.03 % Favored : 88.78 % Rotamer: Outliers : 3.15 % Allowed : 18.67 % Favored : 78.18 % 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 are not related in a simple way. whole: -2.39 (0.15), residues: 2612 helix: -0.27 (0.19), residues: 808 sheet: -1.22 (0.35), residues: 192 loop : -2.49 (0.14), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 242 TYR 0.048 0.002 TYR B 96 PHE 0.030 0.002 PHE A 162 TRP 0.016 0.002 TRP C 184 HIS 0.005 0.001 HIS K 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (23569) covalent geometry : angle 0.80507 / 0.40 (32275) hydrogen bonds : bond 0.04618 / 2.34 ( 627) hydrogen bonds : angle 5.09303 / 4.01 ( 1734) Misc. bond : bond 0.00317 / 0.16 ( 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 291 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 221 time to evaluate : 0.864 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 56 MET cc_start: 0.8617 (mpp) cc_final: 0.7764 (mpp) REVERT: B 70 HIS cc_start: 0.8484 (m90) cc_final: 0.8197 (m-70) REVERT: B 184 TRP cc_start: 0.8697 (m100) cc_final: 0.8461 (m100) REVERT: B 266 ARG cc_start: 0.8757 (ptt90) cc_final: 0.8327 (ptt90) REVERT: E 10 ILE cc_start: 0.8093 (mp) cc_final: 0.7481 (mm) REVERT: F 149 TRP cc_start: 0.4138 (t-100) cc_final: 0.3815 (t-100) REVERT: H 123 ASN cc_start: 0.8238 (t0) cc_final: 0.7864 (m-40) REVERT: I 97 MET cc_start: 0.7155 (tmm) cc_final: 0.6890 (tmm) REVERT: I 236 ASN cc_start: 0.7880 (m-40) cc_final: 0.7612 (p0) REVERT: J 87 ASP cc_start: 0.7954 (p0) cc_final: 0.7736 (p0) REVERT: K 13 GLU cc_start: 0.8451 (mp0) cc_final: 0.8079 (mp0) REVERT: K 53 GLU cc_start: 0.8930 (pp20) cc_final: 0.8619 (pp20) REVERT: K 58 GLU cc_start: 0.8849 (tm-30) cc_final: 0.8571 (tm-30) REVERT: O 54 LYS cc_start: 0.9401 (tppt) cc_final: 0.9083 (mmpt) REVERT: O 58 GLU cc_start: 0.9046 (pp20) cc_final: 0.8785 (pm20) REVERT: A 70 LYS cc_start: 0.6987 (mmpt) cc_final: 0.6427 (mmpt) outliers start: 70 outliers final: 43 residues processed: 271 average time/residue: 0.1539 time to fit residues: 64.6540 Evaluate side-chains 246 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 203 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 118 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 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 C residue 242 ARG Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 244 THR 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 F residue 301 VAL Chi-restraints excluded: chain G residue 43 ILE 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 43 ILE Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain I residue 49 MET 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 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 45 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 71 optimal weight: 9.9990 chunk 142 optimal weight: 5.9990 chunk 249 optimal weight: 8.9990 chunk 169 optimal weight: 0.4980 chunk 42 optimal weight: 0.8980 chunk 140 optimal weight: 4.9990 chunk 188 optimal weight: 6.9990 chunk 177 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 150 optimal weight: 6.9990 chunk 217 optimal weight: 0.9980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 111 ASN F 32 GLN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 196 ASN ** H 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 272 GLN ** N 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 98 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 = 0.3731 r_free = 0.3731 target = 0.079841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.067197 restraints weight = 112283.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.068939 restraints weight = 65675.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.070087 restraints weight = 45513.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.070869 restraints weight = 35130.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.071306 restraints weight = 29191.329| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 23571 Z= 0.183 Angle : 0.809 16.626 32275 Z= 0.399 Chirality : 0.053 0.522 3508 Planarity : 0.005 0.068 3927 Dihedral : 14.724 171.767 3861 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.22 % Favored : 88.55 % Rotamer: Outliers : 4.00 % Allowed : 19.97 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.16), residues: 2612 helix: -0.15 (0.19), residues: 795 sheet: -1.18 (0.40), residues: 164 loop : -2.47 (0.14), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 21 TYR 0.053 0.002 TYR B 96 PHE 0.026 0.002 PHE I 137 TRP 0.018 0.002 TRP C 184 HIS 0.008 0.001 HIS I 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (23569) covalent geometry : angle 0.80901 / 0.40 (32275) hydrogen bonds : bond 0.04659 / 2.36 ( 627) hydrogen bonds : angle 4.96299 / 3.87 ( 1734) Misc. bond : bond 0.00356 / 0.18 ( 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 295 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 206 time to evaluate : 0.816 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: 0.8475 (m90) cc_final: 0.8178 (m-70) REVERT: B 184 TRP cc_start: 0.8682 (m100) cc_final: 0.8407 (m100) REVERT: B 266 ARG cc_start: 0.8777 (ptt90) cc_final: 0.8387 (ptt90) REVERT: C 55 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8211 (mm-30) REVERT: E 10 ILE cc_start: 0.8087 (mp) cc_final: 0.7657 (mm) REVERT: E 97 MET cc_start: 0.5724 (mpp) cc_final: 0.5377 (mpp) REVERT: G 82 TYR cc_start: 0.7097 (t80) cc_final: 0.6482 (t80) REVERT: G 279 MET cc_start: 0.7286 (OUTLIER) cc_final: 0.5811 (mmm) REVERT: H 107 MET cc_start: 0.8483 (pmm) cc_final: 0.7832 (pmm) REVERT: H 123 ASN cc_start: 0.8317 (t0) cc_final: 0.7805 (m-40) REVERT: I 97 MET cc_start: 0.7039 (tmm) cc_final: 0.6610 (tmm) REVERT: I 222 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8117 (tm) REVERT: I 236 ASN cc_start: 0.7835 (m-40) cc_final: 0.7556 (p0) REVERT: K 13 GLU cc_start: 0.8494 (mp0) cc_final: 0.8108 (mp0) REVERT: K 53 GLU cc_start: 0.8941 (pp20) cc_final: 0.8641 (pp20) REVERT: K 58 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8617 (tm-30) REVERT: O 54 LYS cc_start: 0.9393 (tppt) cc_final: 0.9167 (mmtt) REVERT: A 135 LEU cc_start: 0.8902 (tp) cc_final: 0.8223 (pp) outliers start: 89 outliers final: 56 residues processed: 268 average time/residue: 0.1601 time to fit residues: 66.3742 Evaluate side-chains 254 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 196 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 118 SER 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 251 LEU 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 136 VAL Chi-restraints excluded: chain C residue 153 THR 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 242 ARG Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 244 THR 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 F residue 243 LEU Chi-restraints excluded: chain F residue 301 VAL 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 279 MET Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H 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 49 MET Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 142 LEU 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 111 LEU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain N residue 45 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 Chi-restraints excluded: chain A residue 199 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 177 optimal weight: 0.9980 chunk 168 optimal weight: 0.8980 chunk 227 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 262 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 72 optimal weight: 0.0980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 ASN ** H 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 34 GLN ** 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 = 0.3747 r_free = 0.3747 target = 0.080569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.067987 restraints weight = 111778.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.069715 restraints weight = 65408.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.070860 restraints weight = 45338.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.071654 restraints weight = 35034.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.072183 restraints weight = 29133.313| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3092 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= 0.152 Angle : 0.794 12.836 32275 Z= 0.388 Chirality : 0.052 0.522 3508 Planarity : 0.005 0.063 3927 Dihedral : 14.604 172.026 3861 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.95 % Favored : 88.86 % Rotamer: Outliers : 2.92 % Allowed : 22.04 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.16), residues: 2612 helix: -0.15 (0.19), residues: 808 sheet: -1.24 (0.39), residues: 172 loop : -2.48 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 242 TYR 0.059 0.001 TYR B 96 PHE 0.024 0.002 PHE I 137 TRP 0.045 0.002 TRP F 149 HIS 0.005 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (23569) covalent geometry : angle 0.79360 / 0.39 (32275) hydrogen bonds : bond 0.04347 / 2.20 ( 627) hydrogen bonds : angle 4.85582 / 3.78 ( 1734) Misc. bond : bond 0.00338 / 0.17 ( 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 278 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 213 time to evaluate : 0.884 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: 0.8447 (m90) cc_final: 0.8148 (m-70) REVERT: B 184 TRP cc_start: 0.8680 (m100) cc_final: 0.8399 (m100) REVERT: B 266 ARG cc_start: 0.8702 (ptt90) cc_final: 0.8313 (ptt90) REVERT: C 55 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8200 (mm-30) REVERT: E 10 ILE cc_start: 0.8012 (mp) cc_final: 0.7638 (mm) REVERT: E 167 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.7797 (p90) REVERT: F 149 TRP cc_start: 0.3511 (t-100) cc_final: 0.3157 (t60) REVERT: G 82 TYR cc_start: 0.7039 (t80) cc_final: 0.6458 (t80) REVERT: H 123 ASN cc_start: 0.8337 (t0) cc_final: 0.7826 (m-40) REVERT: I 97 MET cc_start: 0.6982 (tmm) cc_final: 0.6541 (tmm) REVERT: I 222 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8086 (tm) REVERT: K 13 GLU cc_start: 0.8548 (mp0) cc_final: 0.8212 (mp0) REVERT: K 53 GLU cc_start: 0.8923 (pp20) cc_final: 0.8649 (pp20) REVERT: K 58 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8640 (tm-30) REVERT: A 135 LEU cc_start: 0.8886 (tp) cc_final: 0.8145 (pp) REVERT: A 222 ASP cc_start: 0.7549 (p0) cc_final: 0.7201 (p0) outliers start: 65 outliers final: 45 residues processed: 257 average time/residue: 0.1654 time to fit residues: 65.6622 Evaluate side-chains 243 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 196 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 102 ASN 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 136 VAL 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 242 ARG 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 167 PHE Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain F residue 27 ASN Chi-restraints excluded: chain F residue 139 GLN 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 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 H residue 43 ILE 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 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 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 45 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 153 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 139 optimal weight: 0.6980 chunk 242 optimal weight: 0.5980 chunk 1 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 63 optimal weight: 0.0370 chunk 171 optimal weight: 2.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 51 ASN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3764 r_free = 0.3764 target = 0.081484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.068875 restraints weight = 111357.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.070639 restraints weight = 65244.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.071819 restraints weight = 45173.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.072595 restraints weight = 34777.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.073126 restraints weight = 28994.935| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 23571 Z= 0.144 Angle : 0.792 12.664 32275 Z= 0.387 Chirality : 0.052 0.523 3508 Planarity : 0.005 0.063 3927 Dihedral : 14.512 172.204 3861 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.80 % Favored : 89.01 % Rotamer: Outliers : 2.79 % Allowed : 22.45 % Favored : 74.76 % 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 are not related in a simple way. whole: -2.28 (0.16), residues: 2612 helix: -0.08 (0.19), residues: 805 sheet: -1.22 (0.40), residues: 157 loop : -2.45 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 242 TYR 0.055 0.001 TYR B 96 PHE 0.044 0.001 PHE J 92 TRP 0.056 0.002 TRP F 259 HIS 0.006 0.001 HIS O 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (23569) covalent geometry : angle 0.79230 / 0.39 (32275) hydrogen bonds : bond 0.04076 / 2.07 ( 627) hydrogen bonds : angle 4.76336 / 3.70 ( 1734) Misc. bond : bond 0.00331 / 0.17 ( 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 273 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 211 time to evaluate : 0.801 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: 0.8458 (m90) cc_final: 0.8148 (m-70) REVERT: B 184 TRP cc_start: 0.8711 (m100) cc_final: 0.8402 (m100) REVERT: E 10 ILE cc_start: 0.8035 (mp) cc_final: 0.7693 (mm) REVERT: E 97 MET cc_start: 0.5894 (mpp) cc_final: 0.5474 (mpp) REVERT: E 167 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.7595 (p90) REVERT: F 21 ARG cc_start: 0.6951 (mtt90) cc_final: 0.6448 (mmt90) REVERT: F 149 TRP cc_start: 0.3481 (t-100) cc_final: 0.2852 (t60) REVERT: G 82 TYR cc_start: 0.6911 (t80) cc_final: 0.6575 (t80) REVERT: H 49 MET cc_start: 0.8686 (mpp) cc_final: 0.8364 (mtm) REVERT: H 123 ASN cc_start: 0.8265 (t0) cc_final: 0.7732 (m-40) REVERT: H 234 GLU cc_start: 0.8264 (pm20) cc_final: 0.7759 (pm20) REVERT: I 97 MET cc_start: 0.7191 (tmm) cc_final: 0.6769 (tmm) REVERT: I 222 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8186 (tm) REVERT: J 89 PHE cc_start: 0.4826 (m-80) cc_final: 0.4537 (m-80) REVERT: K 53 GLU cc_start: 0.8913 (pp20) cc_final: 0.8670 (pp20) REVERT: K 58 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8610 (tm-30) REVERT: A 135 LEU cc_start: 0.8829 (tp) cc_final: 0.8090 (pp) REVERT: A 222 ASP cc_start: 0.7677 (p0) cc_final: 0.7341 (p0) outliers start: 62 outliers final: 39 residues processed: 254 average time/residue: 0.1518 time to fit residues: 60.6287 Evaluate side-chains 234 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 193 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 102 ASN 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 251 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 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 167 PHE Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain F residue 19 ASN Chi-restraints excluded: chain F residue 139 GLN Chi-restraints excluded: chain F residue 198 VAL 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 192 ILE Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 107 MET 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 136 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 111 LEU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain O residue 48 TYR 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: 1.9990 chunk 107 optimal weight: 8.9990 chunk 104 optimal weight: 0.3980 chunk 143 optimal weight: 2.9990 chunk 200 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 249 optimal weight: 10.0000 chunk 137 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 51 ASN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3735 r_free = 0.3735 target = 0.080140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.067561 restraints weight = 112612.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.069275 restraints weight = 66064.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.070438 restraints weight = 45948.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.071205 restraints weight = 35569.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.071711 restraints weight = 29693.054| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 23571 Z= 0.166 Angle : 0.795 12.240 32275 Z= 0.391 Chirality : 0.052 0.537 3508 Planarity : 0.005 0.062 3927 Dihedral : 14.515 172.083 3861 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.64 % Favored : 88.13 % Rotamer: Outliers : 2.61 % Allowed : 23.26 % 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 are not related in a simple way. whole: -2.30 (0.16), residues: 2612 helix: -0.06 (0.19), residues: 800 sheet: -1.31 (0.34), residues: 201 loop : -2.48 (0.14), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 242 TYR 0.031 0.001 TYR B 96 PHE 0.032 0.002 PHE A 162 TRP 0.043 0.002 TRP F 259 HIS 0.006 0.001 HIS O 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 (23569) covalent geometry : angle 0.79470 / 0.39 (32275) hydrogen bonds : bond 0.04315 / 2.19 ( 627) hydrogen bonds : angle 4.80568 / 3.71 ( 1734) Misc. bond : bond 0.00341 / 0.17 ( 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 260 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 202 time to evaluate : 0.879 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: 0.8453 (m90) cc_final: 0.8136 (m-70) REVERT: B 184 TRP cc_start: 0.8678 (m100) cc_final: 0.8381 (m100) REVERT: E 10 ILE cc_start: 0.8112 (mp) cc_final: 0.7788 (mm) REVERT: E 167 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.7737 (p90) REVERT: F 149 TRP cc_start: 0.3609 (t-100) cc_final: 0.2843 (t60) REVERT: G 82 TYR cc_start: 0.7047 (t80) cc_final: 0.6633 (t80) REVERT: H 49 MET cc_start: 0.8702 (mpp) cc_final: 0.8440 (mtm) REVERT: H 82 TYR cc_start: 0.6226 (t80) cc_final: 0.5901 (t80) REVERT: H 123 ASN cc_start: 0.8519 (t0) cc_final: 0.7960 (m-40) REVERT: H 234 GLU cc_start: 0.8257 (pm20) cc_final: 0.7956 (pm20) REVERT: I 97 MET cc_start: 0.7008 (tmm) cc_final: 0.6624 (tmm) REVERT: I 222 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8251 (tm) REVERT: J 89 PHE cc_start: 0.5030 (m-80) cc_final: 0.4715 (m-80) REVERT: K 53 GLU cc_start: 0.8918 (pp20) cc_final: 0.8712 (pp20) REVERT: K 58 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8647 (tm-30) REVERT: A 222 ASP cc_start: 0.7676 (p0) cc_final: 0.7377 (p0) outliers start: 58 outliers final: 49 residues processed: 241 average time/residue: 0.1611 time to fit residues: 60.9818 Evaluate side-chains 239 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 188 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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 102 ASN 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 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 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 167 PHE Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain F residue 19 ASN Chi-restraints excluded: chain F residue 27 ASN Chi-restraints excluded: chain F residue 139 GLN 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 43 ILE Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 139 GLN Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain H residue 43 ILE 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 222 LEU 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 136 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 61 LEU Chi-restraints excluded: chain J residue 111 LEU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain N residue 45 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 245 optimal weight: 7.9990 chunk 186 optimal weight: 0.0270 chunk 181 optimal weight: 0.8980 chunk 171 optimal weight: 9.9990 chunk 118 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 chunk 257 optimal weight: 0.0970 chunk 38 optimal weight: 0.8980 chunk 255 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 overall best weight: 0.5836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 94 GLN ** 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 = 0.3766 r_free = 0.3766 target = 0.081589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.068962 restraints weight = 111849.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.070722 restraints weight = 65826.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.071917 restraints weight = 45753.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.072690 restraints weight = 35264.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.073232 restraints weight = 29485.724| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 23571 Z= 0.140 Angle : 0.780 12.074 32275 Z= 0.381 Chirality : 0.050 0.533 3508 Planarity : 0.005 0.062 3927 Dihedral : 14.454 172.110 3861 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.60 % Favored : 89.17 % Rotamer: Outliers : 2.56 % Allowed : 23.62 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.16), residues: 2612 helix: -0.02 (0.19), residues: 801 sheet: -1.33 (0.36), residues: 185 loop : -2.40 (0.14), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 242 TYR 0.028 0.001 TYR C 226 PHE 0.039 0.001 PHE J 92 TRP 0.033 0.002 TRP F 259 HIS 0.005 0.001 HIS O 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (23569) covalent geometry : angle 0.77992 / 0.38 (32275) hydrogen bonds : bond 0.03903 / 1.98 ( 627) hydrogen bonds : angle 4.65228 / 3.60 ( 1734) Misc. bond : bond 0.00394 / 0.20 ( 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 264 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 207 time to evaluate : 0.822 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: 0.8524 (m90) cc_final: 0.8251 (m-70) REVERT: B 184 TRP cc_start: 0.8666 (m100) cc_final: 0.8356 (m100) REVERT: E 10 ILE cc_start: 0.7969 (mp) cc_final: 0.7713 (mm) REVERT: E 97 MET cc_start: 0.5890 (mpp) cc_final: 0.5571 (mpp) REVERT: E 167 PHE cc_start: 0.8381 (OUTLIER) cc_final: 0.7589 (p90) REVERT: F 149 TRP cc_start: 0.3607 (t-100) cc_final: 0.2887 (t60) REVERT: G 82 TYR cc_start: 0.6913 (t80) cc_final: 0.6619 (t80) REVERT: H 49 MET cc_start: 0.8638 (mpp) cc_final: 0.8372 (mtm) REVERT: H 82 TYR cc_start: 0.6012 (t80) cc_final: 0.5782 (t80) REVERT: H 123 ASN cc_start: 0.8349 (t0) cc_final: 0.7800 (m-40) REVERT: H 234 GLU cc_start: 0.8307 (pm20) cc_final: 0.8014 (pm20) REVERT: H 259 TRP cc_start: 0.6963 (m-10) cc_final: 0.6752 (m-10) REVERT: I 97 MET cc_start: 0.7140 (tmm) cc_final: 0.6694 (tmm) REVERT: I 222 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8215 (tm) REVERT: K 53 GLU cc_start: 0.8875 (pp20) cc_final: 0.8630 (pp20) REVERT: K 58 GLU cc_start: 0.8927 (tm-30) cc_final: 0.8646 (tm-30) REVERT: A 222 ASP cc_start: 0.7675 (p0) cc_final: 0.7466 (p0) outliers start: 57 outliers final: 48 residues processed: 247 average time/residue: 0.1562 time to fit residues: 60.7937 Evaluate side-chains 237 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 187 time to evaluate : 0.864 ------------------------------------------------------------------------------- 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 102 ASN 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 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 167 PHE Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain F residue 19 ASN Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain F residue 139 GLN 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 G residue 192 ILE Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 107 MET Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 167 PHE Chi-restraints excluded: chain H residue 222 LEU 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 136 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 111 LEU Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 97 PHE Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain O residue 48 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 237 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 251 optimal weight: 5.9990 chunk 196 optimal weight: 7.9990 chunk 234 optimal weight: 2.9990 chunk 222 optimal weight: 6.9990 chunk 235 optimal weight: 4.9990 chunk 100 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 27 ASN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3728 r_free = 0.3728 target = 0.079779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.067195 restraints weight = 113051.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.068929 restraints weight = 66289.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.070037 restraints weight = 45954.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.070805 restraints weight = 35768.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.071291 restraints weight = 29870.507| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 23571 Z= 0.172 Angle : 0.790 12.170 32275 Z= 0.388 Chirality : 0.051 0.544 3508 Planarity : 0.005 0.059 3927 Dihedral : 14.476 172.033 3860 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.68 % Favored : 88.06 % Rotamer: Outliers : 2.47 % Allowed : 23.89 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.16), residues: 2612 helix: 0.03 (0.19), residues: 801 sheet: -1.37 (0.34), residues: 202 loop : -2.47 (0.14), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 242 TYR 0.027 0.001 TYR C 226 PHE 0.036 0.002 PHE A 162 TRP 0.049 0.002 TRP F 259 HIS 0.005 0.001 HIS O 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (23569) covalent geometry : angle 0.78989 / 0.39 (32275) hydrogen bonds : bond 0.04154 / 2.10 ( 627) hydrogen bonds : angle 4.74192 / 3.66 ( 1734) Misc. bond : bond 0.00342 / 0.17 ( 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 246 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 191 time to evaluate : 0.837 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: 0.8467 (m90) cc_final: 0.8213 (m-70) REVERT: B 184 TRP cc_start: 0.8681 (m100) cc_final: 0.8384 (m100) REVERT: E 10 ILE cc_start: 0.8119 (mp) cc_final: 0.7812 (mm) REVERT: E 97 MET cc_start: 0.6150 (mpp) cc_final: 0.5757 (mpp) REVERT: E 167 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.7821 (p90) REVERT: F 149 TRP cc_start: 0.3651 (t-100) cc_final: 0.2933 (t60) REVERT: G 82 TYR cc_start: 0.7068 (t80) cc_final: 0.6712 (t80) REVERT: G 282 HIS cc_start: 0.7461 (OUTLIER) cc_final: 0.7210 (t-90) REVERT: H 49 MET cc_start: 0.8695 (mpp) cc_final: 0.8433 (mtm) REVERT: H 82 TYR cc_start: 0.6260 (t80) cc_final: 0.5936 (t80) REVERT: H 123 ASN cc_start: 0.8609 (t0) cc_final: 0.8031 (m-40) REVERT: H 206 TYR cc_start: 0.9198 (OUTLIER) cc_final: 0.8668 (t80) REVERT: H 234 GLU cc_start: 0.8302 (pm20) cc_final: 0.8032 (pm20) REVERT: H 259 TRP cc_start: 0.6998 (m-10) cc_final: 0.6795 (m-10) REVERT: I 97 MET cc_start: 0.6975 (tmm) cc_final: 0.6584 (tmm) REVERT: I 222 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8222 (tm) REVERT: J 74 ASP cc_start: 0.8868 (p0) cc_final: 0.8613 (p0) REVERT: K 53 GLU cc_start: 0.8888 (pp20) cc_final: 0.8679 (pp20) REVERT: K 58 GLU cc_start: 0.8900 (tm-30) cc_final: 0.8627 (tm-30) outliers start: 55 outliers final: 44 residues processed: 230 average time/residue: 0.1607 time to fit residues: 57.6893 Evaluate side-chains 236 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 188 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 102 ASN Chi-restraints excluded: chain B residue 165 THR 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 167 PHE Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain F residue 19 ASN 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 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 282 HIS Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 107 MET Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 167 PHE Chi-restraints excluded: chain H residue 206 TYR 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 136 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 111 LEU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain N residue 45 GLU Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain O residue 48 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 203 optimal weight: 0.9990 chunk 163 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 131 optimal weight: 0.4980 chunk 170 optimal weight: 5.9990 chunk 181 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 159 optimal weight: 0.0170 chunk 77 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 217 optimal weight: 4.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 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 = 0.3730 r_free = 0.3730 target = 0.079857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.067289 restraints weight = 112924.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.069021 restraints weight = 66408.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.070157 restraints weight = 46093.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.070906 restraints weight = 35742.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.071387 restraints weight = 29907.839| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.148 23571 Z= 0.203 Angle : 0.908 59.150 32275 Z= 0.477 Chirality : 0.050 0.541 3508 Planarity : 0.005 0.058 3927 Dihedral : 14.479 172.036 3860 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.72 % Favored : 87.98 % Rotamer: Outliers : 2.29 % Allowed : 24.07 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.16), residues: 2612 helix: 0.05 (0.19), residues: 801 sheet: -1.37 (0.34), residues: 202 loop : -2.48 (0.14), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG E 242 TYR 0.018 0.001 TYR C 226 PHE 0.030 0.002 PHE J 92 TRP 0.042 0.002 TRP F 259 HIS 0.004 0.001 HIS O 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.20 (23569) covalent geometry : angle 0.90840 / 0.48 (32275) hydrogen bonds : bond 0.04131 / 2.09 ( 627) hydrogen bonds : angle 4.73801 / 3.66 ( 1734) Misc. bond : bond 0.00342 / 0.17 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3463.54 seconds wall clock time: 61 minutes 1.30 seconds (3661.30 seconds total)