Starting phenix.real_space_refine on Sat Aug 23 13:43:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rb8_19028/08_2025/8rb8_19028.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rb8_19028/08_2025/8rb8_19028.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8rb8_19028/08_2025/8rb8_19028.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rb8_19028/08_2025/8rb8_19028.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rb8_19028/08_2025/8rb8_19028.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rb8_19028/08_2025/8rb8_19028.map" } resolution = 3.41 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= 0.002 sd= 0.020 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: 6 Type Number sf(0) Gaussians Fe 18 7.16 5 P 3 5.49 5 S 97 5.16 5 C 8088 2.51 5 N 2066 2.21 5 O 2313 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12585 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1394 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 179} Chain: "C" Number of atoms: 3511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3511 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 37, 'TRANS': 438} Chain: "D" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2629 Classifications: {'peptide': 349} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 325} Chain: "E" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1601 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 203} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1482 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "H" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 548 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 4, 'TRANS': 66} Chain: "B" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 811 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain breaks: 2 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FES': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 47 Unusual residues: {'FMN': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 337 Unusual residues: {'FMN': 1, 'LMT': 8, 'RBF': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 140 Unusual residues: {'LMT': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 184 SG CYS A 25 47.481 69.234 56.532 1.00 52.97 S ATOM 8343 SG CYS E 122 45.949 72.224 54.666 1.00 69.51 S ATOM 844 SG CYS A 113 43.755 68.914 51.369 1.00 46.34 S ATOM 7734 SG CYS E 39 44.883 65.904 53.712 1.00 58.14 S ATOM 4124 SG CYS C 376 41.300 55.611 94.622 1.00 68.33 S ATOM 4439 SG CYS C 419 45.656 53.952 95.133 1.00 37.38 S ATOM 4082 SG CYS C 370 44.811 55.253 88.580 1.00 52.12 S ATOM 4107 SG CYS C 373 41.805 50.423 91.849 1.00 37.47 S ATOM 4370 SG CYS C 409 39.574 65.611 99.934 1.00 39.39 S ATOM 4392 SG CYS C 412 37.528 60.572 103.661 1.00 39.61 S ATOM 4408 SG CYS C 415 40.675 59.820 98.074 1.00 64.07 S ATOM 4150 SG CYS C 380 35.062 60.836 97.926 1.00 59.97 S ATOM 11569 SG CYS B 119 55.784 103.085 101.718 1.00 75.59 S ATOM 11742 SG CYS B 145 61.255 101.617 101.791 1.00 78.49 S ATOM 11723 SG CYS B 142 57.360 100.128 96.634 1.00 64.43 S ATOM 11706 SG CYS B 139 57.965 96.390 101.721 1.00 60.88 S ATOM 11493 SG CYS B 109 63.621 106.228 111.629 1.00 91.95 S ATOM 11511 SG CYS B 112 64.811 110.948 106.685 1.00 77.36 S ATOM 11535 SG CYS B 115 60.418 106.339 106.542 1.00 79.14 S ATOM 11772 SG CYS B 149 67.251 106.638 106.114 1.00100.00 S Time building chain proxies: 2.81, per 1000 atoms: 0.22 Number of scatterers: 12585 At special positions: 0 Unit cell: (85.28, 148.42, 154.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 18 26.01 S 97 16.00 P 3 15.00 O 2313 8.00 N 2066 7.00 C 8088 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 530.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 200 " pdb="FE1 FES A 200 " - pdb=" SG CYS E 122 " pdb="FE1 FES A 200 " - pdb=" SG CYS A 25 " pdb="FE2 FES A 200 " - pdb=" SG CYS A 113 " pdb="FE2 FES A 200 " - pdb=" SG CYS E 39 " pdb=" SF4 B 201 " pdb="FE3 SF4 B 201 " - pdb=" SG CYS B 142 " pdb="FE2 SF4 B 201 " - pdb=" SG CYS B 145 " pdb="FE4 SF4 B 201 " - pdb=" SG CYS B 139 " pdb="FE1 SF4 B 201 " - pdb=" SG CYS B 119 " pdb=" SF4 B 202 " pdb="FE2 SF4 B 202 " - pdb=" SG CYS B 112 " pdb="FE4 SF4 B 202 " - pdb=" SG CYS B 149 " pdb="FE3 SF4 B 202 " - pdb=" SG CYS B 115 " pdb="FE1 SF4 B 202 " - pdb=" SG CYS B 109 " pdb=" SF4 C 501 " pdb="FE1 SF4 C 501 " - pdb=" SG CYS C 376 " pdb="FE2 SF4 C 501 " - pdb=" SG CYS C 419 " pdb="FE3 SF4 C 501 " - pdb=" SG CYS C 370 " pdb="FE4 SF4 C 501 " - pdb=" SG CYS C 373 " pdb=" SF4 C 502 " pdb="FE3 SF4 C 502 " - pdb=" SG CYS C 415 " pdb="FE2 SF4 C 502 " - pdb=" SG CYS C 412 " pdb="FE4 SF4 C 502 " - pdb=" SG CYS C 380 " pdb="FE1 SF4 C 502 " - pdb=" SG CYS C 409 " Number of angles added : 54 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2898 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 11 sheets defined 55.1% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 removed outlier: 4.078A pdb=" N PHE A 6 " --> pdb=" O GLU A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 31 removed outlier: 3.728A pdb=" N PHE A 27 " --> pdb=" O GLY A 23 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 31 " --> pdb=" O PHE A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 62 Processing helix chain 'A' and resid 62 through 67 Processing helix chain 'A' and resid 71 through 90 Processing helix chain 'A' and resid 105 through 110 removed outlier: 3.511A pdb=" N THR A 110 " --> pdb=" O PRO A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 126 Proline residue: A 119 - end of helix removed outlier: 3.505A pdb=" N ARG A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 159 removed outlier: 4.048A pdb=" N LEU A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 184 Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'C' and resid 124 through 134 removed outlier: 3.567A pdb=" N LEU C 128 " --> pdb=" O ASP C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 157 removed outlier: 3.535A pdb=" N LYS C 150 " --> pdb=" O PRO C 146 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG C 156 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N HIS C 157 " --> pdb=" O GLN C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 183 removed outlier: 3.515A pdb=" N ARG C 183 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 198 Processing helix chain 'C' and resid 211 through 222 Processing helix chain 'C' and resid 236 through 240 removed outlier: 3.543A pdb=" N MET C 239 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY C 240 " --> pdb=" O TYR C 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 236 through 240' Processing helix chain 'C' and resid 241 through 250 removed outlier: 3.618A pdb=" N GLN C 247 " --> pdb=" O LYS C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 270 through 283 removed outlier: 3.597A pdb=" N TYR C 274 " --> pdb=" O ALA C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 319 removed outlier: 3.668A pdb=" N LEU C 315 " --> pdb=" O PRO C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 395 Processing helix chain 'C' and resid 397 through 404 removed outlier: 3.632A pdb=" N GLU C 403 " --> pdb=" O ASP C 399 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR C 404 " --> pdb=" O GLY C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 removed outlier: 3.570A pdb=" N TYR C 417 " --> pdb=" O GLY C 413 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL C 418 " --> pdb=" O CYS C 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 413 through 418' Processing helix chain 'C' and resid 424 through 478 Processing helix chain 'D' and resid 17 through 41 Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 41 through 67 removed outlier: 3.534A pdb=" N ILE D 45 " --> pdb=" O GLY D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 75 removed outlier: 3.710A pdb=" N ASP D 75 " --> pdb=" O ARG D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 89 removed outlier: 3.693A pdb=" N THR D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 106 removed outlier: 3.832A pdb=" N GLY D 98 " --> pdb=" O PRO D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 114 Processing helix chain 'D' and resid 122 through 135 Processing helix chain 'D' and resid 137 through 141 removed outlier: 4.122A pdb=" N THR D 141 " --> pdb=" O GLN D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 164 Processing helix chain 'D' and resid 178 through 188 Processing helix chain 'D' and resid 191 through 198 removed outlier: 3.656A pdb=" N ILE D 195 " --> pdb=" O THR D 191 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 208 Processing helix chain 'D' and resid 220 through 232 Processing helix chain 'D' and resid 237 through 258 Processing helix chain 'D' and resid 265 through 270 Processing helix chain 'D' and resid 273 through 281 Processing helix chain 'D' and resid 292 through 312 Processing helix chain 'D' and resid 318 through 337 Proline residue: D 331 - end of helix Processing helix chain 'E' and resid 17 through 27 removed outlier: 4.246A pdb=" N PHE E 21 " --> pdb=" O PRO E 17 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU E 25 " --> pdb=" O PHE E 21 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TRP E 26 " --> pdb=" O THR E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 44 removed outlier: 3.656A pdb=" N THR E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 72 Processing helix chain 'E' and resid 73 through 76 removed outlier: 3.657A pdb=" N ILE E 76 " --> pdb=" O ARG E 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 73 through 76' Processing helix chain 'E' and resid 77 through 79 No H-bonds generated for 'chain 'E' and resid 77 through 79' Processing helix chain 'E' and resid 80 through 101 removed outlier: 4.113A pdb=" N VAL E 92 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 112 removed outlier: 3.555A pdb=" N VAL E 110 " --> pdb=" O GLU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'E' and resid 136 through 168 Processing helix chain 'E' and resid 173 through 179 Processing helix chain 'E' and resid 180 through 186 removed outlier: 4.554A pdb=" N TRP E 184 " --> pdb=" O HIS E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 228 removed outlier: 3.993A pdb=" N PHE E 206 " --> pdb=" O PRO E 202 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE E 207 " --> pdb=" O PRO E 203 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL E 208 " --> pdb=" O GLY E 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 79 removed outlier: 5.508A pdb=" N GLY G 63 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N THR G 64 " --> pdb=" O MET G 60 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU G 79 " --> pdb=" O ALA G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 86 Processing helix chain 'G' and resid 89 through 93 removed outlier: 3.826A pdb=" N ASP G 93 " --> pdb=" O PRO G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 163 removed outlier: 4.253A pdb=" N ILE G 162 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU G 163 " --> pdb=" O ASP G 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 159 through 163' Processing helix chain 'G' and resid 168 through 172 Processing helix chain 'G' and resid 202 through 222 Processing helix chain 'G' and resid 223 through 227 removed outlier: 3.590A pdb=" N LEU G 226 " --> pdb=" O ALA G 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 34 Processing helix chain 'H' and resid 34 through 39 removed outlier: 3.593A pdb=" N CYS H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.867A pdb=" N ALA B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 85 Processing helix chain 'B' and resid 113 through 118 Processing sheet with id=AA1, first strand: chain 'C' and resid 34 through 38 removed outlier: 6.562A pdb=" N VAL C 102 " --> pdb=" O VAL C 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 38 Processing sheet with id=AA3, first strand: chain 'C' and resid 48 through 49 Processing sheet with id=AA4, first strand: chain 'C' and resid 161 through 165 Processing sheet with id=AA5, first strand: chain 'C' and resid 206 through 208 Processing sheet with id=AA6, first strand: chain 'C' and resid 288 through 293 Processing sheet with id=AA7, first strand: chain 'C' and resid 328 through 330 removed outlier: 3.930A pdb=" N GLN C 328 " --> pdb=" O LEU C 357 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AA9, first strand: chain 'G' and resid 108 through 109 removed outlier: 6.674A pdb=" N GLU G 133 " --> pdb=" O LEU G 150 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER G 137 " --> pdb=" O GLY G 146 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N GLY G 146 " --> pdb=" O SER G 137 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ASP G 139 " --> pdb=" O ILE G 144 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE G 144 " --> pdb=" O ASP G 139 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 14 through 18 removed outlier: 6.195A pdb=" N SER H 4 " --> pdb=" O ILE H 68 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ILE H 70 " --> pdb=" O SER H 4 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL H 6 " --> pdb=" O ILE H 70 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 100 through 101 641 hydrogen bonds defined for protein. 1830 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.77 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 5077 1.42 - 1.64: 7611 1.64 - 1.85: 121 1.85 - 2.07: 0 2.07 - 2.28: 52 Bond restraints: 12861 Sorted by residual: bond pdb=" O5' FMN C 500 " pdb=" P FMN C 500 " ideal model delta sigma weight residual 1.676 1.827 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" O5' FMN D 410 " pdb=" P FMN D 410 " ideal model delta sigma weight residual 1.676 1.594 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" O5' FMN G 301 " pdb=" P FMN G 301 " ideal model delta sigma weight residual 1.676 1.596 0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C5' FMN C 500 " pdb=" O5' FMN C 500 " ideal model delta sigma weight residual 1.418 1.344 0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" O1P FMN G 301 " pdb=" P FMN G 301 " ideal model delta sigma weight residual 1.542 1.481 0.061 2.00e-02 2.50e+03 9.24e+00 ... (remaining 12856 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 16989 2.01 - 4.03: 366 4.03 - 6.04: 112 6.04 - 8.05: 13 8.05 - 10.07: 40 Bond angle restraints: 17520 Sorted by residual: angle pdb=" C ASN A 112 " pdb=" N CYS A 113 " pdb=" CA CYS A 113 " ideal model delta sigma weight residual 121.54 129.03 -7.49 1.91e+00 2.74e-01 1.54e+01 angle pdb=" C ALA D 170 " pdb=" CA ALA D 170 " pdb=" CB ALA D 170 " ideal model delta sigma weight residual 115.89 110.85 5.04 1.32e+00 5.74e-01 1.46e+01 angle pdb=" C2 LMT E 304 " pdb=" C3 LMT E 304 " pdb=" C4 LMT E 304 " ideal model delta sigma weight residual 117.09 107.02 10.07 3.00e+00 1.11e-01 1.13e+01 angle pdb=" C2 LMT D 401 " pdb=" C3 LMT D 401 " pdb=" C4 LMT D 401 " ideal model delta sigma weight residual 117.09 107.31 9.78 3.00e+00 1.11e-01 1.06e+01 angle pdb=" C2 LMT D 406 " pdb=" C3 LMT D 406 " pdb=" C4 LMT D 406 " ideal model delta sigma weight residual 117.09 107.31 9.78 3.00e+00 1.11e-01 1.06e+01 ... (remaining 17515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.55: 7615 24.55 - 49.10: 356 49.10 - 73.65: 84 73.65 - 98.20: 35 98.20 - 122.75: 49 Dihedral angle restraints: 8139 sinusoidal: 3612 harmonic: 4527 Sorted by residual: dihedral pdb=" CA ILE D 106 " pdb=" C ILE D 106 " pdb=" N GLY D 107 " pdb=" CA GLY D 107 " ideal model delta harmonic sigma weight residual -180.00 -157.92 -22.08 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA ILE C 85 " pdb=" C ILE C 85 " pdb=" N GLY C 86 " pdb=" CA GLY C 86 " ideal model delta harmonic sigma weight residual 180.00 -158.93 -21.07 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" C2B LMT E 303 " pdb=" C1B LMT E 303 " pdb=" O5B LMT E 303 " pdb=" C5B LMT E 303 " ideal model delta sinusoidal sigma weight residual -57.12 65.63 -122.75 1 3.00e+01 1.11e-03 1.64e+01 ... (remaining 8136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.014: 2132 1.014 - 2.029: 0 2.029 - 3.043: 0 3.043 - 4.057: 0 4.057 - 5.072: 4 Chirality restraints: 2136 Sorted by residual: chirality pdb=" C2' FMN G 301 " pdb=" C1' FMN G 301 " pdb=" C3' FMN G 301 " pdb=" O2' FMN G 301 " both_signs ideal model delta sigma weight residual False -2.52 2.55 -5.07 2.00e-01 2.50e+01 6.43e+02 chirality pdb=" CB THR G 202 " pdb=" CA THR G 202 " pdb=" OG1 THR G 202 " pdb=" CG2 THR G 202 " both_signs ideal model delta sigma weight residual False 2.55 -2.46 5.01 2.00e-01 2.50e+01 6.28e+02 chirality pdb=" C4' FMN D 410 " pdb=" C3' FMN D 410 " pdb=" C5' FMN D 410 " pdb=" O4' FMN D 410 " both_signs ideal model delta sigma weight residual False -2.50 2.42 -4.92 2.00e-01 2.50e+01 6.05e+02 ... (remaining 2133 not shown) Planarity restraints: 2122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMN G 301 " -0.112 2.00e-02 2.50e+03 4.16e-02 7.81e+01 pdb=" C10 FMN G 301 " -0.015 2.00e-02 2.50e+03 pdb=" C2 FMN G 301 " 0.035 2.00e-02 2.50e+03 pdb=" C4 FMN G 301 " -0.021 2.00e-02 2.50e+03 pdb=" C4A FMN G 301 " -0.031 2.00e-02 2.50e+03 pdb=" C5A FMN G 301 " -0.026 2.00e-02 2.50e+03 pdb=" C6 FMN G 301 " -0.014 2.00e-02 2.50e+03 pdb=" C7 FMN G 301 " 0.011 2.00e-02 2.50e+03 pdb=" C7M FMN G 301 " 0.024 2.00e-02 2.50e+03 pdb=" C8 FMN G 301 " 0.024 2.00e-02 2.50e+03 pdb=" C8M FMN G 301 " 0.062 2.00e-02 2.50e+03 pdb=" C9 FMN G 301 " 0.011 2.00e-02 2.50e+03 pdb=" C9A FMN G 301 " -0.013 2.00e-02 2.50e+03 pdb=" N1 FMN G 301 " 0.017 2.00e-02 2.50e+03 pdb=" N10 FMN G 301 " -0.019 2.00e-02 2.50e+03 pdb=" N3 FMN G 301 " 0.014 2.00e-02 2.50e+03 pdb=" N5 FMN G 301 " -0.035 2.00e-02 2.50e+03 pdb=" O2 FMN G 301 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FMN D 410 " 0.001 2.00e-02 2.50e+03 1.20e-02 6.53e+00 pdb=" C10 FMN D 410 " -0.003 2.00e-02 2.50e+03 pdb=" C2 FMN D 410 " -0.010 2.00e-02 2.50e+03 pdb=" C4 FMN D 410 " 0.011 2.00e-02 2.50e+03 pdb=" C4A FMN D 410 " 0.006 2.00e-02 2.50e+03 pdb=" C5A FMN D 410 " 0.011 2.00e-02 2.50e+03 pdb=" C6 FMN D 410 " 0.006 2.00e-02 2.50e+03 pdb=" C7 FMN D 410 " -0.001 2.00e-02 2.50e+03 pdb=" C7M FMN D 410 " -0.039 2.00e-02 2.50e+03 pdb=" C8 FMN D 410 " 0.001 2.00e-02 2.50e+03 pdb=" C8M FMN D 410 " 0.010 2.00e-02 2.50e+03 pdb=" C9 FMN D 410 " 0.006 2.00e-02 2.50e+03 pdb=" C9A FMN D 410 " 0.010 2.00e-02 2.50e+03 pdb=" N1 FMN D 410 " -0.012 2.00e-02 2.50e+03 pdb=" N10 FMN D 410 " 0.000 2.00e-02 2.50e+03 pdb=" N3 FMN D 410 " 0.000 2.00e-02 2.50e+03 pdb=" N5 FMN D 410 " 0.012 2.00e-02 2.50e+03 pdb=" O2 FMN D 410 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 78 " -0.011 2.00e-02 2.50e+03 2.11e-02 4.43e+00 pdb=" C VAL A 78 " 0.036 2.00e-02 2.50e+03 pdb=" O VAL A 78 " -0.014 2.00e-02 2.50e+03 pdb=" N VAL A 79 " -0.012 2.00e-02 2.50e+03 ... (remaining 2119 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 383 2.72 - 3.26: 12564 3.26 - 3.81: 20070 3.81 - 4.35: 23997 4.35 - 4.90: 42045 Nonbonded interactions: 99059 Sorted by model distance: nonbonded pdb=" OG1 THR D 191 " pdb=" OE1 GLU D 194 " model vdw 2.169 3.040 nonbonded pdb=" OG SER H 25 " pdb=" OE1 GLN H 28 " model vdw 2.210 3.040 nonbonded pdb=" OG SER C 202 " pdb=" O ALA C 227 " model vdw 2.225 3.040 nonbonded pdb=" O THR D 184 " pdb=" OG1 THR D 187 " model vdw 2.249 3.040 nonbonded pdb=" OG SER D 201 " pdb=" OG SER D 204 " model vdw 2.261 3.040 ... (remaining 99054 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.630 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 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 : 0.006 0.151 12883 Z= 0.320 Angle : 1.098 39.359 17574 Z= 0.363 Chirality : 0.221 5.072 2136 Planarity : 0.004 0.042 2122 Dihedral : 18.684 122.745 5241 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.47 % Favored : 95.34 % Rotamer: Outliers : 1.51 % Allowed : 5.09 % Favored : 93.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.23), residues: 1587 helix: 1.83 (0.19), residues: 805 sheet: -0.62 (0.57), residues: 106 loop : -0.67 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 221 TYR 0.009 0.001 TYR C 237 PHE 0.015 0.001 PHE G 95 TRP 0.009 0.001 TRP D 83 HIS 0.002 0.000 HIS C 268 Details of bonding type rmsd covalent geometry : bond 0.00611 (12861) covalent geometry : angle 0.84016 (17520) hydrogen bonds : bond 0.14334 ( 637) hydrogen bonds : angle 5.76544 ( 1830) metal coordination : bond 0.00811 ( 20) metal coordination : angle 12.79050 ( 54) Misc. bond : bond 0.06989 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 197 time to evaluate : 0.371 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: C 354 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8536 (tt) REVERT: G 67 GLU cc_start: 0.8584 (tp30) cc_final: 0.8299 (tp30) REVERT: B 132 HIS cc_start: 0.5459 (m90) cc_final: 0.5136 (m90) outliers start: 19 outliers final: 4 residues processed: 214 average time/residue: 0.1415 time to fit residues: 40.8515 Evaluate side-chains 122 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 117 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain G residue 202 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 327 GLN G 98 GLN G 225 GLN H 31 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.059887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.042169 restraints weight = 45119.061| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 3.26 r_work: 0.2573 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12883 Z= 0.199 Angle : 0.999 41.182 17574 Z= 0.325 Chirality : 0.046 0.261 2136 Planarity : 0.005 0.046 2122 Dihedral : 16.015 89.915 2555 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.98 % Favored : 94.90 % Rotamer: Outliers : 1.67 % Allowed : 10.73 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.22), residues: 1587 helix: 2.07 (0.19), residues: 807 sheet: -0.34 (0.58), residues: 103 loop : -0.62 (0.25), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 37 TYR 0.018 0.001 TYR C 237 PHE 0.013 0.001 PHE G 121 TRP 0.008 0.001 TRP D 96 HIS 0.002 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00458 (12861) covalent geometry : angle 0.69538 (17520) hydrogen bonds : bond 0.04392 ( 637) hydrogen bonds : angle 4.47376 ( 1830) metal coordination : bond 0.01917 ( 20) metal coordination : angle 12.95034 ( 54) Misc. bond : bond 0.00198 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.317 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: C 354 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8773 (tp) REVERT: E 135 ASN cc_start: 0.8797 (m-40) cc_final: 0.8431 (m110) REVERT: E 227 ARG cc_start: 0.7108 (mtt180) cc_final: 0.6815 (mtt180) REVERT: G 67 GLU cc_start: 0.9319 (tp30) cc_final: 0.8880 (tp30) REVERT: G 70 MET cc_start: 0.9087 (tpp) cc_final: 0.8856 (tpt) REVERT: G 79 GLU cc_start: 0.9052 (tt0) cc_final: 0.8822 (tt0) REVERT: G 101 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8636 (pm20) REVERT: G 106 GLU cc_start: 0.8794 (tp30) cc_final: 0.8532 (tp30) REVERT: H 52 PHE cc_start: 0.8586 (m-80) cc_final: 0.8337 (m-80) REVERT: B 83 LEU cc_start: 0.9046 (tt) cc_final: 0.8764 (mt) outliers start: 21 outliers final: 10 residues processed: 141 average time/residue: 0.1169 time to fit residues: 23.6655 Evaluate side-chains 127 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain B residue 105 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 95 optimal weight: 5.9990 chunk 156 optimal weight: 7.9990 chunk 24 optimal weight: 0.6980 chunk 25 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 74 optimal weight: 0.0670 chunk 56 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 overall best weight: 2.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.061430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.044238 restraints weight = 44069.195| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 3.04 r_work: 0.2678 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12883 Z= 0.138 Angle : 0.930 41.056 17574 Z= 0.288 Chirality : 0.043 0.330 2136 Planarity : 0.004 0.040 2122 Dihedral : 10.979 72.102 2553 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.31 % Allowed : 11.13 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.22), residues: 1587 helix: 2.19 (0.19), residues: 808 sheet: -0.11 (0.59), residues: 99 loop : -0.58 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 103 TYR 0.017 0.001 TYR C 237 PHE 0.011 0.001 PHE E 114 TRP 0.008 0.001 TRP D 83 HIS 0.002 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00316 (12861) covalent geometry : angle 0.61114 (17520) hydrogen bonds : bond 0.03749 ( 637) hydrogen bonds : angle 4.18547 ( 1830) metal coordination : bond 0.01235 ( 20) metal coordination : angle 12.65087 ( 54) Misc. bond : bond 0.00058 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.495 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: A 88 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8495 (tm-30) REVERT: C 134 LYS cc_start: 0.9268 (mtmt) cc_final: 0.9068 (mtmm) REVERT: C 319 CYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8079 (p) REVERT: E 135 ASN cc_start: 0.8846 (m-40) cc_final: 0.8555 (m110) REVERT: E 225 GLU cc_start: 0.9278 (mm-30) cc_final: 0.9055 (tp30) REVERT: E 227 ARG cc_start: 0.7189 (mtt180) cc_final: 0.6886 (mtt180) REVERT: G 67 GLU cc_start: 0.9325 (tp30) cc_final: 0.8866 (tp30) REVERT: G 70 MET cc_start: 0.9227 (tpp) cc_final: 0.8968 (tpt) REVERT: G 79 GLU cc_start: 0.8984 (tt0) cc_final: 0.8762 (tt0) REVERT: G 101 GLU cc_start: 0.9009 (pt0) cc_final: 0.8523 (pm20) REVERT: B 132 HIS cc_start: 0.6987 (m90) cc_final: 0.5998 (m90) outliers start: 29 outliers final: 14 residues processed: 141 average time/residue: 0.1228 time to fit residues: 24.9323 Evaluate side-chains 128 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 173 PHE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain B residue 105 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 12 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.058931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.041733 restraints weight = 44648.766| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 3.03 r_work: 0.2604 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 12883 Z= 0.248 Angle : 1.026 44.736 17574 Z= 0.331 Chirality : 0.045 0.348 2136 Planarity : 0.004 0.050 2122 Dihedral : 9.887 60.314 2549 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.80 % Favored : 94.14 % Rotamer: Outliers : 2.62 % Allowed : 11.92 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.22), residues: 1587 helix: 2.20 (0.19), residues: 806 sheet: -0.43 (0.57), residues: 98 loop : -0.50 (0.25), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 103 TYR 0.021 0.001 TYR C 237 PHE 0.014 0.002 PHE G 121 TRP 0.007 0.001 TRP D 96 HIS 0.003 0.001 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00584 (12861) covalent geometry : angle 0.69095 (17520) hydrogen bonds : bond 0.04390 ( 637) hydrogen bonds : angle 4.36001 ( 1830) metal coordination : bond 0.02395 ( 20) metal coordination : angle 13.71045 ( 54) Misc. bond : bond 0.00165 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.482 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: C 239 MET cc_start: 0.9048 (tpt) cc_final: 0.8841 (tpt) REVERT: C 319 CYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8183 (p) REVERT: E 225 GLU cc_start: 0.9234 (mm-30) cc_final: 0.9005 (tp30) REVERT: E 227 ARG cc_start: 0.7127 (mtt180) cc_final: 0.6837 (mtt180) REVERT: G 67 GLU cc_start: 0.9351 (tp30) cc_final: 0.8990 (tp30) REVERT: G 79 GLU cc_start: 0.9005 (tt0) cc_final: 0.8778 (tt0) REVERT: G 101 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.8553 (pm20) REVERT: G 104 GLU cc_start: 0.9149 (tt0) cc_final: 0.8722 (tp30) REVERT: H 17 SER cc_start: 0.9014 (m) cc_final: 0.8768 (t) REVERT: B 103 ARG cc_start: 0.8460 (mmm160) cc_final: 0.8207 (mmm160) outliers start: 33 outliers final: 20 residues processed: 137 average time/residue: 0.1210 time to fit residues: 24.0648 Evaluate side-chains 132 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 173 PHE Chi-restraints excluded: chain H residue 28 GLN Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 125 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 chunk 123 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 77 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.060586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.043511 restraints weight = 44155.877| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 3.04 r_work: 0.2659 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12883 Z= 0.122 Angle : 0.939 43.429 17574 Z= 0.283 Chirality : 0.041 0.365 2136 Planarity : 0.004 0.040 2122 Dihedral : 9.146 59.948 2548 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.91 % Allowed : 12.96 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.22), residues: 1587 helix: 2.27 (0.19), residues: 815 sheet: -0.20 (0.59), residues: 89 loop : -0.44 (0.25), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 103 TYR 0.021 0.001 TYR C 237 PHE 0.017 0.001 PHE A 143 TRP 0.008 0.001 TRP D 96 HIS 0.001 0.000 HIS C 196 Details of bonding type rmsd covalent geometry : bond 0.00281 (12861) covalent geometry : angle 0.58430 (17520) hydrogen bonds : bond 0.03684 ( 637) hydrogen bonds : angle 4.11440 ( 1830) metal coordination : bond 0.00997 ( 20) metal coordination : angle 13.27627 ( 54) Misc. bond : bond 0.00050 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.497 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: A 155 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8818 (mt-10) REVERT: C 134 LYS cc_start: 0.9302 (mtmt) cc_final: 0.9100 (mtmm) REVERT: C 319 CYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8082 (p) REVERT: D 327 ASN cc_start: 0.9253 (m110) cc_final: 0.8940 (m-40) REVERT: E 135 ASN cc_start: 0.8923 (m-40) cc_final: 0.8616 (m110) REVERT: E 143 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8468 (t0) REVERT: E 225 GLU cc_start: 0.9226 (mm-30) cc_final: 0.9025 (tp30) REVERT: E 227 ARG cc_start: 0.7137 (mtt180) cc_final: 0.6854 (mtt180) REVERT: G 67 GLU cc_start: 0.9331 (tp30) cc_final: 0.8972 (tp30) REVERT: G 70 MET cc_start: 0.9073 (tpp) cc_final: 0.8831 (tpt) REVERT: G 79 GLU cc_start: 0.8995 (tt0) cc_final: 0.8742 (tt0) REVERT: G 101 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8514 (pm20) REVERT: G 133 GLU cc_start: 0.8854 (tp30) cc_final: 0.8543 (tp30) REVERT: B 100 MET cc_start: 0.8527 (tpp) cc_final: 0.8218 (tpp) REVERT: B 103 ARG cc_start: 0.8463 (mmm160) cc_final: 0.8206 (mmm160) REVERT: B 146 ARG cc_start: 0.9189 (mtp85) cc_final: 0.8873 (mmm160) outliers start: 24 outliers final: 17 residues processed: 138 average time/residue: 0.1189 time to fit residues: 24.0536 Evaluate side-chains 134 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 173 PHE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 131 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 54 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 154 optimal weight: 30.0000 chunk 39 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 150 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 chunk 53 optimal weight: 0.2980 chunk 40 optimal weight: 9.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.061650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.044763 restraints weight = 43657.296| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 3.01 r_work: 0.2694 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12883 Z= 0.099 Angle : 0.892 41.021 17574 Z= 0.264 Chirality : 0.040 0.279 2136 Planarity : 0.004 0.040 2122 Dihedral : 8.373 59.931 2548 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.07 % Allowed : 13.59 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.22), residues: 1587 helix: 2.54 (0.19), residues: 801 sheet: -0.17 (0.59), residues: 90 loop : -0.45 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 103 TYR 0.016 0.001 TYR C 237 PHE 0.011 0.001 PHE A 143 TRP 0.008 0.001 TRP D 83 HIS 0.002 0.000 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00216 (12861) covalent geometry : angle 0.54063 (17520) hydrogen bonds : bond 0.03217 ( 637) hydrogen bonds : angle 3.96887 ( 1830) metal coordination : bond 0.00682 ( 20) metal coordination : angle 12.80697 ( 54) Misc. bond : bond 0.00026 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.504 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: A 100 ARG cc_start: 0.9092 (tpp80) cc_final: 0.8804 (tpp80) REVERT: A 131 MET cc_start: 0.9268 (tpp) cc_final: 0.8909 (tpt) REVERT: A 155 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8784 (mt-10) REVERT: C 134 LYS cc_start: 0.9310 (mtmt) cc_final: 0.9087 (mtmm) REVERT: C 319 CYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8083 (p) REVERT: D 327 ASN cc_start: 0.9297 (m110) cc_final: 0.8970 (m-40) REVERT: E 135 ASN cc_start: 0.8883 (m-40) cc_final: 0.8605 (m110) REVERT: E 227 ARG cc_start: 0.7151 (mtt180) cc_final: 0.6886 (mtt180) REVERT: G 67 GLU cc_start: 0.9332 (tp30) cc_final: 0.8969 (tp30) REVERT: G 70 MET cc_start: 0.9140 (tpp) cc_final: 0.8865 (tpt) REVERT: G 79 GLU cc_start: 0.8989 (tt0) cc_final: 0.8739 (tt0) REVERT: G 101 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8485 (pm20) REVERT: H 15 GLN cc_start: 0.8977 (tt0) cc_final: 0.8591 (tt0) REVERT: H 27 GLU cc_start: 0.8641 (mp0) cc_final: 0.8073 (mp0) REVERT: H 28 GLN cc_start: 0.9656 (mt0) cc_final: 0.9427 (mp10) REVERT: B 100 MET cc_start: 0.8478 (tpp) cc_final: 0.8139 (tpp) REVERT: B 103 ARG cc_start: 0.8398 (mmm160) cc_final: 0.8140 (mmm160) REVERT: B 132 HIS cc_start: 0.7036 (m90) cc_final: 0.5814 (m90) outliers start: 26 outliers final: 13 residues processed: 146 average time/residue: 0.1209 time to fit residues: 25.6356 Evaluate side-chains 138 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 131 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 155 optimal weight: 0.2980 chunk 89 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 16 optimal weight: 0.5980 chunk 100 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 61 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.061391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.044439 restraints weight = 43821.107| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 3.02 r_work: 0.2691 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12883 Z= 0.112 Angle : 0.898 41.252 17574 Z= 0.273 Chirality : 0.040 0.218 2136 Planarity : 0.004 0.039 2122 Dihedral : 8.158 59.979 2548 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.41 % Favored : 95.53 % Rotamer: Outliers : 1.83 % Allowed : 13.67 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.22), residues: 1587 helix: 2.59 (0.19), residues: 800 sheet: -0.08 (0.59), residues: 90 loop : -0.43 (0.25), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 92 TYR 0.017 0.001 TYR C 237 PHE 0.009 0.001 PHE D 298 TRP 0.006 0.001 TRP D 96 HIS 0.002 0.000 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00257 (12861) covalent geometry : angle 0.55496 (17520) hydrogen bonds : bond 0.03292 ( 637) hydrogen bonds : angle 3.94397 ( 1830) metal coordination : bond 0.00821 ( 20) metal coordination : angle 12.75260 ( 54) Misc. bond : bond 0.00046 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.512 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: A 59 GLU cc_start: 0.9228 (tm-30) cc_final: 0.8842 (tm-30) REVERT: A 100 ARG cc_start: 0.9050 (tpp80) cc_final: 0.8835 (tpp80) REVERT: A 131 MET cc_start: 0.9280 (tpp) cc_final: 0.8923 (tpt) REVERT: A 155 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8773 (mt-10) REVERT: C 319 CYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8152 (p) REVERT: D 327 ASN cc_start: 0.9280 (m110) cc_final: 0.8952 (m-40) REVERT: E 135 ASN cc_start: 0.8889 (m-40) cc_final: 0.8608 (m110) REVERT: E 227 ARG cc_start: 0.7165 (mtt180) cc_final: 0.6915 (mtt180) REVERT: G 67 GLU cc_start: 0.9342 (tp30) cc_final: 0.8986 (tp30) REVERT: G 70 MET cc_start: 0.9183 (tpp) cc_final: 0.8930 (tpt) REVERT: G 79 GLU cc_start: 0.9007 (tt0) cc_final: 0.8755 (tt0) REVERT: G 95 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.8531 (p90) REVERT: G 101 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8468 (pm20) REVERT: H 27 GLU cc_start: 0.8673 (mp0) cc_final: 0.8053 (mp0) REVERT: B 100 MET cc_start: 0.8557 (tpp) cc_final: 0.8242 (tpp) REVERT: B 103 ARG cc_start: 0.8375 (mmm160) cc_final: 0.8098 (mmm160) REVERT: B 132 HIS cc_start: 0.7042 (m90) cc_final: 0.5795 (m90) outliers start: 23 outliers final: 15 residues processed: 146 average time/residue: 0.1210 time to fit residues: 25.5199 Evaluate side-chains 139 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 95 PHE Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 131 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 55 optimal weight: 0.0010 chunk 113 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 99 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 chunk 156 optimal weight: 0.5980 chunk 81 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.061988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.045130 restraints weight = 43737.948| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 3.03 r_work: 0.2712 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12883 Z= 0.098 Angle : 0.879 40.154 17574 Z= 0.269 Chirality : 0.039 0.156 2136 Planarity : 0.004 0.040 2122 Dihedral : 8.013 59.769 2548 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.22 % Favored : 95.72 % Rotamer: Outliers : 1.59 % Allowed : 13.83 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.22), residues: 1587 helix: 2.61 (0.19), residues: 799 sheet: 0.01 (0.60), residues: 90 loop : -0.40 (0.25), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 103 TYR 0.015 0.001 TYR C 237 PHE 0.016 0.001 PHE A 173 TRP 0.006 0.001 TRP D 96 HIS 0.001 0.000 HIS G 222 Details of bonding type rmsd covalent geometry : bond 0.00211 (12861) covalent geometry : angle 0.54108 (17520) hydrogen bonds : bond 0.03119 ( 637) hydrogen bonds : angle 3.88931 ( 1830) metal coordination : bond 0.00578 ( 20) metal coordination : angle 12.49800 ( 54) Misc. bond : bond 0.00017 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.486 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: A 59 GLU cc_start: 0.9181 (tm-30) cc_final: 0.8880 (tm-30) REVERT: A 100 ARG cc_start: 0.8989 (tpp80) cc_final: 0.8784 (tpp80) REVERT: A 131 MET cc_start: 0.9270 (tpp) cc_final: 0.8922 (tpt) REVERT: A 155 GLU cc_start: 0.9069 (mt-10) cc_final: 0.8781 (mt-10) REVERT: C 319 CYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8209 (p) REVERT: D 327 ASN cc_start: 0.9276 (m110) cc_final: 0.8946 (m-40) REVERT: E 135 ASN cc_start: 0.8863 (m-40) cc_final: 0.8590 (m110) REVERT: E 227 ARG cc_start: 0.7147 (mtt180) cc_final: 0.6890 (mtt180) REVERT: G 67 GLU cc_start: 0.9340 (tp30) cc_final: 0.8959 (tp30) REVERT: G 79 GLU cc_start: 0.8990 (tt0) cc_final: 0.8724 (tt0) REVERT: G 95 PHE cc_start: 0.9026 (OUTLIER) cc_final: 0.8578 (p90) REVERT: G 101 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8468 (pm20) REVERT: B 100 MET cc_start: 0.8592 (tpp) cc_final: 0.8304 (tpp) REVERT: B 103 ARG cc_start: 0.8376 (mmm160) cc_final: 0.8099 (mmm160) REVERT: B 132 HIS cc_start: 0.7035 (m90) cc_final: 0.5795 (m90) outliers start: 20 outliers final: 14 residues processed: 138 average time/residue: 0.1246 time to fit residues: 24.8116 Evaluate side-chains 137 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 95 PHE Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 131 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 53 optimal weight: 7.9990 chunk 58 optimal weight: 0.0670 chunk 144 optimal weight: 20.0000 chunk 101 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 98 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 overall best weight: 2.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.060123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.043081 restraints weight = 44115.788| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 3.02 r_work: 0.2649 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12883 Z= 0.164 Angle : 0.935 42.066 17574 Z= 0.297 Chirality : 0.041 0.182 2136 Planarity : 0.004 0.039 2122 Dihedral : 8.042 59.927 2548 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.91 % Favored : 95.02 % Rotamer: Outliers : 1.91 % Allowed : 14.15 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.23), residues: 1587 helix: 2.49 (0.19), residues: 812 sheet: 0.07 (0.61), residues: 88 loop : -0.28 (0.25), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 103 TYR 0.020 0.001 TYR C 237 PHE 0.015 0.001 PHE A 173 TRP 0.005 0.001 TRP A 56 HIS 0.002 0.001 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00387 (12861) covalent geometry : angle 0.60463 (17520) hydrogen bonds : bond 0.03641 ( 637) hydrogen bonds : angle 4.02303 ( 1830) metal coordination : bond 0.01435 ( 20) metal coordination : angle 12.89113 ( 54) Misc. bond : bond 0.00102 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.496 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: A 59 GLU cc_start: 0.9237 (tm-30) cc_final: 0.8790 (tm-30) REVERT: A 131 MET cc_start: 0.9290 (tpp) cc_final: 0.8936 (tpt) REVERT: A 155 GLU cc_start: 0.9116 (mt-10) cc_final: 0.8812 (mt-10) REVERT: C 319 CYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8206 (p) REVERT: D 327 ASN cc_start: 0.9320 (m110) cc_final: 0.9004 (m-40) REVERT: E 135 ASN cc_start: 0.8905 (m-40) cc_final: 0.8624 (m110) REVERT: E 227 ARG cc_start: 0.7145 (mtt180) cc_final: 0.6908 (mtt180) REVERT: G 67 GLU cc_start: 0.9334 (tp30) cc_final: 0.8974 (tp30) REVERT: G 79 GLU cc_start: 0.9010 (tt0) cc_final: 0.8756 (tt0) REVERT: G 101 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8488 (pm20) REVERT: H 25 SER cc_start: 0.7565 (OUTLIER) cc_final: 0.7067 (t) REVERT: H 27 GLU cc_start: 0.8566 (mp0) cc_final: 0.8308 (mp0) REVERT: H 54 LYS cc_start: 0.8043 (mmmt) cc_final: 0.7823 (mmtt) REVERT: B 100 MET cc_start: 0.8580 (tpp) cc_final: 0.8311 (tpp) REVERT: B 103 ARG cc_start: 0.8379 (mmm160) cc_final: 0.8102 (mmm160) outliers start: 24 outliers final: 16 residues processed: 141 average time/residue: 0.1223 time to fit residues: 25.0439 Evaluate side-chains 137 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 131 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 113 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 chunk 136 optimal weight: 8.9990 chunk 138 optimal weight: 0.9990 chunk 151 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.060205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.043124 restraints weight = 44592.428| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 3.01 r_work: 0.2669 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12883 Z= 0.155 Angle : 0.941 42.415 17574 Z= 0.301 Chirality : 0.041 0.188 2136 Planarity : 0.004 0.040 2122 Dihedral : 7.987 59.906 2548 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.41 % Favored : 95.53 % Rotamer: Outliers : 1.51 % Allowed : 14.86 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.22), residues: 1587 helix: 2.48 (0.19), residues: 813 sheet: 0.02 (0.60), residues: 88 loop : -0.29 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 2 TYR 0.018 0.001 TYR C 237 PHE 0.013 0.001 PHE A 173 TRP 0.007 0.001 TRP D 96 HIS 0.002 0.000 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00366 (12861) covalent geometry : angle 0.61202 (17520) hydrogen bonds : bond 0.03596 ( 637) hydrogen bonds : angle 4.01566 ( 1830) metal coordination : bond 0.01296 ( 20) metal coordination : angle 12.91413 ( 54) Misc. bond : bond 0.00081 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.544 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: A 59 GLU cc_start: 0.9237 (tm-30) cc_final: 0.8790 (tm-30) REVERT: A 131 MET cc_start: 0.9296 (tpp) cc_final: 0.8936 (tpt) REVERT: A 155 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8812 (mt-10) REVERT: C 319 CYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8205 (p) REVERT: D 327 ASN cc_start: 0.9298 (m110) cc_final: 0.8992 (m-40) REVERT: E 135 ASN cc_start: 0.8931 (m-40) cc_final: 0.8661 (m110) REVERT: E 227 ARG cc_start: 0.7060 (mtt180) cc_final: 0.6787 (mtt180) REVERT: G 67 GLU cc_start: 0.9343 (tp30) cc_final: 0.8982 (tp30) REVERT: G 79 GLU cc_start: 0.9006 (tt0) cc_final: 0.8744 (tt0) REVERT: G 101 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8477 (pm20) REVERT: H 25 SER cc_start: 0.7651 (OUTLIER) cc_final: 0.7086 (t) REVERT: H 27 GLU cc_start: 0.8536 (mp0) cc_final: 0.8270 (mp0) REVERT: H 54 LYS cc_start: 0.8047 (mmmt) cc_final: 0.7839 (mmtm) REVERT: B 3 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6810 (pm20) REVERT: B 100 MET cc_start: 0.8590 (tpp) cc_final: 0.8302 (tpp) REVERT: B 103 ARG cc_start: 0.8376 (mmm160) cc_final: 0.8103 (mmm160) outliers start: 19 outliers final: 16 residues processed: 137 average time/residue: 0.1199 time to fit residues: 23.8940 Evaluate side-chains 140 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 153 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 37 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 20 optimal weight: 0.0770 chunk 81 optimal weight: 0.1980 chunk 77 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.061213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.044318 restraints weight = 43677.870| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 3.03 r_work: 0.2689 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12883 Z= 0.112 Angle : 0.922 41.059 17574 Z= 0.298 Chirality : 0.040 0.183 2136 Planarity : 0.004 0.040 2122 Dihedral : 7.826 59.754 2548 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.60 % Favored : 95.34 % Rotamer: Outliers : 1.75 % Allowed : 15.02 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.22), residues: 1587 helix: 2.54 (0.19), residues: 811 sheet: 0.06 (0.60), residues: 88 loop : -0.28 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 37 TYR 0.017 0.001 TYR C 237 PHE 0.015 0.001 PHE A 143 TRP 0.007 0.001 TRP D 96 HIS 0.001 0.000 HIS G 222 Details of bonding type rmsd covalent geometry : bond 0.00258 (12861) covalent geometry : angle 0.60440 (17520) hydrogen bonds : bond 0.03330 ( 637) hydrogen bonds : angle 3.94353 ( 1830) metal coordination : bond 0.00683 ( 20) metal coordination : angle 12.57417 ( 54) Misc. bond : bond 0.00030 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2869.95 seconds wall clock time: 50 minutes 12.00 seconds (3012.00 seconds total)