Starting phenix.real_space_refine on Wed Mar 4 06:10:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zc6_14622/03_2026/7zc6_14622.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zc6_14622/03_2026/7zc6_14622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zc6_14622/03_2026/7zc6_14622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zc6_14622/03_2026/7zc6_14622.map" model { file = "/net/cci-nas-00/data/ceres_data/7zc6_14622/03_2026/7zc6_14622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zc6_14622/03_2026/7zc6_14622.cif" } resolution = 4.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 29 7.16 5 P 3 5.49 5 S 110 5.16 5 C 7337 2.51 5 N 1857 2.21 5 O 2092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11428 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1446 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 184} Chain: "B" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1451 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain breaks: 1 Chain: "C" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3291 Classifications: {'peptide': 435} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 409} Chain: "D" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2282 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 16, 'TRANS': 287} Chain: "E" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1435 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 8, 'TRANS': 185} Chain: "G" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1348 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 6, 'TRANS': 180} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 40 Unusual residues: {'SF4': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'FMN': 1, 'RBF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 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 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 197 SG CYS A 25 74.119 89.930 41.647 1.00 68.15 S ATOM 870 SG CYS A 113 77.837 89.536 39.704 1.00 86.99 S ATOM 8659 SG CYS E 26 76.801 92.203 41.640 1.00 72.84 S ATOM 9273 SG CYS E 109 74.286 91.482 38.436 1.00 74.88 S ATOM 2249 SG CYS B 177 37.926 72.883 46.538 1.00 70.07 S ATOM 2234 SG CYS B 174 41.882 77.587 44.472 1.00 80.54 S ATOM 2217 SG CYS B 171 36.501 78.904 48.010 1.00101.07 S ATOM 2078 SG CYS B 152 42.351 76.972 49.759 1.00 73.24 S ATOM 2276 SG CYS B 181 37.213 64.066 48.403 1.00 60.39 S ATOM 1899 SG CYS B 124 41.917 63.120 49.815 1.00 57.96 S ATOM 2049 SG CYS B 148 40.617 68.951 51.573 1.00 65.89 S ATOM 2013 SG CYS B 142 37.484 63.946 54.134 1.00 52.52 S ATOM 1988 SG CYS B 138 28.277 57.461 53.661 1.00 65.39 S ATOM 1749 SG CYS B 105 31.277 63.446 55.599 1.00 77.65 S ATOM 2414 SG CYS B 199 24.881 62.694 54.758 1.00 83.08 S ATOM 2511 SG CYS B 212 27.646 57.971 57.780 1.00 82.33 S ATOM 2572 SG CYS B 222 13.707 65.162 50.259 1.00110.31 S ATOM 2554 SG CYS B 219 12.993 61.363 54.806 1.00111.20 S ATOM 2534 SG CYS B 216 18.643 61.459 52.209 1.00 97.19 S ATOM 2815 SG CYS B 255 16.109 66.501 55.513 1.00105.47 S ATOM 2604 SG CYS B 226 11.002 73.165 47.062 1.00119.53 S ATOM 2750 SG CYS B 245 15.934 76.629 47.837 1.00121.69 S ATOM 2772 SG CYS B 248 10.150 77.089 51.366 1.00134.21 S ATOM 2789 SG CYS B 251 14.475 73.473 52.896 1.00115.99 S ATOM 5985 SG CYS C 410 58.404 48.702 46.374 1.00 57.86 S ATOM 5729 SG CYS C 375 61.955 46.682 41.136 1.00 60.27 S ATOM 5969 SG CYS C 407 58.117 43.438 43.701 1.00 64.51 S ATOM 5946 SG CYS C 404 55.779 47.850 40.801 1.00 56.81 S ATOM 5681 SG CYS C 368 67.660 51.898 51.719 1.00 62.42 S ATOM 6015 SG CYS C 414 62.114 52.268 53.715 1.00 61.08 S ATOM 5659 SG CYS C 365 64.667 57.398 51.524 1.00 60.44 S ATOM 5700 SG CYS C 371 64.674 52.081 47.522 1.00 54.07 S Time building chain proxies: 2.62, per 1000 atoms: 0.23 Number of scatterers: 11428 At special positions: 0 Unit cell: (136.431, 128.898, 89.559, 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 29 26.01 S 110 16.00 P 3 15.00 O 2092 8.00 N 1857 7.00 C 7337 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: 0.78 Conformation dependent library (CDL) restraints added in 601.1 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B 300 " pdb="FE1 SF4 B 300 " - pdb=" SG CYS B 177 " pdb="FE2 SF4 B 300 " - pdb=" SG CYS B 174 " pdb="FE3 SF4 B 300 " - pdb=" SG CYS B 171 " pdb="FE4 SF4 B 300 " - pdb=" SG CYS B 152 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 142 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 181 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 148 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 124 " pdb=" SF4 B 302 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 212 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 105 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 138 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 199 " pdb=" SF4 B 303 " pdb="FE4 SF4 B 303 " - pdb=" SG CYS B 255 " pdb="FE3 SF4 B 303 " - pdb=" SG CYS B 216 " pdb="FE1 SF4 B 303 " - pdb=" SG CYS B 222 " pdb="FE2 SF4 B 303 " - pdb=" SG CYS B 219 " pdb=" SF4 B 304 " pdb="FE2 SF4 B 304 " - pdb=" SG CYS B 245 " pdb="FE3 SF4 B 304 " - pdb=" SG CYS B 248 " pdb="FE1 SF4 B 304 " - pdb=" SG CYS B 226 " pdb="FE4 SF4 B 304 " - pdb=" SG CYS B 251 " pdb=" SF4 C 501 " pdb="FE1 SF4 C 501 " - pdb=" SG CYS C 410 " pdb="FE4 SF4 C 501 " - pdb=" SG CYS C 404 " pdb="FE3 SF4 C 501 " - pdb=" SG CYS C 407 " pdb="FE2 SF4 C 501 " - pdb=" SG CYS C 375 " pdb=" SF4 C 502 " pdb="FE1 SF4 C 502 " - pdb=" SG CYS C 368 " pdb="FE2 SF4 C 502 " - pdb=" SG CYS C 414 " pdb="FE3 SF4 C 502 " - pdb=" SG CYS C 365 " pdb="FE4 SF4 C 502 " - pdb=" SG CYS C 371 " Number of angles added : 84 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2730 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 11 sheets defined 51.8% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 removed outlier: 3.840A pdb=" N ILE A 8 " --> pdb=" O PHE A 4 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER A 9 " --> pdb=" O THR A 5 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA A 10 " --> pdb=" O ILE A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 28 removed outlier: 3.799A pdb=" N PHE A 27 " --> pdb=" O GLY A 23 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 28 " --> pdb=" O ILE A 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 23 through 28' Processing helix chain 'A' and resid 33 through 61 removed outlier: 4.897A pdb=" N GLY A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET A 40 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL A 58 " --> pdb=" O MET A 54 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 67 Processing helix chain 'A' and resid 69 through 74 removed outlier: 4.057A pdb=" N THR A 73 " --> pdb=" O TYR A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 86 removed outlier: 3.806A pdb=" N VAL A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 92 removed outlier: 3.659A pdb=" N VAL A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 99 removed outlier: 3.751A pdb=" N LEU A 98 " --> pdb=" O SER A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 112 through 123 removed outlier: 3.880A pdb=" N LEU A 116 " --> pdb=" O ASN A 112 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY A 117 " --> pdb=" O CYS A 113 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE A 121 " --> pdb=" O GLY A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 158 removed outlier: 3.815A pdb=" N LYS A 156 " --> pdb=" O GLY A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 168 Processing helix chain 'A' and resid 169 through 185 removed outlier: 4.294A pdb=" N THR A 173 " --> pdb=" O GLY A 169 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'B' and resid 4 through 12 removed outlier: 4.108A pdb=" N VAL B 8 " --> pdb=" O LEU B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 21 Processing helix chain 'B' and resid 22 through 27 Processing helix chain 'B' and resid 108 through 112 removed outlier: 3.516A pdb=" N ALA B 112 " --> pdb=" O CYS B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 129 removed outlier: 3.904A pdb=" N ALA B 128 " --> pdb=" O VAL B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 removed outlier: 3.649A pdb=" N VAL B 149 " --> pdb=" O GLY B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 181 removed outlier: 4.342A pdb=" N SER B 179 " --> pdb=" O GLY B 175 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N CYS B 181 " --> pdb=" O CYS B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 210 removed outlier: 3.595A pdb=" N ASN B 210 " --> pdb=" O ILE B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 Processing helix chain 'B' and resid 250 through 255 removed outlier: 3.504A pdb=" N LYS B 254 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS B 255 " --> pdb=" O CYS B 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 250 through 255' Processing helix chain 'C' and resid 15 through 19 removed outlier: 3.659A pdb=" N TYR C 18 " --> pdb=" O GLY C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 40 No H-bonds generated for 'chain 'C' and resid 38 through 40' Processing helix chain 'C' and resid 119 through 131 Processing helix chain 'C' and resid 141 through 146 removed outlier: 3.994A pdb=" N LYS C 145 " --> pdb=" O PRO C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 178 removed outlier: 3.709A pdb=" N ARG C 173 " --> pdb=" O THR C 169 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N MET C 174 " --> pdb=" O CYS C 170 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS C 178 " --> pdb=" O MET C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 193 Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 206 through 214 Processing helix chain 'C' and resid 215 through 220 removed outlier: 3.701A pdb=" N LYS C 218 " --> pdb=" O GLU C 215 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASN C 219 " --> pdb=" O ALA C 216 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE C 220 " --> pdb=" O VAL C 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 215 through 220' Processing helix chain 'C' and resid 236 through 244 removed outlier: 3.604A pdb=" N LEU C 240 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE C 241 " --> pdb=" O GLU C 237 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR C 242 " --> pdb=" O LYS C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 276 Processing helix chain 'C' and resid 306 through 314 Processing helix chain 'C' and resid 353 through 358 removed outlier: 3.613A pdb=" N GLU C 358 " --> pdb=" O LYS C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 375 removed outlier: 3.547A pdb=" N GLN C 373 " --> pdb=" O GLY C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 391 removed outlier: 3.968A pdb=" N LEU C 384 " --> pdb=" O MET C 380 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA C 389 " --> pdb=" O ALA C 385 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL C 390 " --> pdb=" O THR C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 399 removed outlier: 3.562A pdb=" N PHE C 396 " --> pdb=" O ASN C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 413 removed outlier: 3.581A pdb=" N PHE C 412 " --> pdb=" O GLY C 408 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL C 413 " --> pdb=" O CYS C 409 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 408 through 413' Processing helix chain 'C' and resid 420 through 434 removed outlier: 3.653A pdb=" N SER C 432 " --> pdb=" O LYS C 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 32 removed outlier: 4.077A pdb=" N ASP D 27 " --> pdb=" O SER D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 41 removed outlier: 3.823A pdb=" N TYR D 41 " --> pdb=" O ILE D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 67 removed outlier: 3.808A pdb=" N ILE D 51 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP D 65 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS D 67 " --> pdb=" O TYR D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 77 Processing helix chain 'D' and resid 78 through 88 removed outlier: 4.317A pdb=" N VAL D 82 " --> pdb=" O TYR D 78 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 110 removed outlier: 3.588A pdb=" N VAL D 110 " --> pdb=" O PHE D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 137 Processing helix chain 'D' and resid 137 through 142 Processing helix chain 'D' and resid 153 through 160 removed outlier: 3.784A pdb=" N ILE D 157 " --> pdb=" O THR D 153 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS D 159 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY D 160 " --> pdb=" O ALA D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 177 removed outlier: 4.318A pdb=" N PHE D 175 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE D 176 " --> pdb=" O MET D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 201 removed outlier: 3.783A pdb=" N TYR D 200 " --> pdb=" O ALA D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 224 Processing helix chain 'D' and resid 230 through 235 removed outlier: 4.139A pdb=" N PHE D 234 " --> pdb=" O VAL D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 242 Processing helix chain 'D' and resid 255 through 275 removed outlier: 4.043A pdb=" N ILE D 260 " --> pdb=" O PRO D 256 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLY D 267 " --> pdb=" O GLY D 263 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL D 268 " --> pdb=" O VAL D 264 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE D 269 " --> pdb=" O GLY D 265 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER D 271 " --> pdb=" O GLY D 267 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU D 272 " --> pdb=" O VAL D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 293 removed outlier: 4.063A pdb=" N VAL D 289 " --> pdb=" O TYR D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 301 removed outlier: 3.957A pdb=" N TRP D 300 " --> pdb=" O LEU D 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 14 removed outlier: 3.540A pdb=" N LYS E 14 " --> pdb=" O ASN E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 31 removed outlier: 4.102A pdb=" N THR E 28 " --> pdb=" O GLY E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 60 removed outlier: 3.627A pdb=" N GLY E 38 " --> pdb=" O SER E 34 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL E 55 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU E 58 " --> pdb=" O VAL E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 63 No H-bonds generated for 'chain 'E' and resid 61 through 63' Processing helix chain 'E' and resid 64 through 68 removed outlier: 3.946A pdb=" N ARG E 68 " --> pdb=" O ASP E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 88 Processing helix chain 'E' and resid 101 through 106 removed outlier: 3.859A pdb=" N ILE E 105 " --> pdb=" O ILE E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 116 removed outlier: 4.352A pdb=" N LEU E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 152 removed outlier: 3.939A pdb=" N PHE E 128 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE E 129 " --> pdb=" O GLY E 125 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ASP E 130 " --> pdb=" O ALA E 126 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE E 148 " --> pdb=" O ALA E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 160 Processing helix chain 'E' and resid 177 through 194 removed outlier: 4.153A pdb=" N PHE E 181 " --> pdb=" O PRO E 177 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR E 182 " --> pdb=" O GLY E 178 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA E 188 " --> pdb=" O GLY E 184 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG E 193 " --> pdb=" O ILE E 189 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS E 194 " --> pdb=" O LEU E 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 51 removed outlier: 3.722A pdb=" N ALA G 32 " --> pdb=" O ASN G 28 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N GLU G 33 " --> pdb=" O GLN G 29 " (cutoff:3.500A) Proline residue: G 34 - end of helix Processing helix chain 'G' and resid 129 through 134 Processing helix chain 'G' and resid 135 through 137 No H-bonds generated for 'chain 'G' and resid 135 through 137' Processing helix chain 'G' and resid 163 through 185 Processing sheet with id=AA1, first strand: chain 'B' and resid 99 through 103 Processing sheet with id=AA2, first strand: chain 'B' and resid 157 through 160 Processing sheet with id=AA3, first strand: chain 'B' and resid 195 through 197 Processing sheet with id=AA4, first strand: chain 'B' and resid 231 through 232 Processing sheet with id=AA5, first strand: chain 'C' and resid 33 through 36 removed outlier: 4.378A pdb=" N ASN C 82 " --> pdb=" O ILE C 98 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N GLU C 100 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL C 80 " --> pdb=" O GLU C 100 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 86 through 87 Processing sheet with id=AA7, first strand: chain 'C' and resid 156 through 158 Processing sheet with id=AA8, first strand: chain 'C' and resid 283 through 285 removed outlier: 3.606A pdb=" N ARG C 284 " --> pdb=" O PHE C 301 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 323 through 326 removed outlier: 4.273A pdb=" N LYS C 323 " --> pdb=" O LEU C 352 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU C 352 " --> pdb=" O LYS C 323 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 56 through 59 removed outlier: 6.618A pdb=" N THR G 73 " --> pdb=" O TYR G 84 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N TYR G 84 " --> pdb=" O THR G 73 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLY G 75 " --> pdb=" O LYS G 82 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP G 80 " --> pdb=" O SER G 77 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY G 111 " --> pdb=" O GLY G 102 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N SER G 104 " --> pdb=" O VAL G 109 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL G 109 " --> pdb=" O SER G 104 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS G 139 " --> pdb=" O VAL G 109 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 145 through 147 removed outlier: 6.257A pdb=" N LYS G 145 " --> pdb=" O ILE G 157 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 443 hydrogen bonds defined for protein. 1251 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: 1.47 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 4359 1.40 - 1.62: 7084 1.62 - 1.84: 122 1.84 - 2.06: 4 2.06 - 2.28: 84 Bond restraints: 11653 Sorted by residual: bond pdb=" N PRO C 194 " pdb=" CA PRO C 194 " ideal model delta sigma weight residual 1.469 1.707 -0.238 1.28e-02 6.10e+03 3.46e+02 bond pdb=" C4 FMN G 300 " pdb=" O4 FMN G 300 " ideal model delta sigma weight residual 1.221 1.402 -0.181 2.00e-02 2.50e+03 8.18e+01 bond pdb=" C2 FMN D 400 " pdb=" O2 FMN D 400 " ideal model delta sigma weight residual 1.227 1.398 -0.171 2.00e-02 2.50e+03 7.27e+01 bond pdb=" C4 FMN C 503 " pdb=" O4 FMN C 503 " ideal model delta sigma weight residual 1.221 1.391 -0.170 2.00e-02 2.50e+03 7.25e+01 bond pdb=" C4 FMN D 400 " pdb=" O4 FMN D 400 " ideal model delta sigma weight residual 1.221 1.388 -0.167 2.00e-02 2.50e+03 7.00e+01 ... (remaining 11648 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.67: 14760 3.67 - 7.33: 980 7.33 - 11.00: 111 11.00 - 14.67: 10 14.67 - 18.34: 1 Bond angle restraints: 15862 Sorted by residual: angle pdb=" C PHE C 193 " pdb=" N PRO C 194 " pdb=" CA PRO C 194 " ideal model delta sigma weight residual 119.84 138.18 -18.34 1.25e+00 6.40e-01 2.15e+02 angle pdb=" CA PRO C 194 " pdb=" N PRO C 194 " pdb=" CD PRO C 194 " ideal model delta sigma weight residual 112.00 100.66 11.34 1.40e+00 5.10e-01 6.56e+01 angle pdb=" N LEU A 170 " pdb=" CA LEU A 170 " pdb=" C LEU A 170 " ideal model delta sigma weight residual 112.75 122.10 -9.35 1.36e+00 5.41e-01 4.73e+01 angle pdb=" CA THR A 176 " pdb=" CB THR A 176 " pdb=" OG1 THR A 176 " ideal model delta sigma weight residual 109.60 99.51 10.09 1.50e+00 4.44e-01 4.52e+01 angle pdb=" CA PRO D 295 " pdb=" N PRO D 295 " pdb=" CD PRO D 295 " ideal model delta sigma weight residual 112.00 102.74 9.26 1.40e+00 5.10e-01 4.37e+01 ... (remaining 15857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 5903 17.99 - 35.97: 735 35.97 - 53.96: 213 53.96 - 71.94: 68 71.94 - 89.93: 13 Dihedral angle restraints: 6932 sinusoidal: 2656 harmonic: 4276 Sorted by residual: dihedral pdb=" CA VAL D 91 " pdb=" C VAL D 91 " pdb=" N PRO D 92 " pdb=" CA PRO D 92 " ideal model delta harmonic sigma weight residual 180.00 150.49 29.51 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA THR E 33 " pdb=" C THR E 33 " pdb=" N SER E 34 " pdb=" CA SER E 34 " ideal model delta harmonic sigma weight residual 180.00 150.57 29.43 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA VAL B 16 " pdb=" C VAL B 16 " pdb=" N VAL B 17 " pdb=" CA VAL B 17 " ideal model delta harmonic sigma weight residual 180.00 -150.61 -29.39 0 5.00e+00 4.00e-02 3.46e+01 ... (remaining 6929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.261: 1892 4.261 - 8.523: 0 8.523 - 12.784: 0 12.784 - 17.045: 0 17.045 - 21.307: 28 Chirality restraints: 1920 Sorted by residual: chirality pdb="FE2 SF4 B 300 " pdb=" S1 SF4 B 300 " pdb=" S3 SF4 B 300 " pdb=" S4 SF4 B 300 " both_signs ideal model delta sigma weight residual False 10.55 -10.75 21.31 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE2 SF4 B 303 " pdb=" S1 SF4 B 303 " pdb=" S3 SF4 B 303 " pdb=" S4 SF4 B 303 " both_signs ideal model delta sigma weight residual False 10.55 -10.71 21.27 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE1 SF4 B 304 " pdb=" S2 SF4 B 304 " pdb=" S3 SF4 B 304 " pdb=" S4 SF4 B 304 " both_signs ideal model delta sigma weight residual False -10.55 10.67 -21.23 2.00e-01 2.50e+01 1.13e+04 ... (remaining 1917 not shown) Planarity restraints: 1949 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG E 7 " -0.026 2.00e-02 2.50e+03 5.27e-02 2.78e+01 pdb=" C ARG E 7 " 0.091 2.00e-02 2.50e+03 pdb=" O ARG E 7 " -0.035 2.00e-02 2.50e+03 pdb=" N LEU E 8 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL G 146 " 0.027 2.00e-02 2.50e+03 5.27e-02 2.77e+01 pdb=" C VAL G 146 " -0.091 2.00e-02 2.50e+03 pdb=" O VAL G 146 " 0.034 2.00e-02 2.50e+03 pdb=" N VAL G 147 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 248 " -0.022 2.00e-02 2.50e+03 4.49e-02 2.01e+01 pdb=" CG ASP D 248 " 0.078 2.00e-02 2.50e+03 pdb=" OD1 ASP D 248 " -0.028 2.00e-02 2.50e+03 pdb=" OD2 ASP D 248 " -0.028 2.00e-02 2.50e+03 ... (remaining 1946 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 242 2.66 - 3.22: 10177 3.22 - 3.78: 17580 3.78 - 4.34: 22629 4.34 - 4.90: 35634 Nonbonded interactions: 86262 Sorted by model distance: nonbonded pdb=" CG2 VAL B 234 " pdb=" OD1 ASN B 235 " model vdw 2.098 3.460 nonbonded pdb=" O2' FMN G 300 " pdb=" O4' FMN G 300 " model vdw 2.161 3.040 nonbonded pdb=" SG CYS A 25 " pdb="FE FE A 200 " model vdw 2.301 2.620 nonbonded pdb=" NZ LYS G 139 " pdb=" O GLY G 153 " model vdw 2.308 3.120 nonbonded pdb=" SG CYS E 26 " pdb="FE FE A 200 " model vdw 2.312 2.620 ... (remaining 86257 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=0.00 max=1.00 mean=0.91 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.410 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 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 : 0.015 0.238 11683 Z= 0.741 Angle : 2.543 46.457 15946 Z= 1.179 Chirality : 2.554 21.307 1920 Planarity : 0.014 0.127 1949 Dihedral : 18.465 89.926 4202 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.80 % Allowed : 6.14 % Favored : 93.06 % Rotamer: Outliers : 10.79 % Allowed : 9.16 % Favored : 80.05 % Cbeta Deviations : 0.88 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.22), residues: 1499 helix: -2.83 (0.16), residues: 610 sheet: -2.47 (0.48), residues: 96 loop : 0.94 (0.24), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 114 TYR 0.037 0.005 TYR C 167 PHE 0.041 0.005 PHE B 18 TRP 0.026 0.005 TRP D 65 HIS 0.009 0.003 HIS C 419 Details of bonding type rmsd covalent geometry : bond 0.01424 (11653) covalent geometry : angle 1.95824 (15862) hydrogen bonds : bond 0.20990 ( 443) hydrogen bonds : angle 8.72876 ( 1251) metal coordination : bond 0.08277 ( 28) metal coordination : angle 22.43099 ( 84) Misc. bond : bond 0.09303 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 279 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.6867 (t80) cc_final: 0.5944 (t80) REVERT: A 125 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8181 (mm-30) REVERT: A 168 LYS cc_start: 0.8524 (mttt) cc_final: 0.8119 (mmtt) REVERT: B 119 TYR cc_start: 0.8830 (t80) cc_final: 0.8567 (t80) REVERT: B 122 MET cc_start: 0.8303 (mtm) cc_final: 0.8066 (mmt) REVERT: B 158 HIS cc_start: 0.7723 (m-70) cc_final: 0.7248 (m90) REVERT: B 160 GLU cc_start: 0.8276 (pm20) cc_final: 0.8030 (pm20) REVERT: B 231 ILE cc_start: 0.8634 (tp) cc_final: 0.8263 (mp) REVERT: B 238 PRO cc_start: 0.9337 (Cg_endo) cc_final: 0.9032 (Cg_exo) REVERT: B 241 ASP cc_start: 0.8278 (t0) cc_final: 0.7849 (t70) REVERT: C 230 THR cc_start: 0.8177 (OUTLIER) cc_final: 0.7971 (t) REVERT: C 323 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8025 (ttmt) REVERT: D 249 TYR cc_start: 0.6844 (m-10) cc_final: 0.6620 (m-10) REVERT: E 57 SER cc_start: 0.8779 (OUTLIER) cc_final: 0.8428 (t) REVERT: E 122 ASN cc_start: 0.7988 (OUTLIER) cc_final: 0.7574 (m110) REVERT: E 167 PHE cc_start: 0.6125 (OUTLIER) cc_final: 0.5433 (t80) REVERT: E 174 ILE cc_start: 0.7525 (mm) cc_final: 0.7212 (mm) outliers start: 132 outliers final: 46 residues processed: 374 average time/residue: 0.0994 time to fit residues: 53.7495 Evaluate side-chains 240 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 189 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 7.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 GLN C 73 HIS C 172 HIS C 364 ASN C 419 HIS D 66 GLN ** D 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN D 161 ASN ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 161 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.132084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.111723 restraints weight = 18166.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.112915 restraints weight = 14136.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.113564 restraints weight = 11786.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.114060 restraints weight = 10448.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.114490 restraints weight = 9637.980| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.261 11683 Z= 0.686 Angle : 4.545 56.650 15946 Z= 2.582 Chirality : 0.763 6.447 1920 Planarity : 0.006 0.052 1949 Dihedral : 8.589 89.484 1619 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.25 % Allowed : 5.97 % Favored : 93.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.20), residues: 1499 helix: -1.48 (0.17), residues: 639 sheet: -2.16 (0.51), residues: 85 loop : -0.29 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 308 TYR 0.021 0.002 TYR C 167 PHE 0.021 0.002 PHE B 18 TRP 0.011 0.001 TRP D 65 HIS 0.006 0.001 HIS C 172 Details of bonding type rmsd covalent geometry : bond 0.02026 (11653) covalent geometry : angle 3.90357 (15862) hydrogen bonds : bond 0.05139 ( 443) hydrogen bonds : angle 5.37383 ( 1251) metal coordination : bond 0.02806 ( 28) metal coordination : angle 32.30926 ( 84) Misc. bond : bond 0.00140 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 249 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 158 HIS cc_start: 0.7342 (m-70) cc_final: 0.7098 (m90) REVERT: B 241 ASP cc_start: 0.8314 (t0) cc_final: 0.8009 (t70) REVERT: C 165 GLU cc_start: 0.7964 (tt0) cc_final: 0.7711 (tt0) REVERT: C 202 ILE cc_start: 0.8659 (mp) cc_final: 0.8280 (mm) REVERT: C 429 LYS cc_start: 0.8369 (mttt) cc_final: 0.7931 (mptt) REVERT: D 133 LEU cc_start: 0.8391 (tp) cc_final: 0.8162 (tp) REVERT: D 249 TYR cc_start: 0.7466 (m-10) cc_final: 0.7023 (m-10) REVERT: E 10 ASN cc_start: 0.8582 (t0) cc_final: 0.8368 (t0) outliers start: 3 outliers final: 1 residues processed: 251 average time/residue: 0.0831 time to fit residues: 31.4986 Evaluate side-chains 180 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 87 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 142 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 5 optimal weight: 0.0000 chunk 72 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 overall best weight: 2.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN C 143 HIS C 172 HIS C 239 GLN C 422 GLN D 121 ASN ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.129009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.108347 restraints weight = 18450.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.109424 restraints weight = 14792.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.109923 restraints weight = 12479.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.110484 restraints weight = 11302.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.110551 restraints weight = 10371.901| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.244 11683 Z= 0.678 Angle : 4.527 51.871 15946 Z= 2.577 Chirality : 0.761 6.419 1920 Planarity : 0.005 0.055 1949 Dihedral : 7.706 81.779 1619 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.25 % Allowed : 4.74 % Favored : 95.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.21), residues: 1499 helix: -0.69 (0.19), residues: 651 sheet: -1.63 (0.59), residues: 78 loop : -0.53 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 68 TYR 0.021 0.002 TYR D 7 PHE 0.022 0.002 PHE D 234 TRP 0.008 0.001 TRP D 65 HIS 0.007 0.001 HIS C 143 Details of bonding type rmsd covalent geometry : bond 0.02014 (11653) covalent geometry : angle 3.89138 (15862) hydrogen bonds : bond 0.04389 ( 443) hydrogen bonds : angle 4.83816 ( 1251) metal coordination : bond 0.01732 ( 28) metal coordination : angle 32.11483 ( 84) Misc. bond : bond 0.00257 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 231 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.6859 (t80) cc_final: 0.6470 (t80) REVERT: C 165 GLU cc_start: 0.8142 (tt0) cc_final: 0.7646 (tt0) REVERT: C 202 ILE cc_start: 0.8562 (mp) cc_final: 0.8119 (mm) REVERT: C 261 ILE cc_start: 0.7555 (mt) cc_final: 0.7190 (mt) REVERT: C 335 MET cc_start: 0.7483 (mmm) cc_final: 0.6953 (mmt) REVERT: C 429 LYS cc_start: 0.8572 (mttt) cc_final: 0.8100 (mptt) REVERT: D 64 ILE cc_start: 0.8995 (mm) cc_final: 0.8699 (mm) REVERT: D 249 TYR cc_start: 0.7613 (m-10) cc_final: 0.7244 (m-80) REVERT: E 25 MET cc_start: 0.7920 (mmm) cc_final: 0.7637 (mmt) REVERT: E 187 MET cc_start: 0.8520 (ttp) cc_final: 0.7965 (ttp) outliers start: 3 outliers final: 1 residues processed: 233 average time/residue: 0.0918 time to fit residues: 31.9068 Evaluate side-chains 167 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 126 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 35 optimal weight: 20.0000 chunk 140 optimal weight: 20.0000 chunk 85 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 ASN D 121 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.123628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.100100 restraints weight = 19436.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.100356 restraints weight = 16413.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.100810 restraints weight = 14972.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.100951 restraints weight = 12965.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.101129 restraints weight = 12520.329| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.240 11683 Z= 0.695 Angle : 4.587 57.371 15946 Z= 2.594 Chirality : 0.762 6.411 1920 Planarity : 0.006 0.059 1949 Dihedral : 7.997 80.848 1619 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.16 % Allowed : 7.20 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.21), residues: 1499 helix: -0.73 (0.19), residues: 640 sheet: -1.40 (0.60), residues: 77 loop : -0.75 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 284 TYR 0.023 0.003 TYR C 232 PHE 0.039 0.003 PHE D 89 TRP 0.011 0.002 TRP D 65 HIS 0.005 0.002 HIS C 419 Details of bonding type rmsd covalent geometry : bond 0.02015 (11653) covalent geometry : angle 3.93049 (15862) hydrogen bonds : bond 0.04518 ( 443) hydrogen bonds : angle 5.13965 ( 1251) metal coordination : bond 0.02628 ( 28) metal coordination : angle 32.80902 ( 84) Misc. bond : bond 0.00131 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 226 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.7633 (mmt) cc_final: 0.7103 (mmp) REVERT: A 99 TYR cc_start: 0.7341 (t80) cc_final: 0.6877 (t80) REVERT: B 122 MET cc_start: 0.8344 (mmt) cc_final: 0.8090 (mmt) REVERT: C 60 LYS cc_start: 0.8677 (ptpp) cc_final: 0.8386 (mttt) REVERT: C 125 ASN cc_start: 0.8481 (m-40) cc_final: 0.8116 (m110) REVERT: C 165 GLU cc_start: 0.8430 (tt0) cc_final: 0.7945 (tt0) REVERT: C 335 MET cc_start: 0.8114 (mmm) cc_final: 0.7449 (mmt) REVERT: C 429 LYS cc_start: 0.8703 (mttt) cc_final: 0.8220 (mptt) REVERT: D 64 ILE cc_start: 0.9104 (mm) cc_final: 0.8855 (mm) REVERT: E 187 MET cc_start: 0.8732 (ttp) cc_final: 0.8405 (ttp) outliers start: 2 outliers final: 0 residues processed: 227 average time/residue: 0.1001 time to fit residues: 33.2351 Evaluate side-chains 165 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 105 optimal weight: 0.9980 chunk 131 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 128 optimal weight: 0.0370 chunk 108 optimal weight: 5.9990 overall best weight: 1.0060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 ASN C 172 HIS D 121 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.129402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.108556 restraints weight = 18496.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.108332 restraints weight = 16602.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.108516 restraints weight = 16072.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.108692 restraints weight = 14543.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.108900 restraints weight = 13713.775| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.247 11683 Z= 0.683 Angle : 4.513 50.623 15946 Z= 2.573 Chirality : 0.761 6.390 1920 Planarity : 0.005 0.057 1949 Dihedral : 7.240 74.867 1619 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.08 % Allowed : 2.86 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.21), residues: 1499 helix: -0.44 (0.20), residues: 656 sheet: -1.25 (0.60), residues: 77 loop : -0.86 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 284 TYR 0.024 0.002 TYR D 7 PHE 0.014 0.001 PHE D 234 TRP 0.008 0.001 TRP D 144 HIS 0.004 0.001 HIS C 172 Details of bonding type rmsd covalent geometry : bond 0.02033 (11653) covalent geometry : angle 3.88617 (15862) hydrogen bonds : bond 0.03929 ( 443) hydrogen bonds : angle 4.61770 ( 1251) metal coordination : bond 0.01807 ( 28) metal coordination : angle 31.85422 ( 84) Misc. bond : bond 0.00010 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 229 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 60 LYS cc_start: 0.8483 (ptpp) cc_final: 0.8268 (mttt) REVERT: C 121 GLU cc_start: 0.7416 (tp30) cc_final: 0.7023 (tp30) REVERT: C 125 ASN cc_start: 0.8450 (m-40) cc_final: 0.7608 (m-40) REVERT: C 165 GLU cc_start: 0.8339 (tt0) cc_final: 0.7936 (tt0) REVERT: C 335 MET cc_start: 0.7771 (mmm) cc_final: 0.7096 (mmt) REVERT: C 429 LYS cc_start: 0.8327 (mttt) cc_final: 0.7976 (mptt) REVERT: D 41 TYR cc_start: 0.6854 (p90) cc_final: 0.5061 (t80) REVERT: D 64 ILE cc_start: 0.9036 (mm) cc_final: 0.8824 (mm) REVERT: D 133 LEU cc_start: 0.8434 (tp) cc_final: 0.8108 (tt) REVERT: D 211 SER cc_start: 0.8948 (p) cc_final: 0.8725 (t) REVERT: E 121 LYS cc_start: 0.7769 (mtmm) cc_final: 0.7431 (mtmm) REVERT: E 187 MET cc_start: 0.8595 (ttp) cc_final: 0.8291 (ttp) outliers start: 1 outliers final: 1 residues processed: 230 average time/residue: 0.0943 time to fit residues: 32.1442 Evaluate side-chains 166 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 56 optimal weight: 2.9990 chunk 106 optimal weight: 0.0370 chunk 22 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 45 optimal weight: 0.4980 overall best weight: 1.7064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 264 ASN ** C 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.128786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.106260 restraints weight = 18783.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.106902 restraints weight = 14807.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.107046 restraints weight = 12879.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.107050 restraints weight = 12109.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.107109 restraints weight = 11543.471| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.244 11683 Z= 0.678 Angle : 4.517 53.145 15946 Z= 2.574 Chirality : 0.761 6.368 1920 Planarity : 0.004 0.046 1949 Dihedral : 6.896 71.959 1619 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.08 % Allowed : 2.37 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.21), residues: 1499 helix: -0.25 (0.20), residues: 649 sheet: -1.12 (0.62), residues: 72 loop : -0.89 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 284 TYR 0.023 0.002 TYR D 7 PHE 0.016 0.002 PHE D 219 TRP 0.006 0.001 TRP D 144 HIS 0.002 0.001 HIS D 14 Details of bonding type rmsd covalent geometry : bond 0.02017 (11653) covalent geometry : angle 3.88740 (15862) hydrogen bonds : bond 0.03766 ( 443) hydrogen bonds : angle 4.52632 ( 1251) metal coordination : bond 0.01397 ( 28) metal coordination : angle 31.93804 ( 84) Misc. bond : bond 0.00043 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 221 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.7891 (mmm) cc_final: 0.7661 (tpt) REVERT: C 60 LYS cc_start: 0.8617 (ptpp) cc_final: 0.8298 (mttt) REVERT: C 121 GLU cc_start: 0.7575 (tp30) cc_final: 0.7129 (tp30) REVERT: C 125 ASN cc_start: 0.8506 (m-40) cc_final: 0.7645 (m-40) REVERT: C 165 GLU cc_start: 0.8383 (tt0) cc_final: 0.7883 (tt0) REVERT: C 273 ASN cc_start: 0.8056 (m-40) cc_final: 0.7736 (m-40) REVERT: C 331 MET cc_start: 0.8277 (mtp) cc_final: 0.7991 (mtt) REVERT: C 429 LYS cc_start: 0.8363 (mttt) cc_final: 0.8038 (mptt) REVERT: D 41 TYR cc_start: 0.6956 (p90) cc_final: 0.5094 (t80) REVERT: D 133 LEU cc_start: 0.8253 (tp) cc_final: 0.7877 (tt) REVERT: E 121 LYS cc_start: 0.7714 (mtmm) cc_final: 0.7463 (mtmm) REVERT: E 187 MET cc_start: 0.8649 (ttp) cc_final: 0.8397 (ttp) outliers start: 1 outliers final: 0 residues processed: 222 average time/residue: 0.0955 time to fit residues: 31.3686 Evaluate side-chains 165 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 86 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 104 optimal weight: 0.7980 chunk 127 optimal weight: 0.0050 chunk 81 optimal weight: 0.9980 chunk 142 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 137 optimal weight: 20.0000 chunk 79 optimal weight: 2.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** C 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.131185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.109891 restraints weight = 18623.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.110251 restraints weight = 16916.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.110400 restraints weight = 13902.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.110547 restraints weight = 13222.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.110738 restraints weight = 12616.870| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.246 11683 Z= 0.682 Angle : 4.500 50.582 15946 Z= 2.570 Chirality : 0.761 6.395 1920 Planarity : 0.004 0.041 1949 Dihedral : 6.590 67.382 1619 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.21), residues: 1499 helix: -0.16 (0.20), residues: 664 sheet: -1.09 (0.60), residues: 77 loop : -0.91 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 284 TYR 0.024 0.001 TYR D 7 PHE 0.013 0.001 PHE D 293 TRP 0.006 0.001 TRP D 137 HIS 0.004 0.001 HIS C 172 Details of bonding type rmsd covalent geometry : bond 0.02032 (11653) covalent geometry : angle 3.88023 (15862) hydrogen bonds : bond 0.03569 ( 443) hydrogen bonds : angle 4.38966 ( 1251) metal coordination : bond 0.01924 ( 28) metal coordination : angle 31.65127 ( 84) Misc. bond : bond 0.00017 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 MET cc_start: 0.8327 (mmm) cc_final: 0.7966 (mmm) REVERT: C 60 LYS cc_start: 0.8515 (ptpp) cc_final: 0.8264 (mttt) REVERT: C 121 GLU cc_start: 0.7452 (tp30) cc_final: 0.7042 (tp30) REVERT: C 125 ASN cc_start: 0.8482 (m-40) cc_final: 0.7565 (m-40) REVERT: C 135 MET cc_start: 0.8105 (ptp) cc_final: 0.7384 (mtm) REVERT: C 165 GLU cc_start: 0.8337 (tt0) cc_final: 0.7893 (tt0) REVERT: C 322 LEU cc_start: 0.8568 (pt) cc_final: 0.8111 (pp) REVERT: C 330 MET cc_start: 0.8260 (mtm) cc_final: 0.8006 (mtm) REVERT: C 331 MET cc_start: 0.8330 (mtp) cc_final: 0.8103 (ttt) REVERT: C 429 LYS cc_start: 0.8298 (mttt) cc_final: 0.7961 (mptt) REVERT: D 41 TYR cc_start: 0.6934 (p90) cc_final: 0.5091 (t80) REVERT: D 64 ILE cc_start: 0.9003 (mm) cc_final: 0.8770 (mm) REVERT: E 25 MET cc_start: 0.7597 (mmm) cc_final: 0.7315 (tpp) REVERT: E 121 LYS cc_start: 0.7644 (mtmm) cc_final: 0.7411 (mtmm) REVERT: E 187 MET cc_start: 0.8617 (ttp) cc_final: 0.8386 (ttp) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.0851 time to fit residues: 29.9141 Evaluate side-chains 167 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 98 optimal weight: 0.5980 chunk 79 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 92 optimal weight: 0.0010 chunk 39 optimal weight: 0.7980 chunk 83 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 20.0000 chunk 61 optimal weight: 5.9990 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 HIS ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.130953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.108735 restraints weight = 19169.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.108825 restraints weight = 16448.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.109206 restraints weight = 14141.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.109505 restraints weight = 12449.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.109750 restraints weight = 11653.913| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.244 11683 Z= 0.680 Angle : 4.500 51.172 15946 Z= 2.570 Chirality : 0.760 6.416 1920 Planarity : 0.004 0.041 1949 Dihedral : 6.382 64.648 1619 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.21), residues: 1499 helix: -0.14 (0.20), residues: 668 sheet: -0.91 (0.63), residues: 72 loop : -0.88 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 149 TYR 0.022 0.001 TYR D 7 PHE 0.011 0.001 PHE D 219 TRP 0.004 0.001 TRP D 65 HIS 0.001 0.000 HIS C 172 Details of bonding type rmsd covalent geometry : bond 0.02028 (11653) covalent geometry : angle 3.87984 (15862) hydrogen bonds : bond 0.03518 ( 443) hydrogen bonds : angle 4.34009 ( 1251) metal coordination : bond 0.01424 ( 28) metal coordination : angle 31.63566 ( 84) Misc. bond : bond 0.00024 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 60 LYS cc_start: 0.8563 (ptpp) cc_final: 0.8262 (mttt) REVERT: C 121 GLU cc_start: 0.7526 (tp30) cc_final: 0.7084 (tp30) REVERT: C 125 ASN cc_start: 0.8502 (m-40) cc_final: 0.7573 (m-40) REVERT: C 135 MET cc_start: 0.8272 (ptp) cc_final: 0.7378 (mtm) REVERT: C 165 GLU cc_start: 0.8369 (tt0) cc_final: 0.7926 (tt0) REVERT: C 322 LEU cc_start: 0.8614 (pt) cc_final: 0.8188 (pp) REVERT: C 330 MET cc_start: 0.8249 (mtm) cc_final: 0.8026 (mtm) REVERT: C 429 LYS cc_start: 0.8295 (mttt) cc_final: 0.7977 (mptt) REVERT: D 41 TYR cc_start: 0.6921 (p90) cc_final: 0.5119 (t80) REVERT: D 64 ILE cc_start: 0.8961 (mm) cc_final: 0.8742 (mm) REVERT: E 121 LYS cc_start: 0.7691 (mtmm) cc_final: 0.7464 (mtmm) REVERT: E 187 MET cc_start: 0.8656 (ttp) cc_final: 0.8420 (ttp) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.0838 time to fit residues: 27.4144 Evaluate side-chains 163 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 127 optimal weight: 6.9990 chunk 89 optimal weight: 0.6980 chunk 121 optimal weight: 0.2980 chunk 11 optimal weight: 7.9990 chunk 131 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 133 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.131303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.109523 restraints weight = 19041.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.110075 restraints weight = 16446.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.110381 restraints weight = 13184.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.110566 restraints weight = 12064.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.110710 restraints weight = 11384.992| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.243 11683 Z= 0.680 Angle : 4.504 52.140 15946 Z= 2.572 Chirality : 0.760 6.406 1920 Planarity : 0.004 0.042 1949 Dihedral : 6.212 61.631 1619 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.21), residues: 1499 helix: -0.17 (0.20), residues: 670 sheet: -0.84 (0.64), residues: 72 loop : -0.86 (0.22), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 284 TYR 0.019 0.001 TYR D 7 PHE 0.011 0.001 PHE D 293 TRP 0.009 0.001 TRP D 137 HIS 0.008 0.001 HIS C 172 Details of bonding type rmsd covalent geometry : bond 0.02026 (11653) covalent geometry : angle 3.88599 (15862) hydrogen bonds : bond 0.03490 ( 443) hydrogen bonds : angle 4.39133 ( 1251) metal coordination : bond 0.01397 ( 28) metal coordination : angle 31.61773 ( 84) Misc. bond : bond 0.00029 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.7632 (tpp) cc_final: 0.7306 (tpt) REVERT: C 60 LYS cc_start: 0.8539 (ptpp) cc_final: 0.8231 (mttt) REVERT: C 121 GLU cc_start: 0.7453 (tp30) cc_final: 0.7045 (tp30) REVERT: C 125 ASN cc_start: 0.8473 (m-40) cc_final: 0.7530 (m-40) REVERT: C 135 MET cc_start: 0.8255 (ptp) cc_final: 0.7903 (mtm) REVERT: C 165 GLU cc_start: 0.8290 (tt0) cc_final: 0.7920 (tt0) REVERT: C 322 LEU cc_start: 0.8581 (pt) cc_final: 0.8167 (pp) REVERT: C 429 LYS cc_start: 0.8192 (mttt) cc_final: 0.7976 (mptt) REVERT: D 41 TYR cc_start: 0.6932 (p90) cc_final: 0.5136 (t80) REVERT: D 64 ILE cc_start: 0.8969 (mm) cc_final: 0.8765 (mm) REVERT: E 21 GLN cc_start: 0.7791 (mt0) cc_final: 0.7527 (mp10) REVERT: E 121 LYS cc_start: 0.7675 (mtmm) cc_final: 0.7429 (mtmm) REVERT: E 187 MET cc_start: 0.8668 (ttp) cc_final: 0.8467 (ttp) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.0833 time to fit residues: 26.6961 Evaluate side-chains 163 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 58 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 123 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 121 optimal weight: 0.0070 chunk 107 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 HIS ** C 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.132244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.109997 restraints weight = 18913.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.110235 restraints weight = 17129.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.110648 restraints weight = 13871.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.110822 restraints weight = 12249.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.111047 restraints weight = 11600.970| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.4970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.243 11683 Z= 0.681 Angle : 4.503 54.757 15946 Z= 2.571 Chirality : 0.760 6.392 1920 Planarity : 0.004 0.039 1949 Dihedral : 6.048 58.088 1619 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.21), residues: 1499 helix: -0.16 (0.20), residues: 676 sheet: -0.84 (0.63), residues: 72 loop : -0.81 (0.23), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 130 TYR 0.019 0.001 TYR D 7 PHE 0.010 0.001 PHE C 89 TRP 0.005 0.001 TRP D 144 HIS 0.002 0.001 HIS C 172 Details of bonding type rmsd covalent geometry : bond 0.02031 (11653) covalent geometry : angle 3.88419 (15862) hydrogen bonds : bond 0.03441 ( 443) hydrogen bonds : angle 4.30079 ( 1251) metal coordination : bond 0.01580 ( 28) metal coordination : angle 31.61842 ( 84) Misc. bond : bond 0.00018 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2998 Ramachandran restraints generated. 1499 Oldfield, 0 Emsley, 1499 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.7624 (tpp) cc_final: 0.7278 (tpt) REVERT: C 60 LYS cc_start: 0.8588 (ptpp) cc_final: 0.8261 (mttt) REVERT: C 121 GLU cc_start: 0.7511 (tp30) cc_final: 0.7077 (tp30) REVERT: C 125 ASN cc_start: 0.8494 (m-40) cc_final: 0.7546 (m-40) REVERT: C 135 MET cc_start: 0.7489 (ptp) cc_final: 0.7055 (mtm) REVERT: C 165 GLU cc_start: 0.8323 (tt0) cc_final: 0.7864 (tt0) REVERT: C 322 LEU cc_start: 0.8514 (pt) cc_final: 0.8022 (pp) REVERT: C 331 MET cc_start: 0.8117 (mtp) cc_final: 0.7880 (ttt) REVERT: C 429 LYS cc_start: 0.8302 (mttt) cc_final: 0.7982 (mptt) REVERT: D 41 TYR cc_start: 0.6930 (p90) cc_final: 0.5156 (t80) REVERT: D 64 ILE cc_start: 0.8972 (mm) cc_final: 0.8748 (mm) REVERT: E 121 LYS cc_start: 0.7626 (mtmm) cc_final: 0.7375 (mtmm) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.0820 time to fit residues: 27.5972 Evaluate side-chains 162 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 46 optimal weight: 30.0000 chunk 10 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 128 optimal weight: 0.0000 chunk 57 optimal weight: 5.9990 chunk 132 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 chunk 118 optimal weight: 0.0570 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.126081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.105486 restraints weight = 18540.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.105152 restraints weight = 15311.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.105295 restraints weight = 15046.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.105443 restraints weight = 13714.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.105562 restraints weight = 13208.691| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.5008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.241 11683 Z= 0.677 Angle : 4.520 54.369 15946 Z= 2.576 Chirality : 0.761 6.414 1920 Planarity : 0.004 0.040 1949 Dihedral : 6.009 57.175 1619 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.08 % Allowed : 0.33 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.21), residues: 1499 helix: -0.16 (0.20), residues: 656 sheet: -0.83 (0.63), residues: 72 loop : -0.88 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 299 TYR 0.017 0.002 TYR D 7 PHE 0.012 0.002 PHE D 262 TRP 0.008 0.001 TRP D 65 HIS 0.008 0.001 HIS C 172 Details of bonding type rmsd covalent geometry : bond 0.02008 (11653) covalent geometry : angle 3.89244 (15862) hydrogen bonds : bond 0.03657 ( 443) hydrogen bonds : angle 4.42516 ( 1251) metal coordination : bond 0.01525 ( 28) metal coordination : angle 31.88937 ( 84) Misc. bond : bond 0.00049 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1669.37 seconds wall clock time: 29 minutes 38.74 seconds (1778.74 seconds total)