Starting phenix.real_space_refine on Sat Jul 4 19:28:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8h7q_34524/07_2026/8h7q_34524.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h7q_34524/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8h7q_34524/07_2026/8h7q_34524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h7q_34524/07_2026/8h7q_34524.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h7q_34524/07_2026/8h7q_34524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h7q_34524/07_2026/8h7q_34524.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8h7q_34524/07_2026/8h7q_34524.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8h7q_34524/07_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-dev-6108/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: {'RNA': 36} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 8, 'rna3p_pur': 8, 'rna3p_pyr': 15} Link IDs: {'rna2p': 13, 'rna3p': 22} Chain: "L" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 725 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "M" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 231 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "B" Number of atoms: 1992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1992 Classifications: {'peptide': 251} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 236} Chain breaks: 3 Chain: "C" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2366 Classifications: {'peptide': 299} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 283} Chain: "E" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2366 Classifications: {'peptide': 299} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 283} Chain: "F" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2366 Classifications: {'peptide': 299} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 283} Chain: "G" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2366 Classifications: {'peptide': 299} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 283} Chain: "H" Number of atoms: 2366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2366 Classifications: {'peptide': 299} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 283} Chain: "I" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2334 Classifications: {'peptide': 295} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 279} Chain breaks: 1 Chain: "J" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 925 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 3, 'TRANS': 107} Chain: "K" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 890 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain: "N" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 883 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 2, 'TRANS': 103} Chain: "O" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 704 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain breaks: 2 Chain: "A" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1617 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 184} Chain breaks: 2 Time building chain proxies: 5.01, per 1000 atoms: 0.22 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: 2.03 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: 2.08 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: 3.20 Time building geometry restraints manager: 2.60 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: 31765 2.85 - 5.69: 436 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: 13615 35.06 - 70.12: 403 70.12 - 105.17: 29 105.17 - 140.23: 2 140.23 - 175.29: 5 Dihedral angle restraints: 14054 sinusoidal: 6249 harmonic: 7805 Sorted by residual: dihedral pdb=" O4' U D 38 " pdb=" C1' U D 38 " pdb=" N1 U D 38 " pdb=" C2 U D 38 " ideal model delta sinusoidal sigma weight residual 200.00 45.93 154.07 1 1.50e+01 4.44e-03 8.10e+01 dihedral pdb=" O4' C D 14 " pdb=" C1' C D 14 " pdb=" N1 C D 14 " pdb=" C2 C D 14 " ideal model delta sinusoidal sigma weight residual 200.00 50.59 149.41 1 1.50e+01 4.44e-03 7.94e+01 dihedral pdb=" O4' U D 41 " pdb=" C1' U D 41 " pdb=" N1 U D 41 " pdb=" C2 U D 41 " ideal model delta sinusoidal sigma weight residual -160.00 -77.75 -82.25 1 1.50e+01 4.44e-03 3.69e+01 ... (remaining 14051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 3315 0.098 - 0.196: 172 0.196 - 0.294: 11 0.294 - 0.392: 7 0.392 - 0.491: 3 Chirality restraints: 3508 Sorted by residual: chirality pdb=" CA VAL I 223 " pdb=" N VAL I 223 " pdb=" C VAL I 223 " pdb=" CB VAL I 223 " both_signs ideal model delta sigma weight residual False 2.44 1.95 0.49 2.00e-01 2.50e+01 6.02e+00 chirality pdb=" CA TRP A 204 " pdb=" N TRP A 204 " pdb=" C TRP A 204 " pdb=" CB TRP A 204 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.54e+00 chirality pdb=" CA ASN C 19 " pdb=" N ASN C 19 " pdb=" C ASN C 19 " pdb=" CB ASN C 19 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.28e+00 ... (remaining 3505 not shown) Planarity restraints: 3927 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 210 " 0.091 5.00e-02 4.00e+02 1.42e-01 3.21e+01 pdb=" N PRO C 211 " -0.245 5.00e-02 4.00e+02 pdb=" CA PRO C 211 " 0.081 5.00e-02 4.00e+02 pdb=" CD PRO C 211 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 219 " -0.082 5.00e-02 4.00e+02 1.27e-01 2.58e+01 pdb=" N PRO A 220 " 0.220 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN E 84 " 0.077 5.00e-02 4.00e+02 1.13e-01 2.03e+01 pdb=" N PRO E 85 " -0.194 5.00e-02 4.00e+02 pdb=" CA PRO E 85 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO E 85 " 0.062 5.00e-02 4.00e+02 ... (remaining 3924 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.13: 25 2.13 - 2.83: 7195 2.83 - 3.52: 32744 3.52 - 4.21: 50573 4.21 - 4.90: 83844 Nonbonded interactions: 174381 Sorted by model distance: nonbonded pdb=" O TRP A 184 " pdb=" CB SER A 221 " model vdw 1.442 3.440 nonbonded pdb=" CD2 LEU A 160 " pdb=" OD1 ASN A 166 " model vdw 1.549 3.460 nonbonded pdb=" CD PRO G 141 " pdb=" O ALA G 156 " model vdw 1.759 3.440 nonbonded pdb=" O CYS A 199 " pdb=" CG2 ILE A 215 " model vdw 1.793 3.460 nonbonded pdb=" O ALA G 191 " pdb=" O GLU G 194 " model vdw 1.798 3.040 ... (remaining 174376 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 3 through 248 or resid 253 through 301)) selection = (chain 'I' and (resid 3 through 18 or resid 30 through 133 or resid 163 through \ 198 or resid 207 through 301)) } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = (chain 'J' and resid 10 through 115) selection = (chain 'K' and resid 10 through 115) selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.260 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.760 ------------------------------------------------------------------------------- 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= 0.325 Angle : 0.851 14.237 32275 Z= 0.512 Chirality : 0.050 0.491 3508 Planarity : 0.007 0.142 3927 Dihedral : 16.750 175.288 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 0.00350 / 0.23 (23569) covalent geometry : angle 0.85102 / 0.51 (32275) hydrogen bonds : bond 0.21958 / 13.01 ( 627) hydrogen bonds : angle 7.68368 / 7.07 ( 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 : 0.821 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: 0.1622 time to fit residues: 84.0125 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 : 0.570 ------------------------------------------------------------------------------- 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 256 ASN C 286 ASN ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN F 196 ASN G 196 ASN G 282 HIS H 196 ASN I 19 ASN ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.081852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.069168 restraints weight = 111882.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.070930 restraints weight = 65347.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.072090 restraints weight = 45245.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.072877 restraints weight = 34875.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.073411 restraints weight = 29022.848| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1694 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= 0.191 Angle : 0.778 10.731 32275 Z= 0.409 Chirality : 0.045 0.229 3508 Planarity : 0.006 0.085 3927 Dihedral : 15.325 171.146 3871 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.72 % Favored : 89.17 % Rotamer: Outliers : 1.80 % Allowed : 13.59 % Favored : 84.62 % 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: -0.26 (0.19), residues: 793 sheet: -1.37 (0.32), residues: 233 loop : -2.49 (0.14), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 157 TYR 0.041 0.002 TYR B 96 PHE 0.025 0.002 PHE G 209 TRP 0.026 0.002 TRP C 184 HIS 0.006 0.001 HIS K 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 (23569) covalent geometry : angle 0.77792 / 0.41 (32275) hydrogen bonds : bond 0.05840 / 3.47 ( 627) hydrogen bonds : angle 5.62013 / 5.05 ( 1734) Misc. bond : bond 0.00875 / 0.44 ( 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 287 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 247 time to evaluate : 0.787 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 97 MET cc_start: 0.5661 (mpp) cc_final: 0.5343 (mpp) REVERT: B 184 TRP cc_start: 0.8739 (m100) cc_final: 0.8466 (m100) REVERT: B 258 PHE cc_start: 0.3269 (t80) cc_final: 0.3054 (t80) REVERT: B 268 MET cc_start: 0.7238 (mpp) cc_final: 0.6357 (mmp) REVERT: C 209 PHE cc_start: 0.3768 (OUTLIER) cc_final: 0.3422 (p90) REVERT: C 279 MET cc_start: 0.8104 (mpp) cc_final: 0.7847 (mpp) REVERT: E 97 MET cc_start: 0.5794 (mpp) cc_final: 0.5545 (mpp) REVERT: F 149 TRP cc_start: 0.3983 (t-100) cc_final: 0.3564 (t-100) REVERT: H 123 ASN cc_start: 0.8046 (t0) cc_final: 0.7811 (t0) REVERT: H 181 LYS cc_start: 0.5674 (ttmt) cc_final: 0.5408 (ttmt) REVERT: H 279 MET cc_start: 0.7844 (mpp) cc_final: 0.7631 (mpp) REVERT: H 282 HIS cc_start: 0.7426 (OUTLIER) cc_final: 0.7213 (m-70) REVERT: I 222 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8230 (tp) REVERT: J 97 PHE cc_start: 0.8144 (m-10) cc_final: 0.7691 (m-10) REVERT: K 13 GLU cc_start: 0.8550 (mp0) cc_final: 0.8314 (mp0) REVERT: K 53 GLU cc_start: 0.8923 (pp20) cc_final: 0.8662 (pp20) REVERT: K 58 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8584 (tm-30) REVERT: K 91 ASP cc_start: 0.8893 (p0) cc_final: 0.8693 (p0) REVERT: O 54 LYS cc_start: 0.9396 (tppt) cc_final: 0.9189 (mmtt) REVERT: O 58 GLU cc_start: 0.8998 (pp20) cc_final: 0.8755 (pm20) REVERT: O 98 GLN cc_start: 0.7395 (pm20) cc_final: 0.6942 (pm20) REVERT: A 70 LYS cc_start: 0.7077 (mmtt) cc_final: 0.6822 (mmpt) REVERT: A 217 VAL cc_start: 0.1634 (OUTLIER) cc_final: 0.1355 (t) outliers start: 40 outliers final: 20 residues processed: 271 average time/residue: 0.1640 time to fit residues: 68.0721 Evaluate side-chains 226 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 202 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 F residue 10 ILE Chi-restraints excluded: chain F residue 27 ASN Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain F residue 139 GLN Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 139 GLN Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain H residue 282 HIS Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain I residue 222 LEU Chi-restraints excluded: chain J residue 61 LEU Chi-restraints excluded: chain J residue 111 LEU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 217 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 36 optimal weight: 8.9990 chunk 186 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 227 optimal weight: 2.9990 chunk 197 optimal weight: 0.9990 chunk 237 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 198 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 64 ASN F 32 GLN G 51 ASN ** H 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 ASN ** H 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.081778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.069057 restraints weight = 112873.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.070853 restraints weight = 66057.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.072022 restraints weight = 45597.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.072799 restraints weight = 35122.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.073338 restraints weight = 29229.590| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2045 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= 0.156 Angle : 0.718 9.253 32275 Z= 0.377 Chirality : 0.043 0.231 3508 Planarity : 0.005 0.083 3927 Dihedral : 15.294 171.078 3863 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.38 % Favored : 89.51 % Rotamer: Outliers : 1.98 % Allowed : 16.91 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.16), residues: 2612 helix: -0.27 (0.19), residues: 804 sheet: -1.31 (0.33), residues: 225 loop : -2.48 (0.14), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 242 TYR 0.041 0.001 TYR B 96 PHE 0.026 0.002 PHE A 218 TRP 0.021 0.002 TRP I 237 HIS 0.010 0.001 HIS G 282 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (23569) covalent geometry : angle 0.71823 / 0.38 (32275) hydrogen bonds : bond 0.05009 / 2.95 ( 627) hydrogen bonds : angle 5.24963 / 4.69 ( 1734) Misc. bond : bond 0.00695 / 0.35 ( 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 269 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 225 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 HIS cc_start: 0.8833 (m90) cc_final: 0.8590 (m-70) REVERT: B 97 MET cc_start: 0.5919 (mpp) cc_final: 0.5703 (mpp) REVERT: B 112 ARG cc_start: 0.8419 (ppt170) cc_final: 0.8198 (ppt170) REVERT: B 184 TRP cc_start: 0.8742 (m100) cc_final: 0.8456 (m100) REVERT: B 258 PHE cc_start: 0.3527 (t80) cc_final: 0.3184 (t80) REVERT: B 266 ARG cc_start: 0.8645 (ptt90) cc_final: 0.8309 (ptt90) REVERT: C 198 VAL cc_start: 0.8436 (OUTLIER) cc_final: 0.8222 (p) REVERT: E 10 ILE cc_start: 0.7715 (mp) cc_final: 0.7145 (mm) REVERT: E 97 MET cc_start: 0.5471 (mpp) cc_final: 0.5135 (mpp) REVERT: F 149 TRP cc_start: 0.4324 (t-100) cc_final: 0.3833 (t-100) REVERT: G 207 TYR cc_start: 0.8120 (t80) cc_final: 0.7859 (t80) REVERT: G 279 MET cc_start: 0.6834 (OUTLIER) cc_final: 0.5376 (mmm) REVERT: H 123 ASN cc_start: 0.8067 (t0) cc_final: 0.7741 (m-40) REVERT: H 181 LYS cc_start: 0.5640 (ttmt) cc_final: 0.5220 (ttmt) REVERT: H 282 HIS cc_start: 0.7313 (OUTLIER) cc_final: 0.7077 (m-70) REVERT: I 222 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8323 (tp) REVERT: I 236 ASN cc_start: 0.7813 (m-40) cc_final: 0.7583 (p0) REVERT: K 13 GLU cc_start: 0.8455 (mp0) cc_final: 0.8205 (mp0) REVERT: K 53 GLU cc_start: 0.8922 (pp20) cc_final: 0.8623 (pp20) REVERT: K 58 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8583 (tm-30) REVERT: O 54 LYS cc_start: 0.9406 (tppt) cc_final: 0.9177 (mmtt) REVERT: O 58 GLU cc_start: 0.9020 (pp20) cc_final: 0.8756 (pm20) REVERT: A 135 LEU cc_start: 0.8910 (tp) cc_final: 0.8228 (pp) outliers start: 44 outliers final: 31 residues processed: 254 average time/residue: 0.1545 time to fit residues: 60.1216 Evaluate side-chains 234 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 199 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 118 SER Chi-restraints excluded: chain B residue 163 THR 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 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 219 THR Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain F residue 19 ASN 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 282 HIS Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain I residue 222 LEU Chi-restraints excluded: chain J residue 61 LEU Chi-restraints excluded: chain J residue 111 LEU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain A residue 83 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 37 optimal weight: 0.0970 chunk 202 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 161 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 215 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** O 98 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 = 0.3771 r_free = 0.3771 target = 0.081666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.068914 restraints weight = 111965.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.070709 restraints weight = 65654.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.071903 restraints weight = 45104.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.072691 restraints weight = 34724.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.073219 restraints weight = 28831.255| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2314 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= 0.149 Angle : 0.705 12.096 32275 Z= 0.367 Chirality : 0.042 0.256 3508 Planarity : 0.005 0.075 3927 Dihedral : 15.270 171.537 3863 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.38 % Favored : 89.47 % Rotamer: Outliers : 2.97 % Allowed : 18.89 % Favored : 78.14 % 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: -2.35 (0.16), residues: 2612 helix: -0.17 (0.19), residues: 809 sheet: -1.38 (0.34), residues: 206 loop : -2.47 (0.14), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 242 TYR 0.020 0.001 TYR C 226 PHE 0.026 0.002 PHE A 162 TRP 0.015 0.001 TRP A 184 HIS 0.005 0.001 HIS K 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 (23569) covalent geometry : angle 0.70481 / 0.37 (32275) hydrogen bonds : bond 0.04543 / 2.67 ( 627) hydrogen bonds : angle 5.04244 / 4.46 ( 1734) Misc. bond : bond 0.00448 / 0.22 ( 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 290 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 224 time to evaluate : 0.745 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 56 MET cc_start: 0.8575 (mpp) cc_final: 0.7749 (mpp) REVERT: B 70 HIS cc_start: 0.8819 (m90) cc_final: 0.8558 (m-70) REVERT: B 184 TRP cc_start: 0.8737 (m100) cc_final: 0.8507 (m100) REVERT: B 258 PHE cc_start: 0.3013 (t80) cc_final: 0.2798 (t80) REVERT: B 266 ARG cc_start: 0.8691 (ptt90) cc_final: 0.8312 (ptt90) REVERT: C 55 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8330 (mm-30) REVERT: E 10 ILE cc_start: 0.7958 (mp) cc_final: 0.7511 (mm) REVERT: F 149 TRP cc_start: 0.4310 (t-100) cc_final: 0.3892 (t-100) REVERT: H 123 ASN cc_start: 0.8109 (t0) cc_final: 0.7759 (m-40) REVERT: H 181 LYS cc_start: 0.5638 (ttmt) cc_final: 0.5324 (ttmt) REVERT: I 97 MET cc_start: 0.7134 (tmm) cc_final: 0.6738 (tmm) REVERT: I 236 ASN cc_start: 0.7872 (m-40) cc_final: 0.7641 (p0) REVERT: I 242 ARG cc_start: 0.8786 (mmt180) cc_final: 0.8424 (mmt180) REVERT: J 87 ASP cc_start: 0.7975 (p0) cc_final: 0.7739 (p0) REVERT: K 13 GLU cc_start: 0.8492 (mp0) cc_final: 0.8227 (mp0) REVERT: K 53 GLU cc_start: 0.8918 (pp20) cc_final: 0.8601 (pp20) REVERT: K 58 GLU cc_start: 0.8864 (tm-30) cc_final: 0.8584 (tm-30) REVERT: O 54 LYS cc_start: 0.9408 (tppt) cc_final: 0.9092 (mmpt) REVERT: O 58 GLU cc_start: 0.9031 (pp20) cc_final: 0.8780 (pm20) outliers start: 66 outliers final: 42 residues processed: 269 average time/residue: 0.1611 time to fit residues: 67.1620 Evaluate side-chains 251 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 209 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 102 ASN Chi-restraints excluded: chain B residue 107 MET 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 B residue 279 MET Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain 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 F residue 10 ILE Chi-restraints excluded: chain F residue 27 ASN Chi-restraints excluded: chain F residue 139 GLN Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain G residue 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 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 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: 3.9990 chunk 142 optimal weight: 0.9990 chunk 249 optimal weight: 7.9990 chunk 169 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 140 optimal weight: 4.9990 chunk 188 optimal weight: 0.7980 chunk 177 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 150 optimal weight: 0.6980 chunk 217 optimal weight: 0.1980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 ASN ** H 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.081780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.069049 restraints weight = 110984.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.070803 restraints weight = 65275.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.071986 restraints weight = 45324.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.072775 restraints weight = 35088.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.073327 restraints weight = 29250.849| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 23571 Z= 0.139 Angle : 0.699 10.854 32275 Z= 0.363 Chirality : 0.042 0.340 3508 Planarity : 0.005 0.072 3927 Dihedral : 15.190 171.871 3861 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.53 % Favored : 89.28 % Rotamer: Outliers : 2.97 % Allowed : 20.29 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.16), residues: 2612 helix: -0.15 (0.19), residues: 807 sheet: -1.18 (0.36), residues: 194 loop : -2.43 (0.14), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 242 TYR 0.025 0.001 TYR B 96 PHE 0.028 0.001 PHE J 92 TRP 0.015 0.001 TRP I 237 HIS 0.005 0.001 HIS K 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (23569) covalent geometry : angle 0.69906 / 0.36 (32275) hydrogen bonds : bond 0.04270 / 2.49 ( 627) hydrogen bonds : angle 4.87710 / 4.31 ( 1734) Misc. bond : bond 0.00453 / 0.23 ( 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 291 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 225 time to evaluate : 0.700 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 56 MET cc_start: 0.8556 (mpp) cc_final: 0.7790 (mpp) REVERT: B 70 HIS cc_start: 0.8788 (m90) cc_final: 0.8521 (m-70) REVERT: B 184 TRP cc_start: 0.8650 (m100) cc_final: 0.8336 (m100) REVERT: B 258 PHE cc_start: 0.3049 (t80) cc_final: 0.2713 (t80) REVERT: B 266 ARG cc_start: 0.8680 (ptt90) cc_final: 0.8291 (ptt90) REVERT: C 55 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8247 (mm-30) REVERT: E 10 ILE cc_start: 0.8047 (mp) cc_final: 0.7673 (mm) REVERT: E 97 MET cc_start: 0.5490 (mpp) cc_final: 0.5142 (mpp) REVERT: F 149 TRP cc_start: 0.4503 (t-100) cc_final: 0.4141 (t-100) REVERT: G 82 TYR cc_start: 0.6915 (t80) cc_final: 0.6510 (t80) REVERT: H 123 ASN cc_start: 0.8106 (t0) cc_final: 0.7742 (m-40) REVERT: I 97 MET cc_start: 0.7104 (tmm) cc_final: 0.6773 (tmm) REVERT: I 222 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8155 (tm) REVERT: I 236 ASN cc_start: 0.7790 (m-40) cc_final: 0.7575 (p0) REVERT: I 242 ARG cc_start: 0.8750 (mmt180) cc_final: 0.8348 (mmt180) REVERT: K 13 GLU cc_start: 0.8517 (mp0) cc_final: 0.8241 (mp0) REVERT: K 53 GLU cc_start: 0.8919 (pp20) cc_final: 0.8614 (pp20) REVERT: K 58 GLU cc_start: 0.8883 (tm-30) cc_final: 0.8601 (tm-30) REVERT: O 54 LYS cc_start: 0.9408 (tppt) cc_final: 0.9082 (mmpt) REVERT: O 58 GLU cc_start: 0.9023 (pp20) cc_final: 0.8777 (pm20) REVERT: A 135 LEU cc_start: 0.8886 (tp) cc_final: 0.8294 (pp) outliers start: 66 outliers final: 44 residues processed: 268 average time/residue: 0.1559 time to fit residues: 63.6538 Evaluate side-chains 252 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 207 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 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 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 165 THR Chi-restraints excluded: chain E residue 219 THR 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 44 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 G residue 279 MET 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 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 77 VAL Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain A residue 83 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 51 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 177 optimal weight: 4.9990 chunk 168 optimal weight: 0.7980 chunk 227 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 262 optimal weight: 9.9990 chunk 95 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 72 optimal weight: 0.4980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** 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** ** K 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 34 GLN ** O 98 GLN ** 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 = 0.3754 r_free = 0.3754 target = 0.081026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.068265 restraints weight = 111386.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.070011 restraints weight = 65908.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.071177 restraints weight = 45863.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.071964 restraints weight = 35482.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.072498 restraints weight = 29540.522| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.2845 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 : 0.695 10.524 32275 Z= 0.361 Chirality : 0.042 0.230 3508 Planarity : 0.005 0.070 3927 Dihedral : 15.090 171.924 3861 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.80 % Favored : 89.01 % Rotamer: Outliers : 3.15 % Allowed : 20.83 % 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: -2.28 (0.16), residues: 2612 helix: -0.16 (0.19), residues: 808 sheet: -1.16 (0.36), residues: 194 loop : -2.43 (0.14), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 242 TYR 0.032 0.001 TYR B 96 PHE 0.030 0.002 PHE J 92 TRP 0.016 0.001 TRP C 184 HIS 0.005 0.001 HIS K 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (23569) covalent geometry : angle 0.69504 / 0.36 (32275) hydrogen bonds : bond 0.04286 / 2.49 ( 627) hydrogen bonds : angle 4.86798 / 4.26 ( 1734) Misc. bond : bond 0.00396 / 0.20 ( 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 289 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 219 time to evaluate : 0.759 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: 0.8798 (m90) cc_final: 0.8523 (m-70) REVERT: B 184 TRP cc_start: 0.8686 (m100) cc_final: 0.8392 (m100) REVERT: B 266 ARG cc_start: 0.8692 (ptt90) cc_final: 0.8326 (ptt90) REVERT: C 55 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8232 (mm-30) REVERT: E 10 ILE cc_start: 0.8073 (mp) cc_final: 0.7746 (mm) REVERT: F 149 TRP cc_start: 0.4273 (t-100) cc_final: 0.4048 (t-100) REVERT: G 82 TYR cc_start: 0.7048 (t80) cc_final: 0.6613 (t80) REVERT: H 49 MET cc_start: 0.8597 (ptp) cc_final: 0.8283 (mtm) REVERT: H 123 ASN cc_start: 0.8185 (t0) cc_final: 0.7797 (m-40) REVERT: I 97 MET cc_start: 0.7263 (tmm) cc_final: 0.6900 (tmm) REVERT: I 222 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8158 (tm) REVERT: J 97 PHE cc_start: 0.8222 (m-10) cc_final: 0.7955 (m-80) REVERT: K 13 GLU cc_start: 0.8530 (mp0) cc_final: 0.8256 (mp0) REVERT: K 53 GLU cc_start: 0.8942 (pp20) cc_final: 0.8741 (pp20) REVERT: K 58 GLU cc_start: 0.8911 (tm-30) cc_final: 0.8642 (tm-30) REVERT: O 54 LYS cc_start: 0.9404 (tppt) cc_final: 0.9063 (mmpt) REVERT: O 58 GLU cc_start: 0.9042 (pp20) cc_final: 0.8798 (pm20) REVERT: A 135 LEU cc_start: 0.8767 (tp) cc_final: 0.8145 (pp) outliers start: 70 outliers final: 47 residues processed: 268 average time/residue: 0.1572 time to fit residues: 64.7677 Evaluate side-chains 249 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 201 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 167 PHE Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 229 TYR 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 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 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 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 237 TRP 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 283 LEU Chi-restraints excluded: chain I residue 49 MET Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 222 LEU Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 153 optimal weight: 0.9980 chunk 9 optimal weight: 0.4980 chunk 94 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 139 optimal weight: 0.8980 chunk 242 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 63 optimal weight: 0.4980 chunk 171 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 111 ASN ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 GLN ** H 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.081837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.069147 restraints weight = 111322.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.070891 restraints weight = 65582.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.072050 restraints weight = 45657.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.072835 restraints weight = 35395.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.073366 restraints weight = 29515.955| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 23571 Z= 0.136 Angle : 0.697 11.545 32275 Z= 0.360 Chirality : 0.042 0.238 3508 Planarity : 0.005 0.068 3927 Dihedral : 14.999 171.977 3861 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.80 % Favored : 89.01 % Rotamer: Outliers : 2.65 % Allowed : 21.86 % Favored : 75.48 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.16), residues: 2612 helix: -0.15 (0.19), residues: 808 sheet: -1.13 (0.36), residues: 194 loop : -2.41 (0.14), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 242 TYR 0.037 0.001 TYR B 96 PHE 0.046 0.001 PHE J 92 TRP 0.014 0.001 TRP F 259 HIS 0.005 0.001 HIS O 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (23569) covalent geometry : angle 0.69744 / 0.36 (32275) hydrogen bonds : bond 0.04070 / 2.38 ( 627) hydrogen bonds : angle 4.74910 / 4.17 ( 1734) Misc. bond : bond 0.00401 / 0.20 ( 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 271 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 212 time to evaluate : 0.719 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: 0.8796 (m90) cc_final: 0.8513 (m-70) REVERT: B 184 TRP cc_start: 0.8669 (m100) cc_final: 0.8369 (m100) REVERT: B 266 ARG cc_start: 0.8678 (ptt90) cc_final: 0.8325 (ptt90) REVERT: E 10 ILE cc_start: 0.8068 (mp) cc_final: 0.7839 (mm) REVERT: E 97 MET cc_start: 0.5723 (mpp) cc_final: 0.5342 (mpp) REVERT: G 82 TYR cc_start: 0.6874 (t80) cc_final: 0.6534 (t80) REVERT: H 49 MET cc_start: 0.8560 (ptp) cc_final: 0.8254 (mtm) REVERT: H 123 ASN cc_start: 0.8132 (t0) cc_final: 0.7713 (m-40) REVERT: H 259 TRP cc_start: 0.6931 (m-10) cc_final: 0.6657 (m-10) REVERT: I 97 MET cc_start: 0.7180 (tmm) cc_final: 0.6817 (tmm) REVERT: I 222 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8155 (tm) REVERT: K 13 GLU cc_start: 0.8477 (mp0) cc_final: 0.8246 (mp0) REVERT: K 53 GLU cc_start: 0.8920 (pp20) cc_final: 0.8685 (pp20) REVERT: K 58 GLU cc_start: 0.8907 (tm-30) cc_final: 0.8617 (tm-30) REVERT: O 54 LYS cc_start: 0.9385 (tppt) cc_final: 0.9150 (mmtt) REVERT: O 58 GLU cc_start: 0.9031 (pp20) cc_final: 0.8783 (pm20) REVERT: A 135 LEU cc_start: 0.8702 (tp) cc_final: 0.8088 (pp) REVERT: A 222 ASP cc_start: 0.7513 (p0) cc_final: 0.7144 (p0) outliers start: 59 outliers final: 44 residues processed: 252 average time/residue: 0.1631 time to fit residues: 63.2423 Evaluate side-chains 243 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 198 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 218 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 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 58 ILE Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 219 THR 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 44 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 67 THR 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 222 LEU Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 111 LEU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 199 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 127 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 143 optimal weight: 0.8980 chunk 200 optimal weight: 4.9990 chunk 173 optimal weight: 0.7980 chunk 206 optimal weight: 0.0270 chunk 145 optimal weight: 2.9990 chunk 249 optimal weight: 0.9990 chunk 137 optimal weight: 0.6980 chunk 152 optimal weight: 0.5980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 62 GLN ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 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 = 0.3780 r_free = 0.3780 target = 0.082185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.069502 restraints weight = 111181.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.071257 restraints weight = 65526.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.072419 restraints weight = 45669.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.073210 restraints weight = 35392.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.073752 restraints weight = 29530.261| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 23571 Z= 0.135 Angle : 0.705 13.628 32275 Z= 0.362 Chirality : 0.042 0.235 3508 Planarity : 0.005 0.066 3927 Dihedral : 14.905 172.058 3861 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.68 % Favored : 89.09 % Rotamer: Outliers : 2.65 % Allowed : 22.63 % Favored : 74.72 % 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: -2.21 (0.16), residues: 2612 helix: -0.09 (0.19), residues: 808 sheet: -1.13 (0.36), residues: 194 loop : -2.39 (0.14), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 242 TYR 0.025 0.001 TYR C 226 PHE 0.033 0.001 PHE A 162 TRP 0.057 0.002 TRP F 149 HIS 0.007 0.001 HIS O 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (23569) covalent geometry : angle 0.70492 / 0.36 (32275) hydrogen bonds : bond 0.03984 / 2.32 ( 627) hydrogen bonds : angle 4.70938 / 4.11 ( 1734) Misc. bond : bond 0.00389 / 0.19 ( 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 269 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 210 time to evaluate : 0.604 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: 0.8790 (m90) cc_final: 0.8489 (m-70) REVERT: B 184 TRP cc_start: 0.8662 (m100) cc_final: 0.8364 (m100) REVERT: E 97 MET cc_start: 0.5621 (mpp) cc_final: 0.5219 (mpp) REVERT: F 149 TRP cc_start: 0.3733 (t-100) cc_final: 0.3082 (t60) REVERT: G 82 TYR cc_start: 0.6857 (t80) cc_final: 0.6538 (t80) REVERT: H 49 MET cc_start: 0.8528 (ptp) cc_final: 0.8226 (mtm) REVERT: H 123 ASN cc_start: 0.8108 (t0) cc_final: 0.7688 (m-40) REVERT: H 234 GLU cc_start: 0.8359 (pm20) cc_final: 0.7870 (pm20) REVERT: H 259 TRP cc_start: 0.6936 (m-10) cc_final: 0.6714 (m-10) REVERT: I 97 MET cc_start: 0.7132 (tmm) cc_final: 0.6778 (tmm) REVERT: I 222 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8128 (tm) REVERT: K 13 GLU cc_start: 0.8549 (mp0) cc_final: 0.8334 (mp0) REVERT: K 53 GLU cc_start: 0.8920 (pp20) cc_final: 0.8677 (pp20) REVERT: K 58 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8625 (tm-30) REVERT: O 54 LYS cc_start: 0.9328 (tppt) cc_final: 0.9117 (mmtt) REVERT: O 58 GLU cc_start: 0.9015 (pp20) cc_final: 0.8791 (pm20) REVERT: A 135 LEU cc_start: 0.8682 (tp) cc_final: 0.8062 (pp) REVERT: A 222 ASP cc_start: 0.7490 (p0) cc_final: 0.7132 (p0) outliers start: 59 outliers final: 40 residues processed: 250 average time/residue: 0.1596 time to fit residues: 62.4151 Evaluate side-chains 239 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 198 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 163 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 167 PHE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain C residue 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 F residue 58 ILE Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain G residue 44 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 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 283 LEU Chi-restraints excluded: chain I residue 49 MET Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 222 LEU Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 111 LEU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 102 GLU Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain A residue 83 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 245 optimal weight: 6.9990 chunk 186 optimal weight: 10.0000 chunk 181 optimal weight: 0.8980 chunk 171 optimal weight: 7.9990 chunk 118 optimal weight: 0.4980 chunk 126 optimal weight: 3.9990 chunk 257 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 255 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 152 optimal weight: 0.6980 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 62 GLN C 286 ASN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.079284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.066545 restraints weight = 113063.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.068267 restraints weight = 66687.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.069379 restraints weight = 46404.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.070117 restraints weight = 36144.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.070642 restraints weight = 30349.704| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3407 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= 0.201 Angle : 0.760 13.529 32275 Z= 0.396 Chirality : 0.044 0.248 3508 Planarity : 0.005 0.063 3927 Dihedral : 14.892 171.743 3861 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.56 % Favored : 88.21 % Rotamer: Outliers : 2.47 % Allowed : 23.08 % Favored : 74.45 % 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: -2.32 (0.16), residues: 2612 helix: -0.09 (0.19), residues: 807 sheet: -1.25 (0.33), residues: 213 loop : -2.51 (0.14), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 112 TYR 0.020 0.002 TYR C 226 PHE 0.027 0.002 PHE I 137 TRP 0.026 0.002 TRP F 149 HIS 0.005 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 (23569) covalent geometry : angle 0.75989 / 0.40 (32275) hydrogen bonds : bond 0.04589 / 2.68 ( 627) hydrogen bonds : angle 4.92964 / 4.30 ( 1734) Misc. bond : bond 0.00329 / 0.16 ( 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 253 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 198 time to evaluate : 0.866 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: 0.8790 (m90) cc_final: 0.8499 (m-70) REVERT: B 184 TRP cc_start: 0.8697 (m100) cc_final: 0.8419 (m100) REVERT: F 149 TRP cc_start: 0.3841 (t-100) cc_final: 0.3137 (t60) REVERT: G 82 TYR cc_start: 0.7110 (t80) cc_final: 0.6692 (t80) REVERT: H 49 MET cc_start: 0.8582 (ptp) cc_final: 0.8272 (mtm) REVERT: H 123 ASN cc_start: 0.8490 (t0) cc_final: 0.7941 (m-40) REVERT: H 234 GLU cc_start: 0.8291 (pm20) cc_final: 0.8010 (pm20) REVERT: I 97 MET cc_start: 0.7078 (tmm) cc_final: 0.6717 (tmm) REVERT: I 222 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8213 (tm) REVERT: K 13 GLU cc_start: 0.8488 (mp0) cc_final: 0.8255 (mp0) REVERT: K 53 GLU cc_start: 0.8957 (pp20) cc_final: 0.8726 (pp20) REVERT: K 58 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8607 (tm-30) REVERT: O 54 LYS cc_start: 0.9365 (tppt) cc_final: 0.9104 (mmtt) REVERT: O 109 LEU cc_start: 0.8519 (mp) cc_final: 0.8209 (mp) REVERT: A 118 ILE cc_start: 0.7873 (OUTLIER) cc_final: 0.7542 (mm) outliers start: 55 outliers final: 45 residues processed: 236 average time/residue: 0.1523 time to fit residues: 56.1588 Evaluate side-chains 234 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 187 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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 218 LEU Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 229 TYR Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain F residue 27 ASN Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain F residue 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 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 282 HIS Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain I residue 49 MET Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 165 THR Chi-restraints excluded: chain I residue 207 TYR 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 K residue 102 GLU Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 133 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 237 optimal weight: 0.8980 chunk 176 optimal weight: 0.0870 chunk 48 optimal weight: 0.6980 chunk 251 optimal weight: 7.9990 chunk 196 optimal weight: 3.9990 chunk 234 optimal weight: 4.9990 chunk 222 optimal weight: 0.8980 chunk 235 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 81 optimal weight: 0.0980 chunk 95 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 51 ASN ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 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 = 0.3760 r_free = 0.3760 target = 0.081298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.068512 restraints weight = 111665.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.070238 restraints weight = 65964.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.071409 restraints weight = 46027.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.072188 restraints weight = 35745.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.072714 restraints weight = 29839.761| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 23571 Z= 0.140 Angle : 0.739 12.645 32275 Z= 0.378 Chirality : 0.042 0.249 3508 Planarity : 0.005 0.061 3927 Dihedral : 14.804 171.974 3861 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.26 % Favored : 89.51 % Rotamer: Outliers : 2.20 % Allowed : 23.26 % Favored : 74.54 % 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: -2.24 (0.16), residues: 2612 helix: -0.10 (0.19), residues: 808 sheet: -1.23 (0.36), residues: 184 loop : -2.39 (0.14), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 242 TYR 0.041 0.001 TYR E 169 PHE 0.038 0.001 PHE A 162 TRP 0.076 0.002 TRP F 259 HIS 0.005 0.001 HIS O 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (23569) covalent geometry : angle 0.73876 / 0.38 (32275) hydrogen bonds : bond 0.04042 / 2.35 ( 627) hydrogen bonds : angle 4.72985 / 4.12 ( 1734) Misc. bond : bond 0.00382 / 0.19 ( 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 257 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 208 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 HIS cc_start: 0.8789 (m90) cc_final: 0.8501 (m-70) REVERT: B 184 TRP cc_start: 0.8664 (m100) cc_final: 0.8380 (m100) REVERT: E 97 MET cc_start: 0.5793 (mpp) cc_final: 0.5444 (mpp) REVERT: F 149 TRP cc_start: 0.3652 (t-100) cc_final: 0.2950 (t60) REVERT: G 82 TYR cc_start: 0.6930 (t80) cc_final: 0.6609 (t80) REVERT: H 49 MET cc_start: 0.8534 (ptp) cc_final: 0.8231 (mtm) REVERT: H 82 TYR cc_start: 0.6007 (t80) cc_final: 0.5762 (t80) REVERT: H 123 ASN cc_start: 0.8286 (t0) cc_final: 0.7732 (m-40) REVERT: H 234 GLU cc_start: 0.8269 (pm20) cc_final: 0.7967 (pm20) REVERT: H 259 TRP cc_start: 0.6896 (m-10) cc_final: 0.6689 (m-10) REVERT: I 97 MET cc_start: 0.7140 (tmm) cc_final: 0.6723 (tmm) REVERT: I 222 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8252 (tm) REVERT: J 74 ASP cc_start: 0.8877 (p0) cc_final: 0.8614 (p0) REVERT: K 13 GLU cc_start: 0.8557 (mp0) cc_final: 0.8356 (mp0) REVERT: K 53 GLU cc_start: 0.8866 (pp20) cc_final: 0.8625 (pp20) REVERT: K 58 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8638 (tm-30) REVERT: O 54 LYS cc_start: 0.9393 (tppt) cc_final: 0.9128 (mmtt) REVERT: A 222 ASP cc_start: 0.7436 (p0) cc_final: 0.7113 (p0) outliers start: 49 outliers final: 44 residues processed: 240 average time/residue: 0.1586 time to fit residues: 59.3645 Evaluate side-chains 240 residues out of total 2223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 195 time to evaluate : 0.599 ------------------------------------------------------------------------------- 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 218 LEU Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 167 PHE Chi-restraints excluded: chain C residue 209 PHE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain F residue 58 ILE Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain 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 158 LEU 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 181 LYS Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain I residue 49 MET Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 165 THR Chi-restraints excluded: chain I residue 222 LEU Chi-restraints excluded: chain I residue 228 THR Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 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 77 VAL Chi-restraints excluded: chain A residue 83 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 203 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 118 optimal weight: 0.5980 chunk 131 optimal weight: 0.9990 chunk 170 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 84 optimal weight: 0.0270 chunk 217 optimal weight: 2.9990 overall best weight: 0.9244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 51 ASN F 27 ASN ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.080963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.068231 restraints weight = 113844.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.069931 restraints weight = 67564.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.071109 restraints weight = 47188.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.071865 restraints weight = 36692.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.072333 restraints weight = 30797.282| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3579 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= 0.140 Angle : 0.722 12.589 32275 Z= 0.370 Chirality : 0.042 0.236 3508 Planarity : 0.005 0.061 3927 Dihedral : 14.751 172.143 3861 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.03 % Favored : 88.71 % Rotamer: Outliers : 2.29 % Allowed : 23.35 % Favored : 74.36 % 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: -2.17 (0.16), residues: 2612 helix: 0.01 (0.19), residues: 803 sheet: -1.27 (0.36), residues: 188 loop : -2.36 (0.14), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 242 TYR 0.029 0.001 TYR C 226 PHE 0.029 0.001 PHE I 137 TRP 0.102 0.002 TRP F 259 HIS 0.004 0.001 HIS O 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (23569) covalent geometry : angle 0.72150 / 0.37 (32275) hydrogen bonds : bond 0.03941 / 2.29 ( 627) hydrogen bonds : angle 4.70760 / 4.08 ( 1734) Misc. bond : bond 0.00366 / 0.18 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3378.07 seconds wall clock time: 59 minutes 20.64 seconds (3560.64 seconds total)