Starting phenix.real_space_refine on Fri Jul 3 06:19:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9erk_19919/07_2026/9erk_19919.cif Found real_map, /net/cci-nas-00/data/ceres_data/9erk_19919/07_2026/9erk_19919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9erk_19919/07_2026/9erk_19919.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9erk_19919/07_2026/9erk_19919.map" model { file = "/net/cci-nas-00/data/ceres_data/9erk_19919/07_2026/9erk_19919.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9erk_19919/07_2026/9erk_19919.cif" } resolution = 2.8 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= 0.010 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: 7 Type Number sf(0) Gaussians Fe 42 7.16 5 P 3 5.49 5 S 158 5.16 5 Na 7 4.78 5 C 8074 2.51 5 N 2063 2.21 5 O 2320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 12667 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1433 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 6, 'TRANS': 184} Chain: "B" Number of atoms: 2394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2394 Classifications: {'peptide': 333} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 315} Chain: "C" Number of atoms: 3287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3287 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 29, 'TRANS': 413} Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2374 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 302} Chain: "E" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1439 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 9, 'TRANS': 186} Chain: "G" Number of atoms: 1531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1531 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Ad-hoc single atom residues: {' NA': 3} Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain breaks: 3 Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 64 Unusual residues: {'SF4': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 47 Unusual residues: {'FMN': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'FMN': 1, 'RBF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 0 Ad-hoc single atom residues: {' NA': 4} Chain breaks: 4 Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 199 SG CYS A 25 50.419 61.184 58.327 1.00 6.17 S ATOM 10283 SG CYS E 108 48.138 63.150 56.147 1.00 27.39 S ATOM 857 SG CYS A 113 48.117 58.742 52.699 1.00 24.80 S ATOM 9687 SG CYS E 25 50.813 57.306 55.167 1.00 19.46 S ATOM 2824 SG CYS B 200 58.968 82.975 112.703 1.00 5.95 S ATOM 2373 SG CYS B 138 59.130 76.521 113.635 1.00 2.51 S ATOM 2927 SG CYS B 213 64.447 79.670 113.512 1.00 2.10 S ATOM 2142 SG CYS B 106 60.930 79.041 107.949 1.00 4.28 S ATOM 2447 SG CYS B 148 58.258 74.896 97.137 1.00 4.62 S ATOM 2406 SG CYS B 142 60.752 74.967 103.188 1.00 2.01 S ATOM 2288 SG CYS B 125 57.802 69.816 101.081 1.00 5.42 S ATOM 2688 SG CYS B 182 54.322 75.335 101.840 1.00 5.99 S ATOM 1840 SG CYS B 58 44.107 79.507 78.029 1.00174.01 S ATOM 1797 SG CYS B 50 47.816 79.748 84.056 1.00124.56 S ATOM 1811 SG CYS B 53 43.368 77.500 83.555 1.00155.01 S ATOM 1945 SG CYS B 75 44.372 84.330 82.210 1.00171.76 S ATOM 2474 SG CYS B 152 57.145 77.380 88.892 1.00 6.80 S ATOM 2642 SG CYS B 175 51.331 80.412 88.791 1.00 57.13 S ATOM 2623 SG CYS B 172 56.034 83.996 90.312 1.00 12.14 S ATOM 2661 SG CYS B 178 54.137 79.233 94.125 1.00 8.52 S ATOM 3219 SG CYS B 252 58.927 97.775 110.214 1.00 17.08 S ATOM 3013 SG CYS B 227 53.673 101.094 110.951 1.00 24.25 S ATOM 3166 SG CYS B 246 55.465 98.894 104.879 1.00 39.75 S ATOM 3249 SG CYS B 256 62.372 91.522 115.074 1.00 24.87 S ATOM 2971 SG CYS B 220 59.393 92.062 120.562 1.00 23.30 S ATOM 2952 SG CYS B 217 57.166 87.695 116.129 1.00 26.87 S ATOM 2986 SG CYS B 223 56.623 94.217 115.458 1.00 13.79 S ATOM 3650 SG CYS B 310 61.559 113.343 107.094 1.00107.43 S ATOM 3686 SG CYS B 316 57.749 115.277 101.854 1.00103.02 S ATOM 3488 SG CYS B 289 56.502 117.495 107.341 1.00157.38 S ATOM 3668 SG CYS B 313 56.236 110.822 105.646 1.00 82.75 S ATOM 3720 SG CYS B 320 54.661 120.148 99.007 1.00168.60 S ATOM 3442 SG CYS B 282 55.259 126.658 99.454 1.00167.88 S ATOM 3423 SG CYS B 279 57.885 125.670 97.368 1.00173.26 S ATOM 3442 SG CYS B 282 55.259 126.658 99.454 1.00167.88 S ATOM 3460 SG CYS B 285 57.902 123.153 103.112 1.00166.72 S ATOM 6541 SG CYS C 369 54.841 47.472 90.675 1.00 8.45 S ATOM 6565 SG CYS C 372 54.720 41.469 93.256 1.00 3.75 S ATOM 6584 SG CYS C 375 49.949 45.176 94.554 1.00 4.00 S ATOM 6915 SG CYS C 418 55.926 46.329 96.892 1.00 4.53 S ATOM 6867 SG CYS C 411 44.585 46.331 104.997 1.00 6.69 S ATOM 6844 SG CYS C 408 43.326 51.861 101.989 1.00 0.06 S ATOM 6608 SG CYS C 379 42.689 45.920 99.024 1.00 2.91 S ATOM 6883 SG CYS C 414 48.551 48.418 100.699 1.00 6.30 S Time building chain proxies: 3.01, per 1000 atoms: 0.24 Number of scatterers: 12667 At special positions: 0 Unit cell: (91.2, 143.64, 158.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 42 26.01 S 158 16.00 P 3 15.00 Na 7 11.00 O 2320 8.00 N 2063 7.00 C 8074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 672.7 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 204 " pdb="FE2 FES A 204 " - pdb=" SG CYS E 25 " pdb="FE1 FES A 204 " - pdb=" SG CYS E 108 " pdb="FE1 FES A 204 " - pdb=" SG CYS A 25 " pdb="FE2 FES A 204 " - pdb=" SG CYS A 113 " pdb=" SF4 B 401 " pdb="FE4 SF4 B 401 " - pdb=" SG CYS B 106 " pdb="FE2 SF4 B 401 " - pdb=" SG CYS B 138 " pdb="FE1 SF4 B 401 " - pdb=" SG CYS B 200 " pdb="FE3 SF4 B 401 " - pdb=" SG CYS B 213 " pdb=" SF4 B 402 " pdb="FE2 SF4 B 402 " - pdb=" SG CYS B 142 " pdb="FE4 SF4 B 402 " - pdb=" SG CYS B 182 " pdb="FE3 SF4 B 402 " - pdb=" SG CYS B 125 " pdb="FE1 SF4 B 402 " - pdb=" SG CYS B 148 " pdb=" SF4 B 403 " pdb="FE2 SF4 B 403 " - pdb=" SG CYS B 50 " pdb="FE1 SF4 B 403 " - pdb=" SG CYS B 58 " pdb="FE4 SF4 B 403 " - pdb=" SG CYS B 75 " pdb="FE3 SF4 B 403 " - pdb=" SG CYS B 53 " pdb=" SF4 B 404 " pdb="FE2 SF4 B 404 " - pdb=" SG CYS B 175 " pdb="FE1 SF4 B 404 " - pdb=" SG CYS B 152 " pdb="FE3 SF4 B 404 " - pdb=" SG CYS B 172 " pdb="FE4 SF4 B 404 " - pdb=" SG CYS B 178 " pdb=" SF4 B 405 " pdb="FE3 SF4 B 405 " - pdb=" SG CYS B 227 " pdb="FE4 SF4 B 405 " - pdb=" SG CYS B 246 " pdb="FE1 SF4 B 405 " - pdb=" SG CYS B 252 " pdb=" SF4 B 406 " pdb="FE2 SF4 B 406 " - pdb=" SG CYS B 220 " pdb="FE4 SF4 B 406 " - pdb=" SG CYS B 223 " pdb="FE1 SF4 B 406 " - pdb=" SG CYS B 256 " pdb="FE3 SF4 B 406 " - pdb=" SG CYS B 217 " pdb=" SF4 B 407 " pdb="FE1 SF4 B 407 " - pdb=" SG CYS B 310 " pdb="FE4 SF4 B 407 " - pdb=" SG CYS B 313 " pdb="FE2 SF4 B 407 " - pdb=" SG CYS B 316 " pdb="FE3 SF4 B 407 " - pdb=" SG CYS B 289 " pdb=" SF4 B 408 " pdb="FE4 SF4 B 408 " - pdb=" SG CYS B 285 " pdb="FE1 SF4 B 408 " - pdb=" SG CYS B 320 " pdb="FE3 SF4 B 408 " - pdb=" SG CYS B 282 " pdb="FE3 SF4 B 408 " - pdb=" SG CYS B 279 " pdb=" SF4 C 501 " pdb="FE2 SF4 C 501 " - pdb=" SG CYS C 372 " pdb="FE4 SF4 C 501 " - pdb=" SG CYS C 418 " pdb="FE1 SF4 C 501 " - pdb=" SG CYS C 369 " pdb="FE3 SF4 C 501 " - pdb=" SG CYS C 375 " pdb=" SF4 C 502 " pdb="FE2 SF4 C 502 " - pdb=" SG CYS C 408 " pdb="FE1 SF4 C 502 " - pdb=" SG CYS C 411 " pdb="FE3 SF4 C 502 " - pdb=" SG CYS C 379 " pdb="FE4 SF4 C 502 " - pdb=" SG CYS C 414 " Number of angles added : 123 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3050 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 12 sheets defined 50.8% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 33 through 62 removed outlier: 3.620A pdb=" N ALA A 37 " --> pdb=" O GLN A 33 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ALA A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 67 removed outlier: 3.689A pdb=" N LEU A 66 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A 67 " --> pdb=" O ASP A 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 63 through 67' Processing helix chain 'A' and resid 68 through 70 No H-bonds generated for 'chain 'A' and resid 68 through 70' Processing helix chain 'A' and resid 71 through 94 removed outlier: 3.979A pdb=" N LYS A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS A 93 " --> pdb=" O MET A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 106 through 112 removed outlier: 3.579A pdb=" N ILE A 109 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N THR A 110 " --> pdb=" O PRO A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 125 Processing helix chain 'A' and resid 128 through 158 Processing helix chain 'A' and resid 167 through 185 Processing helix chain 'B' and resid 2 through 28 Proline residue: B 8 - end of helix removed outlier: 3.918A pdb=" N LYS B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 64 Processing helix chain 'B' and resid 79 through 88 Processing helix chain 'B' and resid 124 through 131 removed outlier: 3.582A pdb=" N ALA B 131 " --> pdb=" O GLU B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 152 Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 221 through 227 removed outlier: 3.762A pdb=" N LYS B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA B 226 " --> pdb=" O ALA B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 256 Processing helix chain 'B' and resid 315 through 320 removed outlier: 4.032A pdb=" N CYS B 320 " --> pdb=" O CYS B 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 21 removed outlier: 3.718A pdb=" N SER C 20 " --> pdb=" O ARG C 17 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR C 21 " --> pdb=" O LYS C 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 17 through 21' Processing helix chain 'C' and resid 118 through 121 removed outlier: 3.585A pdb=" N ASP C 121 " --> pdb=" O THR C 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 118 through 121' Processing helix chain 'C' and resid 122 through 134 removed outlier: 4.000A pdb=" N ALA C 126 " --> pdb=" O MET C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 150 removed outlier: 3.619A pdb=" N LYS C 149 " --> pdb=" O PRO C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 182 Processing helix chain 'C' and resid 182 through 198 Processing helix chain 'C' and resid 210 through 222 removed outlier: 3.590A pdb=" N GLY C 222 " --> pdb=" O VAL C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 240 removed outlier: 3.846A pdb=" N GLN C 238 " --> pdb=" O LYS C 235 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY C 239 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA C 240 " --> pdb=" O PRO C 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 235 through 240' Processing helix chain 'C' and resid 242 through 249 Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 269 through 282 Processing helix chain 'C' and resid 310 through 318 removed outlier: 3.616A pdb=" N VAL C 314 " --> pdb=" O PRO C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 379 removed outlier: 3.591A pdb=" N GLY C 377 " --> pdb=" O GLY C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 393 removed outlier: 3.581A pdb=" N ILE C 388 " --> pdb=" O GLN C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 403 Processing helix chain 'C' and resid 412 through 417 Processing helix chain 'C' and resid 423 through 442 removed outlier: 3.701A pdb=" N ARG C 440 " --> pdb=" O ILE C 436 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 43 removed outlier: 3.568A pdb=" N ILE D 23 " --> pdb=" O SER D 19 " (cutoff:3.500A) Proline residue: D 33 - end of helix Processing helix chain 'D' and resid 43 through 68 removed outlier: 4.071A pdb=" N LEU D 47 " --> pdb=" O GLY D 43 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 88 removed outlier: 3.706A pdb=" N VAL D 81 " --> pdb=" O TRP D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 109 removed outlier: 4.468A pdb=" N GLY D 99 " --> pdb=" O PRO D 95 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL D 100 " --> pdb=" O TRP D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 136 Processing helix chain 'D' and resid 137 through 140 removed outlier: 3.520A pdb=" N MET D 140 " --> pdb=" O PRO D 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 137 through 140' Processing helix chain 'D' and resid 156 through 163 Processing helix chain 'D' and resid 171 through 178 Processing helix chain 'D' and resid 190 through 204 removed outlier: 3.925A pdb=" N LEU D 194 " --> pdb=" O SER D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 226 removed outlier: 3.646A pdb=" N VAL D 226 " --> pdb=" O PHE D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 236 Processing helix chain 'D' and resid 238 through 245 Processing helix chain 'D' and resid 256 through 278 Processing helix chain 'D' and resid 283 through 294 Processing helix chain 'D' and resid 294 through 300 removed outlier: 3.913A pdb=" N ARG D 300 " --> pdb=" O PRO D 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 13 removed outlier: 4.367A pdb=" N GLY E 10 " --> pdb=" O ASN E 6 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ILE E 11 " --> pdb=" O LEU E 7 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE E 12 " --> pdb=" O THR E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 31 removed outlier: 3.694A pdb=" N THR E 27 " --> pdb=" O GLY E 23 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR E 31 " --> pdb=" O THR E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 57 removed outlier: 3.896A pdb=" N GLY E 37 " --> pdb=" O SER E 33 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N MET E 38 " --> pdb=" O ALA E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 90 removed outlier: 3.632A pdb=" N ALA E 70 " --> pdb=" O ILE E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 97 Processing helix chain 'E' and resid 101 through 106 removed outlier: 4.036A pdb=" N VAL E 105 " --> pdb=" O PRO E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 115 Processing helix chain 'E' and resid 117 through 121 removed outlier: 3.575A pdb=" N SER E 120 " --> pdb=" O PHE E 117 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASN E 121 " --> pdb=" O ALA E 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 117 through 121' Processing helix chain 'E' and resid 122 through 154 removed outlier: 3.593A pdb=" N ALA E 128 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU E 151 " --> pdb=" O ILE E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 192 removed outlier: 3.604A pdb=" N ALA E 178 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N PHE E 179 " --> pdb=" O PRO E 175 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU E 180 " --> pdb=" O PRO E 176 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR E 181 " --> pdb=" O GLY E 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 6 removed outlier: 3.706A pdb=" N LYS G 6 " --> pdb=" O GLU G 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2 through 6' Processing helix chain 'G' and resid 8 through 58 removed outlier: 3.660A pdb=" N LYS G 12 " --> pdb=" O GLN G 8 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL G 14 " --> pdb=" O ASP G 10 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE G 20 " --> pdb=" O LYS G 16 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU G 21 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU G 34 " --> pdb=" O CYS G 30 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLY G 41 " --> pdb=" O TYR G 37 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N THR G 42 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 79 Processing helix chain 'G' and resid 144 through 148 removed outlier: 3.959A pdb=" N ALA G 147 " --> pdb=" O GLY G 144 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER G 148 " --> pdb=" O ALA G 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 144 through 148' Processing helix chain 'G' and resid 149 through 156 removed outlier: 3.754A pdb=" N GLN G 154 " --> pdb=" O TRP G 151 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE G 155 " --> pdb=" O ASN G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 206 Processing sheet with id=AA1, first strand: chain 'B' and resid 100 through 104 Processing sheet with id=AA2, first strand: chain 'B' and resid 118 through 119 removed outlier: 6.219A pdb=" N GLU B 118 " --> pdb=" O VAL D 8 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 157 through 159 Processing sheet with id=AA4, first strand: chain 'B' and resid 232 through 235 Processing sheet with id=AA5, first strand: chain 'C' and resid 3 through 6 removed outlier: 6.430A pdb=" N LYS C 4 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLY C 202 " --> pdb=" O GLU C 228 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N TYR C 230 " --> pdb=" O GLY C 202 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE C 204 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N LEU C 232 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL C 206 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 27 through 28 removed outlier: 8.225A pdb=" N ILE C 353 " --> pdb=" O TYR C 289 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR C 291 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N CYS C 355 " --> pdb=" O THR C 291 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N THR C 293 " --> pdb=" O CYS C 355 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N THR C 357 " --> pdb=" O THR C 293 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY C 352 " --> pdb=" O SER C 330 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N SER C 330 " --> pdb=" O GLY C 352 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU C 354 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL C 328 " --> pdb=" O LEU C 354 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU C 356 " --> pdb=" O GLY C 326 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 34 through 38 removed outlier: 3.713A pdb=" N ALA C 84 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLU C 102 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N VAL C 82 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY C 80 " --> pdb=" O VAL C 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 34 through 38 Processing sheet with id=AA9, first strand: chain 'C' and resid 48 through 49 removed outlier: 6.516A pdb=" N VAL C 74 " --> pdb=" O VAL C 63 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 155 through 156 Processing sheet with id=AB2, first strand: chain 'G' and resid 64 through 67 removed outlier: 4.027A pdb=" N GLY G 102 " --> pdb=" O GLY G 94 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N SER G 96 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL G 100 " --> pdb=" O SER G 96 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLN G 118 " --> pdb=" O ILE G 135 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY G 122 " --> pdb=" O GLY G 131 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLY G 131 " --> pdb=" O GLY G 122 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N SER G 124 " --> pdb=" O ILE G 129 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ILE G 129 " --> pdb=" O SER G 124 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 165 through 167 removed outlier: 6.328A pdb=" N VAL G 165 " --> pdb=" O ILE G 178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 586 hydrogen bonds defined for protein. 1704 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: 2.03 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 4945 1.42 - 1.64: 7682 1.64 - 1.85: 171 1.85 - 2.07: 0 2.07 - 2.29: 124 Bond restraints: 12922 Sorted by residual: bond pdb=" C4 FMN D 401 " pdb=" C4A FMN D 401 " ideal model delta sigma weight residual 1.485 1.406 0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" C4 FMN C 503 " pdb=" C4A FMN C 503 " ideal model delta sigma weight residual 1.485 1.406 0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C4 FMN G 301 " pdb=" C4A FMN G 301 " ideal model delta sigma weight residual 1.485 1.406 0.079 2.00e-02 2.50e+03 1.55e+01 bond pdb=" O5' FMN C 503 " pdb=" P FMN C 503 " ideal model delta sigma weight residual 1.676 1.610 0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" O5' FMN G 301 " pdb=" P FMN G 301 " ideal model delta sigma weight residual 1.676 1.616 0.060 2.00e-02 2.50e+03 8.88e+00 ... (remaining 12917 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.96: 17544 3.96 - 7.91: 78 7.91 - 11.87: 5 11.87 - 15.83: 0 15.83 - 19.79: 1 Bond angle restraints: 17628 Sorted by residual: angle pdb=" CB MET B 92 " pdb=" CG MET B 92 " pdb=" SD MET B 92 " ideal model delta sigma weight residual 112.70 132.49 -19.79 3.00e+00 1.11e-01 4.35e+01 angle pdb=" CA GLU G 86 " pdb=" CB GLU G 86 " pdb=" CG GLU G 86 " ideal model delta sigma weight residual 114.10 125.43 -11.33 2.00e+00 2.50e-01 3.21e+01 angle pdb=" C ILE B 65 " pdb=" N VAL B 66 " pdb=" CA VAL B 66 " ideal model delta sigma weight residual 121.97 129.77 -7.80 1.80e+00 3.09e-01 1.88e+01 angle pdb=" CA MET B 92 " pdb=" CB MET B 92 " pdb=" CG MET B 92 " ideal model delta sigma weight residual 114.10 122.44 -8.34 2.00e+00 2.50e-01 1.74e+01 angle pdb=" C THR D 153 " pdb=" N THR D 154 " pdb=" CA THR D 154 " ideal model delta sigma weight residual 121.54 128.89 -7.35 1.91e+00 2.74e-01 1.48e+01 ... (remaining 17623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 6652 17.51 - 35.01: 798 35.01 - 52.52: 181 52.52 - 70.02: 39 70.02 - 87.53: 10 Dihedral angle restraints: 7680 sinusoidal: 2904 harmonic: 4776 Sorted by residual: dihedral pdb=" CA CYS B 289 " pdb=" C CYS B 289 " pdb=" N PRO B 290 " pdb=" CA PRO B 290 " ideal model delta harmonic sigma weight residual -180.00 -133.01 -46.99 0 5.00e+00 4.00e-02 8.83e+01 dihedral pdb=" CA ARG E 9 " pdb=" C ARG E 9 " pdb=" N GLY E 10 " pdb=" CA GLY E 10 " ideal model delta harmonic sigma weight residual 180.00 142.34 37.66 0 5.00e+00 4.00e-02 5.67e+01 dihedral pdb=" CA LEU B 45 " pdb=" C LEU B 45 " pdb=" N PRO B 46 " pdb=" CA PRO B 46 " ideal model delta harmonic sigma weight residual -180.00 -146.74 -33.26 0 5.00e+00 4.00e-02 4.42e+01 ... (remaining 7677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1822 0.065 - 0.130: 291 0.130 - 0.196: 21 0.196 - 0.261: 2 0.261 - 0.326: 1 Chirality restraints: 2137 Sorted by residual: chirality pdb=" CB VAL B 66 " pdb=" CA VAL B 66 " pdb=" CG1 VAL B 66 " pdb=" CG2 VAL B 66 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CA GLU G 86 " pdb=" N GLU G 86 " pdb=" C GLU G 86 " pdb=" CB GLU G 86 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA PRO B 290 " pdb=" N PRO B 290 " pdb=" C PRO B 290 " pdb=" CB PRO B 290 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 2134 not shown) Planarity restraints: 2169 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 45 " 0.080 5.00e-02 4.00e+02 1.21e-01 2.34e+01 pdb=" N PRO B 46 " -0.209 5.00e-02 4.00e+02 pdb=" CA PRO B 46 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO B 46 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 289 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.43e+00 pdb=" C CYS B 289 " 0.044 2.00e-02 2.50e+03 pdb=" O CYS B 289 " -0.016 2.00e-02 2.50e+03 pdb=" N PRO B 290 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 60 " 0.013 2.00e-02 2.50e+03 2.51e-02 6.29e+00 pdb=" C THR D 60 " -0.043 2.00e-02 2.50e+03 pdb=" O THR D 60 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU D 61 " 0.015 2.00e-02 2.50e+03 ... (remaining 2166 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3417 2.81 - 3.33: 10925 3.33 - 3.86: 19234 3.86 - 4.38: 22225 4.38 - 4.90: 39775 Nonbonded interactions: 95576 Sorted by model distance: nonbonded pdb=" OG SER D 78 " pdb=" O2' RBF D 402 " model vdw 2.289 3.040 nonbonded pdb=" O ILE B 294 " pdb=" NZ LYS B 299 " model vdw 2.291 3.120 nonbonded pdb=" O THR B 173 " pdb=" OG1 THR B 173 " model vdw 2.292 3.040 nonbonded pdb=" ND2 ASN C 268 " pdb=" O2 FMN C 503 " model vdw 2.297 3.120 nonbonded pdb=" O THR D 151 " pdb=" OG1 THR D 151 " model vdw 2.317 3.040 ... (remaining 95571 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.650 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 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 : 0.004 0.079 12967 Z= 0.209 Angle : 1.134 64.414 17751 Z= 0.394 Chirality : 0.047 0.326 2137 Planarity : 0.007 0.121 2169 Dihedral : 16.189 87.531 4630 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.54 % Allowed : 7.04 % Favored : 92.42 % Rotamer: Outliers : 2.82 % Allowed : 17.74 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 2.47 % Twisted General : 0.06 % 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: -0.70 (0.20), residues: 1676 helix: 0.83 (0.19), residues: 757 sheet: 0.71 (0.52), residues: 95 loop : -1.94 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 62 TYR 0.021 0.001 TYR D 263 PHE 0.014 0.001 PHE E 179 TRP 0.007 0.001 TRP D 97 HIS 0.004 0.001 HIS D 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.20 (12922) covalent geometry : angle 0.72522 / 0.39 (17628) hydrogen bonds : bond 0.16561 / 10.90 ( 582) hydrogen bonds : angle 6.28231 / 4.51 ( 1704) metal coordination : bond 0.00647 / 0.40 ( 43) metal coordination : angle 10.49781 / 7.37 ( 123) Misc. bond : bond 0.04704 / 2.35 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: B 305 ILE cc_start: -0.4554 (OUTLIER) cc_final: -0.5014 (mt) REVERT: B 327 MET cc_start: 0.6644 (mmt) cc_final: 0.6269 (mmp) REVERT: G 179 GLN cc_start: 0.7751 (tt0) cc_final: 0.7541 (tp40) outliers start: 38 outliers final: 18 residues processed: 169 average time/residue: 0.5882 time to fit residues: 107.7634 Evaluate side-chains 137 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 252 SER Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 184 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.0670 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.0980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.117127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.074127 restraints weight = 20446.776| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 2.65 r_work: 0.2764 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12967 Z= 0.126 Angle : 1.042 68.496 17751 Z= 0.323 Chirality : 0.043 0.220 2137 Planarity : 0.005 0.119 2169 Dihedral : 5.907 58.588 1837 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.38 % Favored : 93.14 % Rotamer: Outliers : 2.82 % Allowed : 18.78 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.21), residues: 1676 helix: 1.65 (0.20), residues: 766 sheet: 0.58 (0.52), residues: 102 loop : -1.97 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 55 TYR 0.016 0.001 TYR D 263 PHE 0.019 0.001 PHE A 21 TRP 0.006 0.001 TRP D 45 HIS 0.001 0.000 HIS C 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 (12922) covalent geometry : angle 0.59452 / 0.31 (17628) hydrogen bonds : bond 0.05710 / 3.70 ( 582) hydrogen bonds : angle 4.39269 / 3.11 ( 1704) metal coordination : bond 0.00559 / 0.37 ( 43) metal coordination : angle 10.29536 / 7.32 ( 123) Misc. bond : bond 0.00122 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: B 30 PHE cc_start: 0.7017 (OUTLIER) cc_final: 0.6814 (t80) REVERT: B 305 ILE cc_start: -0.1068 (OUTLIER) cc_final: -0.1914 (mt) REVERT: C 342 THR cc_start: 0.8458 (OUTLIER) cc_final: 0.8167 (m) REVERT: G 179 GLN cc_start: 0.7897 (tt0) cc_final: 0.7293 (tp40) outliers start: 38 outliers final: 13 residues processed: 155 average time/residue: 0.4807 time to fit residues: 81.7908 Evaluate side-chains 133 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 197 MET Chi-restraints excluded: chain G residue 198 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 76 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 142 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.110582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.069817 restraints weight = 20745.723| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 2.65 r_work: 0.2634 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2520 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 12967 Z= 0.194 Angle : 1.171 50.406 17751 Z= 0.356 Chirality : 0.046 0.173 2137 Planarity : 0.006 0.118 2169 Dihedral : 5.577 55.484 1819 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.46 % Favored : 92.24 % Rotamer: Outliers : 3.49 % Allowed : 18.49 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.13 (0.21), residues: 1676 helix: 1.77 (0.20), residues: 762 sheet: 0.50 (0.48), residues: 112 loop : -2.16 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 17 TYR 0.024 0.002 TYR D 263 PHE 0.017 0.002 PHE A 21 TRP 0.008 0.001 TRP D 97 HIS 0.004 0.001 HIS D 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.19 (12922) covalent geometry : angle 0.65685 / 0.35 (17628) hydrogen bonds : bond 0.07877 / 5.11 ( 582) hydrogen bonds : angle 4.39580 / 3.11 ( 1704) metal coordination : bond 0.01011 / 0.71 ( 43) metal coordination : angle 11.66398 / 7.70 ( 123) Misc. bond : bond 0.00043 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 121 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: B 30 PHE cc_start: 0.7329 (OUTLIER) cc_final: 0.7120 (t80) REVERT: B 305 ILE cc_start: -0.0943 (OUTLIER) cc_final: -0.1721 (mt) REVERT: C 123 ASP cc_start: 0.5846 (OUTLIER) cc_final: 0.5619 (p0) REVERT: E 1 MET cc_start: 0.5058 (OUTLIER) cc_final: 0.4639 (pp-130) REVERT: G 179 GLN cc_start: 0.7911 (tt0) cc_final: 0.7323 (tp40) outliers start: 47 outliers final: 24 residues processed: 156 average time/residue: 0.5341 time to fit residues: 91.2916 Evaluate side-chains 144 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 198 SER Chi-restraints excluded: chain G residue 201 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 127 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 159 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 chunk 28 optimal weight: 8.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 200 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.110194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.067079 restraints weight = 20674.934| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 2.63 r_work: 0.2637 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2526 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 12967 Z= 0.181 Angle : 1.103 45.201 17751 Z= 0.342 Chirality : 0.046 0.185 2137 Planarity : 0.005 0.117 2169 Dihedral : 5.523 57.673 1819 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.98 % Favored : 92.72 % Rotamer: Outliers : 3.34 % Allowed : 19.67 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.07 (0.21), residues: 1676 helix: 1.88 (0.20), residues: 762 sheet: 0.45 (0.48), residues: 112 loop : -2.19 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 55 TYR 0.022 0.002 TYR G 37 PHE 0.020 0.001 PHE A 21 TRP 0.010 0.001 TRP G 11 HIS 0.003 0.001 HIS D 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.18 (12922) covalent geometry : angle 0.63182 / 0.33 (17628) hydrogen bonds : bond 0.07207 / 4.67 ( 582) hydrogen bonds : angle 4.28755 / 3.02 ( 1704) metal coordination : bond 0.00991 / 0.74 ( 43) metal coordination : angle 10.88019 / 7.37 ( 123) Misc. bond : bond 0.00022 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 118 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: B 30 PHE cc_start: 0.7414 (OUTLIER) cc_final: 0.7118 (t80) REVERT: B 305 ILE cc_start: -0.0793 (OUTLIER) cc_final: -0.1552 (mt) REVERT: C 123 ASP cc_start: 0.5854 (OUTLIER) cc_final: 0.5630 (p0) REVERT: E 159 PHE cc_start: 0.5743 (t80) cc_final: 0.5480 (m-10) REVERT: G 162 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7675 (pm20) REVERT: G 179 GLN cc_start: 0.7898 (tt0) cc_final: 0.7240 (tp40) outliers start: 45 outliers final: 28 residues processed: 157 average time/residue: 0.4996 time to fit residues: 86.3392 Evaluate side-chains 146 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 162 GLU Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 198 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 17 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 156 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 86 optimal weight: 0.0010 chunk 117 optimal weight: 0.5980 chunk 147 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 64 ASN ** B 330 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 = 0.3523 r_free = 0.3523 target = 0.113803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.073034 restraints weight = 20805.929| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.78 r_work: 0.2706 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 12967 Z= 0.121 Angle : 1.044 40.612 17751 Z= 0.310 Chirality : 0.043 0.164 2137 Planarity : 0.005 0.116 2169 Dihedral : 5.231 49.840 1819 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.62 % Favored : 93.08 % Rotamer: Outliers : 3.19 % Allowed : 20.71 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.15 (0.21), residues: 1676 helix: 2.10 (0.20), residues: 767 sheet: 0.44 (0.50), residues: 106 loop : -2.12 (0.20), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 440 TYR 0.025 0.001 TYR G 37 PHE 0.011 0.001 PHE B 30 TRP 0.006 0.001 TRP D 97 HIS 0.001 0.000 HIS C 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (12922) covalent geometry : angle 0.57542 / 0.30 (17628) hydrogen bonds : bond 0.05381 / 3.46 ( 582) hydrogen bonds : angle 4.03006 / 2.81 ( 1704) metal coordination : bond 0.00619 / 0.46 ( 43) metal coordination : angle 10.48472 / 7.13 ( 123) Misc. bond : bond 0.00061 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 119 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 21 PHE cc_start: 0.8386 (m-80) cc_final: 0.8169 (m-80) REVERT: B 30 PHE cc_start: 0.7431 (OUTLIER) cc_final: 0.7123 (t80) REVERT: B 305 ILE cc_start: -0.0914 (OUTLIER) cc_final: -0.1684 (mt) REVERT: C 123 ASP cc_start: 0.5732 (OUTLIER) cc_final: 0.5528 (p0) REVERT: E 1 MET cc_start: 0.4872 (OUTLIER) cc_final: 0.4337 (pp-130) REVERT: E 159 PHE cc_start: 0.5765 (t80) cc_final: 0.5551 (m-10) REVERT: G 162 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7670 (pm20) REVERT: G 179 GLN cc_start: 0.7803 (tt0) cc_final: 0.7201 (tp40) outliers start: 43 outliers final: 21 residues processed: 154 average time/residue: 0.5134 time to fit residues: 86.8935 Evaluate side-chains 141 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 162 GLU Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 198 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 60 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 64 ASN ** B 330 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 = 0.3498 r_free = 0.3498 target = 0.111672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.068858 restraints weight = 20540.713| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 2.62 r_work: 0.2675 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12967 Z= 0.141 Angle : 1.034 37.927 17751 Z= 0.319 Chirality : 0.044 0.211 2137 Planarity : 0.005 0.115 2169 Dihedral : 5.042 48.051 1816 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.40 % Favored : 92.36 % Rotamer: Outliers : 3.19 % Allowed : 20.79 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.17 (0.21), residues: 1676 helix: 2.11 (0.20), residues: 765 sheet: 0.47 (0.48), residues: 112 loop : -2.10 (0.20), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 55 TYR 0.025 0.001 TYR G 37 PHE 0.011 0.001 PHE D 131 TRP 0.008 0.001 TRP G 11 HIS 0.002 0.001 HIS C 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (12922) covalent geometry : angle 0.59215 / 0.31 (17628) hydrogen bonds : bond 0.06055 / 3.91 ( 582) hydrogen bonds : angle 4.05953 / 2.83 ( 1704) metal coordination : bond 0.00719 / 0.52 ( 43) metal coordination : angle 10.20746 / 6.95 ( 123) Misc. bond : bond 0.00014 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 114 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 21 PHE cc_start: 0.8352 (m-80) cc_final: 0.8024 (m-80) REVERT: B 30 PHE cc_start: 0.7471 (OUTLIER) cc_final: 0.7138 (t80) REVERT: B 251 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.6930 (mt-10) REVERT: C 123 ASP cc_start: 0.5955 (OUTLIER) cc_final: 0.5736 (p0) REVERT: E 1 MET cc_start: 0.4791 (OUTLIER) cc_final: 0.4206 (pp-130) REVERT: E 159 PHE cc_start: 0.5980 (t80) cc_final: 0.5673 (m-10) REVERT: G 179 GLN cc_start: 0.7815 (tt0) cc_final: 0.7169 (tp40) outliers start: 43 outliers final: 24 residues processed: 151 average time/residue: 0.4886 time to fit residues: 80.8439 Evaluate side-chains 141 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 198 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 5 optimal weight: 0.9980 chunk 163 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 143 optimal weight: 0.0970 chunk 141 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 156 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 136 optimal weight: 0.0970 chunk 84 optimal weight: 1.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 64 ASN ** B 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 200 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.114081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.071401 restraints weight = 20559.130| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 2.62 r_work: 0.2728 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 12967 Z= 0.118 Angle : 1.008 35.664 17751 Z= 0.306 Chirality : 0.043 0.198 2137 Planarity : 0.005 0.114 2169 Dihedral : 4.893 42.040 1814 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.68 % Favored : 93.08 % Rotamer: Outliers : 2.45 % Allowed : 21.53 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.30 (0.21), residues: 1676 helix: 2.22 (0.20), residues: 769 sheet: 0.46 (0.50), residues: 106 loop : -2.03 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 440 TYR 0.026 0.001 TYR G 37 PHE 0.009 0.001 PHE E 179 TRP 0.009 0.001 TRP G 11 HIS 0.001 0.000 HIS D 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (12922) covalent geometry : angle 0.57940 / 0.30 (17628) hydrogen bonds : bond 0.04969 / 3.19 ( 582) hydrogen bonds : angle 3.90433 / 2.71 ( 1704) metal coordination : bond 0.00617 / 0.46 ( 43) metal coordination : angle 9.92660 / 6.76 ( 123) Misc. bond : bond 0.00045 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 21 PHE cc_start: 0.8225 (m-80) cc_final: 0.7793 (m-80) REVERT: A 164 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.6930 (pptt) REVERT: C 123 ASP cc_start: 0.5782 (OUTLIER) cc_final: 0.5571 (p0) REVERT: E 1 MET cc_start: 0.4802 (OUTLIER) cc_final: 0.4212 (pp-130) REVERT: E 159 PHE cc_start: 0.5904 (t80) cc_final: 0.5658 (m-10) REVERT: E 192 LYS cc_start: 0.7575 (tptt) cc_final: 0.7355 (tppt) REVERT: G 162 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7676 (pm20) REVERT: G 179 GLN cc_start: 0.7832 (tt0) cc_final: 0.7209 (tp40) outliers start: 33 outliers final: 21 residues processed: 146 average time/residue: 0.4796 time to fit residues: 76.7792 Evaluate side-chains 142 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 162 GLU Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 198 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 116 optimal weight: 1.9990 chunk 144 optimal weight: 0.0870 chunk 101 optimal weight: 0.6980 chunk 136 optimal weight: 0.8980 chunk 164 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 85 optimal weight: 0.0020 chunk 128 optimal weight: 0.9990 chunk 86 optimal weight: 0.0270 chunk 4 optimal weight: 2.9990 chunk 81 optimal weight: 0.0980 overall best weight: 0.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 64 ASN ** B 330 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 = 0.3599 r_free = 0.3599 target = 0.119245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.077236 restraints weight = 20420.479| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.64 r_work: 0.2834 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 12967 Z= 0.103 Angle : 0.977 36.062 17751 Z= 0.293 Chirality : 0.042 0.203 2137 Planarity : 0.005 0.113 2169 Dihedral : 4.557 30.282 1814 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.38 % Favored : 93.38 % Rotamer: Outliers : 2.45 % Allowed : 21.46 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.50 (0.22), residues: 1676 helix: 2.39 (0.20), residues: 766 sheet: 0.40 (0.50), residues: 113 loop : -1.91 (0.21), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 439 TYR 0.025 0.001 TYR G 37 PHE 0.010 0.001 PHE B 30 TRP 0.008 0.001 TRP D 209 HIS 0.001 0.000 HIS D 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (12922) covalent geometry : angle 0.55960 / 0.29 (17628) hydrogen bonds : bond 0.03453 / 2.21 ( 582) hydrogen bonds : angle 3.68486 / 2.52 ( 1704) metal coordination : bond 0.00681 / 0.50 ( 43) metal coordination : angle 9.63120 / 6.44 ( 123) Misc. bond : bond 0.00042 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 128 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 21 PHE cc_start: 0.8060 (m-80) cc_final: 0.7720 (m-80) REVERT: A 164 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.6471 (pmtt) REVERT: B 212 SER cc_start: 0.6938 (m) cc_final: 0.6682 (p) REVERT: C 123 ASP cc_start: 0.5431 (OUTLIER) cc_final: 0.5225 (p0) REVERT: D 141 THR cc_start: 0.8766 (m) cc_final: 0.8440 (p) REVERT: E 1 MET cc_start: 0.4551 (OUTLIER) cc_final: 0.3942 (pp-130) REVERT: G 179 GLN cc_start: 0.7787 (tt0) cc_final: 0.7161 (tp40) outliers start: 33 outliers final: 18 residues processed: 153 average time/residue: 0.4833 time to fit residues: 81.2006 Evaluate side-chains 143 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 198 SER Chi-restraints excluded: chain G residue 201 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 47 optimal weight: 6.9990 chunk 60 optimal weight: 0.0670 chunk 83 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 64 ASN B 292 ASN C 182 GLN D 89 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.108131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.067317 restraints weight = 20636.198| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 2.80 r_work: 0.2589 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2476 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 12967 Z= 0.238 Angle : 1.081 36.450 17751 Z= 0.373 Chirality : 0.048 0.223 2137 Planarity : 0.005 0.113 2169 Dihedral : 5.129 35.596 1813 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.00 % Favored : 91.77 % Rotamer: Outliers : 2.30 % Allowed : 22.35 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.12 (0.21), residues: 1676 helix: 2.04 (0.20), residues: 767 sheet: 0.56 (0.49), residues: 112 loop : -2.13 (0.20), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 228 TYR 0.028 0.002 TYR G 37 PHE 0.013 0.001 PHE D 131 TRP 0.016 0.002 TRP G 11 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.24 (12922) covalent geometry : angle 0.70409 / 0.37 (17628) hydrogen bonds : bond 0.08355 / 5.44 ( 582) hydrogen bonds : angle 4.26695 / 2.98 ( 1704) metal coordination : bond 0.01058 / 0.70 ( 43) metal coordination : angle 9.87402 / 6.74 ( 123) Misc. bond : bond 0.00056 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: A 21 PHE cc_start: 0.8257 (m-80) cc_final: 0.7660 (m-80) REVERT: B 212 SER cc_start: 0.7253 (m) cc_final: 0.6905 (p) REVERT: B 228 ARG cc_start: 0.9203 (ptp-110) cc_final: 0.8920 (ptp90) REVERT: B 251 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7053 (mt-10) REVERT: C 123 ASP cc_start: 0.6151 (OUTLIER) cc_final: 0.5937 (p0) REVERT: E 1 MET cc_start: 0.4688 (OUTLIER) cc_final: 0.4053 (pp-130) REVERT: G 179 GLN cc_start: 0.7791 (tt0) cc_final: 0.7204 (tp40) outliers start: 31 outliers final: 18 residues processed: 143 average time/residue: 0.5468 time to fit residues: 85.3568 Evaluate side-chains 136 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 105 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 198 SER Chi-restraints excluded: chain G residue 201 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 154 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 149 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.113555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.070479 restraints weight = 20077.104| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.61 r_work: 0.2842 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12967 Z= 0.134 Angle : 1.013 34.950 17751 Z= 0.327 Chirality : 0.044 0.200 2137 Planarity : 0.005 0.113 2169 Dihedral : 4.898 35.484 1812 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.74 % Favored : 93.02 % Rotamer: Outliers : 1.78 % Allowed : 22.87 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.06 % 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: 0.25 (0.21), residues: 1676 helix: 2.15 (0.20), residues: 777 sheet: 0.43 (0.51), residues: 108 loop : -2.07 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 228 TYR 0.026 0.001 TYR G 37 PHE 0.010 0.001 PHE D 131 TRP 0.012 0.001 TRP G 11 HIS 0.002 0.001 HIS C 147 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (12922) covalent geometry : angle 0.62217 / 0.32 (17628) hydrogen bonds : bond 0.05682 / 3.68 ( 582) hydrogen bonds : angle 3.99201 / 2.76 ( 1704) metal coordination : bond 0.00635 / 0.46 ( 43) metal coordination : angle 9.62793 / 6.61 ( 123) Misc. bond : bond 0.00040 / 0.02 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3352 Ramachandran restraints generated. 1676 Oldfield, 0 Emsley, 1676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: A 21 PHE cc_start: 0.8061 (m-80) cc_final: 0.7420 (m-80) REVERT: A 164 LYS cc_start: 0.8046 (tppt) cc_final: 0.6973 (pptt) REVERT: B 251 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7304 (mt-10) REVERT: C 123 ASP cc_start: 0.6706 (OUTLIER) cc_final: 0.6479 (p0) REVERT: E 1 MET cc_start: 0.4425 (OUTLIER) cc_final: 0.3726 (pp-130) REVERT: G 179 GLN cc_start: 0.7992 (tt0) cc_final: 0.7343 (tp40) outliers start: 24 outliers final: 18 residues processed: 134 average time/residue: 0.5756 time to fit residues: 84.3502 Evaluate side-chains 135 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 182 THR Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain G residue 198 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 11 optimal weight: 0.7980 chunk 112 optimal weight: 0.3980 chunk 25 optimal weight: 10.0000 chunk 128 optimal weight: 0.0030 chunk 159 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.113408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.070524 restraints weight = 20030.181| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.59 r_work: 0.2848 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12967 Z= 0.138 Angle : 1.005 34.922 17751 Z= 0.326 Chirality : 0.044 0.205 2137 Planarity : 0.005 0.112 2169 Dihedral : 4.830 33.208 1812 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.64 % Favored : 92.12 % Rotamer: Outliers : 1.86 % Allowed : 23.16 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.21), residues: 1676 helix: 2.18 (0.19), residues: 776 sheet: 0.38 (0.51), residues: 108 loop : -2.06 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 440 TYR 0.028 0.001 TYR G 37 PHE 0.010 0.001 PHE D 131 TRP 0.010 0.001 TRP G 11 HIS 0.002 0.001 HIS D 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (12922) covalent geometry : angle 0.62076 / 0.32 (17628) hydrogen bonds : bond 0.05748 / 3.72 ( 582) hydrogen bonds : angle 3.99152 / 2.76 ( 1704) metal coordination : bond 0.00674 / 0.49 ( 43) metal coordination : angle 9.52144 / 6.54 ( 123) Misc. bond : bond 0.00018 / 0.01 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5012.01 seconds wall clock time: 86 minutes 4.46 seconds (5164.46 seconds total)