Starting phenix.real_space_refine on Sun Sep 13 02:45:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7uzz_26923/09_2026/7uzz_26923.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uzz_26923/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7uzz_26923/09_2026/7uzz_26923.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uzz_26923/09_2026/7uzz_26923.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7uzz_26923/09_2026/7uzz_26923.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7uzz_26923/09_2026/7uzz_26923.cif" model { file = "/net/cci-nas-00/data/ceres_data/7uzz_26923/09_2026/7uzz_26923.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uzz_26923/09_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-2.2.1-6174/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: {'RNAv2': 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: 4.20, 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: 1.84 Conformation dependent library (CDL) restraints added in 835.6 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: 2.27 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: 3.55 Time building geometry restraints manager: 2.42 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: 25568 1.95 - 3.91: 1816 3.91 - 5.86: 138 5.86 - 7.82: 20 7.82 - 9.77: 4 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=" 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 angle pdb=" N PHE I 16 " pdb=" CA PHE I 16 " pdb=" C PHE I 16 " ideal model delta sigma weight residual 113.18 107.49 5.69 1.21e+00 6.83e-01 2.21e+01 ... (remaining 27541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.98: 11223 15.98 - 31.97: 684 31.97 - 47.95: 193 47.95 - 63.93: 79 63.93 - 79.92: 30 Dihedral angle restraints: 12209 sinusoidal: 5272 harmonic: 6937 Sorted by residual: dihedral pdb=" C4' A G 27 " pdb=" C3' A G 27 " pdb=" C2' A G 27 " pdb=" C1' A G 27 " ideal model delta sinusoidal sigma weight residual 36.35 -43.57 79.92 1 3.10e+00 1.04e-01 8.24e+02 dihedral pdb=" C4' A G 9 " pdb=" C3' A G 9 " pdb=" C2' A G 9 " pdb=" C1' A G 9 " ideal model delta sinusoidal sigma weight residual 36.34 -39.46 75.81 1 3.10e+00 1.04e-01 7.54e+02 dihedral pdb=" C4' G G 3 " pdb=" C3' G G 3 " pdb=" C2' G G 3 " pdb=" C1' G G 3 " ideal model delta sinusoidal sigma weight residual 36.35 -39.09 75.44 1 3.10e+00 1.04e-01 7.48e+02 ... (remaining 12206 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 2738 0.110 - 0.220: 263 0.220 - 0.330: 26 0.330 - 0.439: 0 0.439 - 0.549: 3 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 2.17 -2.72 -0.55 2.00e-01 2.50e+01 7.54e+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 2.17 -2.72 -0.55 2.00e-01 2.50e+01 7.53e+00 chirality pdb=" P G G 11 " pdb=" OP1 G G 11 " pdb=" OP2 G G 11 " pdb=" O5' G G 11 " both_signs ideal model delta sigma weight residual True 2.17 -2.67 -0.50 2.00e-01 2.50e+01 6.19e+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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.300 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.960 ------------------------------------------------------------------------------- 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= 0.573 Angle : 1.092 70.431 27550 Z= 0.709 Chirality : 0.068 0.549 3030 Planarity : 0.005 0.080 3415 Dihedral : 12.937 79.916 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 0.00850 / 0.57 (20390) covalent geometry : angle 1.00467 / 0.68 (27546) SS BOND : bond 0.18928 / 9.46 ( 2) SS BOND : angle 35.53686 / 11.85 ( 4) hydrogen bonds : bond 0.15448 / 8.28 ( 947) hydrogen bonds : angle 6.96333 / 4.22 ( 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 : 0.777 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: 0.1896 time to fit residues: 99.3444 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 : 0.737 ------------------------------------------------------------------------------- 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: 7.9990 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 D 155 ASN 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 17 HIS ** 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 685 GLN ** F 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 722 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.040964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.032193 restraints weight = 205299.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.033116 restraints weight = 136578.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.033786 restraints weight = 100386.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.034256 restraints weight = 79997.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.034628 restraints weight = 67372.935| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20392 Z= 0.182 Angle : 0.768 18.421 27550 Z= 0.378 Chirality : 0.066 1.184 3030 Planarity : 0.004 0.053 3415 Dihedral : 9.509 125.590 2925 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.19 % Favored : 96.77 % Rotamer: Outliers : 0.24 % Allowed : 1.74 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.17), residues: 2320 helix: 1.11 (0.15), residues: 1101 sheet: 0.46 (0.27), residues: 373 loop : -1.59 (0.19), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 78 TYR 0.035 0.002 TYR K 59 PHE 0.029 0.002 PHE F 589 TRP 0.025 0.002 TRP F 184 HIS 0.010 0.001 HIS D 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.18 (20390) covalent geometry : angle 0.76804 / 0.38 (27546) SS BOND : bond 0.00600 / 0.30 ( 2) SS BOND : angle 2.12470 / 0.71 ( 4) hydrogen bonds : bond 0.04279 / 2.35 ( 947) hydrogen bonds : angle 5.26846 / 3.27 ( 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 208 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 203 time to evaluate : 0.532 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: J 81 LEU cc_start: 0.9639 (tp) cc_final: 0.9324 (tt) REVERT: J 85 PHE cc_start: 0.9210 (m-80) cc_final: 0.8549 (m-80) REVERT: J 120 PHE cc_start: 0.9674 (t80) cc_final: 0.9463 (t80) REVERT: J 127 PHE cc_start: 0.9714 (t80) cc_final: 0.9202 (t80) REVERT: I 14 MET cc_start: 0.8827 (tpp) cc_final: 0.8437 (tpp) REVERT: I 27 ASN cc_start: 0.7746 (t0) cc_final: 0.7485 (t0) REVERT: I 52 MET cc_start: 0.9445 (tpt) cc_final: 0.9208 (tpt) REVERT: I 63 PHE cc_start: 0.9737 (t80) cc_final: 0.9463 (t80) REVERT: I 66 ASN cc_start: 0.9540 (m-40) cc_final: 0.9201 (p0) REVERT: I 80 TYR cc_start: 0.9064 (m-80) cc_final: 0.8532 (m-80) REVERT: I 86 TYR cc_start: 0.9399 (m-80) cc_final: 0.9098 (m-80) REVERT: I 109 ASP cc_start: 0.9276 (m-30) cc_final: 0.9036 (m-30) REVERT: K 52 MET cc_start: 0.9697 (mtt) cc_final: 0.9082 (tpt) REVERT: K 64 ASN cc_start: 0.9301 (m-40) cc_final: 0.9086 (m110) REVERT: K 69 GLN cc_start: 0.9062 (tp40) cc_final: 0.8611 (tm-30) REVERT: K 85 PHE cc_start: 0.9920 (m-80) cc_final: 0.9510 (m-80) REVERT: K 109 ASP cc_start: 0.9728 (t0) cc_final: 0.9283 (m-30) REVERT: K 120 PHE cc_start: 0.9866 (t80) cc_final: 0.9642 (t80) REVERT: K 127 PHE cc_start: 0.9597 (t80) cc_final: 0.9030 (t80) REVERT: E 186 MET cc_start: 0.8614 (mmp) cc_final: 0.7980 (mmp) REVERT: E 260 LEU cc_start: 0.8978 (mm) cc_final: 0.8500 (mm) REVERT: D 88 LYS cc_start: 0.9206 (tttt) cc_final: 0.8961 (ptpt) REVERT: D 113 GLN cc_start: 0.9336 (mt0) cc_final: 0.8925 (pt0) REVERT: D 181 LEU cc_start: 0.9507 (pp) cc_final: 0.8914 (mp) REVERT: C 17 LEU cc_start: 0.9848 (tt) cc_final: 0.9213 (mm) REVERT: C 40 GLN cc_start: 0.9486 (tt0) cc_final: 0.8383 (pt0) REVERT: A 55 MET cc_start: 0.9640 (mtm) cc_final: 0.9163 (mtp) REVERT: A 82 LEU cc_start: 0.9205 (mt) cc_final: 0.8842 (mt) REVERT: B 55 MET cc_start: 0.9533 (mmp) cc_final: 0.9314 (mmp) REVERT: B 96 LEU cc_start: 0.9764 (tp) cc_final: 0.8948 (pp) REVERT: B 115 ASP cc_start: 0.9112 (t0) cc_final: 0.8871 (t0) REVERT: H 28 MET cc_start: 0.9322 (ttm) cc_final: 0.8751 (pmm) REVERT: H 208 LEU cc_start: 0.9950 (tt) cc_final: 0.9611 (mt) REVERT: F 257 MET cc_start: 0.9711 (mpp) cc_final: 0.9374 (mpp) REVERT: F 363 MET cc_start: 0.8862 (mtp) cc_final: 0.8466 (mmm) REVERT: F 495 TRP cc_start: 0.8096 (m-90) cc_final: 0.6979 (m100) REVERT: F 535 ASN cc_start: 0.9289 (t0) cc_final: 0.8962 (t0) REVERT: F 634 MET cc_start: 0.8867 (mmp) cc_final: 0.8362 (mmm) REVERT: F 697 MET cc_start: 0.9796 (mmp) cc_final: 0.9542 (mmm) outliers start: 5 outliers final: 2 residues processed: 208 average time/residue: 0.1600 time to fit residues: 49.2430 Evaluate side-chains 150 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 148 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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: 0.9990 chunk 188 optimal weight: 0.0050 chunk 176 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 230 optimal weight: 10.0000 chunk 148 optimal weight: 3.9990 chunk 135 optimal weight: 7.9990 chunk 211 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 overall best weight: 3.8002 ------------------------------------------------------------------------------- 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 D 114 ASN C 114 ASN ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 GLN B 138 GLN B 193 GLN ** H 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 HIS H 129 GLN F 2 ASN F 33 HIS ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 375 ASN ** F 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.038312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.030336 restraints weight = 228907.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.031184 restraints weight = 149576.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.031811 restraints weight = 109049.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.032266 restraints weight = 85566.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.032596 restraints weight = 71374.111| |-----------------------------------------------------------------------------| r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4525 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= 0.265 Angle : 0.731 11.855 27550 Z= 0.378 Chirality : 0.051 0.593 3030 Planarity : 0.004 0.044 3415 Dihedral : 9.497 138.028 2925 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.22 % Favored : 95.73 % Rotamer: Outliers : 0.24 % Allowed : 2.40 % Favored : 97.37 % 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: -0.10 (0.17), residues: 2320 helix: 1.03 (0.15), residues: 1089 sheet: 0.22 (0.26), residues: 399 loop : -1.68 (0.19), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 78 TYR 0.033 0.002 TYR J 87 PHE 0.017 0.002 PHE F 589 TRP 0.017 0.002 TRP F 184 HIS 0.009 0.002 HIS H 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.26 (20390) covalent geometry : angle 0.73041 / 0.38 (27546) SS BOND : bond 0.00941 / 0.47 ( 2) SS BOND : angle 1.80187 / 0.60 ( 4) hydrogen bonds : bond 0.04225 / 2.34 ( 947) hydrogen bonds : angle 5.26460 / 3.28 ( 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 154 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 149 time to evaluate : 0.833 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: J 49 ARG cc_start: 0.9539 (ptp-170) cc_final: 0.8900 (ptp-110) REVERT: J 81 LEU cc_start: 0.9688 (tp) cc_final: 0.9295 (tt) REVERT: J 85 PHE cc_start: 0.9245 (m-80) cc_final: 0.8464 (m-80) REVERT: J 127 PHE cc_start: 0.9764 (t80) cc_final: 0.9402 (t80) REVERT: I 14 MET cc_start: 0.8451 (tpp) cc_final: 0.7751 (tpp) REVERT: I 52 MET cc_start: 0.8620 (tpt) cc_final: 0.8134 (tpt) REVERT: I 64 ASN cc_start: 0.8198 (m110) cc_final: 0.7605 (m110) REVERT: I 66 ASN cc_start: 0.9324 (m-40) cc_final: 0.8992 (p0) REVERT: I 80 TYR cc_start: 0.9159 (m-80) cc_final: 0.8576 (m-80) REVERT: I 86 TYR cc_start: 0.9361 (m-80) cc_final: 0.9013 (m-80) REVERT: I 104 MET cc_start: 0.9879 (mmt) cc_final: 0.9610 (mmm) REVERT: I 109 ASP cc_start: 0.9066 (m-30) cc_final: 0.8787 (m-30) REVERT: I 127 PHE cc_start: 0.9775 (t80) cc_final: 0.9367 (t80) REVERT: K 52 MET cc_start: 0.9641 (mtt) cc_final: 0.9154 (tpt) REVERT: K 54 GLN cc_start: 0.9630 (OUTLIER) cc_final: 0.9373 (pm20) REVERT: K 76 ASP cc_start: 0.9581 (m-30) cc_final: 0.9375 (m-30) REVERT: K 85 PHE cc_start: 0.9907 (m-80) cc_final: 0.9528 (m-80) REVERT: K 109 ASP cc_start: 0.9768 (t0) cc_final: 0.9081 (m-30) REVERT: K 112 ILE cc_start: 0.9549 (pt) cc_final: 0.8920 (pt) REVERT: K 123 TYR cc_start: 0.9560 (t80) cc_final: 0.9289 (t80) REVERT: K 127 PHE cc_start: 0.9489 (t80) cc_final: 0.8937 (t80) REVERT: E 40 MET cc_start: 0.9367 (tpt) cc_final: 0.9164 (tpp) REVERT: E 186 MET cc_start: 0.8708 (mmp) cc_final: 0.8060 (mmp) REVERT: E 300 MET cc_start: 0.2162 (mtt) cc_final: 0.1882 (mtt) REVERT: D 55 MET cc_start: 0.9600 (mmp) cc_final: 0.9229 (mmm) REVERT: C 17 LEU cc_start: 0.9905 (tt) cc_final: 0.9332 (mm) REVERT: C 72 HIS cc_start: 0.9189 (t70) cc_final: 0.8949 (t70) REVERT: A 55 MET cc_start: 0.9537 (mtm) cc_final: 0.9149 (mtp) REVERT: H 28 MET cc_start: 0.9417 (ttm) cc_final: 0.8852 (pmm) REVERT: H 179 MET cc_start: 0.9723 (tpt) cc_final: 0.9414 (tpp) REVERT: F 1 MET cc_start: 0.8472 (tpt) cc_final: 0.7689 (tpp) REVERT: F 8 MET cc_start: 0.9710 (mtm) cc_final: 0.9353 (ptt) REVERT: F 160 MET cc_start: 0.9683 (mtt) cc_final: 0.9429 (mmt) REVERT: F 184 TRP cc_start: 0.8114 (m100) cc_final: 0.7869 (m100) REVERT: F 252 PHE cc_start: 0.9427 (m-80) cc_final: 0.8810 (m-80) REVERT: F 257 MET cc_start: 0.9682 (mpp) cc_final: 0.9264 (mpp) REVERT: F 288 MET cc_start: 0.9067 (mmp) cc_final: 0.8809 (mmm) REVERT: F 495 TRP cc_start: 0.8199 (m-90) cc_final: 0.7732 (m100) REVERT: F 634 MET cc_start: 0.8852 (mmp) cc_final: 0.8385 (mmm) REVERT: F 697 MET cc_start: 0.9747 (mmp) cc_final: 0.9535 (mmm) outliers start: 5 outliers final: 0 residues processed: 154 average time/residue: 0.1670 time to fit residues: 38.3105 Evaluate side-chains 119 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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: 2.9990 chunk 172 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 210 optimal weight: 0.9980 chunk 224 optimal weight: 6.9990 chunk 216 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 57 optimal weight: 0.0980 chunk 197 optimal weight: 7.9990 chunk 142 optimal weight: 2.9990 chunk 223 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 HIS ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 708 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.038522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.030450 restraints weight = 219485.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.031364 restraints weight = 140541.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.032021 restraints weight = 101766.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.032494 restraints weight = 79472.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.032840 restraints weight = 65869.010| |-----------------------------------------------------------------------------| r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20392 Z= 0.121 Angle : 0.587 13.890 27550 Z= 0.298 Chirality : 0.049 0.655 3030 Planarity : 0.003 0.042 3415 Dihedral : 9.082 136.337 2925 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.15 % Favored : 96.81 % Rotamer: Outliers : 0.05 % Allowed : 1.88 % Favored : 98.07 % 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: 1.42 (0.16), residues: 1082 sheet: 0.38 (0.26), residues: 403 loop : -1.47 (0.19), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 191 TYR 0.033 0.001 TYR K 59 PHE 0.019 0.001 PHE I 98 TRP 0.009 0.001 TRP F 184 HIS 0.008 0.001 HIS E 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (20390) covalent geometry : angle 0.58583 / 0.30 (27546) SS BOND : bond 0.01044 / 0.52 ( 2) SS BOND : angle 3.11601 / 1.04 ( 4) hydrogen bonds : bond 0.03381 / 1.88 ( 947) hydrogen bonds : angle 4.90155 / 3.04 ( 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 154 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 0.738 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: J 120 PHE cc_start: 0.9714 (t80) cc_final: 0.9454 (t80) REVERT: I 14 MET cc_start: 0.8445 (tpp) cc_final: 0.7662 (tpp) REVERT: I 52 MET cc_start: 0.8854 (tpt) cc_final: 0.8468 (tpt) REVERT: I 63 PHE cc_start: 0.9758 (t80) cc_final: 0.9377 (t80) REVERT: I 64 ASN cc_start: 0.8692 (m110) cc_final: 0.7918 (m110) REVERT: I 66 ASN cc_start: 0.9318 (m-40) cc_final: 0.8987 (p0) REVERT: I 80 TYR cc_start: 0.9131 (m-80) cc_final: 0.8544 (m-80) REVERT: I 86 TYR cc_start: 0.9343 (m-80) cc_final: 0.8968 (m-80) REVERT: I 104 MET cc_start: 0.9811 (mmt) cc_final: 0.9564 (mmm) REVERT: I 109 ASP cc_start: 0.9107 (m-30) cc_final: 0.8883 (m-30) REVERT: I 127 PHE cc_start: 0.9756 (t80) cc_final: 0.9319 (t80) REVERT: K 52 MET cc_start: 0.9687 (mtt) cc_final: 0.8934 (tpt) REVERT: K 69 GLN cc_start: 0.8784 (tp40) cc_final: 0.8242 (tm-30) REVERT: K 85 PHE cc_start: 0.9916 (m-80) cc_final: 0.9570 (m-80) REVERT: K 109 ASP cc_start: 0.9787 (t0) cc_final: 0.9202 (m-30) REVERT: K 112 ILE cc_start: 0.9629 (pt) cc_final: 0.9055 (pt) REVERT: K 127 PHE cc_start: 0.9420 (t80) cc_final: 0.8805 (t80) REVERT: E 119 MET cc_start: 0.7717 (mmp) cc_final: 0.6326 (mmm) REVERT: E 186 MET cc_start: 0.8771 (mmp) cc_final: 0.8149 (mmp) REVERT: E 300 MET cc_start: 0.2044 (mtt) cc_final: 0.1792 (mtt) REVERT: D 55 MET cc_start: 0.9762 (mmp) cc_final: 0.9368 (mmm) REVERT: C 17 LEU cc_start: 0.9892 (tt) cc_final: 0.9247 (mm) REVERT: C 40 GLN cc_start: 0.9549 (tt0) cc_final: 0.8337 (pt0) REVERT: A 40 GLN cc_start: 0.9248 (tt0) cc_final: 0.9027 (tt0) REVERT: A 55 MET cc_start: 0.9592 (mtm) cc_final: 0.9163 (mtp) REVERT: B 55 MET cc_start: 0.9537 (mmp) cc_final: 0.9309 (mmp) REVERT: H 28 MET cc_start: 0.9303 (ttm) cc_final: 0.8778 (pmm) REVERT: H 179 MET cc_start: 0.9716 (tpt) cc_final: 0.9302 (tpp) REVERT: H 208 LEU cc_start: 0.9957 (tt) cc_final: 0.9637 (mt) REVERT: F 1 MET cc_start: 0.8511 (tpt) cc_final: 0.7655 (tpp) REVERT: F 160 MET cc_start: 0.9674 (mtt) cc_final: 0.9436 (mmt) REVERT: F 252 PHE cc_start: 0.9668 (m-80) cc_final: 0.9067 (m-80) REVERT: F 352 MET cc_start: 0.8465 (mpp) cc_final: 0.8222 (mpp) REVERT: F 495 TRP cc_start: 0.8091 (m-90) cc_final: 0.7683 (m100) REVERT: F 571 HIS cc_start: 0.9755 (t70) cc_final: 0.9225 (t70) REVERT: F 634 MET cc_start: 0.9285 (mmp) cc_final: 0.9007 (mmm) outliers start: 1 outliers final: 0 residues processed: 154 average time/residue: 0.1690 time to fit residues: 39.3588 Evaluate side-chains 122 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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: 0.8980 chunk 35 optimal weight: 0.2980 chunk 121 optimal weight: 5.9990 chunk 155 optimal weight: 8.9990 chunk 189 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 225 optimal weight: 6.9990 chunk 48 optimal weight: 8.9990 chunk 203 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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** E 27 GLN ** D 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 HIS ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.037871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.029669 restraints weight = 212909.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.030566 restraints weight = 138005.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.031219 restraints weight = 100400.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.031693 restraints weight = 78701.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.032043 restraints weight = 65287.191| |-----------------------------------------------------------------------------| r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.5224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20392 Z= 0.126 Angle : 0.566 13.995 27550 Z= 0.287 Chirality : 0.046 0.622 3030 Planarity : 0.003 0.040 3415 Dihedral : 8.852 134.659 2925 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.28 % Favored : 96.68 % 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: 0.53 (0.17), residues: 2320 helix: 1.56 (0.16), residues: 1083 sheet: 0.51 (0.26), residues: 396 loop : -1.35 (0.19), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 57 TYR 0.026 0.001 TYR J 123 PHE 0.020 0.001 PHE I 98 TRP 0.010 0.001 TRP E 89 HIS 0.004 0.001 HIS H 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.13 (20390) covalent geometry : angle 0.56598 / 0.29 (27546) SS BOND : bond 0.00669 / 0.33 ( 2) SS BOND : angle 2.03439 / 0.68 ( 4) hydrogen bonds : bond 0.03260 / 1.84 ( 947) hydrogen bonds : angle 4.78085 / 2.99 ( 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 153 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 152 time to evaluate : 0.865 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: J 49 ARG cc_start: 0.9671 (ptp-170) cc_final: 0.9269 (ptm-80) REVERT: J 81 LEU cc_start: 0.9796 (tp) cc_final: 0.9312 (tt) REVERT: J 85 PHE cc_start: 0.9191 (m-80) cc_final: 0.8397 (m-80) REVERT: J 88 GLU cc_start: 0.9696 (mm-30) cc_final: 0.9421 (mm-30) REVERT: J 120 PHE cc_start: 0.9708 (t80) cc_final: 0.9371 (t80) REVERT: J 127 PHE cc_start: 0.9695 (t80) cc_final: 0.9306 (t80) REVERT: I 14 MET cc_start: 0.8637 (tpp) cc_final: 0.7930 (tpp) REVERT: I 52 MET cc_start: 0.8878 (tpt) cc_final: 0.8392 (tpt) REVERT: I 63 PHE cc_start: 0.9722 (t80) cc_final: 0.9317 (t80) REVERT: I 64 ASN cc_start: 0.8789 (m110) cc_final: 0.8243 (m110) REVERT: I 66 ASN cc_start: 0.9411 (m-40) cc_final: 0.9034 (p0) REVERT: I 80 TYR cc_start: 0.9116 (m-80) cc_final: 0.8596 (m-80) REVERT: I 86 TYR cc_start: 0.9357 (m-80) cc_final: 0.8964 (m-80) REVERT: I 104 MET cc_start: 0.9847 (mmt) cc_final: 0.9611 (mmm) REVERT: I 109 ASP cc_start: 0.9079 (m-30) cc_final: 0.8778 (m-30) REVERT: I 127 PHE cc_start: 0.9753 (t80) cc_final: 0.9237 (t80) REVERT: K 52 MET cc_start: 0.9711 (mtt) cc_final: 0.9164 (tpt) REVERT: K 69 GLN cc_start: 0.8798 (tp40) cc_final: 0.8543 (tp40) REVERT: K 76 ASP cc_start: 0.9559 (m-30) cc_final: 0.9352 (m-30) REVERT: K 85 PHE cc_start: 0.9914 (m-80) cc_final: 0.9552 (m-80) REVERT: K 109 ASP cc_start: 0.9769 (t0) cc_final: 0.9187 (m-30) REVERT: K 112 ILE cc_start: 0.9647 (pt) cc_final: 0.9109 (pt) REVERT: K 120 PHE cc_start: 0.9838 (t80) cc_final: 0.9624 (t80) REVERT: K 123 TYR cc_start: 0.9585 (t80) cc_final: 0.9259 (t80) REVERT: K 127 PHE cc_start: 0.9588 (t80) cc_final: 0.9116 (t80) REVERT: E 40 MET cc_start: 0.9368 (tpt) cc_final: 0.9164 (tpp) REVERT: E 119 MET cc_start: 0.8021 (mmp) cc_final: 0.7546 (mmm) REVERT: E 186 MET cc_start: 0.8668 (mmp) cc_final: 0.8161 (mmp) REVERT: E 300 MET cc_start: 0.2094 (mtt) cc_final: 0.1835 (mtt) REVERT: D 55 MET cc_start: 0.9779 (mmp) cc_final: 0.9436 (mmm) REVERT: C 40 GLN cc_start: 0.9590 (tt0) cc_final: 0.9376 (tt0) REVERT: A 40 GLN cc_start: 0.9295 (tt0) cc_final: 0.9042 (tt0) REVERT: A 55 MET cc_start: 0.9558 (mtm) cc_final: 0.9176 (mtp) REVERT: B 55 MET cc_start: 0.9494 (mmp) cc_final: 0.9284 (mmm) REVERT: B 115 ASP cc_start: 0.9165 (t0) cc_final: 0.8781 (t0) REVERT: H 28 MET cc_start: 0.9294 (ttm) cc_final: 0.8983 (pmm) REVERT: H 179 MET cc_start: 0.9680 (tpt) cc_final: 0.9287 (tpp) REVERT: H 208 LEU cc_start: 0.9953 (tt) cc_final: 0.9624 (mt) REVERT: F 1 MET cc_start: 0.8589 (tpt) cc_final: 0.7670 (tpp) REVERT: F 288 MET cc_start: 0.9074 (mmp) cc_final: 0.8784 (mmm) REVERT: F 571 HIS cc_start: 0.9737 (t70) cc_final: 0.9179 (t70) REVERT: F 634 MET cc_start: 0.9282 (mmp) cc_final: 0.9007 (mmm) outliers start: 1 outliers final: 0 residues processed: 153 average time/residue: 0.1727 time to fit residues: 39.9335 Evaluate side-chains 124 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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: 9.9990 chunk 124 optimal weight: 0.8980 chunk 228 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 31 optimal weight: 0.1980 chunk 52 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 232 optimal weight: 0.6980 chunk 158 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 37 GLN ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 183 GLN ** F 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 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 = 0.3076 r_free = 0.3076 target = 0.038075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.030023 restraints weight = 213876.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.030941 restraints weight = 136656.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.031616 restraints weight = 98315.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.032108 restraints weight = 76469.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.032459 restraints weight = 62791.324| |-----------------------------------------------------------------------------| r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.5463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20392 Z= 0.105 Angle : 0.551 14.010 27550 Z= 0.280 Chirality : 0.046 0.595 3030 Planarity : 0.003 0.035 3415 Dihedral : 8.767 132.808 2925 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.84 % Favored : 97.11 % Rotamer: Outliers : 0.05 % Allowed : 1.27 % Favored : 98.68 % 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: 0.63 (0.17), residues: 2320 helix: 1.62 (0.16), residues: 1076 sheet: 0.55 (0.26), residues: 396 loop : -1.24 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG I 91 TYR 0.027 0.001 TYR I 87 PHE 0.029 0.001 PHE F 565 TRP 0.008 0.001 TRP E 89 HIS 0.004 0.001 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.11 (20390) covalent geometry : angle 0.55082 / 0.28 (27546) SS BOND : bond 0.00586 / 0.29 ( 2) SS BOND : angle 1.93692 / 0.65 ( 4) hydrogen bonds : bond 0.03093 / 1.75 ( 947) hydrogen bonds : angle 4.67403 / 2.91 ( 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 151 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 0.802 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: 0.9666 (ptp-170) cc_final: 0.9283 (ptm-80) REVERT: J 81 LEU cc_start: 0.9784 (tp) cc_final: 0.9374 (tt) REVERT: J 85 PHE cc_start: 0.9277 (m-80) cc_final: 0.8396 (m-10) REVERT: J 88 GLU cc_start: 0.9667 (mm-30) cc_final: 0.9380 (mm-30) REVERT: J 120 PHE cc_start: 0.9721 (t80) cc_final: 0.9337 (t80) REVERT: J 127 PHE cc_start: 0.9709 (t80) cc_final: 0.9146 (t80) REVERT: I 14 MET cc_start: 0.8379 (tpp) cc_final: 0.7839 (tpp) REVERT: I 52 MET cc_start: 0.8687 (tpt) cc_final: 0.8060 (tpt) REVERT: I 63 PHE cc_start: 0.9673 (t80) cc_final: 0.9253 (t80) REVERT: I 64 ASN cc_start: 0.8756 (m110) cc_final: 0.8202 (m110) REVERT: I 66 ASN cc_start: 0.9423 (m-40) cc_final: 0.9055 (p0) REVERT: I 80 TYR cc_start: 0.9204 (m-80) cc_final: 0.8675 (m-80) REVERT: I 86 TYR cc_start: 0.9352 (m-80) cc_final: 0.8918 (m-80) REVERT: I 127 PHE cc_start: 0.9762 (t80) cc_final: 0.9276 (t80) REVERT: K 52 MET cc_start: 0.9725 (mtt) cc_final: 0.9111 (tpt) REVERT: K 69 GLN cc_start: 0.8780 (tp40) cc_final: 0.8527 (tp40) REVERT: K 76 ASP cc_start: 0.9553 (m-30) cc_final: 0.9344 (m-30) REVERT: K 85 PHE cc_start: 0.9914 (m-80) cc_final: 0.9554 (m-80) REVERT: K 109 ASP cc_start: 0.9759 (t0) cc_final: 0.9182 (m-30) REVERT: K 112 ILE cc_start: 0.9633 (pt) cc_final: 0.9098 (pt) REVERT: K 127 PHE cc_start: 0.9550 (t80) cc_final: 0.9071 (t80) REVERT: E 119 MET cc_start: 0.8158 (mmp) cc_final: 0.7614 (mmm) REVERT: E 186 MET cc_start: 0.8905 (mmp) cc_final: 0.8235 (mmp) REVERT: E 300 MET cc_start: 0.2192 (mtt) cc_final: 0.1934 (mtt) REVERT: E 327 MET cc_start: 0.9510 (ptp) cc_final: 0.9006 (pmm) REVERT: D 55 MET cc_start: 0.9784 (mmp) cc_final: 0.9448 (mmm) REVERT: D 102 PHE cc_start: 0.9123 (t80) cc_final: 0.8495 (t80) REVERT: A 40 GLN cc_start: 0.9319 (tt0) cc_final: 0.9030 (tt0) REVERT: A 55 MET cc_start: 0.9607 (mtm) cc_final: 0.9162 (mtp) REVERT: B 115 ASP cc_start: 0.9112 (t0) cc_final: 0.8717 (t0) REVERT: H 28 MET cc_start: 0.9235 (ttm) cc_final: 0.8984 (pmm) REVERT: H 35 LEU cc_start: 0.9920 (tp) cc_final: 0.9572 (pp) REVERT: H 179 MET cc_start: 0.9704 (tpt) cc_final: 0.9344 (tpp) REVERT: H 208 LEU cc_start: 0.9950 (tt) cc_final: 0.9623 (mt) REVERT: H 258 MET cc_start: 0.7640 (mmt) cc_final: 0.6965 (pmm) REVERT: F 1 MET cc_start: 0.8909 (tpt) cc_final: 0.8059 (tpp) REVERT: F 160 MET cc_start: 0.9711 (mtt) cc_final: 0.9476 (mmt) REVERT: F 252 PHE cc_start: 0.9394 (m-80) cc_final: 0.8640 (m-80) REVERT: F 259 MET cc_start: 0.8758 (tpt) cc_final: 0.8493 (tpp) REVERT: F 288 MET cc_start: 0.9019 (mmp) cc_final: 0.8704 (mmm) REVERT: F 452 MET cc_start: 0.7712 (mmp) cc_final: 0.7509 (mmm) REVERT: F 571 HIS cc_start: 0.9738 (t70) cc_final: 0.9295 (t70) REVERT: F 634 MET cc_start: 0.9283 (mmp) cc_final: 0.9020 (mmm) REVERT: F 697 MET cc_start: 0.9741 (mmp) cc_final: 0.9441 (mmm) outliers start: 1 outliers final: 0 residues processed: 151 average time/residue: 0.1603 time to fit residues: 37.5774 Evaluate side-chains 119 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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: 5.9990 chunk 53 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 224 optimal weight: 10.0000 chunk 194 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 chunk 81 optimal weight: 0.5980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 37 GLN ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** D 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** F 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 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 = 0.3049 r_free = 0.3049 target = 0.037326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.029551 restraints weight = 224945.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.030461 restraints weight = 142293.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.031103 restraints weight = 101981.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.031569 restraints weight = 79230.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.031904 restraints weight = 65200.745| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.5829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20392 Z= 0.142 Angle : 0.569 12.487 27550 Z= 0.290 Chirality : 0.045 0.484 3030 Planarity : 0.003 0.035 3415 Dihedral : 8.889 132.273 2925 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.49 % Favored : 96.47 % Rotamer: Outliers : 0.05 % Allowed : 1.13 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.17), residues: 2320 helix: 1.59 (0.16), residues: 1079 sheet: 0.60 (0.27), residues: 389 loop : -1.20 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 91 TYR 0.031 0.001 TYR K 59 PHE 0.031 0.001 PHE J 74 TRP 0.008 0.001 TRP F 339 HIS 0.005 0.001 HIS F 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (20390) covalent geometry : angle 0.56874 / 0.29 (27546) SS BOND : bond 0.00730 / 0.36 ( 2) SS BOND : angle 1.56500 / 0.52 ( 4) hydrogen bonds : bond 0.03235 / 1.81 ( 947) hydrogen bonds : angle 4.72992 / 2.95 ( 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 139 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.803 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: 0.9714 (ptp-170) cc_final: 0.9351 (ptm-80) REVERT: J 81 LEU cc_start: 0.9765 (tp) cc_final: 0.9303 (tt) REVERT: J 85 PHE cc_start: 0.9315 (m-80) cc_final: 0.8515 (m-80) REVERT: J 88 GLU cc_start: 0.9754 (mm-30) cc_final: 0.9538 (mm-30) REVERT: J 120 PHE cc_start: 0.9706 (t80) cc_final: 0.9321 (t80) REVERT: J 127 PHE cc_start: 0.9713 (t80) cc_final: 0.9144 (t80) REVERT: I 14 MET cc_start: 0.8421 (tpp) cc_final: 0.7862 (tpp) REVERT: I 52 MET cc_start: 0.8797 (tpt) cc_final: 0.8314 (tpt) REVERT: I 63 PHE cc_start: 0.9594 (t80) cc_final: 0.9008 (t80) REVERT: I 64 ASN cc_start: 0.8714 (m110) cc_final: 0.8158 (m110) REVERT: I 66 ASN cc_start: 0.9404 (m-40) cc_final: 0.9035 (p0) REVERT: I 80 TYR cc_start: 0.9218 (m-80) cc_final: 0.8711 (m-80) REVERT: I 85 PHE cc_start: 0.9846 (m-10) cc_final: 0.9612 (m-80) REVERT: I 86 TYR cc_start: 0.9328 (m-80) cc_final: 0.8903 (m-80) REVERT: I 127 PHE cc_start: 0.9773 (t80) cc_final: 0.9189 (t80) REVERT: K 52 MET cc_start: 0.9707 (mtt) cc_final: 0.9115 (tpt) REVERT: K 69 GLN cc_start: 0.8788 (tp40) cc_final: 0.8582 (tp40) REVERT: K 76 ASP cc_start: 0.9526 (m-30) cc_final: 0.9325 (m-30) REVERT: K 85 PHE cc_start: 0.9913 (m-80) cc_final: 0.9579 (m-80) REVERT: K 109 ASP cc_start: 0.9780 (t0) cc_final: 0.9255 (m-30) REVERT: K 120 PHE cc_start: 0.9830 (t80) cc_final: 0.9612 (t80) REVERT: K 123 TYR cc_start: 0.9520 (t80) cc_final: 0.9240 (t80) REVERT: K 127 PHE cc_start: 0.9523 (t80) cc_final: 0.9042 (t80) REVERT: E 119 MET cc_start: 0.8014 (mmp) cc_final: 0.7759 (mmm) REVERT: E 186 MET cc_start: 0.8908 (mmp) cc_final: 0.8390 (mmp) REVERT: E 327 MET cc_start: 0.9433 (ptp) cc_final: 0.9078 (ptp) REVERT: D 55 MET cc_start: 0.9769 (mmp) cc_final: 0.9435 (mmm) REVERT: D 102 PHE cc_start: 0.9155 (t80) cc_final: 0.8851 (t80) REVERT: C 17 LEU cc_start: 0.9853 (tp) cc_final: 0.9358 (mm) REVERT: C 40 GLN cc_start: 0.9680 (tt0) cc_final: 0.9341 (tt0) REVERT: A 40 GLN cc_start: 0.9300 (tt0) cc_final: 0.8979 (tt0) REVERT: A 55 MET cc_start: 0.9490 (mtm) cc_final: 0.9158 (mtp) REVERT: B 55 MET cc_start: 0.9500 (mmp) cc_final: 0.9284 (mmm) REVERT: B 115 ASP cc_start: 0.9157 (t0) cc_final: 0.8786 (t0) REVERT: H 28 MET cc_start: 0.9298 (ttm) cc_final: 0.9031 (pmm) REVERT: H 35 LEU cc_start: 0.9925 (tp) cc_final: 0.9530 (pp) REVERT: H 208 LEU cc_start: 0.9947 (tt) cc_final: 0.9610 (mt) REVERT: H 258 MET cc_start: 0.7675 (mmt) cc_final: 0.7011 (pmm) REVERT: F 1 MET cc_start: 0.8580 (tpt) cc_final: 0.7474 (tpp) REVERT: F 160 MET cc_start: 0.9684 (mtt) cc_final: 0.9419 (mmt) REVERT: F 252 PHE cc_start: 0.9613 (m-80) cc_final: 0.9128 (m-80) REVERT: F 259 MET cc_start: 0.8813 (tpt) cc_final: 0.8598 (tpp) REVERT: F 288 MET cc_start: 0.8913 (mmp) cc_final: 0.8655 (mmm) REVERT: F 571 HIS cc_start: 0.9717 (t70) cc_final: 0.9185 (t70) REVERT: F 634 MET cc_start: 0.9264 (mmp) cc_final: 0.9001 (mmm) REVERT: F 697 MET cc_start: 0.9750 (mmp) cc_final: 0.9455 (mmm) outliers start: 1 outliers final: 0 residues processed: 139 average time/residue: 0.1654 time to fit residues: 35.0888 Evaluate side-chains 115 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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: 0.8980 chunk 50 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 176 optimal weight: 7.9990 chunk 178 optimal weight: 0.2980 chunk 184 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.037287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.029127 restraints weight = 215709.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.030031 restraints weight = 139043.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.030693 restraints weight = 100584.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.031166 restraints weight = 78584.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.031510 restraints weight = 65177.172| |-----------------------------------------------------------------------------| r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.5994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20392 Z= 0.115 Angle : 0.546 13.584 27550 Z= 0.280 Chirality : 0.045 0.528 3030 Planarity : 0.003 0.036 3415 Dihedral : 8.840 131.733 2925 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.10 % Favored : 96.85 % Rotamer: Outliers : 0.05 % Allowed : 0.80 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.18), residues: 2320 helix: 1.59 (0.16), residues: 1081 sheet: 0.74 (0.27), residues: 381 loop : -1.17 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 91 TYR 0.028 0.001 TYR K 59 PHE 0.022 0.001 PHE I 98 TRP 0.008 0.001 TRP E 89 HIS 0.012 0.001 HIS I 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (20390) covalent geometry : angle 0.54555 / 0.28 (27546) SS BOND : bond 0.00543 / 0.27 ( 2) SS BOND : angle 1.72968 / 0.58 ( 4) hydrogen bonds : bond 0.03135 / 1.75 ( 947) hydrogen bonds : angle 4.72590 / 2.92 ( 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 : 0.831 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: J 49 ARG cc_start: 0.9731 (ptp-170) cc_final: 0.9288 (mtm110) REVERT: J 81 LEU cc_start: 0.9759 (tp) cc_final: 0.9265 (tt) REVERT: J 85 PHE cc_start: 0.9362 (m-80) cc_final: 0.8825 (m-80) REVERT: J 88 GLU cc_start: 0.9761 (mm-30) cc_final: 0.9463 (pt0) REVERT: J 120 PHE cc_start: 0.9739 (t80) cc_final: 0.9398 (t80) REVERT: J 127 PHE cc_start: 0.9708 (t80) cc_final: 0.9136 (t80) REVERT: I 14 MET cc_start: 0.8456 (tpp) cc_final: 0.7871 (tpp) REVERT: I 52 MET cc_start: 0.8770 (tpt) cc_final: 0.8265 (tpt) REVERT: I 63 PHE cc_start: 0.9280 (t80) cc_final: 0.8917 (t80) REVERT: I 64 ASN cc_start: 0.8709 (m110) cc_final: 0.8211 (m110) REVERT: I 66 ASN cc_start: 0.9417 (m-40) cc_final: 0.9041 (p0) REVERT: I 80 TYR cc_start: 0.9200 (m-80) cc_final: 0.8707 (m-80) REVERT: I 86 TYR cc_start: 0.9343 (m-80) cc_final: 0.8918 (m-80) REVERT: I 123 TYR cc_start: 0.9542 (t80) cc_final: 0.9245 (t80) REVERT: I 127 PHE cc_start: 0.9741 (t80) cc_final: 0.9047 (t80) REVERT: K 52 MET cc_start: 0.9709 (mtt) cc_final: 0.9409 (tpt) REVERT: K 69 GLN cc_start: 0.8767 (tp40) cc_final: 0.8559 (tp40) REVERT: K 85 PHE cc_start: 0.9913 (m-80) cc_final: 0.9575 (m-80) REVERT: K 109 ASP cc_start: 0.9772 (t0) cc_final: 0.9259 (m-30) REVERT: K 120 PHE cc_start: 0.9807 (t80) cc_final: 0.9549 (t80) REVERT: K 123 TYR cc_start: 0.9585 (t80) cc_final: 0.9270 (t80) REVERT: K 127 PHE cc_start: 0.9421 (t80) cc_final: 0.8975 (t80) REVERT: E 119 MET cc_start: 0.6332 (mmp) cc_final: 0.6049 (mmm) REVERT: E 186 MET cc_start: 0.8919 (mmp) cc_final: 0.8247 (mmp) REVERT: E 327 MET cc_start: 0.9447 (ptp) cc_final: 0.9059 (ptp) REVERT: D 55 MET cc_start: 0.9779 (mmp) cc_final: 0.9455 (mmm) REVERT: C 17 LEU cc_start: 0.9714 (tp) cc_final: 0.8925 (mm) REVERT: C 40 GLN cc_start: 0.9634 (tt0) cc_final: 0.9226 (tt0) REVERT: A 40 GLN cc_start: 0.9305 (tt0) cc_final: 0.8953 (tt0) REVERT: A 55 MET cc_start: 0.9629 (mtm) cc_final: 0.9083 (mtp) REVERT: B 55 MET cc_start: 0.9514 (mmp) cc_final: 0.9290 (mmm) REVERT: B 115 ASP cc_start: 0.9136 (t0) cc_final: 0.8762 (t0) REVERT: H 35 LEU cc_start: 0.9920 (tp) cc_final: 0.9527 (pp) REVERT: H 179 MET cc_start: 0.9620 (mmp) cc_final: 0.9284 (mmm) REVERT: H 208 LEU cc_start: 0.9944 (tt) cc_final: 0.9612 (mt) REVERT: H 258 MET cc_start: 0.7869 (mmt) cc_final: 0.7160 (pmm) REVERT: F 1 MET cc_start: 0.8616 (tpt) cc_final: 0.7718 (tpp) REVERT: F 160 MET cc_start: 0.9686 (mtt) cc_final: 0.9420 (mmt) REVERT: F 252 PHE cc_start: 0.9688 (m-80) cc_final: 0.9162 (m-80) REVERT: F 259 MET cc_start: 0.8937 (tpt) cc_final: 0.8601 (tpp) REVERT: F 288 MET cc_start: 0.8915 (mmp) cc_final: 0.8678 (mmm) REVERT: F 341 MET cc_start: 0.9460 (tpt) cc_final: 0.9255 (tpp) REVERT: F 452 MET cc_start: 0.7887 (mmp) cc_final: 0.7654 (mmm) REVERT: F 571 HIS cc_start: 0.9723 (t70) cc_final: 0.9289 (t70) REVERT: F 634 MET cc_start: 0.9229 (mmp) cc_final: 0.8987 (mmm) REVERT: F 697 MET cc_start: 0.9730 (mmp) cc_final: 0.9429 (mmm) outliers start: 1 outliers final: 0 residues processed: 137 average time/residue: 0.1621 time to fit residues: 34.2247 Evaluate side-chains 113 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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: 9.9990 chunk 124 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 233 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 46 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 37 GLN K 24 ASN ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 5 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.036789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.029008 restraints weight = 221110.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.029882 restraints weight = 141497.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.030503 restraints weight = 101306.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.030951 restraints weight = 79186.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.031282 restraints weight = 65587.269| |-----------------------------------------------------------------------------| r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.6477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20392 Z= 0.155 Angle : 0.583 11.364 27550 Z= 0.300 Chirality : 0.045 0.403 3030 Planarity : 0.003 0.036 3415 Dihedral : 8.992 131.972 2925 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % 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: 0.59 (0.17), residues: 2320 helix: 1.54 (0.16), residues: 1080 sheet: 0.56 (0.27), residues: 386 loop : -1.19 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 91 TYR 0.029 0.001 TYR J 87 PHE 0.017 0.001 PHE I 98 TRP 0.010 0.002 TRP F 184 HIS 0.006 0.001 HIS F 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 (20390) covalent geometry : angle 0.58313 / 0.30 (27546) SS BOND : bond 0.00771 / 0.39 ( 2) SS BOND : angle 1.55251 / 0.52 ( 4) hydrogen bonds : bond 0.03277 / 1.82 ( 947) hydrogen bonds : angle 4.80324 / 2.98 ( 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 133 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 49 ARG cc_start: 0.9722 (ptp-170) cc_final: 0.9398 (ptm-80) REVERT: J 81 LEU cc_start: 0.9752 (tp) cc_final: 0.9283 (tt) REVERT: J 85 PHE cc_start: 0.9399 (m-80) cc_final: 0.9069 (m-80) REVERT: J 88 GLU cc_start: 0.9814 (mm-30) cc_final: 0.9505 (mm-30) REVERT: J 120 PHE cc_start: 0.9743 (t80) cc_final: 0.9406 (t80) REVERT: J 127 PHE cc_start: 0.9747 (t80) cc_final: 0.9190 (t80) REVERT: I 14 MET cc_start: 0.8625 (tpp) cc_final: 0.7955 (tpp) REVERT: I 52 MET cc_start: 0.8582 (tpt) cc_final: 0.8060 (tpt) REVERT: I 63 PHE cc_start: 0.9318 (t80) cc_final: 0.8972 (t80) REVERT: I 64 ASN cc_start: 0.8636 (m110) cc_final: 0.8115 (m110) REVERT: I 66 ASN cc_start: 0.9394 (m-40) cc_final: 0.9004 (p0) REVERT: I 80 TYR cc_start: 0.9377 (m-80) cc_final: 0.8806 (m-80) REVERT: I 86 TYR cc_start: 0.9344 (m-80) cc_final: 0.8942 (m-80) REVERT: I 109 ASP cc_start: 0.9344 (m-30) cc_final: 0.9086 (m-30) REVERT: I 127 PHE cc_start: 0.9750 (t80) cc_final: 0.9208 (t80) REVERT: K 52 MET cc_start: 0.9684 (mtt) cc_final: 0.9405 (tpt) REVERT: K 76 ASP cc_start: 0.9520 (m-30) cc_final: 0.9308 (m-30) REVERT: K 85 PHE cc_start: 0.9908 (m-80) cc_final: 0.9580 (m-80) REVERT: K 109 ASP cc_start: 0.9786 (t0) cc_final: 0.9262 (m-30) REVERT: K 120 PHE cc_start: 0.9827 (t80) cc_final: 0.9546 (t80) REVERT: K 123 TYR cc_start: 0.9570 (t80) cc_final: 0.9239 (t80) REVERT: K 127 PHE cc_start: 0.9490 (t80) cc_final: 0.9045 (t80) REVERT: E 119 MET cc_start: 0.6557 (mmp) cc_final: 0.6275 (mmm) REVERT: E 186 MET cc_start: 0.8920 (mmp) cc_final: 0.8398 (mmp) REVERT: E 327 MET cc_start: 0.9543 (ptp) cc_final: 0.9229 (ptp) REVERT: D 55 MET cc_start: 0.9770 (mmp) cc_final: 0.9463 (mmm) REVERT: D 102 PHE cc_start: 0.9236 (t80) cc_final: 0.8938 (t80) REVERT: A 40 GLN cc_start: 0.9381 (tt0) cc_final: 0.9062 (tt0) REVERT: A 55 MET cc_start: 0.9662 (mtm) cc_final: 0.9307 (mtp) REVERT: B 115 ASP cc_start: 0.9160 (t0) cc_final: 0.8821 (t0) REVERT: H 179 MET cc_start: 0.9707 (mmp) cc_final: 0.9203 (mmm) REVERT: H 208 LEU cc_start: 0.9943 (tt) cc_final: 0.9616 (mt) REVERT: H 258 MET cc_start: 0.7887 (mmt) cc_final: 0.7161 (pmm) REVERT: F 1 MET cc_start: 0.8601 (tpt) cc_final: 0.7521 (tpp) REVERT: F 252 PHE cc_start: 0.9722 (m-80) cc_final: 0.9194 (m-80) REVERT: F 259 MET cc_start: 0.9109 (tpt) cc_final: 0.8796 (tpp) REVERT: F 288 MET cc_start: 0.9010 (mmp) cc_final: 0.8794 (mmm) REVERT: F 452 MET cc_start: 0.8070 (mmp) cc_final: 0.7853 (mmm) REVERT: F 571 HIS cc_start: 0.9745 (t70) cc_final: 0.9378 (t-90) REVERT: F 634 MET cc_start: 0.9192 (mmp) cc_final: 0.8959 (mmm) REVERT: F 697 MET cc_start: 0.9735 (mmp) cc_final: 0.9451 (mmm) outliers start: 1 outliers final: 0 residues processed: 133 average time/residue: 0.1561 time to fit residues: 31.9043 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 : 0.819 ------------------------------------------------------------------------------- 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: 3.9990 chunk 130 optimal weight: 0.0980 chunk 104 optimal weight: 0.8980 chunk 228 optimal weight: 0.0270 chunk 34 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 96 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 211 optimal weight: 7.9990 chunk 206 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 overall best weight: 1.0042 ------------------------------------------------------------------------------- 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** ** 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 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 549 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.036966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.028849 restraints weight = 215281.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.029754 restraints weight = 138233.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.030398 restraints weight = 99420.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.030876 restraints weight = 77581.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.031229 restraints weight = 64066.527| |-----------------------------------------------------------------------------| r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.6534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20392 Z= 0.105 Angle : 0.541 13.237 27550 Z= 0.276 Chirality : 0.045 0.471 3030 Planarity : 0.003 0.037 3415 Dihedral : 8.835 131.254 2925 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.05 % Allowed : 0.09 % Favored : 99.86 % 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: 0.69 (0.18), residues: 2320 helix: 1.61 (0.16), residues: 1080 sheet: 0.72 (0.27), residues: 380 loop : -1.17 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 91 TYR 0.024 0.001 TYR K 59 PHE 0.019 0.001 PHE I 98 TRP 0.011 0.001 TRP E 89 HIS 0.005 0.001 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.11 (20390) covalent geometry : angle 0.54061 / 0.28 (27546) SS BOND : bond 0.00686 / 0.34 ( 2) SS BOND : angle 1.85546 / 0.62 ( 4) hydrogen bonds : bond 0.03029 / 1.69 ( 947) hydrogen bonds : angle 4.66178 / 2.89 ( 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 135 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.935 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: J 49 ARG cc_start: 0.9725 (ptp-170) cc_final: 0.9291 (mtm110) REVERT: J 88 GLU cc_start: 0.9799 (mm-30) cc_final: 0.9554 (mm-30) REVERT: J 120 PHE cc_start: 0.9741 (t80) cc_final: 0.9402 (t80) REVERT: J 127 PHE cc_start: 0.9679 (t80) cc_final: 0.9054 (t80) REVERT: I 14 MET cc_start: 0.8584 (tpp) cc_final: 0.7935 (tpp) REVERT: I 52 MET cc_start: 0.8566 (tpt) cc_final: 0.8054 (tpt) REVERT: I 63 PHE cc_start: 0.9296 (t80) cc_final: 0.8958 (t80) REVERT: I 64 ASN cc_start: 0.8654 (m110) cc_final: 0.8130 (m110) REVERT: I 66 ASN cc_start: 0.9470 (m-40) cc_final: 0.9117 (p0) REVERT: I 80 TYR cc_start: 0.9377 (m-80) cc_final: 0.8800 (m-80) REVERT: I 85 PHE cc_start: 0.9868 (m-80) cc_final: 0.9663 (m-80) REVERT: I 86 TYR cc_start: 0.9290 (m-80) cc_final: 0.8898 (m-80) REVERT: I 127 PHE cc_start: 0.9769 (t80) cc_final: 0.9184 (t80) REVERT: K 52 MET cc_start: 0.9695 (mtt) cc_final: 0.9412 (tpt) REVERT: K 76 ASP cc_start: 0.9530 (m-30) cc_final: 0.9319 (m-30) REVERT: K 85 PHE cc_start: 0.9909 (m-80) cc_final: 0.9578 (m-80) REVERT: K 109 ASP cc_start: 0.9763 (t0) cc_final: 0.9257 (m-30) REVERT: K 120 PHE cc_start: 0.9786 (t80) cc_final: 0.9540 (t80) REVERT: K 123 TYR cc_start: 0.9571 (t80) cc_final: 0.9264 (t80) REVERT: K 127 PHE cc_start: 0.9494 (t80) cc_final: 0.9043 (t80) REVERT: E 327 MET cc_start: 0.9498 (ptp) cc_final: 0.9188 (ptp) REVERT: D 55 MET cc_start: 0.9781 (mmp) cc_final: 0.9480 (mmm) REVERT: D 102 PHE cc_start: 0.9296 (t80) cc_final: 0.9084 (t80) REVERT: C 17 LEU cc_start: 0.9801 (tp) cc_final: 0.9210 (mm) REVERT: A 55 MET cc_start: 0.9622 (mtm) cc_final: 0.9133 (mtp) REVERT: B 55 MET cc_start: 0.9502 (mmp) cc_final: 0.9287 (mmm) REVERT: B 115 ASP cc_start: 0.9148 (t0) cc_final: 0.8759 (t0) REVERT: H 35 LEU cc_start: 0.9925 (tp) cc_final: 0.9683 (pp) REVERT: H 179 MET cc_start: 0.9658 (mmp) cc_final: 0.9180 (mmm) REVERT: H 208 LEU cc_start: 0.9941 (tt) cc_final: 0.9617 (mt) REVERT: H 258 MET cc_start: 0.7972 (mmt) cc_final: 0.7169 (pmm) REVERT: F 1 MET cc_start: 0.8637 (tpt) cc_final: 0.7538 (tpp) REVERT: F 252 PHE cc_start: 0.9721 (m-80) cc_final: 0.9236 (m-80) REVERT: F 259 MET cc_start: 0.9184 (tpt) cc_final: 0.8780 (tpp) REVERT: F 288 MET cc_start: 0.9018 (mmp) cc_final: 0.8813 (mmm) REVERT: F 571 HIS cc_start: 0.9749 (t70) cc_final: 0.9371 (t-90) REVERT: F 634 MET cc_start: 0.9167 (mmp) cc_final: 0.8946 (mmm) REVERT: F 697 MET cc_start: 0.9711 (mmp) cc_final: 0.9426 (mmm) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.1635 time to fit residues: 34.1969 Evaluate side-chains 112 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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: 6.9990 chunk 191 optimal weight: 4.9990 chunk 230 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 193 optimal weight: 0.6980 chunk 98 optimal weight: 0.0570 chunk 201 optimal weight: 7.9990 chunk 232 optimal weight: 0.0770 chunk 52 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 overall best weight: 0.9258 ------------------------------------------------------------------------------- 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 E 254 ASN D 90 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 = 0.3061 r_free = 0.3061 target = 0.037289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.029545 restraints weight = 230330.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.030458 restraints weight = 146263.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.031106 restraints weight = 104335.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.031560 restraints weight = 81187.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.031888 restraints weight = 66937.091| |-----------------------------------------------------------------------------| r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.6641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20392 Z= 0.104 Angle : 0.535 12.530 27550 Z= 0.273 Chirality : 0.045 0.438 3030 Planarity : 0.003 0.038 3415 Dihedral : 8.798 130.807 2925 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.05 % Allowed : 0.28 % Favored : 99.67 % 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: 0.74 (0.18), residues: 2320 helix: 1.63 (0.16), residues: 1080 sheet: 0.73 (0.27), residues: 383 loop : -1.12 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 91 TYR 0.023 0.001 TYR K 59 PHE 0.016 0.001 PHE K 63 TRP 0.010 0.001 TRP E 89 HIS 0.005 0.001 HIS C 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (20390) covalent geometry : angle 0.53466 / 0.27 (27546) SS BOND : bond 0.00543 / 0.27 ( 2) SS BOND : angle 1.63614 / 0.55 ( 4) hydrogen bonds : bond 0.03013 / 1.67 ( 947) hydrogen bonds : angle 4.60092 / 2.84 ( 2769) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2887.12 seconds wall clock time: 51 minutes 21.31 seconds (3081.31 seconds total)