Starting phenix.real_space_refine on Fri Jul 3 01:37:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zc6_14622/07_2026/7zc6_14622.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zc6_14622/07_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_14622/07_2026/7zc6_14622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zc6_14622/07_2026/7zc6_14622.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7zc6_14622/07_2026/7zc6_14622.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zc6_14622/07_2026/7zc6_14622.cif" model { file = "/net/cci-nas-00/data/ceres_data/7zc6_14622/07_2026/7zc6_14622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zc6_14622/07_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-6108/lib/python3.11/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 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 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: 2.15, per 1000 atoms: 0.19 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: 0.90 Conformation dependent library (CDL) restraints added in 470.6 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: 0.32 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: 1.61 Time building geometry restraints manager: 1.21 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 1.230 1.402 -0.172 2.00e-02 2.50e+03 7.39e+01 bond pdb=" C2 FMN D 400 " pdb=" O2 FMN D 400 " ideal model delta sigma weight residual 1.230 1.398 -0.168 2.00e-02 2.50e+03 7.02e+01 bond pdb=" C2 FMN G 300 " pdb=" O2 FMN G 300 " ideal model delta sigma weight residual 1.230 1.394 -0.164 2.00e-02 2.50e+03 6.72e+01 bond pdb=" C2 FMN C 503 " pdb=" O2 FMN C 503 " ideal model delta sigma weight residual 1.230 1.392 -0.162 2.00e-02 2.50e+03 6.58e+01 ... (remaining 11648 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.67: 14773 3.67 - 7.33: 968 7.33 - 11.00: 110 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 - 34.69: 6577 34.69 - 69.37: 316 69.37 - 104.06: 16 104.06 - 138.74: 1 138.74 - 173.42: 3 Dihedral angle restraints: 6913 sinusoidal: 2637 harmonic: 4276 Sorted by residual: dihedral pdb=" C10 FMN D 400 " pdb=" C1' FMN D 400 " pdb=" N10 FMN D 400 " pdb=" C2' FMN D 400 " ideal model delta sinusoidal sigma weight residual -102.41 71.02 -173.42 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C10 FMN G 300 " pdb=" C1' FMN G 300 " pdb=" N10 FMN G 300 " pdb=" C2' FMN G 300 " ideal model delta sinusoidal sigma weight residual 257.59 93.16 164.43 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" C10 FMN C 503 " pdb=" C1' FMN C 503 " pdb=" N10 FMN C 503 " pdb=" C2' FMN C 503 " ideal model delta sinusoidal sigma weight residual 257.59 102.47 155.12 1 2.00e+01 2.50e-03 4.58e+01 ... (remaining 6910 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: 1946 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 1943 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.150 Find NCS groups from input model: 0.070 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 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= 0.734 Angle : 2.534 46.457 15946 Z= 1.177 Chirality : 2.554 21.307 1920 Planarity : 0.014 0.127 1946 Dihedral : 19.197 173.425 4183 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/Z covalent geometry : bond 0.01409 / 0.72 (11653) covalent geometry : angle 1.94700 / 1.17 (15862) hydrogen bonds : bond 0.20990 / 13.21 ( 443) hydrogen bonds : angle 8.72876 / 6.12 ( 1251) metal coordination : bond 0.08277 / 4.64 ( 28) metal coordination : angle 22.43099 / 15.25 ( 84) Misc. bond : bond 0.09303 / 4.79 ( 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: 0.0913 time to fit residues: 49.6168 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 : 0.482 ------------------------------------------------------------------------------- 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... C 39 GLN C 73 HIS C 172 HIS C 419 HIS D 66 GLN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.131890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.111562 restraints weight = 18200.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.112774 restraints weight = 14208.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.113402 restraints weight = 11824.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.113816 restraints weight = 10535.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.114301 restraints weight = 9723.903| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.021 0.261 11683 Z= 0.695 Angle : 4.544 54.922 15946 Z= 2.580 Chirality : 0.765 6.483 1920 Planarity : 0.006 0.054 1946 Dihedral : 11.657 167.783 1600 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.33 % Allowed : 5.23 % Favored : 94.44 % 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: -1.53 (0.20), residues: 1499 helix: -1.54 (0.17), residues: 637 sheet: -2.17 (0.51), residues: 85 loop : -0.22 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 308 TYR 0.024 0.002 TYR C 167 PHE 0.023 0.002 PHE B 18 TRP 0.011 0.001 TRP D 65 HIS 0.004 0.001 HIS D 14 Details of bonding type rmsd/Z covalent geometry : bond 0.02053 / 0.69 (11653) covalent geometry : angle 3.90190 / 2.58 (15862) hydrogen bonds : bond 0.05510 / 3.58 ( 443) hydrogen bonds : angle 5.48476 / 3.74 ( 1251) metal coordination : bond 0.02855 / 1.98 ( 28) metal coordination : angle 32.31348 / 21.96 ( 84) Misc. bond : bond 0.00057 / 0.03 ( 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 251 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 247 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: B 158 HIS cc_start: 0.7366 (m-70) cc_final: 0.7091 (m90) REVERT: B 241 ASP cc_start: 0.8291 (t0) cc_final: 0.7986 (t70) REVERT: C 239 GLN cc_start: 0.8564 (mm-40) cc_final: 0.8354 (mm-40) REVERT: C 429 LYS cc_start: 0.8323 (mttt) cc_final: 0.7898 (mptt) REVERT: D 133 LEU cc_start: 0.8408 (tp) cc_final: 0.8149 (tp) REVERT: D 249 TYR cc_start: 0.7453 (m-10) cc_final: 0.7087 (m-10) REVERT: E 10 ASN cc_start: 0.8531 (t0) cc_final: 0.8309 (t0) REVERT: E 187 MET cc_start: 0.8175 (ttp) cc_final: 0.7668 (ttp) outliers start: 4 outliers final: 2 residues processed: 250 average time/residue: 0.0867 time to fit residues: 32.8016 Evaluate side-chains 176 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 174 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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: 0.0040 chunk 75 optimal weight: 8.9990 chunk 110 optimal weight: 0.3980 chunk 142 optimal weight: 20.0000 chunk 127 optimal weight: 1.9990 chunk 5 optimal weight: 0.0270 chunk 72 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 overall best weight: 0.8854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 143 HIS C 172 HIS C 422 GLN D 121 ASN ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.132621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.114266 restraints weight = 18148.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.114382 restraints weight = 17763.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.114728 restraints weight = 15397.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.115131 restraints weight = 13888.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.115252 restraints weight = 12393.261| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.3450 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= 0.682 Angle : 4.518 52.363 15946 Z= 2.574 Chirality : 0.761 6.381 1920 Planarity : 0.005 0.046 1946 Dihedral : 10.653 167.620 1600 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.25 % Allowed : 4.66 % Favored : 95.09 % 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: -1.17 (0.20), residues: 1499 helix: -0.73 (0.19), residues: 654 sheet: -1.72 (0.56), residues: 85 loop : -0.55 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 68 TYR 0.021 0.002 TYR D 7 PHE 0.019 0.001 PHE B 18 TRP 0.006 0.001 TRP D 65 HIS 0.010 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.02029 / 0.68 (11653) covalent geometry : angle 3.88681 / 2.57 (15862) hydrogen bonds : bond 0.04267 / 2.84 ( 443) hydrogen bonds : angle 4.78180 / 3.20 ( 1251) metal coordination : bond 0.02016 / 1.38 ( 28) metal coordination : angle 31.96481 / 21.65 ( 84) Misc. bond : bond 0.00038 / 0.02 ( 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 237 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 234 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.6664 (t80) cc_final: 0.6034 (t80) REVERT: C 125 ASN cc_start: 0.8042 (m110) cc_final: 0.7807 (m110) REVERT: C 335 MET cc_start: 0.7320 (mmm) cc_final: 0.6864 (mmt) REVERT: C 429 LYS cc_start: 0.8377 (mttt) cc_final: 0.7979 (mptt) REVERT: D 64 ILE cc_start: 0.9000 (mm) cc_final: 0.8732 (mm) REVERT: D 133 LEU cc_start: 0.8333 (tp) cc_final: 0.8020 (tt) REVERT: D 249 TYR cc_start: 0.7394 (m-10) cc_final: 0.7140 (m-10) REVERT: E 25 MET cc_start: 0.7784 (mmm) cc_final: 0.7479 (tpp) outliers start: 3 outliers final: 1 residues processed: 236 average time/residue: 0.0758 time to fit residues: 27.5408 Evaluate side-chains 172 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 171 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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: 9.9990 chunk 82 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 110 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 140 optimal weight: 20.0000 chunk 85 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 HIS C 71 ASN C 239 GLN D 121 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.123734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.103342 restraints weight = 18800.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.103640 restraints weight = 20836.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.104625 restraints weight = 16415.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.104738 restraints weight = 13344.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.104816 restraints weight = 13212.199| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3903 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= 0.688 Angle : 4.569 54.534 15946 Z= 2.588 Chirality : 0.760 6.380 1920 Planarity : 0.005 0.050 1946 Dihedral : 10.529 170.195 1600 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.25 % Allowed : 5.72 % Favored : 94.03 % 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: -1.15 (0.21), residues: 1499 helix: -0.61 (0.20), residues: 648 sheet: -1.44 (0.61), residues: 76 loop : -0.72 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 308 TYR 0.023 0.003 TYR E 72 PHE 0.030 0.003 PHE D 89 TRP 0.010 0.002 TRP D 65 HIS 0.005 0.002 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.02013 / 0.69 (11653) covalent geometry : angle 3.91776 / 2.59 (15862) hydrogen bonds : bond 0.04300 / 2.85 ( 443) hydrogen bonds : angle 4.96090 / 3.34 ( 1251) metal coordination : bond 0.02303 / 1.34 ( 28) metal coordination : angle 32.63711 / 21.80 ( 84) Misc. bond : bond 0.00488 / 0.23 ( 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: 3 poor density : 225 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.6961 (t80) cc_final: 0.6735 (t80) REVERT: C 125 ASN cc_start: 0.8210 (m110) cc_final: 0.7961 (m110) REVERT: C 165 GLU cc_start: 0.8260 (tt0) cc_final: 0.7735 (tt0) REVERT: C 210 ILE cc_start: 0.8027 (pt) cc_final: 0.7792 (tp) REVERT: C 239 GLN cc_start: 0.8620 (mp10) cc_final: 0.8267 (mp10) REVERT: C 335 MET cc_start: 0.7937 (mmm) cc_final: 0.7362 (mmt) REVERT: C 429 LYS cc_start: 0.8626 (mttt) cc_final: 0.8193 (mptt) REVERT: D 64 ILE cc_start: 0.9056 (mm) cc_final: 0.8831 (mm) REVERT: E 25 MET cc_start: 0.7727 (mmm) cc_final: 0.7432 (tpp) outliers start: 3 outliers final: 1 residues processed: 227 average time/residue: 0.0964 time to fit residues: 32.4570 Evaluate side-chains 172 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 171 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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: 5.9990 chunk 131 optimal weight: 0.0980 chunk 98 optimal weight: 0.0000 chunk 19 optimal weight: 8.9990 chunk 127 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 139 optimal weight: 20.0000 chunk 128 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN D 121 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 = 0.3701 r_free = 0.3701 target = 0.129618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.107688 restraints weight = 18575.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.107975 restraints weight = 15252.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.108196 restraints weight = 12680.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.108508 restraints weight = 11305.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.108623 restraints weight = 10736.539| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.245 11683 Z= 0.676 Angle : 4.517 53.333 15946 Z= 2.573 Chirality : 0.762 6.358 1920 Planarity : 0.005 0.121 1946 Dihedral : 10.277 170.244 1600 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % 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: -1.03 (0.21), residues: 1499 helix: -0.36 (0.20), residues: 649 sheet: -1.32 (0.59), residues: 77 loop : -0.80 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 284 TYR 0.023 0.002 TYR D 7 PHE 0.013 0.001 PHE D 234 TRP 0.006 0.001 TRP D 144 HIS 0.003 0.001 HIS D 14 Details of bonding type rmsd/Z covalent geometry : bond 0.02011 / 0.68 (11653) covalent geometry : angle 3.88492 / 2.57 (15862) hydrogen bonds : bond 0.03907 / 2.59 ( 443) hydrogen bonds : angle 4.64187 / 3.12 ( 1251) metal coordination : bond 0.01603 / 1.19 ( 28) metal coordination : angle 31.99851 / 21.51 ( 84) Misc. bond : bond 0.00106 / 0.05 ( 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 225 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.6940 (t80) cc_final: 0.6347 (t80) REVERT: B 149 VAL cc_start: 0.8048 (m) cc_final: 0.7210 (t) REVERT: B 158 HIS cc_start: 0.7496 (m90) cc_final: 0.7287 (m90) REVERT: C 107 GLU cc_start: 0.6755 (pp20) cc_final: 0.6484 (pp20) REVERT: C 121 GLU cc_start: 0.7318 (tp30) cc_final: 0.7031 (tp30) REVERT: C 125 ASN cc_start: 0.8307 (m110) cc_final: 0.7406 (m110) REVERT: C 165 GLU cc_start: 0.8321 (tt0) cc_final: 0.7788 (tt0) REVERT: C 429 LYS cc_start: 0.8506 (mttt) cc_final: 0.8032 (mptt) REVERT: D 211 SER cc_start: 0.8915 (p) cc_final: 0.8706 (t) REVERT: E 25 MET cc_start: 0.7839 (mmm) cc_final: 0.7478 (tpp) REVERT: E 187 MET cc_start: 0.8758 (ttm) cc_final: 0.8472 (ttp) outliers start: 1 outliers final: 1 residues processed: 225 average time/residue: 0.0946 time to fit residues: 31.6980 Evaluate side-chains 169 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 168 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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: 10.0000 chunk 106 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN 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 = 0.3638 r_free = 0.3638 target = 0.124852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.103234 restraints weight = 18985.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.103721 restraints weight = 14187.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.103695 restraints weight = 12379.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.103770 restraints weight = 11755.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.103912 restraints weight = 11219.529| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.242 11683 Z= 0.681 Angle : 4.546 54.387 15946 Z= 2.581 Chirality : 0.761 6.407 1920 Planarity : 0.005 0.046 1946 Dihedral : 10.346 176.205 1600 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.08 % Allowed : 3.92 % Favored : 95.99 % 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: -0.95 (0.21), residues: 1499 helix: -0.28 (0.20), residues: 631 sheet: -1.02 (0.64), residues: 70 loop : -0.81 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 284 TYR 0.022 0.002 TYR D 7 PHE 0.026 0.002 PHE D 89 TRP 0.009 0.002 TRP D 65 HIS 0.003 0.001 HIS C 172 Details of bonding type rmsd/Z covalent geometry : bond 0.02003 / 0.68 (11653) covalent geometry : angle 3.90321 / 2.58 (15862) hydrogen bonds : bond 0.04120 / 2.74 ( 443) hydrogen bonds : angle 4.78930 / 3.22 ( 1251) metal coordination : bond 0.01827 / 1.16 ( 28) metal coordination : angle 32.33683 / 21.63 ( 84) Misc. bond : bond 0.00169 / 0.09 ( 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 224 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 223 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.7118 (t80) cc_final: 0.6918 (t80) REVERT: B 122 MET cc_start: 0.8428 (mmt) cc_final: 0.7977 (mmt) REVERT: C 107 GLU cc_start: 0.6864 (pp20) cc_final: 0.6289 (pp20) REVERT: C 125 ASN cc_start: 0.8278 (m110) cc_final: 0.8014 (m110) REVERT: C 165 GLU cc_start: 0.8384 (tt0) cc_final: 0.7826 (tt0) REVERT: C 239 GLN cc_start: 0.8656 (mp-120) cc_final: 0.8352 (mp10) REVERT: C 335 MET cc_start: 0.7669 (mmm) cc_final: 0.7089 (mmt) REVERT: C 429 LYS cc_start: 0.8623 (mttt) cc_final: 0.8118 (mptt) REVERT: D 41 TYR cc_start: 0.7106 (p90) cc_final: 0.5290 (t80) REVERT: D 64 ILE cc_start: 0.9029 (mm) cc_final: 0.8775 (mm) REVERT: E 25 MET cc_start: 0.7865 (mmm) cc_final: 0.7503 (tpp) REVERT: E 187 MET cc_start: 0.8759 (ttm) cc_final: 0.8532 (ttp) outliers start: 1 outliers final: 0 residues processed: 224 average time/residue: 0.0984 time to fit residues: 32.7673 Evaluate side-chains 164 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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: 1.9990 chunk 26 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 chunk 127 optimal weight: 0.0370 chunk 81 optimal weight: 0.5980 chunk 142 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 137 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 overall best weight: 0.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 239 GLN C 263 GLN ** C 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.129968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.107618 restraints weight = 18384.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.108498 restraints weight = 16915.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.109503 restraints weight = 13002.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.109519 restraints weight = 11115.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.109587 restraints weight = 10698.305| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4572 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= 0.681 Angle : 4.507 52.904 15946 Z= 2.571 Chirality : 0.761 6.438 1920 Planarity : 0.004 0.041 1946 Dihedral : 10.056 171.166 1600 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.08 % Allowed : 2.53 % Favored : 97.38 % 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: -0.95 (0.21), residues: 1499 helix: -0.20 (0.20), residues: 661 sheet: -1.04 (0.61), residues: 77 loop : -0.89 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 284 TYR 0.025 0.001 TYR D 7 PHE 0.013 0.001 PHE D 293 TRP 0.006 0.001 TRP D 144 HIS 0.003 0.001 HIS D 14 Details of bonding type rmsd/Z covalent geometry : bond 0.02030 / 0.68 (11653) covalent geometry : angle 3.88241 / 2.57 (15862) hydrogen bonds : bond 0.03683 / 2.46 ( 443) hydrogen bonds : angle 4.52880 / 3.05 ( 1251) metal coordination : bond 0.01630 / 1.13 ( 28) metal coordination : angle 31.77722 / 21.45 ( 84) Misc. bond : bond 0.00032 / 0.02 ( 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 222 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 221 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 107 GLU cc_start: 0.6722 (pp20) cc_final: 0.6161 (pp20) REVERT: C 121 GLU cc_start: 0.7470 (tp30) cc_final: 0.7103 (tp30) REVERT: C 125 ASN cc_start: 0.8388 (m110) cc_final: 0.7400 (m110) REVERT: C 165 GLU cc_start: 0.8268 (tt0) cc_final: 0.7818 (tt0) REVERT: C 322 LEU cc_start: 0.8648 (pt) cc_final: 0.8242 (pp) REVERT: C 330 MET cc_start: 0.8555 (mtm) cc_final: 0.8277 (mtm) REVERT: C 429 LYS cc_start: 0.8317 (mttt) cc_final: 0.7934 (mptt) REVERT: D 41 TYR cc_start: 0.7056 (p90) cc_final: 0.5173 (t80) REVERT: D 64 ILE cc_start: 0.9005 (mm) cc_final: 0.8794 (mm) REVERT: E 25 MET cc_start: 0.7777 (mmm) cc_final: 0.7392 (tpp) REVERT: E 187 MET cc_start: 0.8715 (ttm) cc_final: 0.8465 (ttp) outliers start: 1 outliers final: 1 residues processed: 222 average time/residue: 0.0863 time to fit residues: 28.9628 Evaluate side-chains 157 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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: 4.9990 chunk 79 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 39 optimal weight: 0.0170 chunk 83 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN B 264 ASN C 73 HIS ** D 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.130483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.108397 restraints weight = 18689.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.108788 restraints weight = 13515.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.109071 restraints weight = 11746.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.109419 restraints weight = 10640.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.109598 restraints weight = 10571.836| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.245 11683 Z= 0.681 Angle : 4.504 51.484 15946 Z= 2.572 Chirality : 0.760 6.399 1920 Planarity : 0.004 0.040 1946 Dihedral : 9.925 173.187 1600 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.08 % Allowed : 1.23 % 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: -0.88 (0.22), residues: 1499 helix: -0.13 (0.20), residues: 666 sheet: -1.04 (0.61), residues: 77 loop : -0.86 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 284 TYR 0.023 0.002 TYR D 7 PHE 0.012 0.001 PHE D 219 TRP 0.004 0.001 TRP D 144 HIS 0.002 0.001 HIS C 172 Details of bonding type rmsd/Z covalent geometry : bond 0.02030 / 0.68 (11653) covalent geometry : angle 3.88480 / 2.57 (15862) hydrogen bonds : bond 0.03629 / 2.39 ( 443) hydrogen bonds : angle 4.42285 / 2.97 ( 1251) metal coordination : bond 0.01485 / 1.06 ( 28) metal coordination : angle 31.65128 / 21.35 ( 84) Misc. bond : bond 0.00048 / 0.02 ( 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 217 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 GLU cc_start: 0.7925 (mp0) cc_final: 0.7685 (mp0) REVERT: C 121 GLU cc_start: 0.7540 (tp30) cc_final: 0.7167 (tp30) REVERT: C 125 ASN cc_start: 0.8379 (m110) cc_final: 0.7368 (m110) REVERT: C 165 GLU cc_start: 0.8256 (tt0) cc_final: 0.7719 (tt0) REVERT: C 168 LEU cc_start: 0.8801 (mp) cc_final: 0.8510 (mp) REVERT: C 211 LYS cc_start: 0.8000 (pttp) cc_final: 0.7381 (mmmt) REVERT: C 322 LEU cc_start: 0.8610 (pt) cc_final: 0.8213 (pp) REVERT: C 331 MET cc_start: 0.8298 (mtp) cc_final: 0.7891 (ttm) REVERT: C 429 LYS cc_start: 0.8362 (mttt) cc_final: 0.7948 (mptt) REVERT: D 41 TYR cc_start: 0.6977 (p90) cc_final: 0.5175 (t80) REVERT: D 64 ILE cc_start: 0.8954 (mm) cc_final: 0.8733 (mm) REVERT: E 187 MET cc_start: 0.8770 (ttm) cc_final: 0.8516 (ttp) outliers start: 1 outliers final: 0 residues processed: 217 average time/residue: 0.0837 time to fit residues: 27.9539 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 : 0.385 ------------------------------------------------------------------------------- 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: 5.9990 chunk 89 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 131 optimal weight: 30.0000 chunk 102 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 133 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 60 optimal weight: 8.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 419 HIS D 121 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 = 0.3667 r_free = 0.3667 target = 0.127181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.105047 restraints weight = 18511.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.105167 restraints weight = 14323.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.105301 restraints weight = 12535.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.105425 restraints weight = 11803.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.105496 restraints weight = 11472.576| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.4779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.242 11683 Z= 0.679 Angle : 4.528 55.483 15946 Z= 2.578 Chirality : 0.760 6.412 1920 Planarity : 0.004 0.041 1946 Dihedral : 9.947 172.543 1600 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.08 % Allowed : 0.65 % Favored : 99.26 % 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: -0.91 (0.22), residues: 1499 helix: -0.21 (0.20), residues: 664 sheet: -0.85 (0.65), residues: 72 loop : -0.85 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 284 TYR 0.020 0.002 TYR D 7 PHE 0.014 0.002 PHE D 262 TRP 0.007 0.001 TRP D 65 HIS 0.004 0.001 HIS C 73 Details of bonding type rmsd/Z covalent geometry : bond 0.02010 / 0.68 (11653) covalent geometry : angle 3.89696 / 2.58 (15862) hydrogen bonds : bond 0.03744 / 2.50 ( 443) hydrogen bonds : angle 4.53176 / 3.06 ( 1251) metal coordination : bond 0.01518 / 1.07 ( 28) metal coordination : angle 32.01747 / 21.42 ( 84) Misc. bond : bond 0.00045 / 0.02 ( 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 212 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 211 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.7575 (tpp) cc_final: 0.7199 (tpt) REVERT: B 158 HIS cc_start: 0.7895 (m90) cc_final: 0.7693 (m90) REVERT: B 207 GLU cc_start: 0.8059 (mp0) cc_final: 0.7789 (mp0) REVERT: C 125 ASN cc_start: 0.8356 (m110) cc_final: 0.8064 (m110) REVERT: C 165 GLU cc_start: 0.8333 (tt0) cc_final: 0.7762 (tt0) REVERT: C 168 LEU cc_start: 0.8817 (mp) cc_final: 0.8553 (mp) REVERT: C 211 LYS cc_start: 0.8056 (pttp) cc_final: 0.7407 (mmmt) REVERT: C 331 MET cc_start: 0.8530 (mtp) cc_final: 0.8129 (mtt) REVERT: C 429 LYS cc_start: 0.8492 (mttt) cc_final: 0.8043 (mptt) REVERT: D 41 TYR cc_start: 0.7189 (p90) cc_final: 0.5340 (t80) REVERT: E 187 MET cc_start: 0.8729 (ttm) cc_final: 0.8527 (ttp) outliers start: 1 outliers final: 0 residues processed: 212 average time/residue: 0.0815 time to fit residues: 26.0215 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 : 0.356 ------------------------------------------------------------------------------- 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: 0.3980 chunk 3 optimal weight: 6.9990 chunk 113 optimal weight: 7.9990 chunk 123 optimal weight: 0.0070 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 121 optimal weight: 0.1980 chunk 107 optimal weight: 0.9980 chunk 111 optimal weight: 0.0970 chunk 44 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3727 r_free = 0.3727 target = 0.131560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.108930 restraints weight = 18388.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.109558 restraints weight = 14856.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.110082 restraints weight = 12479.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.110237 restraints weight = 10666.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.110353 restraints weight = 10622.477| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.4963 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= 0.682 Angle : 4.500 50.969 15946 Z= 2.571 Chirality : 0.761 6.388 1920 Planarity : 0.004 0.039 1946 Dihedral : 9.792 171.385 1600 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % 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: -0.83 (0.22), residues: 1499 helix: -0.12 (0.20), residues: 670 sheet: -0.91 (0.63), residues: 72 loop : -0.84 (0.23), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 284 TYR 0.021 0.001 TYR D 7 PHE 0.010 0.001 PHE C 89 TRP 0.006 0.001 TRP D 206 HIS 0.005 0.001 HIS C 419 Details of bonding type rmsd/Z covalent geometry : bond 0.02033 / 0.68 (11653) covalent geometry : angle 3.88420 / 2.57 (15862) hydrogen bonds : bond 0.03496 / 2.32 ( 443) hydrogen bonds : angle 4.36891 / 2.95 ( 1251) metal coordination : bond 0.01758 / 1.25 ( 28) metal coordination : angle 31.54757 / 21.23 ( 84) Misc. bond : bond 0.00029 / 0.01 ( 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 216 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 215 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 207 GLU cc_start: 0.8104 (mp0) cc_final: 0.7857 (mp0) REVERT: C 121 GLU cc_start: 0.7579 (tp30) cc_final: 0.7176 (tp30) REVERT: C 125 ASN cc_start: 0.8364 (m110) cc_final: 0.7355 (m110) REVERT: C 135 MET cc_start: 0.7967 (ptp) cc_final: 0.6979 (mtm) REVERT: C 165 GLU cc_start: 0.8215 (tt0) cc_final: 0.7735 (tt0) REVERT: C 168 LEU cc_start: 0.8793 (mp) cc_final: 0.8543 (mp) REVERT: C 211 LYS cc_start: 0.7946 (pttp) cc_final: 0.7336 (mmmt) REVERT: C 322 LEU cc_start: 0.8572 (pt) cc_final: 0.8093 (pp) REVERT: C 330 MET cc_start: 0.8241 (mtm) cc_final: 0.7977 (mtm) REVERT: C 331 MET cc_start: 0.8258 (mtp) cc_final: 0.7850 (mtt) REVERT: C 429 LYS cc_start: 0.8219 (mttt) cc_final: 0.7841 (mptt) REVERT: D 25 MET cc_start: 0.7792 (mmt) cc_final: 0.7137 (mmt) REVERT: D 41 TYR cc_start: 0.6938 (p90) cc_final: 0.5205 (t80) REVERT: D 64 ILE cc_start: 0.8963 (mm) cc_final: 0.8726 (mm) REVERT: E 187 MET cc_start: 0.8661 (ttm) cc_final: 0.8419 (ttp) outliers start: 1 outliers final: 0 residues processed: 216 average time/residue: 0.0776 time to fit residues: 25.4966 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 : 0.318 ------------------------------------------------------------------------------- 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: 20.0000 chunk 10 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 128 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 94 optimal weight: 0.7980 chunk 118 optimal weight: 0.0030 overall best weight: 2.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 263 GLN ** D 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 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 = 0.3644 r_free = 0.3644 target = 0.125317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.104694 restraints weight = 18555.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.104807 restraints weight = 16132.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.105021 restraints weight = 13403.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.105187 restraints weight = 12694.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.105377 restraints weight = 11864.243| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.4988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.242 11683 Z= 0.677 Angle : 4.520 53.536 15946 Z= 2.576 Chirality : 0.761 6.400 1920 Planarity : 0.004 0.040 1946 Dihedral : 9.837 173.839 1600 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.08 % Allowed : 0.25 % Favored : 99.67 % 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: -0.85 (0.22), residues: 1499 helix: -0.15 (0.20), residues: 667 sheet: -0.84 (0.64), residues: 72 loop : -0.82 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 284 TYR 0.018 0.002 TYR D 7 PHE 0.014 0.002 PHE D 262 TRP 0.010 0.001 TRP D 137 HIS 0.006 0.001 HIS C 172 Details of bonding type rmsd/Z covalent geometry : bond 0.02010 / 0.68 (11653) covalent geometry : angle 3.89343 / 2.57 (15862) hydrogen bonds : bond 0.03604 / 2.36 ( 443) hydrogen bonds : angle 4.42207 / 2.99 ( 1251) metal coordination : bond 0.01383 / 1.01 ( 28) metal coordination : angle 31.85973 / 21.36 ( 84) Misc. bond : bond 0.00027 / 0.01 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1680.95 seconds wall clock time: 29 minutes 48.66 seconds (1788.66 seconds total)