Starting phenix.real_space_refine on Fri Jun 5 19:03:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oyh_71021/06_2026/9oyh_71021.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oyh_71021/06_2026/9oyh_71021.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oyh_71021/06_2026/9oyh_71021.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oyh_71021/06_2026/9oyh_71021.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oyh_71021/06_2026/9oyh_71021.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oyh_71021/06_2026/9oyh_71021.map" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 53 5.49 5 Mg 3 5.21 5 S 117 5.16 5 C 14137 2.51 5 N 4057 2.21 5 O 4330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22701 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2726 Classifications: {'peptide': 343} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "B" Number of atoms: 2840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2840 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 16, 'TRANS': 348} Chain: "C" Number of atoms: 2865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2865 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain: "D" Number of atoms: 2799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2799 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 14, 'TRANS': 345} Chain: "E" Number of atoms: 2602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2602 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 313} Chain: "F" Number of atoms: 2835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2835 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 20, 'TRANS': 344} Chain: "G" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2844 Classifications: {'peptide': 366} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 345} Chain: "H" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 489 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "I" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "J" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1024 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 11, 'TRANS': 120} Chain: "L" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1166 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 6, 'TRANS': 139} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3209 SG CYS B 64 92.146 86.115 121.245 1.00 71.59 S ATOM 3269 SG CYS B 73 95.930 85.458 121.487 1.00 83.10 S ATOM 3286 SG CYS B 76 93.815 83.274 123.228 1.00 99.19 S ATOM 3308 SG CYS B 79 93.558 83.195 119.325 1.00 77.18 S ATOM 6049 SG CYS C 64 114.279 56.253 93.607 1.00 51.88 S ATOM 6109 SG CYS C 73 115.789 53.463 91.917 1.00 64.43 S ATOM 6126 SG CYS C 76 112.779 52.674 94.378 1.00 57.78 S ATOM 6148 SG CYS C 79 112.193 54.453 91.091 1.00 42.50 S ATOM 8914 SG CYS D 64 92.174 29.644 62.395 1.00 53.00 S ATOM 8974 SG CYS D 73 90.252 27.101 60.466 1.00 57.47 S ATOM 8991 SG CYS D 76 89.022 27.758 63.895 1.00 57.51 S ATOM 9013 SG CYS D 79 88.617 30.545 61.490 1.00 51.18 S ATOM 11637 SG CYS E 50 46.777 34.283 54.784 1.00 55.74 S ATOM 11706 SG CYS E 59 43.256 33.139 55.479 1.00 65.02 S ATOM 11726 SG CYS E 62 45.558 33.390 58.409 1.00 54.95 S ATOM 11747 SG CYS E 65 44.617 36.587 56.800 1.00 49.60 S Time building chain proxies: 5.52, per 1000 atoms: 0.24 Number of scatterers: 22701 At special positions: 0 Unit cell: (126.684, 153.18, 157.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 117 16.00 P 53 15.00 Mg 3 11.99 O 4330 8.00 N 4057 7.00 C 14137 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=0, symmetry=0 Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 76 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 73 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 64 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 79 " pdb=" ZN C 701 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 79 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 64 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 73 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 76 " pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 76 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 73 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 79 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 64 " pdb=" ZN E 401 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 65 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 62 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 50 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 59 " Number of angles added : 24 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5234 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 18 sheets defined 54.1% alpha, 14.6% beta 18 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 2.86 Creating SS restraints... Processing helix chain 'A' and resid 5 through 7 No H-bonds generated for 'chain 'A' and resid 5 through 7' Processing helix chain 'A' and resid 8 through 15 removed outlier: 3.671A pdb=" N GLN A 12 " --> pdb=" O GLN A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 45 Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.571A pdb=" N ILE A 64 " --> pdb=" O ASP A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 104 removed outlier: 4.156A pdb=" N GLN A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 103 " --> pdb=" O THR A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 124 through 130 Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 163 through 174 Processing helix chain 'A' and resid 177 through 192 Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 213 through 224 Processing helix chain 'A' and resid 225 through 240 Processing helix chain 'A' and resid 242 through 264 removed outlier: 3.663A pdb=" N LEU A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU A 253 " --> pdb=" O THR A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 Processing helix chain 'A' and resid 279 through 293 removed outlier: 4.333A pdb=" N GLY A 284 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N MET A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 315 Processing helix chain 'A' and resid 320 through 332 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'B' and resid 5 through 10 Processing helix chain 'B' and resid 21 through 35 removed outlier: 4.039A pdb=" N ALA B 27 " --> pdb=" O HIS B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 63 Processing helix chain 'B' and resid 76 through 84 Processing helix chain 'B' and resid 100 through 109 Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'B' and resid 132 through 145 removed outlier: 4.179A pdb=" N GLU B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 162 Processing helix chain 'B' and resid 163 through 168 removed outlier: 3.958A pdb=" N LEU B 167 " --> pdb=" O VAL B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 194 Processing helix chain 'B' and resid 199 through 211 removed outlier: 3.859A pdb=" N GLU B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 228 Processing helix chain 'B' and resid 233 through 244 Processing helix chain 'B' and resid 247 through 259 Processing helix chain 'B' and resid 260 through 275 Processing helix chain 'B' and resid 277 through 298 Processing helix chain 'B' and resid 299 through 302 Processing helix chain 'B' and resid 303 through 307 removed outlier: 3.680A pdb=" N MET B 306 " --> pdb=" O GLY B 303 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA B 307 " --> pdb=" O ASN B 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 303 through 307' Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 321 through 338 Processing helix chain 'B' and resid 339 through 342 Processing helix chain 'B' and resid 344 through 358 Processing helix chain 'C' and resid 5 through 10 Processing helix chain 'C' and resid 14 through 18 removed outlier: 3.563A pdb=" N VAL C 18 " --> pdb=" O PHE C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 35 Processing helix chain 'C' and resid 50 through 63 Processing helix chain 'C' and resid 76 through 84 Processing helix chain 'C' and resid 100 through 110 removed outlier: 4.166A pdb=" N ASN C 110 " --> pdb=" O ASP C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 131 Processing helix chain 'C' and resid 132 through 145 removed outlier: 4.434A pdb=" N LYS C 141 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 162 Processing helix chain 'C' and resid 163 through 169 removed outlier: 3.706A pdb=" N ARG C 169 " --> pdb=" O THR C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 194 Processing helix chain 'C' and resid 199 through 211 removed outlier: 3.957A pdb=" N GLU C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 228 Processing helix chain 'C' and resid 233 through 242 Processing helix chain 'C' and resid 245 through 258 removed outlier: 3.538A pdb=" N ALA C 249 " --> pdb=" O ASP C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 273 Processing helix chain 'C' and resid 277 through 298 Processing helix chain 'C' and resid 299 through 302 removed outlier: 4.134A pdb=" N LEU C 302 " --> pdb=" O PRO C 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 299 through 302' Processing helix chain 'C' and resid 303 through 307 removed outlier: 3.554A pdb=" N ALA C 307 " --> pdb=" O ASN C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 321 through 339 Processing helix chain 'C' and resid 340 through 342 No H-bonds generated for 'chain 'C' and resid 340 through 342' Processing helix chain 'C' and resid 344 through 359 Processing helix chain 'D' and resid 5 through 10 Processing helix chain 'D' and resid 21 through 34 Processing helix chain 'D' and resid 50 through 63 Processing helix chain 'D' and resid 76 through 84 Processing helix chain 'D' and resid 96 through 99 removed outlier: 4.119A pdb=" N THR D 99 " --> pdb=" O ALA D 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 96 through 99' Processing helix chain 'D' and resid 100 through 111 Processing helix chain 'D' and resid 127 through 131 Processing helix chain 'D' and resid 132 through 145 removed outlier: 4.704A pdb=" N LYS D 141 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N THR D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 162 Processing helix chain 'D' and resid 163 through 170 removed outlier: 3.585A pdb=" N ARG D 169 " --> pdb=" O THR D 165 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N CYS D 170 " --> pdb=" O ILE D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 194 Processing helix chain 'D' and resid 199 through 211 removed outlier: 3.791A pdb=" N GLU D 211 " --> pdb=" O ALA D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 228 Processing helix chain 'D' and resid 233 through 242 Processing helix chain 'D' and resid 245 through 259 Processing helix chain 'D' and resid 260 through 274 Processing helix chain 'D' and resid 277 through 298 Processing helix chain 'D' and resid 299 through 302 removed outlier: 4.197A pdb=" N LEU D 302 " --> pdb=" O PRO D 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 299 through 302' Processing helix chain 'D' and resid 303 through 307 Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 321 through 339 Processing helix chain 'D' and resid 340 through 342 No H-bonds generated for 'chain 'D' and resid 340 through 342' Processing helix chain 'D' and resid 344 through 358 removed outlier: 3.777A pdb=" N ALA D 358 " --> pdb=" O LEU D 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 6 No H-bonds generated for 'chain 'E' and resid 4 through 6' Processing helix chain 'E' and resid 7 through 20 removed outlier: 3.585A pdb=" N SER E 17 " --> pdb=" O LYS E 13 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA E 20 " --> pdb=" O ALA E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 50 Processing helix chain 'E' and resid 62 through 70 Processing helix chain 'E' and resid 89 through 101 removed outlier: 3.596A pdb=" N ASN E 101 " --> pdb=" O THR E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 120 Processing helix chain 'E' and resid 121 through 127 Processing helix chain 'E' and resid 128 through 134 Processing helix chain 'E' and resid 147 through 151 Processing helix chain 'E' and resid 152 through 158 removed outlier: 3.592A pdb=" N ARG E 158 " --> pdb=" O THR E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 178 removed outlier: 3.712A pdb=" N ARG E 178 " --> pdb=" O THR E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 194 Processing helix chain 'E' and resid 197 through 204 Processing helix chain 'E' and resid 208 through 227 Proline residue: E 225 - end of helix Processing helix chain 'E' and resid 228 through 231 Processing helix chain 'E' and resid 232 through 237 Processing helix chain 'E' and resid 240 through 260 Processing helix chain 'E' and resid 270 through 281 Processing helix chain 'E' and resid 282 through 303 Processing helix chain 'E' and resid 307 through 323 Processing helix chain 'F' and resid 7 through 18 removed outlier: 4.698A pdb=" N LYS F 12 " --> pdb=" O GLU F 8 " (cutoff:3.500A) Proline residue: F 13 - end of helix Processing helix chain 'F' and resid 27 through 30 Processing helix chain 'F' and resid 72 through 82 Processing helix chain 'F' and resid 112 through 116 Processing helix chain 'F' and resid 131 through 143 removed outlier: 3.845A pdb=" N THR F 142 " --> pdb=" O LEU F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 146 No H-bonds generated for 'chain 'F' and resid 144 through 146' Processing helix chain 'F' and resid 152 through 157 removed outlier: 3.509A pdb=" N GLY F 157 " --> pdb=" O TYR F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 207 Processing helix chain 'F' and resid 259 through 274 removed outlier: 3.562A pdb=" N LEU F 273 " --> pdb=" O ARG F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 332 Processing helix chain 'G' and resid 7 through 18 removed outlier: 4.312A pdb=" N LYS G 12 " --> pdb=" O GLU G 8 " (cutoff:3.500A) Proline residue: G 13 - end of helix Processing helix chain 'G' and resid 71 through 81 Processing helix chain 'G' and resid 131 through 141 Processing helix chain 'G' and resid 142 through 146 Processing helix chain 'G' and resid 152 through 155 Processing helix chain 'G' and resid 197 through 207 Processing helix chain 'G' and resid 243 through 248 Processing helix chain 'G' and resid 260 through 271 Processing helix chain 'G' and resid 321 through 332 Processing helix chain 'J' and resid 4 through 12 Processing helix chain 'J' and resid 21 through 25 Processing helix chain 'J' and resid 51 through 61 Processing helix chain 'J' and resid 64 through 68 Processing helix chain 'J' and resid 72 through 79 removed outlier: 3.772A pdb=" N MET J 78 " --> pdb=" O GLU J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 112 Processing helix chain 'J' and resid 114 through 127 removed outlier: 3.866A pdb=" N ARG J 118 " --> pdb=" O ASN J 114 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 133 Processing helix chain 'L' and resid 19 through 24 removed outlier: 3.586A pdb=" N GLN L 23 " --> pdb=" O SER L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 34 Processing helix chain 'L' and resid 48 through 56 removed outlier: 4.475A pdb=" N GLU L 54 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA L 55 " --> pdb=" O ARG L 51 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 110 Processing helix chain 'L' and resid 120 through 122 No H-bonds generated for 'chain 'L' and resid 120 through 122' Processing helix chain 'L' and resid 123 through 131 removed outlier: 4.592A pdb=" N GLU L 129 " --> pdb=" O GLN L 125 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG L 130 " --> pdb=" O LEU L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 137 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 removed outlier: 3.652A pdb=" N ILE A 2 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TYR A 21 " --> pdb=" O VAL A 112 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N GLY A 114 " --> pdb=" O TYR A 21 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU A 23 " --> pdb=" O GLY A 114 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ARG A 77 " --> pdb=" O PHE A 47 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU A 49 " --> pdb=" O ARG A 77 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 161 through 162 removed outlier: 6.125A pdb=" N GLU A 161 " --> pdb=" O LEU A 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 90 through 94 removed outlier: 6.088A pdb=" N LYS B 121 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N LEU B 153 " --> pdb=" O LYS B 121 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N TYR B 123 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ALA B 155 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE B 125 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TYR B 41 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N THR B 156 " --> pdb=" O TYR B 41 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N PHE B 43 " --> pdb=" O THR B 156 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ALA B 40 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N PHE B 173 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU B 42 " --> pdb=" O PHE B 173 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 197 through 198 removed outlier: 6.795A pdb=" N ALA B 197 " --> pdb=" O VAL B 232 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 359 through 361 Processing sheet with id=AA6, first strand: chain 'C' and resid 90 through 94 Processing sheet with id=AA7, first strand: chain 'D' and resid 90 through 94 removed outlier: 6.210A pdb=" N LYS D 121 " --> pdb=" O LYS D 151 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N LEU D 153 " --> pdb=" O LYS D 121 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TYR D 123 " --> pdb=" O LEU D 153 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ALA D 155 " --> pdb=" O TYR D 123 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE D 125 " --> pdb=" O ALA D 155 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR D 41 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N THR D 156 " --> pdb=" O TYR D 41 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE D 43 " --> pdb=" O THR D 156 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ALA D 40 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N PHE D 173 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU D 42 " --> pdb=" O PHE D 173 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 76 through 79 Processing sheet with id=AA9, first strand: chain 'F' and resid 2 through 6 removed outlier: 3.653A pdb=" N ARG F 96 " --> pdb=" O GLU F 93 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASN G 295 " --> pdb=" O GLY G 280 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N GLY G 280 " --> pdb=" O ASN G 295 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 66 through 71 removed outlier: 6.536A pdb=" N ASN F 32 " --> pdb=" O THR F 47 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N THR F 47 " --> pdb=" O ASN F 32 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 309 through 310 removed outlier: 15.857A pdb=" N SER F 181 " --> pdb=" O THR F 172 " (cutoff:3.500A) removed outlier: 15.905A pdb=" N THR F 172 " --> pdb=" O SER F 181 " (cutoff:3.500A) removed outlier: 14.603A pdb=" N VAL F 170 " --> pdb=" O PRO F 183 " (cutoff:3.500A) removed outlier: 13.612A pdb=" N GLY F 185 " --> pdb=" O ARG F 168 " (cutoff:3.500A) removed outlier: 14.048A pdb=" N ARG F 168 " --> pdb=" O GLY F 185 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N SER F 187 " --> pdb=" O GLU F 166 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N GLU F 166 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N GLY F 164 " --> pdb=" O PRO F 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 303 through 307 removed outlier: 3.652A pdb=" N MET F 315 " --> pdb=" O VAL F 285 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 2 through 6 Processing sheet with id=AB5, first strand: chain 'G' and resid 66 through 68 Processing sheet with id=AB6, first strand: chain 'G' and resid 254 through 259 removed outlier: 4.362A pdb=" N ASP G 351 " --> pdb=" O ALA G 357 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ALA G 357 " --> pdb=" O ASP G 351 " (cutoff:3.500A) removed outlier: 16.059A pdb=" N SER G 181 " --> pdb=" O THR G 172 " (cutoff:3.500A) removed outlier: 16.125A pdb=" N THR G 172 " --> pdb=" O SER G 181 " (cutoff:3.500A) removed outlier: 14.333A pdb=" N VAL G 170 " --> pdb=" O PRO G 183 " (cutoff:3.500A) removed outlier: 13.759A pdb=" N GLY G 185 " --> pdb=" O ARG G 168 " (cutoff:3.500A) removed outlier: 14.068A pdb=" N ARG G 168 " --> pdb=" O GLY G 185 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N SER G 187 " --> pdb=" O GLU G 166 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N GLU G 166 " --> pdb=" O SER G 187 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N GLY G 164 " --> pdb=" O PRO G 189 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 69 through 71 removed outlier: 5.850A pdb=" N VAL J 40 " --> pdb=" O TRP J 88 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 116 through 117 removed outlier: 6.452A pdb=" N ALA L 4 " --> pdb=" O ASN L 142 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA L 144 " --> pdb=" O ALA L 4 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N PHE L 6 " --> pdb=" O ALA L 144 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 80 through 83 removed outlier: 7.037A pdb=" N VAL L 39 " --> pdb=" O GLU L 81 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N ALA L 83 " --> pdb=" O VAL L 39 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE L 41 " --> pdb=" O ALA L 83 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU L 40 " --> pdb=" O ILE L 97 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 1164 hydrogen bonds defined for protein. 3294 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 4.57 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 7760 1.36 - 1.51: 5934 1.51 - 1.66: 9322 1.66 - 1.80: 133 1.80 - 1.95: 59 Bond restraints: 23208 Sorted by residual: bond pdb=" N ILE J 33 " pdb=" CA ILE J 33 " ideal model delta sigma weight residual 1.462 1.495 -0.033 1.01e-02 9.80e+03 1.07e+01 bond pdb=" N PRO J 34 " pdb=" CA PRO J 34 " ideal model delta sigma weight residual 1.470 1.491 -0.021 1.01e-02 9.80e+03 4.46e+00 bond pdb=" N ALA J 30 " pdb=" CA ALA J 30 " ideal model delta sigma weight residual 1.454 1.480 -0.026 1.27e-02 6.20e+03 4.07e+00 bond pdb=" N ILE J 31 " pdb=" CA ILE J 31 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.76e-02 3.23e+03 3.95e+00 bond pdb=" C PRO J 34 " pdb=" O PRO J 34 " ideal model delta sigma weight residual 1.235 1.250 -0.015 7.90e-03 1.60e+04 3.71e+00 ... (remaining 23203 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 31461 2.59 - 5.18: 226 5.18 - 7.78: 18 7.78 - 10.37: 1 10.37 - 12.96: 3 Bond angle restraints: 31709 Sorted by residual: angle pdb=" CB MET J 78 " pdb=" CG MET J 78 " pdb=" SD MET J 78 " ideal model delta sigma weight residual 112.70 125.66 -12.96 3.00e+00 1.11e-01 1.87e+01 angle pdb=" CA ILE J 31 " pdb=" C ILE J 31 " pdb=" O ILE J 31 " ideal model delta sigma weight residual 122.13 118.13 4.00 1.11e+00 8.12e-01 1.30e+01 angle pdb=" CA LEU J 111 " pdb=" CB LEU J 111 " pdb=" CG LEU J 111 " ideal model delta sigma weight residual 116.30 128.50 -12.20 3.50e+00 8.16e-02 1.21e+01 angle pdb=" CA LEU L 69 " pdb=" CB LEU L 69 " pdb=" CG LEU L 69 " ideal model delta sigma weight residual 116.30 127.97 -11.67 3.50e+00 8.16e-02 1.11e+01 angle pdb=" CA ASP B 247 " pdb=" CB ASP B 247 " pdb=" CG ASP B 247 " ideal model delta sigma weight residual 112.60 115.74 -3.14 1.00e+00 1.00e+00 9.86e+00 ... (remaining 31704 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.40: 13365 34.40 - 68.80: 625 68.80 - 103.20: 41 103.20 - 137.60: 1 137.60 - 172.01: 4 Dihedral angle restraints: 14036 sinusoidal: 5975 harmonic: 8061 Sorted by residual: dihedral pdb=" O1A AGS C 702 " pdb=" O3A AGS C 702 " pdb=" PA AGS C 702 " pdb=" PB AGS C 702 " ideal model delta sinusoidal sigma weight residual -67.73 104.28 -172.01 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" O1A AGS D 702 " pdb=" O3A AGS D 702 " pdb=" PA AGS D 702 " pdb=" PB AGS D 702 " ideal model delta sinusoidal sigma weight residual -67.73 91.96 -159.69 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" O1A AGS B 702 " pdb=" O3A AGS B 702 " pdb=" PA AGS B 702 " pdb=" PB AGS B 702 " ideal model delta sinusoidal sigma weight residual -67.73 88.93 -156.66 1 3.00e+01 1.11e-03 2.05e+01 ... (remaining 14033 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2493 0.033 - 0.065: 837 0.065 - 0.098: 211 0.098 - 0.131: 104 0.131 - 0.163: 9 Chirality restraints: 3654 Sorted by residual: chirality pdb=" CA ILE J 33 " pdb=" N ILE J 33 " pdb=" C ILE J 33 " pdb=" CB ILE J 33 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.68e-01 chirality pdb=" CA ILE J 31 " pdb=" N ILE J 31 " pdb=" C ILE J 31 " pdb=" CB ILE J 31 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.44e-01 chirality pdb=" CA PRO L 85 " pdb=" N PRO L 85 " pdb=" C PRO L 85 " pdb=" CB PRO L 85 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.56e-01 ... (remaining 3651 not shown) Planarity restraints: 3968 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP L 84 " -0.032 5.00e-02 4.00e+02 4.85e-02 3.76e+00 pdb=" N PRO L 85 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO L 85 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO L 85 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 88 " -0.014 2.00e-02 2.50e+03 1.20e-02 3.61e+00 pdb=" CG TRP J 88 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP J 88 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP J 88 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP J 88 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP J 88 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP J 88 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 88 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 88 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP J 88 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP J 51 " -0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO J 52 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO J 52 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO J 52 " -0.025 5.00e-02 4.00e+02 ... (remaining 3965 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 8 2.49 - 3.09: 15281 3.09 - 3.69: 35562 3.69 - 4.30: 53632 4.30 - 4.90: 86966 Nonbonded interactions: 191449 Sorted by model distance: nonbonded pdb=" O2G AGS B 702 " pdb="MG MG B 703 " model vdw 1.884 2.170 nonbonded pdb=" OG1 THR B 52 " pdb="MG MG B 703 " model vdw 1.897 2.170 nonbonded pdb=" OG1 THR D 52 " pdb="MG MG D 703 " model vdw 2.000 2.170 nonbonded pdb=" OG1 THR C 52 " pdb="MG MG C 703 " model vdw 2.002 2.170 nonbonded pdb=" O2G AGS D 702 " pdb="MG MG D 703 " model vdw 2.057 2.170 ... (remaining 191444 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 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 2 through 361 or resid 701 through 703)) selection = (chain 'C' and (resid 2 through 361 or resid 701 through 703)) selection = chain 'D' } ncs_group { reference = chain 'F' selection = (chain 'G' and resid 1 through 365) } 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: 2.160 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 26.660 Find NCS groups from input model: 0.420 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:6.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 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 : 0.003 0.047 23224 Z= 0.129 Angle : 0.579 12.961 31733 Z= 0.292 Chirality : 0.038 0.163 3654 Planarity : 0.004 0.048 3968 Dihedral : 18.056 172.005 8802 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.77 % Allowed : 16.46 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.17), residues: 2761 helix: 1.46 (0.14), residues: 1357 sheet: 1.16 (0.24), residues: 480 loop : 0.53 (0.22), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG L 100 TYR 0.012 0.001 TYR E 47 PHE 0.009 0.001 PHE G 230 TRP 0.031 0.001 TRP J 88 HIS 0.005 0.001 HIS L 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 (23208) covalent geometry : angle 0.56228 / 0.29 (31709) hydrogen bonds : bond 0.14189 / 9.63 ( 1213) hydrogen bonds : angle 5.51597 / 3.99 ( 3392) metal coordination : bond 0.00526 / 0.23 ( 16) metal coordination : angle 4.99868 / 2.90 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 392 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.8033 (m-30) cc_final: 0.7785 (m-30) REVERT: A 48 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7355 (mm-30) REVERT: A 49 GLU cc_start: 0.7964 (tt0) cc_final: 0.7661 (tt0) REVERT: A 60 ASP cc_start: 0.8053 (t0) cc_final: 0.7758 (t0) REVERT: A 242 GLU cc_start: 0.8343 (mm-30) cc_final: 0.7969 (tp30) REVERT: A 313 LYS cc_start: 0.7986 (mttt) cc_final: 0.7761 (mttt) REVERT: A 320 VAL cc_start: 0.8018 (p) cc_final: 0.7749 (m) REVERT: B 105 ARG cc_start: 0.8154 (mtt90) cc_final: 0.7947 (mtt90) REVERT: B 133 ARG cc_start: 0.8331 (ttp-170) cc_final: 0.7994 (ttp80) REVERT: B 136 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.7027 (m-80) REVERT: B 265 MET cc_start: 0.8276 (mmp) cc_final: 0.7922 (mmm) REVERT: C 78 ASN cc_start: 0.8334 (m-40) cc_final: 0.8029 (m110) REVERT: C 83 GLU cc_start: 0.7394 (tt0) cc_final: 0.7170 (tt0) REVERT: C 105 ARG cc_start: 0.8061 (mtm110) cc_final: 0.7545 (mtm-85) REVERT: C 180 VAL cc_start: 0.8551 (t) cc_final: 0.8214 (m) REVERT: C 277 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6724 (mm-30) REVERT: D 181 GLU cc_start: 0.7802 (tp30) cc_final: 0.7479 (tp30) REVERT: D 204 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8197 (mt0) REVERT: D 263 ARG cc_start: 0.8158 (ttt90) cc_final: 0.7815 (ttp80) REVERT: D 277 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7306 (tm-30) REVERT: E 37 ASP cc_start: 0.7810 (p0) cc_final: 0.7566 (p0) REVERT: E 164 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8715 (tp) REVERT: E 206 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8562 (mp-120) REVERT: F 97 MET cc_start: 0.8805 (ttm) cc_final: 0.8383 (ttt) REVERT: F 221 ASN cc_start: 0.8905 (m110) cc_final: 0.8644 (m110) REVERT: F 281 VAL cc_start: 0.6853 (m) cc_final: 0.6595 (t) REVERT: G 136 LYS cc_start: 0.8719 (tttm) cc_final: 0.8461 (ttmt) REVERT: G 140 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7750 (pt0) REVERT: G 286 SER cc_start: 0.8731 (m) cc_final: 0.8377 (p) REVERT: G 287 GLU cc_start: 0.8292 (tp30) cc_final: 0.7996 (mm-30) outliers start: 41 outliers final: 17 residues processed: 409 average time/residue: 0.8554 time to fit residues: 387.5735 Evaluate side-chains 387 residues out of total 2321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 365 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 204 GLN Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 250 LYS Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain L residue 50 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 0.4980 chunk 20 optimal weight: 0.1980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 105 HIS A 136 GLN ** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 GLN A 234 GLN B 231 GLN D 110 ASN D 137 ASN D 160 GLN D 223 GLN D 248 GLN E 54 GLN ** E 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 HIS F 132 GLN F 212 ASN F 221 ASN ** G 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.196229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.170258 restraints weight = 46385.584| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.88 r_work: 0.3476 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.0586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23224 Z= 0.149 Angle : 0.575 11.811 31733 Z= 0.287 Chirality : 0.039 0.149 3654 Planarity : 0.004 0.053 3968 Dihedral : 13.706 172.311 3595 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.63 % Allowed : 16.16 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.17), residues: 2761 helix: 1.57 (0.14), residues: 1374 sheet: 1.17 (0.25), residues: 465 loop : 0.64 (0.22), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 205 TYR 0.020 0.001 TYR L 119 PHE 0.009 0.001 PHE L 110 TRP 0.014 0.001 TRP J 88 HIS 0.004 0.001 HIS F 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (23208) covalent geometry : angle 0.55794 / 0.29 (31709) hydrogen bonds : bond 0.04317 / 2.84 ( 1213) hydrogen bonds : angle 4.44346 / 3.19 ( 3392) metal coordination : bond 0.00638 / 0.28 ( 16) metal coordination : angle 5.05033 / 2.90 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 386 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.8021 (m-30) cc_final: 0.7770 (m-30) REVERT: A 48 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7358 (mm-30) REVERT: A 49 GLU cc_start: 0.7965 (tt0) cc_final: 0.7660 (tt0) REVERT: A 60 ASP cc_start: 0.8007 (t0) cc_final: 0.7717 (t0) REVERT: A 225 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8474 (mmpt) REVERT: A 242 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7924 (tp30) REVERT: A 325 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7354 (mt-10) REVERT: B 133 ARG cc_start: 0.8362 (ttp-170) cc_final: 0.8033 (ttp80) REVERT: B 136 PHE cc_start: 0.7803 (OUTLIER) cc_final: 0.7499 (t80) REVERT: B 188 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8028 (tt0) REVERT: B 247 ASP cc_start: 0.7901 (t70) cc_final: 0.7678 (t0) REVERT: B 265 MET cc_start: 0.8285 (mmp) cc_final: 0.7915 (mmm) REVERT: C 78 ASN cc_start: 0.8408 (m-40) cc_final: 0.8131 (m110) REVERT: C 83 GLU cc_start: 0.7416 (tt0) cc_final: 0.7203 (tt0) REVERT: C 105 ARG cc_start: 0.8046 (mtm110) cc_final: 0.7511 (mtm-85) REVERT: C 180 VAL cc_start: 0.8573 (t) cc_final: 0.8267 (m) REVERT: C 211 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7446 (mp0) REVERT: C 240 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8530 (ttt) REVERT: C 267 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7096 (mp) REVERT: C 277 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6627 (mm-30) REVERT: C 318 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7331 (ptp-110) REVERT: D 181 GLU cc_start: 0.7799 (tp30) cc_final: 0.7523 (tp30) REVERT: D 263 ARG cc_start: 0.8157 (ttt90) cc_final: 0.7841 (ttp80) REVERT: D 277 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7233 (tm-30) REVERT: E 22 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7099 (ttm170) REVERT: E 164 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8739 (tp) REVERT: E 276 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7456 (mm-30) REVERT: F 97 MET cc_start: 0.8895 (ttm) cc_final: 0.8495 (ttt) REVERT: F 123 GLN cc_start: 0.8018 (mm110) cc_final: 0.7815 (mm110) REVERT: F 169 THR cc_start: 0.8784 (OUTLIER) cc_final: 0.8538 (t) REVERT: F 221 ASN cc_start: 0.8911 (m-40) cc_final: 0.8605 (m110) REVERT: F 262 LEU cc_start: 0.4959 (OUTLIER) cc_final: 0.3622 (tm) REVERT: G 136 LYS cc_start: 0.8674 (tttm) cc_final: 0.8294 (tptt) REVERT: G 140 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7752 (pt0) REVERT: G 198 LYS cc_start: 0.8491 (mttp) cc_final: 0.7987 (mptt) REVERT: G 286 SER cc_start: 0.8695 (m) cc_final: 0.8480 (p) REVERT: G 343 SER cc_start: 0.8497 (p) cc_final: 0.8178 (t) REVERT: L 16 ASP cc_start: 0.5239 (m-30) cc_final: 0.4909 (t0) outliers start: 61 outliers final: 20 residues processed: 420 average time/residue: 0.8387 time to fit residues: 391.4645 Evaluate side-chains 410 residues out of total 2321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 376 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 318 ARG Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain E residue 22 ARG Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 135 MET Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain L residue 50 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 274 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 273 optimal weight: 5.9990 chunk 233 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 84 optimal weight: 0.0470 chunk 124 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 139 optimal weight: 1.9990 overall best weight: 1.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 136 GLN ** A 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 GLN C 137 ASN D 160 GLN D 248 GLN E 54 GLN E 61 HIS E 206 GLN F 212 ASN ** G 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 295 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.195948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.169869 restraints weight = 46606.811| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.91 r_work: 0.3470 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23224 Z= 0.152 Angle : 0.574 11.499 31733 Z= 0.283 Chirality : 0.039 0.161 3654 Planarity : 0.004 0.059 3968 Dihedral : 13.622 171.872 3572 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.02 % Allowed : 16.24 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.17), residues: 2761 helix: 1.63 (0.14), residues: 1374 sheet: 1.06 (0.25), residues: 472 loop : 0.63 (0.22), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 205 TYR 0.014 0.001 TYR E 47 PHE 0.008 0.001 PHE L 110 TRP 0.015 0.001 TRP J 88 HIS 0.005 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (23208) covalent geometry : angle 0.55700 / 0.28 (31709) hydrogen bonds : bond 0.03863 / 2.54 ( 1213) hydrogen bonds : angle 4.20632 / 3.02 ( 3392) metal coordination : bond 0.00664 / 0.29 ( 16) metal coordination : angle 5.09585 / 2.95 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 396 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.8013 (m-30) cc_final: 0.7795 (m-30) REVERT: A 48 GLU cc_start: 0.7614 (mm-30) cc_final: 0.7371 (mm-30) REVERT: A 49 GLU cc_start: 0.7929 (tt0) cc_final: 0.7616 (tt0) REVERT: A 60 ASP cc_start: 0.8012 (t0) cc_final: 0.7684 (t0) REVERT: A 225 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8481 (mmpt) REVERT: A 242 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7904 (tp30) REVERT: A 325 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7311 (mt-10) REVERT: B 133 ARG cc_start: 0.8378 (ttp-170) cc_final: 0.8056 (ttp80) REVERT: B 158 ASP cc_start: 0.7805 (p0) cc_final: 0.6500 (t0) REVERT: B 247 ASP cc_start: 0.7902 (t70) cc_final: 0.7598 (t0) REVERT: B 265 MET cc_start: 0.8268 (mmp) cc_final: 0.7958 (mmm) REVERT: C 78 ASN cc_start: 0.8403 (m-40) cc_final: 0.8135 (m110) REVERT: C 83 GLU cc_start: 0.7462 (tt0) cc_final: 0.7254 (tt0) REVERT: C 105 ARG cc_start: 0.8054 (mtm110) cc_final: 0.7534 (mtm-85) REVERT: C 107 LEU cc_start: 0.8449 (tp) cc_final: 0.8212 (tm) REVERT: C 180 VAL cc_start: 0.8574 (t) cc_final: 0.8273 (m) REVERT: C 240 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8556 (ttt) REVERT: C 267 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.7073 (mp) REVERT: C 277 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6576 (mm-30) REVERT: C 318 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7377 (ptp-110) REVERT: D 181 GLU cc_start: 0.7813 (tp30) cc_final: 0.7520 (tp30) REVERT: D 263 ARG cc_start: 0.8141 (ttt90) cc_final: 0.7819 (ttp80) REVERT: E 22 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7077 (ttm170) REVERT: E 164 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8748 (tp) REVERT: E 214 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7987 (tt0) REVERT: F 8 GLU cc_start: 0.7584 (pm20) cc_final: 0.7254 (pt0) REVERT: F 84 GLU cc_start: 0.7833 (tp30) cc_final: 0.7585 (mp0) REVERT: F 97 MET cc_start: 0.8933 (ttm) cc_final: 0.8537 (ttt) REVERT: F 169 THR cc_start: 0.8788 (OUTLIER) cc_final: 0.8536 (t) REVERT: F 221 ASN cc_start: 0.8895 (m-40) cc_final: 0.8554 (m110) REVERT: F 262 LEU cc_start: 0.4922 (OUTLIER) cc_final: 0.3615 (tm) REVERT: F 319 PHE cc_start: 0.7291 (m-80) cc_final: 0.7084 (m-10) REVERT: G 136 LYS cc_start: 0.8684 (tttm) cc_final: 0.8303 (tptt) REVERT: G 140 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7769 (pt0) REVERT: G 198 LYS cc_start: 0.8489 (mttp) cc_final: 0.7971 (mptt) REVERT: L 97 ILE cc_start: 0.6478 (tp) cc_final: 0.6263 (pp) outliers start: 70 outliers final: 29 residues processed: 436 average time/residue: 0.8321 time to fit residues: 403.2113 Evaluate side-chains 408 residues out of total 2321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 368 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 318 ARG Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 22 ARG Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 135 MET Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 250 LYS Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 50 TYR Chi-restraints excluded: chain L residue 106 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 254 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 260 optimal weight: 4.9990 chunk 252 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 212 optimal weight: 8.9990 chunk 108 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 189 optimal weight: 0.3980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 136 GLN A 146 GLN D 137 ASN D 160 GLN D 248 GLN E 54 GLN E 61 HIS E 206 GLN F 212 ASN ** G 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.195897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.171809 restraints weight = 46568.098| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.84 r_work: 0.3461 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23224 Z= 0.143 Angle : 0.564 11.471 31733 Z= 0.277 Chirality : 0.039 0.145 3654 Planarity : 0.004 0.058 3968 Dihedral : 13.552 172.209 3567 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.27 % Allowed : 16.67 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.17), residues: 2761 helix: 1.69 (0.14), residues: 1374 sheet: 1.01 (0.25), residues: 461 loop : 0.62 (0.22), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG L 32 TYR 0.013 0.001 TYR E 47 PHE 0.016 0.001 PHE B 136 TRP 0.010 0.001 TRP B 10 HIS 0.006 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (23208) covalent geometry : angle 0.54659 / 0.28 (31709) hydrogen bonds : bond 0.03617 / 2.38 ( 1213) hydrogen bonds : angle 4.09126 / 2.94 ( 3392) metal coordination : bond 0.00638 / 0.28 ( 16) metal coordination : angle 5.03432 / 2.91 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5522 Ramachandran restraints generated. 2761 Oldfield, 0 Emsley, 2761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 389 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.8029 (m-30) cc_final: 0.7810 (m-30) REVERT: A 48 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7324 (mm-30) REVERT: A 49 GLU cc_start: 0.7860 (tt0) cc_final: 0.7537 (tt0) REVERT: A 60 ASP cc_start: 0.8014 (t0) cc_final: 0.7684 (t0) REVERT: A 225 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8465 (mmpt) REVERT: A 242 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7890 (tp30) REVERT: A 325 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7331 (mt-10) REVERT: B 133 ARG cc_start: 0.8378 (ttp-170) cc_final: 0.8061 (ttp80) REVERT: B 158 ASP cc_start: 0.7821 (p0) cc_final: 0.6495 (t0) REVERT: B 188 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8042 (tt0) REVERT: B 247 ASP cc_start: 0.7967 (t70) cc_final: 0.7602 (t0) REVERT: B 265 MET cc_start: 0.8268 (mmp) cc_final: 0.7887 (mmm) REVERT: C 78 ASN cc_start: 0.8363 (m-40) cc_final: 0.8082 (m110) REVERT: C 83 GLU cc_start: 0.7440 (tt0) cc_final: 0.7227 (tt0) REVERT: C 105 ARG cc_start: 0.8040 (mtm110) cc_final: 0.7506 (mtm-85) REVERT: C 107 LEU cc_start: 0.8469 (tp) cc_final: 0.8194 (tm) REVERT: C 180 VAL cc_start: 0.8582 (t) cc_final: 0.8273 (m) REVERT: C 193 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7774 (mp0) REVERT: C 240 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8534 (ttt) REVERT: C 267 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.7012 (mp) REVERT: C 277 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6529 (mm-30) REVERT: C 318 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7423 (ptp-110) REVERT: D 181 GLU cc_start: 0.7814 (tp30) cc_final: 0.7504 (tp30) REVERT: D 263 ARG cc_start: 0.8124 (ttt90) cc_final: 0.7784 (ttp80) REVERT: D 277 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7120 (tm-30) REVERT: E 22 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7043 (ttm170) REVERT: E 164 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8749 (tp) REVERT: E 214 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.8002 (tt0) REVERT: F 8 GLU cc_start: 0.7590 (pm20) cc_final: 0.7255 (pt0) REVERT: F 84 GLU cc_start: 0.7812 (tp30) cc_final: 0.7540 (mp0) REVERT: F 97 MET cc_start: 0.8919 (ttm) cc_final: 0.8506 (ttt) REVERT: F 169 THR cc_start: 0.8775 (OUTLIER) cc_final: 0.8516 (t) REVERT: F 221 ASN cc_start: 0.8864 (m-40) cc_final: 0.8520 (m110) REVERT: F 262 LEU cc_start: 0.4943 (OUTLIER) cc_final: 0.3609 (tm) REVERT: F 319 PHE cc_start: 0.7267 (m-80) cc_final: 0.7041 (m-10) REVERT: G 136 LYS cc_start: 0.8678 (tttm) cc_final: 0.8280 (tptt) REVERT: G 140 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7730 (pt0) REVERT: G 198 LYS cc_start: 0.8478 (mttp) cc_final: 0.7951 (mptt) REVERT: G 334 GLU cc_start: 0.8217 (tp30) cc_final: 0.7949 (mm-30) REVERT: L 97 ILE cc_start: 0.6431 (tp) cc_final: 0.6179 (pp) outliers start: 76 outliers final: 32 residues processed: 429 average time/residue: 0.8293 time to fit residues: 395.7219 Evaluate side-chains 414 residues out of total 2321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 368 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 310 GLU Chi-restraints excluded: chain C residue 318 ARG Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 22 ARG Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain F residue 2 LYS Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 135 MET Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 250 LYS Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain J residue 40 VAL Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 50 TYR Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 106 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.9467 > 50: distance: 28 - 59: 7.481 distance: 34 - 38: 9.737 distance: 35 - 64: 12.043 distance: 38 - 39: 5.558 distance: 39 - 40: 5.786 distance: 39 - 42: 4.656 distance: 40 - 41: 6.747 distance: 40 - 47: 5.522 distance: 41 - 71: 12.598 distance: 42 - 43: 3.417 distance: 43 - 44: 6.917 distance: 44 - 45: 4.069 distance: 44 - 46: 6.070 distance: 47 - 48: 4.638 distance: 48 - 49: 3.555 distance: 48 - 51: 3.795 distance: 49 - 50: 6.008 distance: 49 - 59: 4.993 distance: 50 - 78: 15.266 distance: 51 - 52: 7.990 distance: 52 - 53: 8.440 distance: 52 - 54: 7.937 distance: 53 - 55: 4.565 distance: 54 - 56: 8.085 distance: 55 - 57: 12.354 distance: 56 - 57: 4.543 distance: 57 - 58: 8.330 distance: 59 - 60: 11.829 distance: 60 - 61: 10.559 distance: 60 - 63: 9.215 distance: 61 - 62: 13.882 distance: 61 - 64: 9.970 distance: 62 - 92: 25.384 distance: 64 - 65: 8.864 distance: 65 - 66: 9.099 distance: 65 - 68: 18.254 distance: 66 - 67: 16.510 distance: 66 - 71: 4.786 distance: 67 - 100: 20.257 distance: 68 - 69: 18.668 distance: 68 - 70: 30.976 distance: 71 - 72: 11.579 distance: 72 - 73: 6.881 distance: 72 - 75: 18.135 distance: 73 - 74: 8.611 distance: 73 - 78: 3.024 distance: 75 - 76: 13.382 distance: 75 - 77: 22.779 distance: 78 - 79: 5.140 distance: 79 - 80: 5.234 distance: 79 - 82: 8.875 distance: 80 - 81: 3.290 distance: 80 - 92: 7.885 distance: 82 - 83: 7.365 distance: 83 - 84: 3.404 distance: 83 - 85: 11.304 distance: 84 - 86: 12.292 distance: 85 - 87: 9.780 distance: 85 - 88: 9.733 distance: 86 - 87: 15.487 distance: 88 - 90: 7.671 distance: 90 - 91: 4.158 distance: 92 - 93: 6.791 distance: 93 - 94: 12.601 distance: 93 - 96: 6.089 distance: 94 - 95: 10.481 distance: 94 - 100: 7.269 distance: 96 - 97: 38.598 distance: 97 - 98: 22.490 distance: 97 - 99: 31.022 distance: 100 - 101: 9.036 distance: 101 - 102: 6.492 distance: 101 - 104: 21.929 distance: 102 - 103: 6.561 distance: 102 - 106: 7.542 distance: 104 - 105: 26.076 distance: 106 - 107: 25.094 distance: 107 - 108: 27.462 distance: 107 - 110: 24.704 distance: 108 - 109: 33.405 distance: 108 - 117: 7.704 distance: 110 - 111: 38.738 distance: 111 - 112: 6.204 distance: 112 - 113: 13.021 distance: 113 - 114: 7.442 distance: 114 - 115: 15.145 distance: 114 - 116: 8.790 distance: 117 - 118: 22.459 distance: 118 - 119: 13.392 distance: 118 - 121: 3.818 distance: 119 - 120: 17.710 distance: 119 - 126: 9.108 distance: 121 - 122: 27.576 distance: 122 - 123: 14.780 distance: 123 - 124: 9.202 distance: 123 - 125: 30.967