Starting phenix.real_space_refine on Sat Jul 4 10:42:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uzz_26923/07_2026/7uzz_26923.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uzz_26923/07_2026/7uzz_26923.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7uzz_26923/07_2026/7uzz_26923.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uzz_26923/07_2026/7uzz_26923.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uzz_26923/07_2026/7uzz_26923.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uzz_26923/07_2026/7uzz_26923.map" model { file = "/net/cci-nas-00/data/ceres_data/7uzz_26923/07_2026/7uzz_26923.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uzz_26923/07_2026/7uzz_26923.cif" } resolution = 4.45 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= -0.001 sd= 0.038 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 30 5.49 5 S 55 5.16 5 C 12617 2.51 5 N 3365 2.21 5 O 3900 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s 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: 19967 Number of models: 1 Model: "" Number of chains: 11 Chain: "G" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 644 Classifications: {'RNA': 30} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 3, 'rna3p_pur': 11, 'rna3p_pyr': 8} Link IDs: {'rna2p': 10, 'rna3p': 19} Chain: "J" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 871 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain breaks: 2 Chain: "I" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 995 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "K" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 995 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "E" Number of atoms: 2398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2398 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 8, 'TRANS': 284} Chain breaks: 4 Chain: "D" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1578 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 4, 'TRANS': 194} Chain breaks: 1 Chain: "C" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1628 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Chain: "A" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1628 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 200} Chain breaks: 1 Chain: "B" Number of atoms: 1523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1523 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 187} Chain breaks: 2 Chain: "H" Number of atoms: 2378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2378 Classifications: {'peptide': 296} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 286} Chain breaks: 1 Chain: "F" Number of atoms: 5329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 654, 5329 Classifications: {'peptide': 654} Link IDs: {'PTRANS': 7, 'TRANS': 646} Chain breaks: 6 Time building chain proxies: 4.26, per 1000 atoms: 0.21 Number of scatterers: 19967 At special positions: 0 Unit cell: (94.0808, 119.739, 211.682, 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 55 16.00 P 30 15.00 O 3900 8.00 N 3365 7.00 C 12617 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS F 407 " - pdb=" SG CYS F 423 " distance=1.76 Simple disulfide: pdb=" SG CYS F 410 " - pdb=" SG CYS F 426 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 960.2 milliseconds 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4466 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 25 sheets defined 48.3% alpha, 16.7% beta 0 base pairs and 3 stacking pairs defined. Time for finding SS restraints: 2.42 Creating SS restraints... Processing helix chain 'J' and resid 17 through 24 removed outlier: 4.235A pdb=" N VAL J 21 " --> pdb=" O ALA J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 61 removed outlier: 3.812A pdb=" N LEU J 48 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ASN J 50 " --> pdb=" O SER J 46 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU J 51 " --> pdb=" O LYS J 47 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE J 61 " --> pdb=" O ARG J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 92 Processing helix chain 'J' and resid 92 through 102 Processing helix chain 'J' and resid 103 through 115 Processing helix chain 'J' and resid 116 through 137 Processing helix chain 'I' and resid 15 through 24 removed outlier: 4.470A pdb=" N GLU I 19 " --> pdb=" O THR I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 47 Processing helix chain 'I' and resid 48 through 65 Processing helix chain 'I' and resid 71 through 92 Processing helix chain 'I' and resid 92 through 102 Processing helix chain 'I' and resid 103 through 115 Processing helix chain 'I' and resid 116 through 137 Processing helix chain 'K' and resid 15 through 24 removed outlier: 4.637A pdb=" N VAL K 21 " --> pdb=" O ALA K 17 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LYS K 22 " --> pdb=" O HIS K 18 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER K 23 " --> pdb=" O GLU K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 47 Processing helix chain 'K' and resid 48 through 65 Processing helix chain 'K' and resid 71 through 92 Processing helix chain 'K' and resid 92 through 102 Processing helix chain 'K' and resid 103 through 115 Processing helix chain 'K' and resid 116 through 137 removed outlier: 3.620A pdb=" N TYR K 137 " --> pdb=" O TYR K 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 53 Processing helix chain 'E' and resid 55 through 65 removed outlier: 3.850A pdb=" N TYR E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 82 Processing helix chain 'E' and resid 85 through 92 Processing helix chain 'E' and resid 130 through 147 Processing helix chain 'E' and resid 150 through 155 removed outlier: 3.603A pdb=" N ILE E 154 " --> pdb=" O LYS E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 169 No H-bonds generated for 'chain 'E' and resid 167 through 169' Processing helix chain 'E' and resid 211 through 230 Processing helix chain 'E' and resid 231 through 235 removed outlier: 3.944A pdb=" N LYS E 235 " --> pdb=" O VAL E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 246 Processing helix chain 'E' and resid 248 through 255 Processing helix chain 'E' and resid 278 through 290 Processing helix chain 'D' and resid 47 through 63 removed outlier: 3.836A pdb=" N ILE D 51 " --> pdb=" O PRO D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 73 Processing helix chain 'D' and resid 76 through 84 Processing helix chain 'D' and resid 104 through 114 Processing helix chain 'D' and resid 161 through 179 Processing helix chain 'C' and resid 47 through 63 removed outlier: 3.648A pdb=" N ILE C 51 " --> pdb=" O PRO C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 84 Processing helix chain 'C' and resid 104 through 113 removed outlier: 3.544A pdb=" N LYS C 108 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 160 No H-bonds generated for 'chain 'C' and resid 158 through 160' Processing helix chain 'C' and resid 161 through 178 removed outlier: 3.551A pdb=" N ASN C 178 " --> pdb=" O HIS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 188 Processing helix chain 'A' and resid 47 through 63 removed outlier: 3.579A pdb=" N ILE A 51 " --> pdb=" O PRO A 47 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 72 Processing helix chain 'A' and resid 76 through 84 Processing helix chain 'A' and resid 104 through 115 Processing helix chain 'A' and resid 162 through 179 Processing helix chain 'B' and resid 47 through 62 removed outlier: 3.618A pdb=" N ILE B 51 " --> pdb=" O PRO B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 84 Processing helix chain 'B' and resid 104 through 115 Processing helix chain 'B' and resid 158 through 160 No H-bonds generated for 'chain 'B' and resid 158 through 160' Processing helix chain 'B' and resid 161 through 178 removed outlier: 3.651A pdb=" N ASN B 178 " --> pdb=" O HIS B 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 47 removed outlier: 3.507A pdb=" N LEU H 35 " --> pdb=" O THR H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 93 removed outlier: 3.523A pdb=" N LYS H 92 " --> pdb=" O LYS H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 107 Processing helix chain 'H' and resid 110 through 121 Processing helix chain 'H' and resid 136 through 141 removed outlier: 3.969A pdb=" N ASP H 140 " --> pdb=" O ALA H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 184 removed outlier: 4.210A pdb=" N TYR H 184 " --> pdb=" O THR H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 194 Processing helix chain 'H' and resid 205 through 213 Processing helix chain 'H' and resid 231 through 236 Processing helix chain 'F' and resid 2 through 13 removed outlier: 3.763A pdb=" N LEU F 13 " --> pdb=" O TYR F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 23 removed outlier: 3.977A pdb=" N ILE F 20 " --> pdb=" O ILE F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 42 Processing helix chain 'F' and resid 49 through 58 Processing helix chain 'F' and resid 60 through 67 removed outlier: 4.156A pdb=" N LYS F 66 " --> pdb=" O LYS F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 86 removed outlier: 3.884A pdb=" N ILE F 77 " --> pdb=" O ASN F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 123 removed outlier: 4.426A pdb=" N ILE F 120 " --> pdb=" O SER F 116 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN F 122 " --> pdb=" O PHE F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 170 removed outlier: 4.088A pdb=" N TYR F 156 " --> pdb=" O SER F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 190 removed outlier: 3.566A pdb=" N GLN F 190 " --> pdb=" O GLU F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 227 Processing helix chain 'F' and resid 231 through 236 Processing helix chain 'F' and resid 239 through 249 Processing helix chain 'F' and resid 261 through 267 Processing helix chain 'F' and resid 273 through 300 removed outlier: 3.585A pdb=" N SER F 280 " --> pdb=" O LYS F 276 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE F 283 " --> pdb=" O ARG F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 305 No H-bonds generated for 'chain 'F' and resid 303 through 305' Processing helix chain 'F' and resid 322 through 344 Processing helix chain 'F' and resid 358 through 363 Processing helix chain 'F' and resid 367 through 386 removed outlier: 3.973A pdb=" N THR F 371 " --> pdb=" O GLY F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 398 removed outlier: 3.514A pdb=" N HIS F 398 " --> pdb=" O LEU F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 424 through 439 removed outlier: 4.171A pdb=" N ARG F 437 " --> pdb=" O SER F 433 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ASP F 438 " --> pdb=" O ASN F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 473 Processing helix chain 'F' and resid 536 through 541 Processing helix chain 'F' and resid 550 through 573 removed outlier: 4.677A pdb=" N LEU F 569 " --> pdb=" O PHE F 565 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ASN F 570 " --> pdb=" O LYS F 566 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU F 573 " --> pdb=" O LEU F 569 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 576 No H-bonds generated for 'chain 'F' and resid 574 through 576' Processing helix chain 'F' and resid 594 through 612 Processing helix chain 'F' and resid 630 through 636 removed outlier: 4.235A pdb=" N PHE F 636 " --> pdb=" O SER F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 665 through 670 Processing helix chain 'F' and resid 674 through 686 Processing helix chain 'F' and resid 690 through 703 Processing helix chain 'F' and resid 705 through 719 Processing helix chain 'F' and resid 722 through 735 Processing helix chain 'F' and resid 735 through 750 Processing sheet with id=AA1, first strand: chain 'J' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'I' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'E' and resid 158 through 160 removed outlier: 4.271A pdb=" N ASN E 256 " --> pdb=" O VAL E 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 23 through 24 removed outlier: 7.069A pdb=" N HIS E 117 " --> pdb=" O GLU E 191 " (cutoff:3.500A) removed outlier: 9.412A pdb=" N ILE E 193 " --> pdb=" O HIS E 117 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LYS E 176 " --> pdb=" O MET E 186 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N LEU E 188 " --> pdb=" O TYR E 174 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N TYR E 174 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG E 190 " --> pdb=" O ALA E 172 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ALA E 172 " --> pdb=" O ARG E 190 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N GLN E 175 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N THR E 315 " --> pdb=" O GLN E 175 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 29 through 31 removed outlier: 3.776A pdb=" N ILE E 30 " --> pdb=" O TYR E 39 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 96 through 103 removed outlier: 5.815A pdb=" N LEU D 96 " --> pdb=" O ASN D 155 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASN D 155 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ILE D 98 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE D 153 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ASP D 100 " --> pdb=" O VAL D 151 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL D 151 " --> pdb=" O ASP D 100 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY D 9 " --> pdb=" O PHE D 150 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N SER D 3 " --> pdb=" O VAL D 156 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LYS D 4 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N THR D 201 " --> pdb=" O LYS D 4 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LYS D 6 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ILE D 199 " --> pdb=" O LYS D 6 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N SER D 8 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR D 197 " --> pdb=" O SER D 8 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 119 through 124 Processing sheet with id=AA8, first strand: chain 'C' and resid 96 through 98 Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 98 removed outlier: 6.869A pdb=" N LYS C 4 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N THR C 10 " --> pdb=" O ASP C 196 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ASP C 196 " --> pdb=" O THR C 10 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLU C 12 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N PHE C 194 " --> pdb=" O GLU C 12 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 119 through 127 Processing sheet with id=AB2, first strand: chain 'A' and resid 37 through 38 removed outlier: 3.629A pdb=" N LEU A 43 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE A 103 " --> pdb=" O PRO A 44 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 46 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N VAL A 151 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA A 101 " --> pdb=" O ASP A 149 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ASP A 149 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N PHE A 103 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N GLU A 147 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LYS A 4 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N THR A 201 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYS A 6 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE A 199 " --> pdb=" O LYS A 6 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N SER A 8 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR A 197 " --> pdb=" O SER A 8 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 119 through 124 Processing sheet with id=AB4, first strand: chain 'B' and resid 45 through 46 removed outlier: 3.620A pdb=" N ILE B 46 " --> pdb=" O ALA B 101 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE B 102 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 45 through 46 removed outlier: 3.620A pdb=" N ILE B 46 " --> pdb=" O ALA B 101 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE B 102 " --> pdb=" O ASP B 149 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER B 3 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LYS B 4 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR B 10 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ASP B 196 " --> pdb=" O THR B 10 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLU B 12 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N PHE B 194 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 119 through 127 Processing sheet with id=AB7, first strand: chain 'H' and resid 58 through 59 removed outlier: 3.609A pdb=" N GLY H 160 " --> pdb=" O TYR H 65 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 58 through 59 Processing sheet with id=AB9, first strand: chain 'H' and resid 71 through 73 Processing sheet with id=AC1, first strand: chain 'H' and resid 125 through 131 Processing sheet with id=AC2, first strand: chain 'H' and resid 239 through 240 removed outlier: 3.601A pdb=" N SER H 219 " --> pdb=" O PHE H 274 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 243 through 248 removed outlier: 3.763A pdb=" N SER H 267 " --> pdb=" O THR H 244 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLY H 248 " --> pdb=" O SER H 263 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N SER H 263 " --> pdb=" O GLY H 248 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 283 through 284 Processing sheet with id=AC5, first strand: chain 'F' and resid 307 through 311 removed outlier: 6.578A pdb=" N TYR F 316 " --> pdb=" O LEU F 308 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N THR F 310 " --> pdb=" O HIS F 314 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N HIS F 314 " --> pdb=" O THR F 310 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 450 through 452 removed outlier: 3.551A pdb=" N LYS F 456 " --> pdb=" O MET F 452 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE F 441 " --> pdb=" O ILE F 461 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ILE F 478 " --> pdb=" O THR F 492 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 578 through 584 removed outlier: 7.122A pdb=" N ILE F 578 " --> pdb=" O ALA F 593 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ALA F 593 " --> pdb=" O ILE F 578 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ALA F 580 " --> pdb=" O ILE F 591 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE F 591 " --> pdb=" O ALA F 580 " (cutoff:3.500A) 953 hydrogen bonds defined for protein. 2769 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 3 stacking parallelities Total time for adding SS restraints: 3.76 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4491 1.33 - 1.45: 4694 1.45 - 1.57: 11049 1.57 - 1.69: 59 1.69 - 1.81: 97 Bond restraints: 20390 Sorted by residual: bond pdb=" N GLY H 186 " pdb=" CA GLY H 186 " ideal model delta sigma weight residual 1.442 1.469 -0.027 7.70e-03 1.69e+04 1.21e+01 bond pdb=" N ILE F 149 " pdb=" CA ILE F 149 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.12e-02 7.97e+03 1.04e+01 bond pdb=" N ILE B 139 " pdb=" CA ILE B 139 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.19e-02 7.06e+03 9.63e+00 bond pdb=" N ILE E 30 " pdb=" CA ILE E 30 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.17e-02 7.31e+03 9.53e+00 bond pdb=" N ILE B 91 " pdb=" CA ILE B 91 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.19e-02 7.06e+03 9.32e+00 ... (remaining 20385 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 25637 1.95 - 3.91: 1779 3.91 - 5.86: 108 5.86 - 7.82: 17 7.82 - 9.77: 5 Bond angle restraints: 27546 Sorted by residual: angle pdb=" C SER H 185 " pdb=" N GLY H 186 " pdb=" CA GLY H 186 " ideal model delta sigma weight residual 122.69 115.86 6.83 1.04e+00 9.25e-01 4.31e+01 angle pdb=" N VAL H 285 " pdb=" CA VAL H 285 " pdb=" C VAL H 285 " ideal model delta sigma weight residual 111.77 105.75 6.02 1.04e+00 9.25e-01 3.36e+01 angle pdb=" C4' C G 8 " pdb=" C3' C G 8 " pdb=" O3' C G 8 " ideal model delta sigma weight residual 113.00 104.98 8.02 1.50e+00 4.44e-01 2.86e+01 angle pdb=" N THR C 131 " pdb=" CA THR C 131 " pdb=" C THR C 131 " ideal model delta sigma weight residual 114.62 108.70 5.92 1.14e+00 7.69e-01 2.70e+01 angle pdb=" C CYS F 426 " pdb=" CA CYS F 426 " pdb=" CB CYS F 426 " ideal model delta sigma weight residual 110.88 103.25 7.63 1.57e+00 4.06e-01 2.36e+01 ... (remaining 27541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.31: 11991 33.31 - 66.62: 190 66.62 - 99.93: 24 99.93 - 133.24: 3 133.24 - 166.55: 1 Dihedral angle restraints: 12209 sinusoidal: 5272 harmonic: 6937 Sorted by residual: dihedral pdb=" O4' C G 10 " pdb=" C1' C G 10 " pdb=" N1 C G 10 " pdb=" C2 C G 10 " ideal model delta sinusoidal sigma weight residual -160.00 -45.68 -114.32 1 1.50e+01 4.44e-03 6.02e+01 dihedral pdb=" O4' C G 2 " pdb=" C1' C G 2 " pdb=" N1 C G 2 " pdb=" C2 C G 2 " ideal model delta sinusoidal sigma weight residual -128.00 -7.64 -120.36 1 1.70e+01 3.46e-03 5.00e+01 dihedral pdb=" O4' U G 14 " pdb=" C1' U G 14 " pdb=" N1 U G 14 " pdb=" C2 U G 14 " ideal model delta sinusoidal sigma weight residual -160.00 -61.07 -98.93 1 1.50e+01 4.44e-03 4.93e+01 ... (remaining 12206 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2245 0.062 - 0.125: 639 0.125 - 0.187: 128 0.187 - 0.250: 13 0.250 - 0.312: 5 Chirality restraints: 3030 Sorted by residual: chirality pdb=" P G G 15 " pdb=" OP1 G G 15 " pdb=" OP2 G G 15 " pdb=" O5' G G 15 " both_signs ideal model delta sigma weight residual True 2.41 -2.72 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" P G G 21 " pdb=" OP1 G G 21 " pdb=" OP2 G G 21 " pdb=" O5' G G 21 " both_signs ideal model delta sigma weight residual True 2.41 -2.72 -0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA CYS F 426 " pdb=" N CYS F 426 " pdb=" C CYS F 426 " pdb=" CB CYS F 426 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 3027 not shown) Planarity restraints: 3415 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS H 17 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C HIS H 17 " 0.060 2.00e-02 2.50e+03 pdb=" O HIS H 17 " -0.022 2.00e-02 2.50e+03 pdb=" N PHE H 18 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 46 " 0.053 5.00e-02 4.00e+02 8.04e-02 1.03e+01 pdb=" N PRO C 47 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO C 47 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 47 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL J 55 " 0.014 2.00e-02 2.50e+03 2.71e-02 7.32e+00 pdb=" C VAL J 55 " -0.047 2.00e-02 2.50e+03 pdb=" O VAL J 55 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN J 56 " 0.016 2.00e-02 2.50e+03 ... (remaining 3412 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.12: 1 2.12 - 2.81: 5768 2.81 - 3.51: 27755 3.51 - 4.20: 44994 4.20 - 4.90: 78263 Nonbonded interactions: 156781 Sorted by model distance: nonbonded pdb=" N7 A G 20 " pdb=" ND2 ASN C 57 " model vdw 1.424 3.200 nonbonded pdb=" O2 C G 8 " pdb=" ND2 ASN B 57 " model vdw 2.126 3.120 nonbonded pdb=" C8 A G 20 " pdb=" ND2 ASN C 57 " model vdw 2.132 3.340 nonbonded pdb=" O PHE K 98 " pdb=" OG1 THR K 102 " model vdw 2.173 3.040 nonbonded pdb=" N GLY C 48 " pdb=" OD1 ASP C 100 " model vdw 2.196 3.120 ... (remaining 156776 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 23 or resid 33 through 63 or resid 76 through 20 \ 8)) selection = (chain 'B' and resid 2 through 208) selection = (chain 'C' and (resid 2 through 23 or resid 33 through 63 or resid 76 through 20 \ 8)) selection = (chain 'D' and (resid 2 through 23 or resid 33 through 63 or resid 76 through 20 \ 8)) } ncs_group { reference = (chain 'I' and (resid 17 through 61 or resid 74 through 139)) selection = chain 'J' selection = (chain 'K' and (resid 17 through 61 or resid 74 through 139)) } 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: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 21.220 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 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 : 0.009 0.267 20392 Z= 0.574 Angle : 1.073 70.431 27550 Z= 0.711 Chirality : 0.061 0.312 3030 Planarity : 0.005 0.080 3415 Dihedral : 12.584 166.549 7737 Min Nonbonded Distance : 1.424 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.96 % Favored : 95.00 % Rotamer: Outliers : 0.75 % Allowed : 1.74 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.16), residues: 2320 helix: 0.65 (0.15), residues: 1030 sheet: 0.18 (0.27), residues: 371 loop : -1.99 (0.17), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 137 TYR 0.029 0.002 TYR F 191 PHE 0.022 0.002 PHE E 92 TRP 0.018 0.002 TRP F 339 HIS 0.013 0.002 HIS H 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00849 / 0.57 (20390) covalent geometry : angle 0.98428 / 0.68 (27546) SS BOND : bond 0.18928 / 9.46 ( 2) SS BOND : angle 35.53686 / 11.85 ( 4) hydrogen bonds : bond 0.15448 / 9.26 ( 947) hydrogen bonds : angle 6.96333 / 4.52 ( 2769) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 352 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: J 81 LEU cc_start: 0.9506 (tp) cc_final: 0.8177 (tt) REVERT: J 104 MET cc_start: 0.9132 (tpp) cc_final: 0.8674 (tpp) REVERT: J 120 PHE cc_start: 0.8616 (t80) cc_final: 0.8398 (t80) REVERT: J 127 PHE cc_start: 0.8819 (t80) cc_final: 0.8449 (t80) REVERT: I 66 ASN cc_start: 0.9233 (m-40) cc_final: 0.8816 (p0) REVERT: I 77 GLU cc_start: 0.9302 (mm-30) cc_final: 0.9056 (mt-10) REVERT: I 86 TYR cc_start: 0.8556 (m-80) cc_final: 0.8156 (m-80) REVERT: K 52 MET cc_start: 0.9392 (mtt) cc_final: 0.8536 (tpt) REVERT: K 76 ASP cc_start: 0.9210 (m-30) cc_final: 0.8227 (m-30) REVERT: K 83 ILE cc_start: 0.9634 (mt) cc_final: 0.9030 (mt) REVERT: K 120 PHE cc_start: 0.9405 (t80) cc_final: 0.9143 (t80) REVERT: E 252 VAL cc_start: 0.7452 (OUTLIER) cc_final: 0.7120 (t) REVERT: C 17 LEU cc_start: 0.9078 (tt) cc_final: 0.8854 (mm) REVERT: C 40 GLN cc_start: 0.9204 (tt0) cc_final: 0.8973 (pt0) REVERT: A 17 LEU cc_start: 0.7175 (tp) cc_final: 0.6857 (tp) REVERT: F 159 LEU cc_start: 0.9084 (tp) cc_final: 0.8824 (mm) REVERT: F 317 LEU cc_start: 0.8988 (mp) cc_final: 0.8742 (tp) REVERT: F 318 LEU cc_start: 0.8244 (tp) cc_final: 0.7895 (tp) REVERT: F 420 ASP cc_start: 0.7497 (m-30) cc_final: 0.7141 (t70) REVERT: F 495 TRP cc_start: 0.7838 (m-90) cc_final: 0.7001 (m100) REVERT: F 624 MET cc_start: 0.8276 (ttm) cc_final: 0.7868 (ttp) outliers start: 16 outliers final: 2 residues processed: 365 average time/residue: 0.1736 time to fit residues: 91.2003 Evaluate side-chains 176 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 173 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 37 GLN ** K 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 ASN K 56 ASN ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 ASN D 110 HIS D 138 GLN C 18 HIS C 135 ASN C 174 HIS A 72 HIS A 110 HIS ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 GLN H 137 GLN H 214 GLN ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 482 ASN F 560 GLN ** F 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.040825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.032193 restraints weight = 208647.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.033104 restraints weight = 138733.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.033772 restraints weight = 101692.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.034259 restraints weight = 80420.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.034622 restraints weight = 67376.421| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20392 Z= 0.176 Angle : 0.601 8.756 27550 Z= 0.329 Chirality : 0.042 0.188 3030 Planarity : 0.004 0.061 3415 Dihedral : 10.805 164.610 2925 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.10 % Favored : 96.85 % Rotamer: Outliers : 0.24 % Allowed : 1.55 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.17), residues: 2320 helix: 1.12 (0.15), residues: 1101 sheet: 0.48 (0.27), residues: 373 loop : -1.58 (0.19), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 78 TYR 0.032 0.002 TYR K 59 PHE 0.030 0.002 PHE F 589 TRP 0.024 0.002 TRP F 184 HIS 0.010 0.001 HIS D 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.18 (20390) covalent geometry : angle 0.60009 / 0.33 (27546) SS BOND : bond 0.00495 / 0.25 ( 2) SS BOND : angle 1.94228 / 0.65 ( 4) hydrogen bonds : bond 0.04428 / 2.69 ( 947) hydrogen bonds : angle 5.29491 / 3.49 ( 2769) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 202 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 37 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.6732 (pp30) REVERT: J 45 THR cc_start: 0.9518 (t) cc_final: 0.9198 (t) REVERT: J 48 LEU cc_start: 0.9904 (mt) cc_final: 0.9682 (pp) REVERT: J 81 LEU cc_start: 0.9630 (tp) cc_final: 0.9316 (tt) REVERT: J 85 PHE cc_start: 0.9195 (m-80) cc_final: 0.8559 (m-80) REVERT: J 120 PHE cc_start: 0.9666 (t80) cc_final: 0.9439 (t80) REVERT: J 127 PHE cc_start: 0.9715 (t80) cc_final: 0.9193 (t80) REVERT: I 14 MET cc_start: 0.8776 (tpp) cc_final: 0.8427 (tpp) REVERT: I 27 ASN cc_start: 0.7730 (t0) cc_final: 0.7477 (t0) REVERT: I 52 MET cc_start: 0.9452 (tpt) cc_final: 0.9212 (tpt) REVERT: I 63 PHE cc_start: 0.9704 (t80) cc_final: 0.9409 (t80) REVERT: I 66 ASN cc_start: 0.9553 (m-40) cc_final: 0.9191 (p0) REVERT: I 80 TYR cc_start: 0.9052 (m-80) cc_final: 0.8327 (m-80) REVERT: I 86 TYR cc_start: 0.9389 (m-80) cc_final: 0.9078 (m-80) REVERT: I 109 ASP cc_start: 0.9280 (m-30) cc_final: 0.9041 (m-30) REVERT: K 52 MET cc_start: 0.9697 (mtt) cc_final: 0.9289 (tpt) REVERT: K 64 ASN cc_start: 0.9239 (m-40) cc_final: 0.8996 (m110) REVERT: K 69 GLN cc_start: 0.9064 (tp40) cc_final: 0.8621 (tm-30) REVERT: K 85 PHE cc_start: 0.9914 (m-80) cc_final: 0.9502 (m-80) REVERT: K 109 ASP cc_start: 0.9729 (t0) cc_final: 0.9285 (m-30) REVERT: K 120 PHE cc_start: 0.9864 (t80) cc_final: 0.9635 (t80) REVERT: K 127 PHE cc_start: 0.9510 (t80) cc_final: 0.8865 (t80) REVERT: E 186 MET cc_start: 0.8609 (mmp) cc_final: 0.7977 (mmp) REVERT: E 260 LEU cc_start: 0.8972 (mm) cc_final: 0.8493 (mm) REVERT: D 88 LYS cc_start: 0.9202 (tttt) cc_final: 0.8951 (ptpt) REVERT: D 113 GLN cc_start: 0.9340 (mt0) cc_final: 0.8927 (pt0) REVERT: D 181 LEU cc_start: 0.9526 (pp) cc_final: 0.8928 (mp) REVERT: C 17 LEU cc_start: 0.9849 (tt) cc_final: 0.9218 (mm) REVERT: C 40 GLN cc_start: 0.9506 (tt0) cc_final: 0.8480 (pt0) REVERT: A 55 MET cc_start: 0.9618 (mtm) cc_final: 0.9135 (mtp) REVERT: A 82 LEU cc_start: 0.9188 (mt) cc_final: 0.8823 (mt) REVERT: B 55 MET cc_start: 0.9524 (mmp) cc_final: 0.9301 (mmp) REVERT: B 96 LEU cc_start: 0.9768 (tp) cc_final: 0.8949 (pp) REVERT: B 115 ASP cc_start: 0.9099 (t0) cc_final: 0.8860 (t0) REVERT: H 208 LEU cc_start: 0.9953 (tt) cc_final: 0.9619 (mt) REVERT: F 257 MET cc_start: 0.9699 (mpp) cc_final: 0.9357 (mpp) REVERT: F 363 MET cc_start: 0.8885 (mtp) cc_final: 0.8487 (mmm) REVERT: F 495 TRP cc_start: 0.8086 (m-90) cc_final: 0.6987 (m100) REVERT: F 535 ASN cc_start: 0.9426 (t0) cc_final: 0.9136 (t0) REVERT: F 634 MET cc_start: 0.8863 (mmp) cc_final: 0.8366 (mmm) REVERT: F 697 MET cc_start: 0.9800 (mmp) cc_final: 0.9544 (mmm) outliers start: 5 outliers final: 1 residues processed: 207 average time/residue: 0.1694 time to fit residues: 51.8104 Evaluate side-chains 156 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 154 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 222 optimal weight: 8.9990 chunk 188 optimal weight: 10.0000 chunk 176 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 29 optimal weight: 0.6980 chunk 230 optimal weight: 7.9990 chunk 148 optimal weight: 0.8980 chunk 135 optimal weight: 8.9990 chunk 211 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 overall best weight: 4.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 37 GLN I 64 ASN ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 ASN D 168 ASN C 114 ASN A 138 GLN ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 193 GLN H 100 HIS H 129 GLN H 183 GLN ** H 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 2 ASN F 33 HIS F 334 ASN F 375 ASN F 549 ASN ** F 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 722 ASN F 735 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.036708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.028995 restraints weight = 231841.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.029828 restraints weight = 150484.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.030416 restraints weight = 108992.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.030825 restraints weight = 85906.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.031116 restraints weight = 72126.043| |-----------------------------------------------------------------------------| r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 20392 Z= 0.330 Angle : 0.781 10.031 27550 Z= 0.426 Chirality : 0.045 0.218 3030 Planarity : 0.005 0.051 3415 Dihedral : 11.092 174.042 2925 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 23.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.78 % Favored : 95.17 % Rotamer: Outliers : 0.24 % Allowed : 3.29 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.16), residues: 2320 helix: 0.48 (0.15), residues: 1086 sheet: 0.01 (0.27), residues: 371 loop : -1.83 (0.19), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 78 TYR 0.033 0.003 TYR J 87 PHE 0.021 0.003 PHE F 265 TRP 0.048 0.003 TRP F 184 HIS 0.011 0.002 HIS F 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00639 / 0.33 (20390) covalent geometry : angle 0.78042 / 0.43 (27546) SS BOND : bond 0.01501 / 0.75 ( 2) SS BOND : angle 2.06294 / 0.69 ( 4) hydrogen bonds : bond 0.04771 / 2.91 ( 947) hydrogen bonds : angle 5.61035 / 3.76 ( 2769) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 143 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 49 ARG cc_start: 0.9528 (ptp-170) cc_final: 0.8880 (ptp-110) REVERT: J 81 LEU cc_start: 0.9632 (tp) cc_final: 0.9266 (tt) REVERT: J 85 PHE cc_start: 0.9248 (m-80) cc_final: 0.8554 (m-80) REVERT: J 87 TYR cc_start: 0.9366 (t80) cc_final: 0.9064 (t80) REVERT: J 88 GLU cc_start: 0.9730 (mm-30) cc_final: 0.9442 (mm-30) REVERT: J 120 PHE cc_start: 0.9669 (t80) cc_final: 0.9468 (t80) REVERT: I 14 MET cc_start: 0.8673 (tpp) cc_final: 0.8021 (tpp) REVERT: I 80 TYR cc_start: 0.9199 (m-80) cc_final: 0.8599 (m-80) REVERT: I 86 TYR cc_start: 0.9339 (m-80) cc_final: 0.9012 (m-80) REVERT: I 104 MET cc_start: 0.9860 (mmt) cc_final: 0.9643 (mmt) REVERT: I 109 ASP cc_start: 0.8960 (m-30) cc_final: 0.8756 (m-30) REVERT: I 127 PHE cc_start: 0.9779 (t80) cc_final: 0.9535 (t80) REVERT: K 52 MET cc_start: 0.9642 (mtt) cc_final: 0.9052 (tpt) REVERT: K 85 PHE cc_start: 0.9891 (m-80) cc_final: 0.9544 (m-80) REVERT: K 109 ASP cc_start: 0.9793 (t0) cc_final: 0.9189 (m-30) REVERT: K 123 TYR cc_start: 0.9499 (t80) cc_final: 0.9247 (t80) REVERT: K 127 PHE cc_start: 0.9494 (t80) cc_final: 0.8821 (t80) REVERT: E 186 MET cc_start: 0.8764 (mmp) cc_final: 0.8266 (mmp) REVERT: D 55 MET cc_start: 0.9630 (mmp) cc_final: 0.9361 (mmp) REVERT: D 113 GLN cc_start: 0.9458 (mt0) cc_final: 0.9172 (pt0) REVERT: A 55 MET cc_start: 0.9507 (mtm) cc_final: 0.9104 (mtp) REVERT: A 192 ILE cc_start: 0.9714 (pt) cc_final: 0.9286 (mm) REVERT: H 28 MET cc_start: 0.8953 (ttt) cc_final: 0.8268 (ttt) REVERT: H 179 MET cc_start: 0.9562 (tpt) cc_final: 0.9093 (tpp) REVERT: F 1 MET cc_start: 0.8465 (tpt) cc_final: 0.7575 (tpp) REVERT: F 160 MET cc_start: 0.9718 (mtm) cc_final: 0.9423 (mpp) REVERT: F 252 PHE cc_start: 0.9669 (m-80) cc_final: 0.8908 (m-80) REVERT: F 288 MET cc_start: 0.9038 (mmp) cc_final: 0.8801 (mmm) REVERT: F 624 MET cc_start: 0.7692 (ttp) cc_final: 0.7309 (tpp) REVERT: F 634 MET cc_start: 0.9295 (mmp) cc_final: 0.8925 (mmm) outliers start: 5 outliers final: 0 residues processed: 148 average time/residue: 0.1669 time to fit residues: 36.4176 Evaluate side-chains 104 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 95 optimal weight: 7.9990 chunk 172 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 210 optimal weight: 0.6980 chunk 224 optimal weight: 4.9990 chunk 216 optimal weight: 30.0000 chunk 99 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 197 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 223 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 37 GLN J 56 ASN ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 HIS A 138 GLN ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 ASN ** F 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.037255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.029256 restraints weight = 219754.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.030152 restraints weight = 139922.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.030792 restraints weight = 99795.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.031258 restraints weight = 77723.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.031614 restraints weight = 64064.749| |-----------------------------------------------------------------------------| r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20392 Z= 0.132 Angle : 0.547 7.000 27550 Z= 0.299 Chirality : 0.041 0.240 3030 Planarity : 0.003 0.045 3415 Dihedral : 10.683 174.074 2925 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.45 % Favored : 96.51 % Rotamer: Outliers : 0.14 % Allowed : 2.07 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.17), residues: 2320 helix: 1.10 (0.16), residues: 1077 sheet: 0.30 (0.27), residues: 386 loop : -1.57 (0.19), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 191 TYR 0.028 0.001 TYR J 87 PHE 0.016 0.001 PHE F 589 TRP 0.038 0.002 TRP F 184 HIS 0.007 0.001 HIS D 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (20390) covalent geometry : angle 0.54602 / 0.30 (27546) SS BOND : bond 0.01132 / 0.57 ( 2) SS BOND : angle 3.28827 / 1.10 ( 4) hydrogen bonds : bond 0.03519 / 2.16 ( 947) hydrogen bonds : angle 5.10092 / 3.40 ( 2769) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 142 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 49 ARG cc_start: 0.9481 (ptp-170) cc_final: 0.8821 (ptp-110) REVERT: J 127 PHE cc_start: 0.9756 (t80) cc_final: 0.9257 (t80) REVERT: I 14 MET cc_start: 0.8548 (tpp) cc_final: 0.7707 (tpp) REVERT: I 52 MET cc_start: 0.9481 (mtm) cc_final: 0.9264 (mtp) REVERT: I 63 PHE cc_start: 0.9752 (t80) cc_final: 0.9367 (t80) REVERT: I 64 ASN cc_start: 0.8564 (m110) cc_final: 0.8084 (m110) REVERT: I 66 ASN cc_start: 0.9383 (m-40) cc_final: 0.9076 (p0) REVERT: I 86 TYR cc_start: 0.9319 (m-80) cc_final: 0.8950 (m-80) REVERT: I 104 MET cc_start: 0.9880 (mmt) cc_final: 0.9592 (mmt) REVERT: I 109 ASP cc_start: 0.8793 (m-30) cc_final: 0.8510 (m-30) REVERT: I 127 PHE cc_start: 0.9767 (t80) cc_final: 0.9471 (t80) REVERT: K 52 MET cc_start: 0.9658 (mtt) cc_final: 0.9140 (tpt) REVERT: K 54 GLN cc_start: 0.9562 (OUTLIER) cc_final: 0.9266 (pm20) REVERT: K 69 GLN cc_start: 0.8801 (tp40) cc_final: 0.8264 (tm-30) REVERT: K 76 ASP cc_start: 0.9598 (m-30) cc_final: 0.9363 (m-30) REVERT: K 85 PHE cc_start: 0.9895 (m-80) cc_final: 0.9564 (m-80) REVERT: K 109 ASP cc_start: 0.9739 (t0) cc_final: 0.9052 (m-30) REVERT: K 112 ILE cc_start: 0.9533 (pt) cc_final: 0.8901 (pt) REVERT: K 120 PHE cc_start: 0.9748 (t80) cc_final: 0.9518 (t80) REVERT: K 127 PHE cc_start: 0.9390 (t80) cc_final: 0.8828 (t80) REVERT: E 40 MET cc_start: 0.9376 (tpt) cc_final: 0.9170 (tpp) REVERT: E 119 MET cc_start: 0.7567 (mmp) cc_final: 0.6302 (mmm) REVERT: D 55 MET cc_start: 0.9645 (mmp) cc_final: 0.9318 (mmm) REVERT: D 113 GLN cc_start: 0.9434 (mt0) cc_final: 0.9068 (pt0) REVERT: C 40 GLN cc_start: 0.9600 (tt0) cc_final: 0.8330 (pt0) REVERT: A 55 MET cc_start: 0.9612 (mtm) cc_final: 0.9084 (mtp) REVERT: H 179 MET cc_start: 0.9659 (tpt) cc_final: 0.9214 (tpp) REVERT: H 208 LEU cc_start: 0.9960 (tt) cc_final: 0.9634 (mt) REVERT: F 1 MET cc_start: 0.8535 (tpt) cc_final: 0.7610 (tpp) REVERT: F 160 MET cc_start: 0.9720 (mtm) cc_final: 0.9394 (mtp) REVERT: F 252 PHE cc_start: 0.9439 (m-80) cc_final: 0.8746 (m-80) REVERT: F 352 MET cc_start: 0.8476 (mpp) cc_final: 0.8105 (mpp) REVERT: F 571 HIS cc_start: 0.9764 (t70) cc_final: 0.9317 (t70) REVERT: F 624 MET cc_start: 0.7694 (ttp) cc_final: 0.7289 (tpp) REVERT: F 634 MET cc_start: 0.9282 (mmp) cc_final: 0.8976 (mmm) REVERT: F 697 MET cc_start: 0.9752 (mmp) cc_final: 0.9535 (mmm) outliers start: 3 outliers final: 1 residues processed: 145 average time/residue: 0.1636 time to fit residues: 35.5443 Evaluate side-chains 115 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 113 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 213 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 121 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 chunk 189 optimal weight: 0.7980 chunk 60 optimal weight: 8.9990 chunk 225 optimal weight: 9.9990 chunk 48 optimal weight: 0.0010 chunk 203 optimal weight: 4.9990 chunk 145 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 37 GLN ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN A 193 GLN ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN H 45 GLN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 708 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.038315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.030389 restraints weight = 217173.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.031271 restraints weight = 141728.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.031905 restraints weight = 102630.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.032357 restraints weight = 80684.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.032704 restraints weight = 67132.331| |-----------------------------------------------------------------------------| r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.5360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20392 Z= 0.105 Angle : 0.523 8.415 27550 Z= 0.283 Chirality : 0.040 0.239 3030 Planarity : 0.003 0.038 3415 Dihedral : 10.402 168.139 2925 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.97 % Favored : 96.98 % Rotamer: Outliers : 0.14 % Allowed : 1.50 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.17), residues: 2320 helix: 1.33 (0.16), residues: 1082 sheet: 0.43 (0.27), residues: 385 loop : -1.33 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 57 TYR 0.033 0.001 TYR K 59 PHE 0.029 0.001 PHE I 98 TRP 0.028 0.001 TRP F 184 HIS 0.004 0.001 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (20390) covalent geometry : angle 0.52256 / 0.28 (27546) SS BOND : bond 0.00542 / 0.27 ( 2) SS BOND : angle 2.19259 / 0.73 ( 4) hydrogen bonds : bond 0.03332 / 2.06 ( 947) hydrogen bonds : angle 4.87691 / 3.28 ( 2769) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 141 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 49 ARG cc_start: 0.9523 (ptp-170) cc_final: 0.9136 (mtm110) REVERT: J 87 TYR cc_start: 0.9021 (t80) cc_final: 0.8819 (t80) REVERT: J 88 GLU cc_start: 0.9666 (mm-30) cc_final: 0.9356 (mm-30) REVERT: J 120 PHE cc_start: 0.9756 (t80) cc_final: 0.9533 (t80) REVERT: J 127 PHE cc_start: 0.9724 (t80) cc_final: 0.9151 (t80) REVERT: I 14 MET cc_start: 0.8693 (tpp) cc_final: 0.7965 (tpp) REVERT: I 52 MET cc_start: 0.9325 (mtm) cc_final: 0.8964 (mtt) REVERT: I 63 PHE cc_start: 0.9700 (t80) cc_final: 0.9273 (t80) REVERT: I 64 ASN cc_start: 0.8508 (m110) cc_final: 0.8028 (m-40) REVERT: I 66 ASN cc_start: 0.9445 (m-40) cc_final: 0.9197 (p0) REVERT: I 85 PHE cc_start: 0.9724 (m-80) cc_final: 0.9484 (m-80) REVERT: I 86 TYR cc_start: 0.9339 (m-80) cc_final: 0.8988 (m-80) REVERT: I 127 PHE cc_start: 0.9783 (t80) cc_final: 0.9526 (t80) REVERT: K 52 MET cc_start: 0.9697 (mtt) cc_final: 0.9173 (tpt) REVERT: K 69 GLN cc_start: 0.8776 (tp40) cc_final: 0.8520 (tp40) REVERT: K 76 ASP cc_start: 0.9562 (m-30) cc_final: 0.9346 (m-30) REVERT: K 85 PHE cc_start: 0.9907 (m-80) cc_final: 0.9558 (m-80) REVERT: K 109 ASP cc_start: 0.9757 (t0) cc_final: 0.9164 (m-30) REVERT: K 112 ILE cc_start: 0.9508 (pt) cc_final: 0.8908 (pt) REVERT: K 123 TYR cc_start: 0.9588 (t80) cc_final: 0.9304 (t80) REVERT: K 127 PHE cc_start: 0.9387 (t80) cc_final: 0.8963 (t80) REVERT: E 119 MET cc_start: 0.8144 (mmp) cc_final: 0.7536 (mmm) REVERT: E 186 MET cc_start: 0.9362 (mmp) cc_final: 0.8718 (mmp) REVERT: D 55 MET cc_start: 0.9707 (mmp) cc_final: 0.9481 (mmm) REVERT: D 113 GLN cc_start: 0.9368 (mt0) cc_final: 0.9047 (pt0) REVERT: C 40 GLN cc_start: 0.9580 (tt0) cc_final: 0.9379 (tt0) REVERT: A 40 GLN cc_start: 0.9221 (tt0) cc_final: 0.8937 (tt0) REVERT: A 55 MET cc_start: 0.9670 (mtm) cc_final: 0.9124 (mtp) REVERT: B 55 MET cc_start: 0.9534 (mmp) cc_final: 0.9297 (mmp) REVERT: H 28 MET cc_start: 0.8634 (ttt) cc_final: 0.8328 (ttt) REVERT: H 179 MET cc_start: 0.9671 (tpt) cc_final: 0.9408 (tpp) REVERT: H 208 LEU cc_start: 0.9956 (tt) cc_final: 0.9657 (mt) REVERT: H 258 MET cc_start: 0.7759 (mmt) cc_final: 0.6921 (pmm) REVERT: F 1 MET cc_start: 0.8650 (tpt) cc_final: 0.7712 (tpp) REVERT: F 160 MET cc_start: 0.9711 (mtm) cc_final: 0.9488 (mpp) REVERT: F 259 MET cc_start: 0.8736 (tpt) cc_final: 0.8424 (tpt) REVERT: F 288 MET cc_start: 0.9085 (mmp) cc_final: 0.8737 (mmm) REVERT: F 571 HIS cc_start: 0.9766 (t70) cc_final: 0.9337 (t70) REVERT: F 624 MET cc_start: 0.7618 (ttp) cc_final: 0.7238 (tpp) REVERT: F 634 MET cc_start: 0.9272 (mmp) cc_final: 0.8980 (mmm) REVERT: F 697 MET cc_start: 0.9746 (mmp) cc_final: 0.9517 (mmm) outliers start: 3 outliers final: 0 residues processed: 144 average time/residue: 0.1709 time to fit residues: 37.0977 Evaluate side-chains 114 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 110 optimal weight: 0.0060 chunk 124 optimal weight: 6.9990 chunk 228 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 196 optimal weight: 3.9990 chunk 232 optimal weight: 0.0980 chunk 158 optimal weight: 1.9990 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 37 GLN ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN E 82 GLN D 155 ASN ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 GLN ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.037432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.029383 restraints weight = 218259.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.030304 restraints weight = 138652.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.030962 restraints weight = 98627.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.031434 restraints weight = 76655.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.031778 restraints weight = 63371.147| |-----------------------------------------------------------------------------| r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.5612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 20392 Z= 0.108 Angle : 0.503 7.441 27550 Z= 0.273 Chirality : 0.040 0.223 3030 Planarity : 0.003 0.066 3415 Dihedral : 10.235 165.009 2925 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.76 % Favored : 97.20 % Rotamer: Outliers : 0.14 % Allowed : 1.65 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.17), residues: 2320 helix: 1.43 (0.16), residues: 1075 sheet: 0.51 (0.27), residues: 385 loop : -1.26 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 241 TYR 0.026 0.001 TYR K 59 PHE 0.013 0.001 PHE I 98 TRP 0.021 0.001 TRP F 184 HIS 0.004 0.001 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (20390) covalent geometry : angle 0.50306 / 0.27 (27546) SS BOND : bond 0.00491 / 0.25 ( 2) SS BOND : angle 1.80952 / 0.60 ( 4) hydrogen bonds : bond 0.03203 / 1.97 ( 947) hydrogen bonds : angle 4.78088 / 3.20 ( 2769) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 136 time to evaluate : 0.786 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: J 49 ARG cc_start: 0.9481 (ptp-170) cc_final: 0.9091 (mtm110) REVERT: J 81 LEU cc_start: 0.9677 (tp) cc_final: 0.9275 (tt) REVERT: J 85 PHE cc_start: 0.9178 (m-80) cc_final: 0.8420 (m-80) REVERT: J 88 GLU cc_start: 0.9646 (mm-30) cc_final: 0.9347 (mm-30) REVERT: J 120 PHE cc_start: 0.9724 (t80) cc_final: 0.9447 (t80) REVERT: J 127 PHE cc_start: 0.9717 (t80) cc_final: 0.9107 (t80) REVERT: I 14 MET cc_start: 0.8691 (tpp) cc_final: 0.7944 (tpp) REVERT: I 52 MET cc_start: 0.9445 (mtm) cc_final: 0.9107 (mtt) REVERT: I 63 PHE cc_start: 0.9675 (t80) cc_final: 0.9229 (t80) REVERT: I 64 ASN cc_start: 0.8496 (m110) cc_final: 0.8033 (m-40) REVERT: I 66 ASN cc_start: 0.9413 (m-40) cc_final: 0.9180 (p0) REVERT: I 85 PHE cc_start: 0.9762 (m-80) cc_final: 0.9465 (m-80) REVERT: I 86 TYR cc_start: 0.9320 (m-80) cc_final: 0.8957 (m-80) REVERT: I 104 MET cc_start: 0.9817 (mmt) cc_final: 0.9585 (mmm) REVERT: I 127 PHE cc_start: 0.9803 (t80) cc_final: 0.9466 (t80) REVERT: K 52 MET cc_start: 0.9668 (mtt) cc_final: 0.9433 (tpt) REVERT: K 69 GLN cc_start: 0.8773 (tp40) cc_final: 0.8536 (tp40) REVERT: K 76 ASP cc_start: 0.9546 (m-30) cc_final: 0.9343 (m-30) REVERT: K 85 PHE cc_start: 0.9907 (m-80) cc_final: 0.9573 (m-80) REVERT: K 109 ASP cc_start: 0.9756 (t0) cc_final: 0.9173 (m-30) REVERT: K 112 ILE cc_start: 0.9535 (pt) cc_final: 0.8944 (pt) REVERT: K 120 PHE cc_start: 0.9832 (t80) cc_final: 0.9627 (t80) REVERT: K 123 TYR cc_start: 0.9535 (t80) cc_final: 0.9270 (t80) REVERT: K 127 PHE cc_start: 0.9531 (t80) cc_final: 0.9047 (t80) REVERT: E 40 MET cc_start: 0.9323 (tpt) cc_final: 0.9112 (tpp) REVERT: E 119 MET cc_start: 0.8028 (mmp) cc_final: 0.7636 (mmm) REVERT: E 186 MET cc_start: 0.9371 (mmp) cc_final: 0.8752 (mmp) REVERT: E 327 MET cc_start: 0.9492 (ptp) cc_final: 0.9034 (pmm) REVERT: D 55 MET cc_start: 0.9697 (mmp) cc_final: 0.9412 (mmm) REVERT: D 113 GLN cc_start: 0.9359 (mt0) cc_final: 0.9045 (pt0) REVERT: A 40 GLN cc_start: 0.9222 (tt0) cc_final: 0.8900 (tt0) REVERT: A 55 MET cc_start: 0.9641 (mtm) cc_final: 0.9115 (mtp) REVERT: B 55 MET cc_start: 0.9452 (mmp) cc_final: 0.9238 (mmm) REVERT: H 179 MET cc_start: 0.9663 (tpt) cc_final: 0.9435 (tpp) REVERT: H 208 LEU cc_start: 0.9952 (tt) cc_final: 0.9628 (mt) REVERT: H 258 MET cc_start: 0.7759 (mmt) cc_final: 0.6922 (pmm) REVERT: F 1 MET cc_start: 0.8907 (tpt) cc_final: 0.8176 (tpp) REVERT: F 160 MET cc_start: 0.9729 (mtm) cc_final: 0.9493 (mtp) REVERT: F 252 PHE cc_start: 0.9369 (m-80) cc_final: 0.8833 (m-80) REVERT: F 259 MET cc_start: 0.8825 (tpt) cc_final: 0.8524 (tpp) REVERT: F 288 MET cc_start: 0.8970 (mmp) cc_final: 0.8697 (mmm) REVERT: F 571 HIS cc_start: 0.9748 (t70) cc_final: 0.9298 (t70) REVERT: F 624 MET cc_start: 0.7639 (ttp) cc_final: 0.7239 (tpp) REVERT: F 634 MET cc_start: 0.9279 (mmp) cc_final: 0.8985 (mmm) REVERT: F 697 MET cc_start: 0.9721 (mmp) cc_final: 0.9494 (mmm) outliers start: 3 outliers final: 0 residues processed: 139 average time/residue: 0.1625 time to fit residues: 34.4406 Evaluate side-chains 111 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 10 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 224 optimal weight: 7.9990 chunk 194 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 37 GLN ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 ASN ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN A 128 ASN A 138 GLN ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 276 ASN H 288 ASN ** F 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.035593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.028120 restraints weight = 230286.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.028953 restraints weight = 148063.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.029532 restraints weight = 106632.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.029937 restraints weight = 83714.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.030242 restraints weight = 69596.130| |-----------------------------------------------------------------------------| r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.6396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20392 Z= 0.270 Angle : 0.673 8.670 27550 Z= 0.367 Chirality : 0.042 0.169 3030 Planarity : 0.005 0.081 3415 Dihedral : 10.758 176.837 2925 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 21.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.91 % Favored : 95.04 % Rotamer: Outliers : 0.05 % Allowed : 1.69 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.17), residues: 2320 helix: 0.90 (0.16), residues: 1078 sheet: 0.39 (0.28), residues: 367 loop : -1.44 (0.19), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG I 91 TYR 0.024 0.002 TYR J 123 PHE 0.023 0.002 PHE F 565 TRP 0.057 0.003 TRP F 184 HIS 0.009 0.002 HIS F 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.27 (20390) covalent geometry : angle 0.67314 / 0.37 (27546) SS BOND : bond 0.01225 / 0.61 ( 2) SS BOND : angle 1.72606 / 0.58 ( 4) hydrogen bonds : bond 0.04104 / 2.48 ( 947) hydrogen bonds : angle 5.29875 / 3.55 ( 2769) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.718 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: J 49 ARG cc_start: 0.9492 (ptp-170) cc_final: 0.9089 (mtm110) REVERT: J 88 GLU cc_start: 0.9755 (mm-30) cc_final: 0.9540 (mm-30) REVERT: J 120 PHE cc_start: 0.9769 (t80) cc_final: 0.9511 (t80) REVERT: J 127 PHE cc_start: 0.9784 (t80) cc_final: 0.9267 (t80) REVERT: I 14 MET cc_start: 0.8629 (tpp) cc_final: 0.7987 (tpp) REVERT: I 52 MET cc_start: 0.9552 (mtm) cc_final: 0.9234 (mtp) REVERT: I 63 PHE cc_start: 0.9619 (t80) cc_final: 0.9059 (t80) REVERT: I 64 ASN cc_start: 0.8496 (m110) cc_final: 0.8003 (m-40) REVERT: I 66 ASN cc_start: 0.9460 (m-40) cc_final: 0.9141 (p0) REVERT: I 85 PHE cc_start: 0.9692 (m-80) cc_final: 0.9335 (m-80) REVERT: I 86 TYR cc_start: 0.9316 (m-80) cc_final: 0.8952 (m-80) REVERT: I 104 MET cc_start: 0.9822 (mmt) cc_final: 0.9619 (mmm) REVERT: I 127 PHE cc_start: 0.9814 (t80) cc_final: 0.9469 (t80) REVERT: K 52 MET cc_start: 0.9727 (mtt) cc_final: 0.9174 (tpt) REVERT: K 85 PHE cc_start: 0.9895 (m-80) cc_final: 0.9574 (m-80) REVERT: K 109 ASP cc_start: 0.9769 (t0) cc_final: 0.9167 (m-30) REVERT: K 120 PHE cc_start: 0.9836 (t80) cc_final: 0.9577 (t80) REVERT: K 127 PHE cc_start: 0.9364 (t80) cc_final: 0.8927 (t80) REVERT: E 119 MET cc_start: 0.8071 (mmp) cc_final: 0.7815 (mmm) REVERT: E 186 MET cc_start: 0.9415 (mmp) cc_final: 0.8775 (mmp) REVERT: D 55 MET cc_start: 0.9620 (mmp) cc_final: 0.9350 (mmm) REVERT: D 113 GLN cc_start: 0.9466 (mt0) cc_final: 0.9115 (pt0) REVERT: A 55 MET cc_start: 0.9624 (mtm) cc_final: 0.9287 (mtp) REVERT: B 115 ASP cc_start: 0.9320 (t0) cc_final: 0.9053 (t0) REVERT: H 258 MET cc_start: 0.7309 (mmt) cc_final: 0.6561 (pmm) REVERT: F 1 MET cc_start: 0.8565 (tpt) cc_final: 0.7492 (tpp) REVERT: F 160 MET cc_start: 0.9724 (mtm) cc_final: 0.9428 (mtm) REVERT: F 163 MET cc_start: 0.9885 (ptp) cc_final: 0.9672 (mpp) REVERT: F 252 PHE cc_start: 0.9728 (m-10) cc_final: 0.9294 (m-80) REVERT: F 288 MET cc_start: 0.9026 (mmp) cc_final: 0.8803 (mmm) REVERT: F 571 HIS cc_start: 0.9756 (t70) cc_final: 0.9386 (t-90) REVERT: F 634 MET cc_start: 0.9236 (mmp) cc_final: 0.8924 (mmm) REVERT: F 697 MET cc_start: 0.9752 (mmp) cc_final: 0.9531 (mmm) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.1633 time to fit residues: 32.6365 Evaluate side-chains 103 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 94 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 176 optimal weight: 9.9990 chunk 178 optimal weight: 0.8980 chunk 184 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 98 optimal weight: 0.1980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 37 GLN ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 ASN A 138 GLN ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN H 288 ASN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.036534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.028619 restraints weight = 224480.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.029540 restraints weight = 140634.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.030187 restraints weight = 99909.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.030660 restraints weight = 77407.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.031001 restraints weight = 63583.196| |-----------------------------------------------------------------------------| r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.6358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20392 Z= 0.107 Angle : 0.530 7.767 27550 Z= 0.287 Chirality : 0.041 0.174 3030 Planarity : 0.003 0.037 3415 Dihedral : 10.458 165.889 2925 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.05 % Allowed : 0.71 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.17), residues: 2320 helix: 1.24 (0.16), residues: 1078 sheet: 0.32 (0.27), residues: 388 loop : -1.25 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 91 TYR 0.034 0.001 TYR J 123 PHE 0.023 0.001 PHE I 98 TRP 0.052 0.002 TRP F 184 HIS 0.005 0.001 HIS I 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 (20390) covalent geometry : angle 0.52965 / 0.29 (27546) SS BOND : bond 0.00553 / 0.28 ( 2) SS BOND : angle 2.03402 / 0.68 ( 4) hydrogen bonds : bond 0.03280 / 2.01 ( 947) hydrogen bonds : angle 4.88586 / 3.27 ( 2769) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 0.792 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: J 49 ARG cc_start: 0.9470 (ptp-170) cc_final: 0.9055 (mtm110) REVERT: J 87 TYR cc_start: 0.9347 (t80) cc_final: 0.9075 (t80) REVERT: J 88 GLU cc_start: 0.9771 (mm-30) cc_final: 0.9465 (mm-30) REVERT: J 91 ARG cc_start: 0.9283 (tpm170) cc_final: 0.8998 (tpp-160) REVERT: J 120 PHE cc_start: 0.9740 (t80) cc_final: 0.9445 (t80) REVERT: J 127 PHE cc_start: 0.9729 (t80) cc_final: 0.9166 (t80) REVERT: I 14 MET cc_start: 0.8568 (tpp) cc_final: 0.7957 (tpp) REVERT: I 52 MET cc_start: 0.9434 (mtm) cc_final: 0.9103 (mtt) REVERT: I 63 PHE cc_start: 0.9583 (t80) cc_final: 0.8995 (t80) REVERT: I 64 ASN cc_start: 0.8460 (m110) cc_final: 0.7993 (m-40) REVERT: I 66 ASN cc_start: 0.9487 (m-40) cc_final: 0.9216 (p0) REVERT: I 85 PHE cc_start: 0.9777 (m-80) cc_final: 0.9448 (m-80) REVERT: I 86 TYR cc_start: 0.9310 (m-80) cc_final: 0.8897 (m-80) REVERT: I 109 ASP cc_start: 0.9699 (t0) cc_final: 0.9447 (m-30) REVERT: I 127 PHE cc_start: 0.9811 (t80) cc_final: 0.9527 (t80) REVERT: K 52 MET cc_start: 0.9728 (mtt) cc_final: 0.9182 (tpt) REVERT: K 69 GLN cc_start: 0.9316 (tp40) cc_final: 0.8985 (tm-30) REVERT: K 76 ASP cc_start: 0.9540 (m-30) cc_final: 0.9330 (m-30) REVERT: K 85 PHE cc_start: 0.9894 (m-80) cc_final: 0.9578 (m-80) REVERT: K 109 ASP cc_start: 0.9767 (t0) cc_final: 0.9255 (m-30) REVERT: K 120 PHE cc_start: 0.9773 (t80) cc_final: 0.9534 (t80) REVERT: K 123 TYR cc_start: 0.9563 (t80) cc_final: 0.9270 (t80) REVERT: K 127 PHE cc_start: 0.9552 (t80) cc_final: 0.9102 (t80) REVERT: E 119 MET cc_start: 0.8087 (mmp) cc_final: 0.7797 (mmm) REVERT: E 186 MET cc_start: 0.9370 (mmp) cc_final: 0.8739 (mmp) REVERT: E 327 MET cc_start: 0.9340 (ptp) cc_final: 0.8676 (pmm) REVERT: D 55 MET cc_start: 0.9722 (mmp) cc_final: 0.9475 (mmm) REVERT: D 113 GLN cc_start: 0.9442 (mt0) cc_final: 0.9109 (pt0) REVERT: C 17 LEU cc_start: 0.9794 (tp) cc_final: 0.9127 (mm) REVERT: C 40 GLN cc_start: 0.9657 (tt0) cc_final: 0.9307 (tt0) REVERT: A 40 GLN cc_start: 0.9273 (tt0) cc_final: 0.8942 (tt0) REVERT: A 55 MET cc_start: 0.9581 (mtm) cc_final: 0.9058 (mtp) REVERT: B 55 MET cc_start: 0.9442 (mmp) cc_final: 0.9223 (mmm) REVERT: B 115 ASP cc_start: 0.9168 (t0) cc_final: 0.8850 (t0) REVERT: H 10 LEU cc_start: 0.9813 (mt) cc_final: 0.9553 (mp) REVERT: H 179 MET cc_start: 0.9676 (mmp) cc_final: 0.9231 (mmm) REVERT: H 208 LEU cc_start: 0.9945 (tt) cc_final: 0.9622 (mt) REVERT: H 258 MET cc_start: 0.7862 (mmt) cc_final: 0.7135 (pmm) REVERT: F 1 MET cc_start: 0.8648 (tpt) cc_final: 0.7584 (tpp) REVERT: F 160 MET cc_start: 0.9707 (mtm) cc_final: 0.9495 (mtp) REVERT: F 259 MET cc_start: 0.9004 (tpt) cc_final: 0.8589 (tpt) REVERT: F 318 LEU cc_start: 0.9726 (tp) cc_final: 0.9239 (tp) REVERT: F 571 HIS cc_start: 0.9750 (t70) cc_final: 0.9363 (t-90) REVERT: F 634 MET cc_start: 0.9189 (mmp) cc_final: 0.8927 (mmm) REVERT: F 697 MET cc_start: 0.9698 (mmp) cc_final: 0.9487 (mmm) outliers start: 1 outliers final: 0 residues processed: 137 average time/residue: 0.1664 time to fit residues: 34.8465 Evaluate side-chains 107 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 84 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 215 optimal weight: 10.0000 chunk 200 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 233 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 GLN ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 703 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 = 0.3005 r_free = 0.3005 target = 0.036464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.028848 restraints weight = 228529.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.029705 restraints weight = 145748.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.030320 restraints weight = 104407.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.030758 restraints weight = 81443.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.031079 restraints weight = 67493.232| |-----------------------------------------------------------------------------| r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.6592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20392 Z= 0.153 Angle : 0.547 10.626 27550 Z= 0.296 Chirality : 0.040 0.162 3030 Planarity : 0.003 0.042 3415 Dihedral : 10.497 166.717 2925 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.05 % Allowed : 0.38 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.17), residues: 2320 helix: 1.29 (0.16), residues: 1077 sheet: 0.27 (0.27), residues: 393 loop : -1.22 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 49 TYR 0.024 0.001 TYR J 123 PHE 0.020 0.001 PHE I 98 TRP 0.048 0.002 TRP F 184 HIS 0.005 0.001 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (20390) covalent geometry : angle 0.54666 / 0.30 (27546) SS BOND : bond 0.00700 / 0.35 ( 2) SS BOND : angle 1.50450 / 0.50 ( 4) hydrogen bonds : bond 0.03386 / 2.06 ( 947) hydrogen bonds : angle 4.93846 / 3.29 ( 2769) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 0.849 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: J 49 ARG cc_start: 0.9466 (ptp-170) cc_final: 0.9063 (mtm110) REVERT: J 88 GLU cc_start: 0.9771 (mm-30) cc_final: 0.9513 (mm-30) REVERT: J 120 PHE cc_start: 0.9783 (t80) cc_final: 0.9528 (t80) REVERT: J 127 PHE cc_start: 0.9758 (t80) cc_final: 0.9190 (t80) REVERT: I 14 MET cc_start: 0.8594 (tpp) cc_final: 0.7958 (tpp) REVERT: I 52 MET cc_start: 0.9452 (mtm) cc_final: 0.9102 (mtt) REVERT: I 63 PHE cc_start: 0.9668 (t80) cc_final: 0.9112 (t80) REVERT: I 64 ASN cc_start: 0.8427 (m110) cc_final: 0.8020 (m-40) REVERT: I 66 ASN cc_start: 0.9479 (m-40) cc_final: 0.9213 (p0) REVERT: I 85 PHE cc_start: 0.9731 (m-80) cc_final: 0.9299 (m-80) REVERT: I 86 TYR cc_start: 0.9297 (m-80) cc_final: 0.8941 (m-80) REVERT: I 109 ASP cc_start: 0.9720 (t0) cc_final: 0.9412 (m-30) REVERT: I 127 PHE cc_start: 0.9832 (t80) cc_final: 0.9534 (t80) REVERT: K 52 MET cc_start: 0.9699 (mtt) cc_final: 0.9140 (tpt) REVERT: K 76 ASP cc_start: 0.9536 (m-30) cc_final: 0.9318 (m-30) REVERT: K 85 PHE cc_start: 0.9895 (m-80) cc_final: 0.9594 (m-80) REVERT: K 109 ASP cc_start: 0.9777 (t0) cc_final: 0.9263 (m-30) REVERT: K 120 PHE cc_start: 0.9784 (t80) cc_final: 0.9551 (t80) REVERT: K 123 TYR cc_start: 0.9544 (t80) cc_final: 0.9241 (t80) REVERT: K 127 PHE cc_start: 0.9499 (t80) cc_final: 0.8977 (t80) REVERT: E 186 MET cc_start: 0.9412 (mmp) cc_final: 0.8783 (mmp) REVERT: E 327 MET cc_start: 0.9303 (ptp) cc_final: 0.9053 (pmm) REVERT: D 55 MET cc_start: 0.9713 (mmp) cc_final: 0.9478 (mmm) REVERT: D 113 GLN cc_start: 0.9460 (mt0) cc_final: 0.9097 (pt0) REVERT: C 17 LEU cc_start: 0.9860 (tp) cc_final: 0.9381 (mm) REVERT: A 40 GLN cc_start: 0.9339 (tt0) cc_final: 0.9059 (tt0) REVERT: A 55 MET cc_start: 0.9610 (mtm) cc_final: 0.9161 (mtp) REVERT: B 55 MET cc_start: 0.9479 (mmp) cc_final: 0.9269 (mmm) REVERT: B 115 ASP cc_start: 0.9230 (t0) cc_final: 0.8935 (t0) REVERT: H 179 MET cc_start: 0.9764 (mmp) cc_final: 0.9268 (mmm) REVERT: H 208 LEU cc_start: 0.9948 (tt) cc_final: 0.9637 (mt) REVERT: H 258 MET cc_start: 0.7898 (mmt) cc_final: 0.6991 (pmm) REVERT: F 160 MET cc_start: 0.9712 (mtm) cc_final: 0.9425 (mpp) REVERT: F 163 MET cc_start: 0.9884 (ptp) cc_final: 0.9665 (mpp) REVERT: F 259 MET cc_start: 0.9064 (tpt) cc_final: 0.8680 (tpt) REVERT: F 288 MET cc_start: 0.9161 (mmp) cc_final: 0.8867 (mmm) REVERT: F 452 MET cc_start: 0.8181 (mmp) cc_final: 0.7935 (mmm) REVERT: F 571 HIS cc_start: 0.9761 (t70) cc_final: 0.9394 (t-90) REVERT: F 634 MET cc_start: 0.9183 (mmp) cc_final: 0.8928 (mmm) REVERT: F 697 MET cc_start: 0.9705 (mmp) cc_final: 0.9479 (mmm) outliers start: 1 outliers final: 0 residues processed: 129 average time/residue: 0.1642 time to fit residues: 32.5473 Evaluate side-chains 105 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 133 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 228 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 211 optimal weight: 0.9990 chunk 206 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 37 GLN ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 ASN A 138 GLN ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 HIS ** F 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.035403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.027790 restraints weight = 230987.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.028660 restraints weight = 145668.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.029288 restraints weight = 103722.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.029739 restraints weight = 80455.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.030058 restraints weight = 66153.512| |-----------------------------------------------------------------------------| r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.6978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20392 Z= 0.157 Angle : 0.554 8.625 27550 Z= 0.300 Chirality : 0.040 0.150 3030 Planarity : 0.003 0.039 3415 Dihedral : 10.616 166.663 2925 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.05 % Allowed : 0.33 % Favored : 99.62 % 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: 0.28 (0.17), residues: 2320 helix: 1.25 (0.16), residues: 1075 sheet: 0.40 (0.28), residues: 370 loop : -1.25 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 121 TYR 0.026 0.001 TYR K 59 PHE 0.021 0.001 PHE I 98 TRP 0.046 0.002 TRP F 184 HIS 0.005 0.001 HIS E 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 (20390) covalent geometry : angle 0.55332 / 0.30 (27546) SS BOND : bond 0.00680 / 0.34 ( 2) SS BOND : angle 1.64617 / 0.55 ( 4) hydrogen bonds : bond 0.03387 / 2.06 ( 947) hydrogen bonds : angle 4.96869 / 3.32 ( 2769) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4640 Ramachandran restraints generated. 2320 Oldfield, 0 Emsley, 2320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.815 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: J 49 ARG cc_start: 0.9454 (ptp-170) cc_final: 0.9041 (mtm110) REVERT: J 88 GLU cc_start: 0.9859 (mm-30) cc_final: 0.9568 (mm-30) REVERT: J 91 ARG cc_start: 0.8858 (tpm170) cc_final: 0.8589 (tpp-160) REVERT: J 120 PHE cc_start: 0.9761 (t80) cc_final: 0.9504 (t80) REVERT: J 127 PHE cc_start: 0.9725 (t80) cc_final: 0.9125 (t80) REVERT: I 14 MET cc_start: 0.8568 (tpp) cc_final: 0.8012 (tpp) REVERT: I 52 MET cc_start: 0.9425 (mtm) cc_final: 0.9081 (mtt) REVERT: I 63 PHE cc_start: 0.9639 (t80) cc_final: 0.9176 (t80) REVERT: I 64 ASN cc_start: 0.8501 (m110) cc_final: 0.8087 (m110) REVERT: I 66 ASN cc_start: 0.9498 (m-40) cc_final: 0.9237 (p0) REVERT: I 85 PHE cc_start: 0.9715 (m-80) cc_final: 0.9223 (m-80) REVERT: I 86 TYR cc_start: 0.9287 (m-80) cc_final: 0.8914 (m-80) REVERT: I 104 MET cc_start: 0.9853 (mmt) cc_final: 0.9601 (mmm) REVERT: I 109 ASP cc_start: 0.9707 (t0) cc_final: 0.9402 (m-30) REVERT: I 127 PHE cc_start: 0.9832 (t80) cc_final: 0.9481 (t80) REVERT: K 52 MET cc_start: 0.9686 (mtt) cc_final: 0.9406 (tpt) REVERT: K 76 ASP cc_start: 0.9524 (m-30) cc_final: 0.9312 (m-30) REVERT: K 85 PHE cc_start: 0.9899 (m-80) cc_final: 0.9661 (m-80) REVERT: K 109 ASP cc_start: 0.9780 (t0) cc_final: 0.9272 (m-30) REVERT: K 120 PHE cc_start: 0.9765 (t80) cc_final: 0.9545 (t80) REVERT: K 123 TYR cc_start: 0.9585 (t80) cc_final: 0.9301 (t80) REVERT: K 127 PHE cc_start: 0.9475 (t80) cc_final: 0.8944 (t80) REVERT: E 119 MET cc_start: 0.8234 (mmp) cc_final: 0.6661 (mmm) REVERT: E 186 MET cc_start: 0.9356 (mmp) cc_final: 0.8808 (mmp) REVERT: E 327 MET cc_start: 0.9194 (ptp) cc_final: 0.8645 (pmm) REVERT: D 55 MET cc_start: 0.9708 (mmp) cc_final: 0.9489 (mmm) REVERT: D 113 GLN cc_start: 0.9436 (mt0) cc_final: 0.9122 (pt0) REVERT: A 40 GLN cc_start: 0.9380 (tt0) cc_final: 0.9095 (tt0) REVERT: A 55 MET cc_start: 0.9672 (mtm) cc_final: 0.9322 (mtp) REVERT: B 115 ASP cc_start: 0.9250 (t0) cc_final: 0.8972 (t0) REVERT: H 179 MET cc_start: 0.9741 (mmp) cc_final: 0.9283 (mmm) REVERT: H 208 LEU cc_start: 0.9944 (tt) cc_final: 0.9631 (mt) REVERT: H 258 MET cc_start: 0.8014 (mmt) cc_final: 0.7221 (pmm) REVERT: F 1 MET cc_start: 0.8631 (tpt) cc_final: 0.7445 (tpp) REVERT: F 160 MET cc_start: 0.9710 (mtm) cc_final: 0.9386 (mpp) REVERT: F 163 MET cc_start: 0.9865 (ptp) cc_final: 0.9644 (mpp) REVERT: F 207 TYR cc_start: 0.8748 (t80) cc_final: 0.7970 (t80) REVERT: F 259 MET cc_start: 0.9171 (tpt) cc_final: 0.8724 (tpt) REVERT: F 288 MET cc_start: 0.9113 (mmp) cc_final: 0.8767 (mmm) REVERT: F 452 MET cc_start: 0.8264 (mmp) cc_final: 0.8056 (mmm) REVERT: F 571 HIS cc_start: 0.9767 (t70) cc_final: 0.9394 (t-90) REVERT: F 634 MET cc_start: 0.9117 (mmp) cc_final: 0.8906 (mmm) outliers start: 1 outliers final: 0 residues processed: 128 average time/residue: 0.1670 time to fit residues: 32.6009 Evaluate side-chains 105 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 51 optimal weight: 0.7980 chunk 234 optimal weight: 7.9990 chunk 191 optimal weight: 7.9990 chunk 230 optimal weight: 10.0000 chunk 91 optimal weight: 0.7980 chunk 193 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 201 optimal weight: 3.9990 chunk 232 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 37 GLN ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN E 254 ASN D 155 ASN ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 GLN ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 549 ASN ** F 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.036019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.028424 restraints weight = 232419.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.029315 restraints weight = 145651.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.029963 restraints weight = 103252.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.030423 restraints weight = 79570.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.030754 restraints weight = 65297.026| |-----------------------------------------------------------------------------| r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.7028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20392 Z= 0.117 Angle : 0.515 8.540 27550 Z= 0.279 Chirality : 0.039 0.148 3030 Planarity : 0.003 0.037 3415 Dihedral : 10.492 162.075 2925 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.05 % Allowed : 0.19 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.18), residues: 2320 helix: 1.39 (0.16), residues: 1078 sheet: 0.32 (0.28), residues: 369 loop : -1.22 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 91 TYR 0.020 0.001 TYR K 59 PHE 0.035 0.001 PHE H 268 TRP 0.044 0.002 TRP F 184 HIS 0.004 0.001 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 (20390) covalent geometry : angle 0.51423 / 0.28 (27546) SS BOND : bond 0.00532 / 0.27 ( 2) SS BOND : angle 1.73921 / 0.58 ( 4) hydrogen bonds : bond 0.03176 / 1.93 ( 947) hydrogen bonds : angle 4.80108 / 3.21 ( 2769) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2852.49 seconds wall clock time: 50 minutes 56.83 seconds (3056.83 seconds total)