Starting phenix.real_space_refine on Wed Jul 30 13:49:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rb8_19028/07_2025/8rb8_19028.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rb8_19028/07_2025/8rb8_19028.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rb8_19028/07_2025/8rb8_19028.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rb8_19028/07_2025/8rb8_19028.map" model { file = "/net/cci-nas-00/data/ceres_data/8rb8_19028/07_2025/8rb8_19028.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rb8_19028/07_2025/8rb8_19028.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 18 7.16 5 P 3 5.49 5 S 97 5.16 5 C 8088 2.51 5 N 2066 2.21 5 O 2313 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12585 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1394 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 179} Chain: "C" Number of atoms: 3511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3511 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 37, 'TRANS': 438} Chain: "D" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2629 Classifications: {'peptide': 349} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 325} Chain: "E" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1601 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 203} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1482 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "H" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 548 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 4, 'TRANS': 66} Chain: "B" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 811 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain breaks: 2 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FES': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 47 Unusual residues: {'FMN': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 337 Unusual residues: {'FMN': 1, 'LMT': 8, 'RBF': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 140 Unusual residues: {'LMT': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 184 SG CYS A 25 47.481 69.234 56.532 1.00 52.97 S ATOM 8343 SG CYS E 122 45.949 72.224 54.666 1.00 69.51 S ATOM 844 SG CYS A 113 43.755 68.914 51.369 1.00 46.34 S ATOM 7734 SG CYS E 39 44.883 65.904 53.712 1.00 58.14 S ATOM 4124 SG CYS C 376 41.300 55.611 94.622 1.00 68.33 S ATOM 4439 SG CYS C 419 45.656 53.952 95.133 1.00 37.38 S ATOM 4082 SG CYS C 370 44.811 55.253 88.580 1.00 52.12 S ATOM 4107 SG CYS C 373 41.805 50.423 91.849 1.00 37.47 S ATOM 4370 SG CYS C 409 39.574 65.611 99.934 1.00 39.39 S ATOM 4392 SG CYS C 412 37.528 60.572 103.661 1.00 39.61 S ATOM 4408 SG CYS C 415 40.675 59.820 98.074 1.00 64.07 S ATOM 4150 SG CYS C 380 35.062 60.836 97.926 1.00 59.97 S ATOM 11569 SG CYS B 119 55.784 103.085 101.718 1.00 75.59 S ATOM 11742 SG CYS B 145 61.255 101.617 101.791 1.00 78.49 S ATOM 11723 SG CYS B 142 57.360 100.128 96.634 1.00 64.43 S ATOM 11706 SG CYS B 139 57.965 96.390 101.721 1.00 60.88 S ATOM 11493 SG CYS B 109 63.621 106.228 111.629 1.00 91.95 S ATOM 11511 SG CYS B 112 64.811 110.948 106.685 1.00 77.36 S ATOM 11535 SG CYS B 115 60.418 106.339 106.542 1.00 79.14 S ATOM 11772 SG CYS B 149 67.251 106.638 106.114 1.00100.00 S Time building chain proxies: 8.10, per 1000 atoms: 0.64 Number of scatterers: 12585 At special positions: 0 Unit cell: (85.28, 148.42, 154.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 18 26.01 S 97 16.00 P 3 15.00 O 2313 8.00 N 2066 7.00 C 8088 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.25 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 200 " pdb="FE1 FES A 200 " - pdb=" SG CYS E 122 " pdb="FE1 FES A 200 " - pdb=" SG CYS A 25 " pdb="FE2 FES A 200 " - pdb=" SG CYS A 113 " pdb="FE2 FES A 200 " - pdb=" SG CYS E 39 " pdb=" SF4 B 201 " pdb="FE3 SF4 B 201 " - pdb=" SG CYS B 142 " pdb="FE2 SF4 B 201 " - pdb=" SG CYS B 145 " pdb="FE4 SF4 B 201 " - pdb=" SG CYS B 139 " pdb="FE1 SF4 B 201 " - pdb=" SG CYS B 119 " pdb=" SF4 B 202 " pdb="FE2 SF4 B 202 " - pdb=" SG CYS B 112 " pdb="FE4 SF4 B 202 " - pdb=" SG CYS B 149 " pdb="FE3 SF4 B 202 " - pdb=" SG CYS B 115 " pdb="FE1 SF4 B 202 " - pdb=" SG CYS B 109 " pdb=" SF4 C 501 " pdb="FE1 SF4 C 501 " - pdb=" SG CYS C 376 " pdb="FE2 SF4 C 501 " - pdb=" SG CYS C 419 " pdb="FE3 SF4 C 501 " - pdb=" SG CYS C 370 " pdb="FE4 SF4 C 501 " - pdb=" SG CYS C 373 " pdb=" SF4 C 502 " pdb="FE3 SF4 C 502 " - pdb=" SG CYS C 415 " pdb="FE2 SF4 C 502 " - pdb=" SG CYS C 412 " pdb="FE4 SF4 C 502 " - pdb=" SG CYS C 380 " pdb="FE1 SF4 C 502 " - pdb=" SG CYS C 409 " Number of angles added : 54 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2898 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 11 sheets defined 55.1% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 removed outlier: 4.078A pdb=" N PHE A 6 " --> pdb=" O GLU A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 31 removed outlier: 3.728A pdb=" N PHE A 27 " --> pdb=" O GLY A 23 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 31 " --> pdb=" O PHE A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 62 Processing helix chain 'A' and resid 62 through 67 Processing helix chain 'A' and resid 71 through 90 Processing helix chain 'A' and resid 105 through 110 removed outlier: 3.511A pdb=" N THR A 110 " --> pdb=" O PRO A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 126 Proline residue: A 119 - end of helix removed outlier: 3.505A pdb=" N ARG A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 159 removed outlier: 4.048A pdb=" N LEU A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 184 Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'C' and resid 124 through 134 removed outlier: 3.567A pdb=" N LEU C 128 " --> pdb=" O ASP C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 157 removed outlier: 3.535A pdb=" N LYS C 150 " --> pdb=" O PRO C 146 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG C 156 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N HIS C 157 " --> pdb=" O GLN C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 183 removed outlier: 3.515A pdb=" N ARG C 183 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 198 Processing helix chain 'C' and resid 211 through 222 Processing helix chain 'C' and resid 236 through 240 removed outlier: 3.543A pdb=" N MET C 239 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY C 240 " --> pdb=" O TYR C 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 236 through 240' Processing helix chain 'C' and resid 241 through 250 removed outlier: 3.618A pdb=" N GLN C 247 " --> pdb=" O LYS C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 270 through 283 removed outlier: 3.597A pdb=" N TYR C 274 " --> pdb=" O ALA C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 319 removed outlier: 3.668A pdb=" N LEU C 315 " --> pdb=" O PRO C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 395 Processing helix chain 'C' and resid 397 through 404 removed outlier: 3.632A pdb=" N GLU C 403 " --> pdb=" O ASP C 399 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR C 404 " --> pdb=" O GLY C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 removed outlier: 3.570A pdb=" N TYR C 417 " --> pdb=" O GLY C 413 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL C 418 " --> pdb=" O CYS C 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 413 through 418' Processing helix chain 'C' and resid 424 through 478 Processing helix chain 'D' and resid 17 through 41 Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 41 through 67 removed outlier: 3.534A pdb=" N ILE D 45 " --> pdb=" O GLY D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 75 removed outlier: 3.710A pdb=" N ASP D 75 " --> pdb=" O ARG D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 89 removed outlier: 3.693A pdb=" N THR D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 106 removed outlier: 3.832A pdb=" N GLY D 98 " --> pdb=" O PRO D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 114 Processing helix chain 'D' and resid 122 through 135 Processing helix chain 'D' and resid 137 through 141 removed outlier: 4.122A pdb=" N THR D 141 " --> pdb=" O GLN D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 164 Processing helix chain 'D' and resid 178 through 188 Processing helix chain 'D' and resid 191 through 198 removed outlier: 3.656A pdb=" N ILE D 195 " --> pdb=" O THR D 191 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 208 Processing helix chain 'D' and resid 220 through 232 Processing helix chain 'D' and resid 237 through 258 Processing helix chain 'D' and resid 265 through 270 Processing helix chain 'D' and resid 273 through 281 Processing helix chain 'D' and resid 292 through 312 Processing helix chain 'D' and resid 318 through 337 Proline residue: D 331 - end of helix Processing helix chain 'E' and resid 17 through 27 removed outlier: 4.246A pdb=" N PHE E 21 " --> pdb=" O PRO E 17 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU E 25 " --> pdb=" O PHE E 21 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TRP E 26 " --> pdb=" O THR E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 44 removed outlier: 3.656A pdb=" N THR E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 72 Processing helix chain 'E' and resid 73 through 76 removed outlier: 3.657A pdb=" N ILE E 76 " --> pdb=" O ARG E 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 73 through 76' Processing helix chain 'E' and resid 77 through 79 No H-bonds generated for 'chain 'E' and resid 77 through 79' Processing helix chain 'E' and resid 80 through 101 removed outlier: 4.113A pdb=" N VAL E 92 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 112 removed outlier: 3.555A pdb=" N VAL E 110 " --> pdb=" O GLU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'E' and resid 136 through 168 Processing helix chain 'E' and resid 173 through 179 Processing helix chain 'E' and resid 180 through 186 removed outlier: 4.554A pdb=" N TRP E 184 " --> pdb=" O HIS E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 228 removed outlier: 3.993A pdb=" N PHE E 206 " --> pdb=" O PRO E 202 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE E 207 " --> pdb=" O PRO E 203 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL E 208 " --> pdb=" O GLY E 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 79 removed outlier: 5.508A pdb=" N GLY G 63 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N THR G 64 " --> pdb=" O MET G 60 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU G 79 " --> pdb=" O ALA G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 86 Processing helix chain 'G' and resid 89 through 93 removed outlier: 3.826A pdb=" N ASP G 93 " --> pdb=" O PRO G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 163 removed outlier: 4.253A pdb=" N ILE G 162 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU G 163 " --> pdb=" O ASP G 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 159 through 163' Processing helix chain 'G' and resid 168 through 172 Processing helix chain 'G' and resid 202 through 222 Processing helix chain 'G' and resid 223 through 227 removed outlier: 3.590A pdb=" N LEU G 226 " --> pdb=" O ALA G 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 34 Processing helix chain 'H' and resid 34 through 39 removed outlier: 3.593A pdb=" N CYS H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.867A pdb=" N ALA B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 85 Processing helix chain 'B' and resid 113 through 118 Processing sheet with id=AA1, first strand: chain 'C' and resid 34 through 38 removed outlier: 6.562A pdb=" N VAL C 102 " --> pdb=" O VAL C 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 38 Processing sheet with id=AA3, first strand: chain 'C' and resid 48 through 49 Processing sheet with id=AA4, first strand: chain 'C' and resid 161 through 165 Processing sheet with id=AA5, first strand: chain 'C' and resid 206 through 208 Processing sheet with id=AA6, first strand: chain 'C' and resid 288 through 293 Processing sheet with id=AA7, first strand: chain 'C' and resid 328 through 330 removed outlier: 3.930A pdb=" N GLN C 328 " --> pdb=" O LEU C 357 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AA9, first strand: chain 'G' and resid 108 through 109 removed outlier: 6.674A pdb=" N GLU G 133 " --> pdb=" O LEU G 150 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER G 137 " --> pdb=" O GLY G 146 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N GLY G 146 " --> pdb=" O SER G 137 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ASP G 139 " --> pdb=" O ILE G 144 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE G 144 " --> pdb=" O ASP G 139 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 14 through 18 removed outlier: 6.195A pdb=" N SER H 4 " --> pdb=" O ILE H 68 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ILE H 70 " --> pdb=" O SER H 4 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL H 6 " --> pdb=" O ILE H 70 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 100 through 101 641 hydrogen bonds defined for protein. 1830 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.39 Time building geometry restraints manager: 4.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 5077 1.42 - 1.64: 7611 1.64 - 1.85: 121 1.85 - 2.07: 0 2.07 - 2.28: 52 Bond restraints: 12861 Sorted by residual: bond pdb=" O5' FMN C 500 " pdb=" P FMN C 500 " ideal model delta sigma weight residual 1.676 1.827 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" O5' FMN D 410 " pdb=" P FMN D 410 " ideal model delta sigma weight residual 1.676 1.594 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" O5' FMN G 301 " pdb=" P FMN G 301 " ideal model delta sigma weight residual 1.676 1.596 0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C5' FMN C 500 " pdb=" O5' FMN C 500 " ideal model delta sigma weight residual 1.418 1.344 0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" O1P FMN G 301 " pdb=" P FMN G 301 " ideal model delta sigma weight residual 1.542 1.481 0.061 2.00e-02 2.50e+03 9.24e+00 ... (remaining 12856 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 16989 2.01 - 4.03: 366 4.03 - 6.04: 112 6.04 - 8.05: 13 8.05 - 10.07: 40 Bond angle restraints: 17520 Sorted by residual: angle pdb=" C ASN A 112 " pdb=" N CYS A 113 " pdb=" CA CYS A 113 " ideal model delta sigma weight residual 121.54 129.03 -7.49 1.91e+00 2.74e-01 1.54e+01 angle pdb=" C ALA D 170 " pdb=" CA ALA D 170 " pdb=" CB ALA D 170 " ideal model delta sigma weight residual 115.89 110.85 5.04 1.32e+00 5.74e-01 1.46e+01 angle pdb=" C2 LMT E 304 " pdb=" C3 LMT E 304 " pdb=" C4 LMT E 304 " ideal model delta sigma weight residual 117.09 107.02 10.07 3.00e+00 1.11e-01 1.13e+01 angle pdb=" C2 LMT D 401 " pdb=" C3 LMT D 401 " pdb=" C4 LMT D 401 " ideal model delta sigma weight residual 117.09 107.31 9.78 3.00e+00 1.11e-01 1.06e+01 angle pdb=" C2 LMT D 406 " pdb=" C3 LMT D 406 " pdb=" C4 LMT D 406 " ideal model delta sigma weight residual 117.09 107.31 9.78 3.00e+00 1.11e-01 1.06e+01 ... (remaining 17515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.55: 7615 24.55 - 49.10: 356 49.10 - 73.65: 84 73.65 - 98.20: 35 98.20 - 122.75: 49 Dihedral angle restraints: 8139 sinusoidal: 3612 harmonic: 4527 Sorted by residual: dihedral pdb=" CA ILE D 106 " pdb=" C ILE D 106 " pdb=" N GLY D 107 " pdb=" CA GLY D 107 " ideal model delta harmonic sigma weight residual -180.00 -157.92 -22.08 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA ILE C 85 " pdb=" C ILE C 85 " pdb=" N GLY C 86 " pdb=" CA GLY C 86 " ideal model delta harmonic sigma weight residual 180.00 -158.93 -21.07 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" C2B LMT E 303 " pdb=" C1B LMT E 303 " pdb=" O5B LMT E 303 " pdb=" C5B LMT E 303 " ideal model delta sinusoidal sigma weight residual -57.12 65.63 -122.75 1 3.00e+01 1.11e-03 1.64e+01 ... (remaining 8136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.014: 2132 1.014 - 2.029: 0 2.029 - 3.043: 0 3.043 - 4.057: 0 4.057 - 5.072: 4 Chirality restraints: 2136 Sorted by residual: chirality pdb=" C2' FMN G 301 " pdb=" C1' FMN G 301 " pdb=" C3' FMN G 301 " pdb=" O2' FMN G 301 " both_signs ideal model delta sigma weight residual False -2.52 2.55 -5.07 2.00e-01 2.50e+01 6.43e+02 chirality pdb=" CB THR G 202 " pdb=" CA THR G 202 " pdb=" OG1 THR G 202 " pdb=" CG2 THR G 202 " both_signs ideal model delta sigma weight residual False 2.55 -2.46 5.01 2.00e-01 2.50e+01 6.28e+02 chirality pdb=" C4' FMN D 410 " pdb=" C3' FMN D 410 " pdb=" C5' FMN D 410 " pdb=" O4' FMN D 410 " both_signs ideal model delta sigma weight residual False -2.50 2.42 -4.92 2.00e-01 2.50e+01 6.05e+02 ... (remaining 2133 not shown) Planarity restraints: 2122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMN G 301 " -0.112 2.00e-02 2.50e+03 4.16e-02 7.81e+01 pdb=" C10 FMN G 301 " -0.015 2.00e-02 2.50e+03 pdb=" C2 FMN G 301 " 0.035 2.00e-02 2.50e+03 pdb=" C4 FMN G 301 " -0.021 2.00e-02 2.50e+03 pdb=" C4A FMN G 301 " -0.031 2.00e-02 2.50e+03 pdb=" C5A FMN G 301 " -0.026 2.00e-02 2.50e+03 pdb=" C6 FMN G 301 " -0.014 2.00e-02 2.50e+03 pdb=" C7 FMN G 301 " 0.011 2.00e-02 2.50e+03 pdb=" C7M FMN G 301 " 0.024 2.00e-02 2.50e+03 pdb=" C8 FMN G 301 " 0.024 2.00e-02 2.50e+03 pdb=" C8M FMN G 301 " 0.062 2.00e-02 2.50e+03 pdb=" C9 FMN G 301 " 0.011 2.00e-02 2.50e+03 pdb=" C9A FMN G 301 " -0.013 2.00e-02 2.50e+03 pdb=" N1 FMN G 301 " 0.017 2.00e-02 2.50e+03 pdb=" N10 FMN G 301 " -0.019 2.00e-02 2.50e+03 pdb=" N3 FMN G 301 " 0.014 2.00e-02 2.50e+03 pdb=" N5 FMN G 301 " -0.035 2.00e-02 2.50e+03 pdb=" O2 FMN G 301 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FMN D 410 " 0.001 2.00e-02 2.50e+03 1.20e-02 6.53e+00 pdb=" C10 FMN D 410 " -0.003 2.00e-02 2.50e+03 pdb=" C2 FMN D 410 " -0.010 2.00e-02 2.50e+03 pdb=" C4 FMN D 410 " 0.011 2.00e-02 2.50e+03 pdb=" C4A FMN D 410 " 0.006 2.00e-02 2.50e+03 pdb=" C5A FMN D 410 " 0.011 2.00e-02 2.50e+03 pdb=" C6 FMN D 410 " 0.006 2.00e-02 2.50e+03 pdb=" C7 FMN D 410 " -0.001 2.00e-02 2.50e+03 pdb=" C7M FMN D 410 " -0.039 2.00e-02 2.50e+03 pdb=" C8 FMN D 410 " 0.001 2.00e-02 2.50e+03 pdb=" C8M FMN D 410 " 0.010 2.00e-02 2.50e+03 pdb=" C9 FMN D 410 " 0.006 2.00e-02 2.50e+03 pdb=" C9A FMN D 410 " 0.010 2.00e-02 2.50e+03 pdb=" N1 FMN D 410 " -0.012 2.00e-02 2.50e+03 pdb=" N10 FMN D 410 " 0.000 2.00e-02 2.50e+03 pdb=" N3 FMN D 410 " 0.000 2.00e-02 2.50e+03 pdb=" N5 FMN D 410 " 0.012 2.00e-02 2.50e+03 pdb=" O2 FMN D 410 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 78 " -0.011 2.00e-02 2.50e+03 2.11e-02 4.43e+00 pdb=" C VAL A 78 " 0.036 2.00e-02 2.50e+03 pdb=" O VAL A 78 " -0.014 2.00e-02 2.50e+03 pdb=" N VAL A 79 " -0.012 2.00e-02 2.50e+03 ... (remaining 2119 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 383 2.72 - 3.26: 12564 3.26 - 3.81: 20070 3.81 - 4.35: 23997 4.35 - 4.90: 42045 Nonbonded interactions: 99059 Sorted by model distance: nonbonded pdb=" OG1 THR D 191 " pdb=" OE1 GLU D 194 " model vdw 2.169 3.040 nonbonded pdb=" OG SER H 25 " pdb=" OE1 GLN H 28 " model vdw 2.210 3.040 nonbonded pdb=" OG SER C 202 " pdb=" O ALA C 227 " model vdw 2.225 3.040 nonbonded pdb=" O THR D 184 " pdb=" OG1 THR D 187 " model vdw 2.249 3.040 nonbonded pdb=" OG SER D 201 " pdb=" OG SER D 204 " model vdw 2.261 3.040 ... (remaining 99054 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 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: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 34.460 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.151 12883 Z= 0.320 Angle : 1.098 39.359 17574 Z= 0.363 Chirality : 0.221 5.072 2136 Planarity : 0.004 0.042 2122 Dihedral : 18.684 122.745 5241 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.47 % Favored : 95.34 % Rotamer: Outliers : 1.51 % Allowed : 5.09 % Favored : 93.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.23), residues: 1587 helix: 1.83 (0.19), residues: 805 sheet: -0.62 (0.57), residues: 106 loop : -0.67 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 83 HIS 0.002 0.000 HIS C 268 PHE 0.015 0.001 PHE G 95 TYR 0.009 0.001 TYR C 237 ARG 0.002 0.000 ARG E 221 Details of bonding type rmsd hydrogen bonds : bond 0.14334 ( 637) hydrogen bonds : angle 5.76544 ( 1830) metal coordination : bond 0.00811 ( 20) metal coordination : angle 12.79050 ( 54) covalent geometry : bond 0.00611 (12861) covalent geometry : angle 0.84016 (17520) Misc. bond : bond 0.06989 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 197 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 354 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8536 (tt) REVERT: G 67 GLU cc_start: 0.8584 (tp30) cc_final: 0.8299 (tp30) REVERT: B 132 HIS cc_start: 0.5459 (m90) cc_final: 0.5134 (m90) outliers start: 19 outliers final: 4 residues processed: 214 average time/residue: 0.3180 time to fit residues: 91.9599 Evaluate side-chains 124 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain G residue 202 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 80 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 47 optimal weight: 0.0370 chunk 74 optimal weight: 0.3980 chunk 91 optimal weight: 4.9990 chunk 142 optimal weight: 10.0000 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 327 GLN G 98 GLN G 225 GLN H 31 GLN H 47 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.063096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.045748 restraints weight = 43759.137| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 3.15 r_work: 0.2701 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12883 Z= 0.117 Angle : 0.938 37.996 17574 Z= 0.300 Chirality : 0.044 0.299 2136 Planarity : 0.005 0.057 2122 Dihedral : 15.122 88.758 2555 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.41 % Favored : 95.46 % Rotamer: Outliers : 1.59 % Allowed : 10.73 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.22), residues: 1587 helix: 2.10 (0.19), residues: 809 sheet: -0.25 (0.60), residues: 103 loop : -0.67 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 96 HIS 0.002 0.000 HIS C 427 PHE 0.013 0.001 PHE H 52 TYR 0.018 0.001 TYR C 237 ARG 0.011 0.001 ARG H 37 Details of bonding type rmsd hydrogen bonds : bond 0.03778 ( 637) hydrogen bonds : angle 4.33671 ( 1830) metal coordination : bond 0.00783 ( 20) metal coordination : angle 12.21759 ( 54) covalent geometry : bond 0.00244 (12861) covalent geometry : angle 0.64930 (17520) Misc. bond : bond 0.00201 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8197 (tm-30) REVERT: E 72 MET cc_start: 0.8871 (ttm) cc_final: 0.8657 (ttm) REVERT: E 135 ASN cc_start: 0.8703 (m-40) cc_final: 0.8438 (m110) REVERT: E 171 PHE cc_start: 0.9140 (m-80) cc_final: 0.8936 (m-80) REVERT: E 227 ARG cc_start: 0.7124 (mtt180) cc_final: 0.6817 (mtt180) REVERT: G 67 GLU cc_start: 0.9297 (tp30) cc_final: 0.8831 (tp30) REVERT: G 70 MET cc_start: 0.9100 (tpp) cc_final: 0.8858 (tpt) REVERT: G 79 GLU cc_start: 0.8949 (tt0) cc_final: 0.8730 (tt0) REVERT: G 95 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.7120 (p90) REVERT: G 101 GLU cc_start: 0.9002 (pt0) cc_final: 0.8632 (pm20) REVERT: H 15 GLN cc_start: 0.8949 (tt0) cc_final: 0.8608 (tt0) REVERT: B 83 LEU cc_start: 0.8956 (tt) cc_final: 0.8709 (mt) REVERT: B 103 ARG cc_start: 0.8078 (tpp-160) cc_final: 0.7723 (mmm160) REVERT: B 132 HIS cc_start: 0.6741 (m90) cc_final: 0.5998 (m90) REVERT: B 146 ARG cc_start: 0.8327 (mmm160) cc_final: 0.8095 (mmm160) outliers start: 20 outliers final: 10 residues processed: 150 average time/residue: 0.2904 time to fit residues: 60.9546 Evaluate side-chains 129 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 95 PHE Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain B residue 105 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 53 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 chunk 31 optimal weight: 0.3980 chunk 124 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.061753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.044515 restraints weight = 44564.449| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 3.07 r_work: 0.2679 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12883 Z= 0.163 Angle : 0.938 40.299 17574 Z= 0.294 Chirality : 0.044 0.311 2136 Planarity : 0.004 0.045 2122 Dihedral : 11.241 75.657 2552 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.91 % Allowed : 11.05 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.22), residues: 1587 helix: 2.15 (0.19), residues: 809 sheet: -0.22 (0.60), residues: 99 loop : -0.61 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 96 HIS 0.002 0.001 HIS A 60 PHE 0.011 0.001 PHE E 114 TYR 0.017 0.001 TYR C 237 ARG 0.007 0.000 ARG H 37 Details of bonding type rmsd hydrogen bonds : bond 0.03863 ( 637) hydrogen bonds : angle 4.19861 ( 1830) metal coordination : bond 0.01513 ( 20) metal coordination : angle 12.61787 ( 54) covalent geometry : bond 0.00377 (12861) covalent geometry : angle 0.62556 (17520) Misc. bond : bond 0.00095 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8456 (tm-30) REVERT: C 319 CYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8141 (p) REVERT: E 135 ASN cc_start: 0.8809 (m-40) cc_final: 0.8497 (m110) REVERT: E 225 GLU cc_start: 0.9257 (mm-30) cc_final: 0.9016 (tp30) REVERT: E 227 ARG cc_start: 0.7181 (mtt180) cc_final: 0.6867 (mtt180) REVERT: G 67 GLU cc_start: 0.9328 (tp30) cc_final: 0.8878 (tp30) REVERT: G 70 MET cc_start: 0.9216 (tpp) cc_final: 0.8960 (tpt) REVERT: G 95 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.7607 (p90) REVERT: G 101 GLU cc_start: 0.9022 (OUTLIER) cc_final: 0.8654 (pm20) REVERT: H 25 SER cc_start: 0.8180 (p) cc_final: 0.7072 (m) REVERT: B 103 ARG cc_start: 0.8167 (tpp-160) cc_final: 0.7839 (mmm160) REVERT: B 132 HIS cc_start: 0.6860 (m90) cc_final: 0.6537 (m90) REVERT: B 146 ARG cc_start: 0.8390 (mmm160) cc_final: 0.8175 (mmm160) outliers start: 24 outliers final: 11 residues processed: 136 average time/residue: 0.2613 time to fit residues: 51.4630 Evaluate side-chains 127 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 95 PHE Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain B residue 105 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 1 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 141 optimal weight: 6.9990 chunk 55 optimal weight: 0.0570 chunk 27 optimal weight: 0.0670 chunk 24 optimal weight: 1.9990 chunk 140 optimal weight: 20.0000 overall best weight: 0.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.062824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.045845 restraints weight = 43796.859| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 3.06 r_work: 0.2725 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12883 Z= 0.104 Angle : 0.879 38.760 17574 Z= 0.269 Chirality : 0.041 0.362 2136 Planarity : 0.004 0.040 2122 Dihedral : 9.594 62.125 2549 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.60 % Favored : 95.34 % Rotamer: Outliers : 1.83 % Allowed : 12.16 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.22), residues: 1587 helix: 2.29 (0.19), residues: 812 sheet: -0.10 (0.61), residues: 96 loop : -0.55 (0.25), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 83 HIS 0.001 0.000 HIS A 60 PHE 0.011 0.001 PHE E 114 TYR 0.018 0.001 TYR C 237 ARG 0.005 0.000 ARG H 37 Details of bonding type rmsd hydrogen bonds : bond 0.03266 ( 637) hydrogen bonds : angle 4.01603 ( 1830) metal coordination : bond 0.00695 ( 20) metal coordination : angle 12.22036 ( 54) covalent geometry : bond 0.00221 (12861) covalent geometry : angle 0.56099 (17520) Misc. bond : bond 0.00024 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9222 (tm-30) cc_final: 0.8820 (tm-30) REVERT: A 88 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8708 (tm-30) REVERT: A 100 ARG cc_start: 0.9057 (tpp80) cc_final: 0.8477 (mmt-90) REVERT: A 155 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8785 (mt-10) REVERT: C 319 CYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8061 (p) REVERT: E 135 ASN cc_start: 0.8761 (m-40) cc_final: 0.8510 (m110) REVERT: E 225 GLU cc_start: 0.9255 (mm-30) cc_final: 0.9031 (tp30) REVERT: E 227 ARG cc_start: 0.7108 (mtt180) cc_final: 0.6781 (mtt180) REVERT: G 60 MET cc_start: 0.9225 (mmm) cc_final: 0.8674 (mtm) REVERT: G 67 GLU cc_start: 0.9333 (tp30) cc_final: 0.8862 (tp30) REVERT: G 95 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.7894 (p90) REVERT: G 101 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8606 (pm20) REVERT: B 103 ARG cc_start: 0.8178 (tpp-160) cc_final: 0.7550 (mmm160) REVERT: B 132 HIS cc_start: 0.6756 (m90) cc_final: 0.5883 (m90) outliers start: 23 outliers final: 13 residues processed: 142 average time/residue: 0.2612 time to fit residues: 53.7325 Evaluate side-chains 134 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 95 PHE Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 125 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 17 optimal weight: 1.9990 chunk 75 optimal weight: 0.0770 chunk 141 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 155 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 overall best weight: 2.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 268 HIS D 189 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.061200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.044111 restraints weight = 44015.956| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 3.03 r_work: 0.2674 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12883 Z= 0.158 Angle : 0.907 40.730 17574 Z= 0.284 Chirality : 0.042 0.352 2136 Planarity : 0.004 0.086 2122 Dihedral : 8.879 59.098 2549 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.67 % Allowed : 13.20 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.22), residues: 1587 helix: 2.36 (0.19), residues: 813 sheet: -0.24 (0.59), residues: 99 loop : -0.51 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 96 HIS 0.002 0.001 HIS C 17 PHE 0.011 0.001 PHE E 114 TYR 0.017 0.001 TYR C 237 ARG 0.008 0.000 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.03598 ( 637) hydrogen bonds : angle 4.04068 ( 1830) metal coordination : bond 0.01439 ( 20) metal coordination : angle 12.42586 ( 54) covalent geometry : bond 0.00373 (12861) covalent geometry : angle 0.59079 (17520) Misc. bond : bond 0.00100 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9261 (tm-30) cc_final: 0.8798 (tm-30) REVERT: A 88 GLU cc_start: 0.8983 (tm-30) cc_final: 0.8692 (tm-30) REVERT: A 92 ARG cc_start: 0.9040 (mmm-85) cc_final: 0.8658 (mmm-85) REVERT: A 100 ARG cc_start: 0.9030 (tpp80) cc_final: 0.8471 (mmt-90) REVERT: A 155 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8800 (mt-10) REVERT: C 319 CYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8101 (p) REVERT: D 327 ASN cc_start: 0.9279 (m110) cc_final: 0.8949 (m-40) REVERT: E 135 ASN cc_start: 0.8840 (m-40) cc_final: 0.8551 (m110) REVERT: E 225 GLU cc_start: 0.9276 (mm-30) cc_final: 0.9048 (tp30) REVERT: E 227 ARG cc_start: 0.7145 (mtt180) cc_final: 0.6837 (mtt180) REVERT: G 67 GLU cc_start: 0.9328 (tp30) cc_final: 0.8887 (tp30) REVERT: G 70 MET cc_start: 0.9083 (tpp) cc_final: 0.8831 (tpt) REVERT: G 95 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.8044 (p90) REVERT: B 132 HIS cc_start: 0.6915 (m90) cc_final: 0.5921 (m90) outliers start: 21 outliers final: 14 residues processed: 136 average time/residue: 0.2463 time to fit residues: 48.6817 Evaluate side-chains 134 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 95 PHE Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 173 PHE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain B residue 15 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 50 optimal weight: 0.0370 chunk 99 optimal weight: 0.0670 chunk 49 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 129 optimal weight: 8.9990 chunk 81 optimal weight: 7.9990 overall best weight: 1.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.061954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.044486 restraints weight = 44501.183| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 3.14 r_work: 0.2699 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12883 Z= 0.110 Angle : 0.866 39.746 17574 Z= 0.266 Chirality : 0.040 0.294 2136 Planarity : 0.004 0.040 2122 Dihedral : 8.274 59.802 2548 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.16 % Favored : 95.78 % Rotamer: Outliers : 2.38 % Allowed : 12.40 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.22), residues: 1587 helix: 2.44 (0.19), residues: 814 sheet: -0.26 (0.59), residues: 98 loop : -0.48 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 96 HIS 0.001 0.000 HIS G 222 PHE 0.010 0.001 PHE E 114 TYR 0.016 0.001 TYR C 237 ARG 0.006 0.000 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.03264 ( 637) hydrogen bonds : angle 3.93275 ( 1830) metal coordination : bond 0.00850 ( 20) metal coordination : angle 12.11671 ( 54) covalent geometry : bond 0.00251 (12861) covalent geometry : angle 0.54714 (17520) Misc. bond : bond 0.00047 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 1.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 GLU cc_start: 0.9055 (tm-30) cc_final: 0.8733 (tm-30) REVERT: A 92 ARG cc_start: 0.9101 (mmm-85) cc_final: 0.8794 (mmm-85) REVERT: A 100 ARG cc_start: 0.8988 (tpp80) cc_final: 0.8505 (mmt-90) REVERT: A 131 MET cc_start: 0.9266 (tpp) cc_final: 0.8908 (tpt) REVERT: A 155 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8807 (mt-10) REVERT: C 319 CYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8108 (p) REVERT: D 327 ASN cc_start: 0.9297 (m110) cc_final: 0.8966 (m-40) REVERT: E 135 ASN cc_start: 0.8839 (m-40) cc_final: 0.8582 (m110) REVERT: E 225 GLU cc_start: 0.9255 (mm-30) cc_final: 0.9049 (tp30) REVERT: E 227 ARG cc_start: 0.7184 (mtt180) cc_final: 0.6908 (mtt180) REVERT: G 67 GLU cc_start: 0.9333 (tp30) cc_final: 0.8881 (tp30) REVERT: G 70 MET cc_start: 0.9129 (tpp) cc_final: 0.8871 (tpt) REVERT: G 95 PHE cc_start: 0.8885 (OUTLIER) cc_final: 0.8254 (p90) REVERT: G 101 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8501 (pm20) REVERT: G 106 GLU cc_start: 0.8721 (tp30) cc_final: 0.8447 (tp30) REVERT: H 54 LYS cc_start: 0.7686 (mmmt) cc_final: 0.7475 (mmtt) REVERT: B 103 ARG cc_start: 0.8328 (tpp-160) cc_final: 0.7843 (mmm160) REVERT: B 114 ARG cc_start: 0.9660 (OUTLIER) cc_final: 0.9444 (ttm110) REVERT: B 132 HIS cc_start: 0.6858 (m90) cc_final: 0.5837 (m90) outliers start: 30 outliers final: 14 residues processed: 144 average time/residue: 0.4204 time to fit residues: 91.4381 Evaluate side-chains 135 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 95 PHE Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 114 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 96 optimal weight: 0.7980 chunk 106 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 134 optimal weight: 7.9990 chunk 138 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 148 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.061954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.044888 restraints weight = 44022.655| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 3.06 r_work: 0.2703 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12883 Z= 0.112 Angle : 0.868 39.668 17574 Z= 0.273 Chirality : 0.040 0.222 2136 Planarity : 0.004 0.040 2122 Dihedral : 8.069 59.989 2548 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.47 % Favored : 95.46 % Rotamer: Outliers : 1.83 % Allowed : 12.96 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.22), residues: 1587 helix: 2.48 (0.19), residues: 813 sheet: -0.25 (0.58), residues: 100 loop : -0.47 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 96 HIS 0.002 0.000 HIS C 17 PHE 0.009 0.001 PHE G 121 TYR 0.016 0.001 TYR C 237 ARG 0.005 0.000 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.03260 ( 637) hydrogen bonds : angle 3.91244 ( 1830) metal coordination : bond 0.00838 ( 20) metal coordination : angle 12.00631 ( 54) covalent geometry : bond 0.00255 (12861) covalent geometry : angle 0.55843 (17520) Misc. bond : bond 0.00049 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 GLU cc_start: 0.9091 (tm-30) cc_final: 0.8747 (tm-30) REVERT: A 92 ARG cc_start: 0.9123 (mmm-85) cc_final: 0.8812 (mmm-85) REVERT: A 100 ARG cc_start: 0.8948 (tpp80) cc_final: 0.8500 (mmt-90) REVERT: A 131 MET cc_start: 0.9258 (tpp) cc_final: 0.8900 (tpt) REVERT: A 155 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8803 (mt-10) REVERT: C 319 CYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8099 (p) REVERT: D 327 ASN cc_start: 0.9285 (m110) cc_final: 0.8950 (m-40) REVERT: E 135 ASN cc_start: 0.8843 (m-40) cc_final: 0.8568 (m110) REVERT: E 227 ARG cc_start: 0.7148 (mtt180) cc_final: 0.6855 (mtt180) REVERT: G 67 GLU cc_start: 0.9336 (tp30) cc_final: 0.8883 (tp30) REVERT: G 70 MET cc_start: 0.9215 (tpp) cc_final: 0.8958 (tpt) REVERT: G 95 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.8343 (p90) REVERT: G 101 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8455 (pm20) REVERT: H 42 ILE cc_start: 0.8541 (mm) cc_final: 0.8201 (pt) REVERT: H 54 LYS cc_start: 0.7732 (mmmt) cc_final: 0.7516 (mmtt) REVERT: B 103 ARG cc_start: 0.8386 (tpp-160) cc_final: 0.7847 (mmm160) REVERT: B 132 HIS cc_start: 0.6819 (m90) cc_final: 0.5674 (m90) outliers start: 23 outliers final: 16 residues processed: 135 average time/residue: 0.2559 time to fit residues: 50.4529 Evaluate side-chains 137 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 95 PHE Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 114 ARG Chi-restraints excluded: chain B residue 131 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 26 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 74 optimal weight: 0.0070 chunk 87 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.061688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.044389 restraints weight = 44746.303| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 3.18 r_work: 0.2665 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12883 Z= 0.097 Angle : 0.847 38.668 17574 Z= 0.265 Chirality : 0.039 0.178 2136 Planarity : 0.004 0.040 2122 Dihedral : 7.840 59.907 2548 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.16 % Favored : 95.78 % Rotamer: Outliers : 1.91 % Allowed : 13.28 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.22), residues: 1587 helix: 2.52 (0.19), residues: 813 sheet: -0.18 (0.59), residues: 98 loop : -0.42 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 96 HIS 0.001 0.000 HIS C 17 PHE 0.013 0.001 PHE A 173 TYR 0.015 0.001 TYR C 237 ARG 0.005 0.000 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.03055 ( 637) hydrogen bonds : angle 3.84019 ( 1830) metal coordination : bond 0.00573 ( 20) metal coordination : angle 11.81693 ( 54) covalent geometry : bond 0.00212 (12861) covalent geometry : angle 0.53736 (17520) Misc. bond : bond 0.00025 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 GLU cc_start: 0.9091 (tm-30) cc_final: 0.8752 (tm-30) REVERT: A 92 ARG cc_start: 0.9104 (mmm-85) cc_final: 0.8784 (mmm-85) REVERT: A 100 ARG cc_start: 0.8917 (tpp80) cc_final: 0.8505 (mmt-90) REVERT: A 131 MET cc_start: 0.9231 (tpp) cc_final: 0.8881 (tpt) REVERT: A 155 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8810 (mt-10) REVERT: C 319 CYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8180 (p) REVERT: D 327 ASN cc_start: 0.9251 (m110) cc_final: 0.8864 (m110) REVERT: E 135 ASN cc_start: 0.8792 (m-40) cc_final: 0.8500 (m110) REVERT: E 227 ARG cc_start: 0.7144 (mtt180) cc_final: 0.6846 (mtt180) REVERT: G 67 GLU cc_start: 0.9333 (tp30) cc_final: 0.8945 (tp30) REVERT: G 95 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8334 (p90) REVERT: G 101 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8691 (pt0) REVERT: G 106 GLU cc_start: 0.8676 (tp30) cc_final: 0.8449 (tp30) REVERT: H 15 GLN cc_start: 0.8928 (tt0) cc_final: 0.8448 (tt0) REVERT: H 42 ILE cc_start: 0.8561 (mm) cc_final: 0.8173 (pt) REVERT: B 103 ARG cc_start: 0.8292 (tpp-160) cc_final: 0.7756 (mmm160) REVERT: B 132 HIS cc_start: 0.6767 (m90) cc_final: 0.5791 (m90) outliers start: 24 outliers final: 16 residues processed: 142 average time/residue: 0.2426 time to fit residues: 50.3696 Evaluate side-chains 136 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 95 PHE Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 114 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 109 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 137 optimal weight: 0.9990 chunk 134 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 chunk 18 optimal weight: 7.9990 chunk 55 optimal weight: 0.0060 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.061890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.044606 restraints weight = 44424.761| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 3.17 r_work: 0.2672 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 12883 Z= 0.099 Angle : 0.847 38.156 17574 Z= 0.271 Chirality : 0.039 0.191 2136 Planarity : 0.004 0.040 2122 Dihedral : 7.648 59.911 2548 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.10 % Favored : 95.84 % Rotamer: Outliers : 2.15 % Allowed : 13.35 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.22), residues: 1587 helix: 2.62 (0.19), residues: 801 sheet: -0.08 (0.59), residues: 98 loop : -0.40 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 96 HIS 0.002 0.000 HIS B 132 PHE 0.014 0.001 PHE A 143 TYR 0.013 0.001 TYR C 237 ARG 0.004 0.000 ARG A 92 Details of bonding type rmsd hydrogen bonds : bond 0.03021 ( 637) hydrogen bonds : angle 3.80899 ( 1830) metal coordination : bond 0.00573 ( 20) metal coordination : angle 11.56864 ( 54) covalent geometry : bond 0.00221 (12861) covalent geometry : angle 0.55399 (17520) Misc. bond : bond 0.00026 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 GLU cc_start: 0.9095 (tm-30) cc_final: 0.8755 (tm-30) REVERT: A 92 ARG cc_start: 0.9099 (mmm-85) cc_final: 0.8807 (mmm-85) REVERT: A 100 ARG cc_start: 0.8871 (tpp80) cc_final: 0.8506 (mmt-90) REVERT: A 131 MET cc_start: 0.9226 (tpp) cc_final: 0.8879 (tpt) REVERT: A 155 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8804 (mt-10) REVERT: C 319 CYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8226 (p) REVERT: D 327 ASN cc_start: 0.9267 (m110) cc_final: 0.8882 (m110) REVERT: E 135 ASN cc_start: 0.8771 (m-40) cc_final: 0.8492 (m110) REVERT: E 227 ARG cc_start: 0.7143 (mtt180) cc_final: 0.6841 (mtt180) REVERT: G 67 GLU cc_start: 0.9323 (tp30) cc_final: 0.8850 (tp30) REVERT: G 95 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.8380 (p90) REVERT: G 101 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8434 (pm20) REVERT: G 106 GLU cc_start: 0.8641 (tp30) cc_final: 0.8387 (tp30) REVERT: H 15 GLN cc_start: 0.8981 (tt0) cc_final: 0.8388 (tt0) REVERT: B 103 ARG cc_start: 0.8225 (tpp-160) cc_final: 0.7895 (mmm160) REVERT: B 132 HIS cc_start: 0.6772 (m90) cc_final: 0.5923 (m90) outliers start: 27 outliers final: 19 residues processed: 136 average time/residue: 0.2544 time to fit residues: 50.3894 Evaluate side-chains 139 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 95 PHE Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 114 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 18 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 54 optimal weight: 9.9990 chunk 155 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 143 optimal weight: 30.0000 chunk 70 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.062381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.045360 restraints weight = 44025.835| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 3.06 r_work: 0.2716 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12883 Z= 0.109 Angle : 0.847 38.342 17574 Z= 0.272 Chirality : 0.039 0.195 2136 Planarity : 0.004 0.039 2122 Dihedral : 7.558 59.985 2548 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.35 % Favored : 95.59 % Rotamer: Outliers : 1.91 % Allowed : 13.59 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.22), residues: 1587 helix: 2.57 (0.19), residues: 812 sheet: -0.01 (0.59), residues: 98 loop : -0.33 (0.25), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 96 HIS 0.002 0.000 HIS B 132 PHE 0.011 0.001 PHE A 173 TYR 0.015 0.001 TYR C 237 ARG 0.008 0.000 ARG H 2 Details of bonding type rmsd hydrogen bonds : bond 0.03112 ( 637) hydrogen bonds : angle 3.83670 ( 1830) metal coordination : bond 0.00779 ( 20) metal coordination : angle 11.53387 ( 54) covalent geometry : bond 0.00251 (12861) covalent geometry : angle 0.55672 (17520) Misc. bond : bond 0.00046 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 GLU cc_start: 0.9121 (tm-30) cc_final: 0.8794 (tm-30) REVERT: A 92 ARG cc_start: 0.9124 (mmm-85) cc_final: 0.8831 (mmm-85) REVERT: A 131 MET cc_start: 0.9247 (tpp) cc_final: 0.8912 (tpt) REVERT: A 155 GLU cc_start: 0.9089 (mt-10) cc_final: 0.8792 (mt-10) REVERT: C 319 CYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8203 (p) REVERT: D 326 MET cc_start: 0.8817 (mmm) cc_final: 0.8609 (mmm) REVERT: D 327 ASN cc_start: 0.9291 (m110) cc_final: 0.8893 (m110) REVERT: E 135 ASN cc_start: 0.8806 (m-40) cc_final: 0.8557 (m110) REVERT: E 227 ARG cc_start: 0.7181 (mtt180) cc_final: 0.6903 (mtt180) REVERT: G 67 GLU cc_start: 0.9338 (tp30) cc_final: 0.8883 (tp30) REVERT: G 95 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.8416 (p90) REVERT: G 101 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8442 (pm20) REVERT: G 106 GLU cc_start: 0.8659 (tp30) cc_final: 0.8397 (tp30) REVERT: H 15 GLN cc_start: 0.9037 (tt0) cc_final: 0.8429 (tt0) REVERT: B 103 ARG cc_start: 0.8214 (tpp-160) cc_final: 0.7879 (mmm160) REVERT: B 132 HIS cc_start: 0.6752 (m90) cc_final: 0.5898 (m90) outliers start: 24 outliers final: 19 residues processed: 135 average time/residue: 0.2626 time to fit residues: 51.2639 Evaluate side-chains 139 residues out of total 1259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 95 PHE Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 110 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 120 optimal weight: 9.9990 chunk 133 optimal weight: 8.9990 chunk 76 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 84 optimal weight: 0.0670 chunk 99 optimal weight: 3.9990 overall best weight: 1.6122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.061973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.044853 restraints weight = 44331.972| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 3.08 r_work: 0.2701 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12883 Z= 0.120 Angle : 0.860 38.841 17574 Z= 0.280 Chirality : 0.039 0.199 2136 Planarity : 0.004 0.039 2122 Dihedral : 7.503 59.959 2548 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.28 % Favored : 95.65 % Rotamer: Outliers : 1.67 % Allowed : 13.91 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.23), residues: 1587 helix: 2.53 (0.19), residues: 816 sheet: 0.02 (0.60), residues: 98 loop : -0.29 (0.25), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 96 HIS 0.002 0.000 HIS C 17 PHE 0.012 0.001 PHE A 173 TYR 0.014 0.001 TYR C 237 ARG 0.006 0.000 ARG G 78 Details of bonding type rmsd hydrogen bonds : bond 0.03208 ( 637) hydrogen bonds : angle 3.84325 ( 1830) metal coordination : bond 0.00906 ( 20) metal coordination : angle 11.57326 ( 54) covalent geometry : bond 0.00280 (12861) covalent geometry : angle 0.57365 (17520) Misc. bond : bond 0.00057 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5818.30 seconds wall clock time: 101 minutes 42.53 seconds (6102.53 seconds total)