Starting phenix.real_space_refine on Thu Jan 15 06:15:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t3b_25653/01_2026/7t3b_25653.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t3b_25653/01_2026/7t3b_25653.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t3b_25653/01_2026/7t3b_25653.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t3b_25653/01_2026/7t3b_25653.map" model { file = "/net/cci-nas-00/data/ceres_data/7t3b_25653/01_2026/7t3b_25653.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t3b_25653/01_2026/7t3b_25653.cif" } resolution = 3.9 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= 0.013 sd= 0.092 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 Al 2 5.89 5 P 4 5.49 5 S 132 5.16 5 C 14891 2.51 5 N 3934 2.21 5 O 4325 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23294 Number of models: 1 Model: "" Number of chains: 14 Chain: "E" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2464 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 7, 'TRANS': 297} Chain: "B" Number of atoms: 2918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2918 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 8104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 989, 8104 Classifications: {'peptide': 989} Link IDs: {'PTRANS': 41, 'TRANS': 947} Chain breaks: 7 Chain: "H" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 934 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 113} Chain: "G" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 936 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "J" Number of atoms: 672 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 91, 666 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Conformer: "B" Number of residues, atoms: 91, 666 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} bond proxies already assigned to first conformer: 665 Chain: "I" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 678 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "F" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 861 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 6, 'TRANS': 104} Chain: "C" Number of atoms: 3234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3234 Classifications: {'peptide': 405} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 384} Chain breaks: 5 Chain: "D" Number of atoms: 2429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2429 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 5, 'TRANS': 290} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'AF3': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'AF3': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ACYS J 23 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS J 23 " occ=0.50 Time building chain proxies: 5.28, per 1000 atoms: 0.23 Number of scatterers: 23294 At special positions: 0 Unit cell: (121.18, 151.89, 199.2, 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) S 132 16.00 P 4 15.00 Al 2 13.00 F 6 9.00 O 4325 8.00 N 3934 7.00 C 14891 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 1.0 seconds 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5544 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 27 sheets defined 41.4% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'E' and resid 73 through 83 Processing helix chain 'E' and resid 86 through 91 removed outlier: 3.526A pdb=" N THR E 90 " --> pdb=" O PRO E 87 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU E 91 " --> pdb=" O ASN E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 136 removed outlier: 4.129A pdb=" N GLY E 136 " --> pdb=" O MET E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 168 Processing helix chain 'E' and resid 184 through 206 Processing helix chain 'E' and resid 223 through 235 removed outlier: 3.846A pdb=" N GLU E 227 " --> pdb=" O HIS E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 252 Processing helix chain 'E' and resid 278 through 299 removed outlier: 3.914A pdb=" N LEU E 284 " --> pdb=" O GLN E 280 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE E 289 " --> pdb=" O CYS E 285 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP E 290 " --> pdb=" O CYS E 286 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR E 299 " --> pdb=" O VAL E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 347 No H-bonds generated for 'chain 'E' and resid 345 through 347' Processing helix chain 'E' and resid 348 through 367 removed outlier: 3.859A pdb=" N TYR E 354 " --> pdb=" O GLY E 350 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS E 361 " --> pdb=" O HIS E 357 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA E 362 " --> pdb=" O CYS E 358 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE E 363 " --> pdb=" O PHE E 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 40 Processing helix chain 'B' and resid 40 through 45 removed outlier: 3.757A pdb=" N ILE B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 117 removed outlier: 4.474A pdb=" N ILE B 101 " --> pdb=" O ALA B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 138 removed outlier: 3.876A pdb=" N GLN B 126 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) Proline residue: B 130 - end of helix removed outlier: 3.866A pdb=" N ILE B 134 " --> pdb=" O PRO B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 184 removed outlier: 3.990A pdb=" N PHE B 184 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 197 Processing helix chain 'B' and resid 198 through 200 No H-bonds generated for 'chain 'B' and resid 198 through 200' Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 216 through 231 Processing helix chain 'B' and resid 249 through 251 No H-bonds generated for 'chain 'B' and resid 249 through 251' Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 258 through 269 removed outlier: 4.184A pdb=" N GLU B 262 " --> pdb=" O LYS B 258 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA B 263 " --> pdb=" O SER B 259 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 287 removed outlier: 4.001A pdb=" N GLN B 283 " --> pdb=" O ARG B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 301 Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.825A pdb=" N GLN B 306 " --> pdb=" O GLN B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 320 removed outlier: 3.500A pdb=" N ILE B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 359 Processing helix chain 'B' and resid 361 through 370 removed outlier: 3.961A pdb=" N ASP B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N GLU B 367 " --> pdb=" O HIS B 363 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG B 368 " --> pdb=" O GLU B 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 77 removed outlier: 3.763A pdb=" N PHE A 77 " --> pdb=" O VAL A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 95 removed outlier: 3.522A pdb=" N ASP A 94 " --> pdb=" O ASP A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 120 removed outlier: 3.717A pdb=" N MET A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TRP A 115 " --> pdb=" O ARG A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 189 removed outlier: 3.763A pdb=" N GLY A 188 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASP A 189 " --> pdb=" O ILE A 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 185 through 189' Processing helix chain 'A' and resid 190 through 211 removed outlier: 4.688A pdb=" N ALA A 201 " --> pdb=" O ASN A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 233 removed outlier: 4.306A pdb=" N GLU A 233 " --> pdb=" O SER A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 269 through 281 removed outlier: 4.113A pdb=" N THR A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 306 through 319 removed outlier: 4.142A pdb=" N LYS A 319 " --> pdb=" O ASN A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 358 removed outlier: 3.694A pdb=" N ILE A 358 " --> pdb=" O LYS A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 749 Processing helix chain 'A' and resid 762 through 770 Processing helix chain 'A' and resid 778 through 784 removed outlier: 3.704A pdb=" N ASP A 784 " --> pdb=" O GLU A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 809 removed outlier: 3.995A pdb=" N PHE A 799 " --> pdb=" O ALA A 795 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU A 800 " --> pdb=" O GLN A 796 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN A 809 " --> pdb=" O GLN A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 916 Processing helix chain 'A' and resid 917 through 927 removed outlier: 3.533A pdb=" N LEU A 921 " --> pdb=" O LYS A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 940 removed outlier: 3.979A pdb=" N LYS A 940 " --> pdb=" O GLU A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 961 Processing helix chain 'A' and resid 977 through 994 removed outlier: 4.464A pdb=" N LEU A 983 " --> pdb=" O GLU A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1185 Processing helix chain 'A' and resid 1207 through 1218 Processing helix chain 'A' and resid 1223 through 1237 removed outlier: 3.829A pdb=" N ALA A1227 " --> pdb=" O THR A1223 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1313 removed outlier: 3.593A pdb=" N LEU A1313 " --> pdb=" O ALA A1310 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1412 Processing helix chain 'A' and resid 1445 through 1449 Processing helix chain 'A' and resid 1461 through 1463 No H-bonds generated for 'chain 'A' and resid 1461 through 1463' Processing helix chain 'A' and resid 1464 through 1480 removed outlier: 4.007A pdb=" N HIS A1470 " --> pdb=" O TRP A1466 " (cutoff:3.500A) Processing helix chain 'A' and resid 1566 through 1581 removed outlier: 4.112A pdb=" N ASP A1570 " --> pdb=" O GLU A1566 " (cutoff:3.500A) Processing helix chain 'A' and resid 1585 through 1596 Processing helix chain 'A' and resid 1597 through 1599 No H-bonds generated for 'chain 'A' and resid 1597 through 1599' Processing helix chain 'H' and resid 4 through 12 Processing helix chain 'H' and resid 41 through 45 removed outlier: 3.619A pdb=" N LEU H 45 " --> pdb=" O GLU H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 51 removed outlier: 3.554A pdb=" N LEU H 50 " --> pdb=" O ARG H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 62 removed outlier: 4.369A pdb=" N LEU H 55 " --> pdb=" O SER H 51 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP H 58 " --> pdb=" O ALA H 54 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN H 59 " --> pdb=" O LEU H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 110 Processing helix chain 'H' and resid 110 through 119 removed outlier: 4.484A pdb=" N GLN H 119 " --> pdb=" O GLU H 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 15 removed outlier: 3.737A pdb=" N ALA G 14 " --> pdb=" O VAL G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 63 removed outlier: 3.769A pdb=" N ASN G 59 " --> pdb=" O ALA G 55 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY G 60 " --> pdb=" O TYR G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 125 removed outlier: 4.191A pdb=" N LEU G 104 " --> pdb=" O GLY G 100 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N GLU G 117 " --> pdb=" O GLN G 113 " (cutoff:3.500A) Proline residue: G 118 - end of helix Processing helix chain 'J' and resid 2 through 14 removed outlier: 4.293A pdb=" N HIS J 8 " --> pdb=" O THR J 4 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU J 9 " --> pdb=" O LEU J 5 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR J 12 " --> pdb=" O HIS J 8 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 42 Processing helix chain 'J' and resid 43 through 54 removed outlier: 3.917A pdb=" N LYS J 54 " --> pdb=" O GLN J 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 12 Processing helix chain 'I' and resid 36 through 52 removed outlier: 4.172A pdb=" N SER I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU I 46 " --> pdb=" O ALA I 42 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL I 47 " --> pdb=" O ILE I 43 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR I 49 " --> pdb=" O GLU I 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 65 Processing helix chain 'F' and resid 79 through 98 removed outlier: 4.065A pdb=" N GLN F 87 " --> pdb=" O ASP F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 120 removed outlier: 4.176A pdb=" N VAL F 118 " --> pdb=" O GLN F 114 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA F 120 " --> pdb=" O HIS F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 144 Processing helix chain 'C' and resid 65 through 74 Processing helix chain 'C' and resid 135 through 161 removed outlier: 3.789A pdb=" N VAL C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 174 Processing helix chain 'C' and resid 193 through 198 removed outlier: 3.602A pdb=" N LYS C 197 " --> pdb=" O HIS C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 213 removed outlier: 4.224A pdb=" N LEU C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N CYS C 212 " --> pdb=" O TYR C 208 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N THR C 213 " --> pdb=" O ASP C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 4.012A pdb=" N GLU C 226 " --> pdb=" O SER C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 274 removed outlier: 3.643A pdb=" N GLU C 273 " --> pdb=" O SER C 269 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C 274 " --> pdb=" O LEU C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 289 removed outlier: 3.794A pdb=" N VAL C 283 " --> pdb=" O SER C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 302 removed outlier: 3.860A pdb=" N GLN C 300 " --> pdb=" O GLN C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 319 Processing helix chain 'C' and resid 346 through 356 Processing helix chain 'C' and resid 360 through 368 Processing helix chain 'C' and resid 383 through 400 removed outlier: 3.572A pdb=" N GLU C 387 " --> pdb=" O PRO C 383 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN C 389 " --> pdb=" O VAL C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 488 Processing helix chain 'C' and resid 491 through 501 removed outlier: 3.983A pdb=" N VAL C 501 " --> pdb=" O ALA C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 506 through 516 removed outlier: 3.546A pdb=" N LEU C 510 " --> pdb=" O ASN C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 534 removed outlier: 3.757A pdb=" N TYR C 531 " --> pdb=" O GLU C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 539 No H-bonds generated for 'chain 'C' and resid 537 through 539' Processing helix chain 'C' and resid 540 through 547 Processing helix chain 'C' and resid 560 through 564 Processing helix chain 'D' and resid 19 through 28 Processing helix chain 'D' and resid 34 through 38 removed outlier: 3.597A pdb=" N ARG D 37 " --> pdb=" O ARG D 34 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG D 38 " --> pdb=" O ASP D 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 34 through 38' Processing helix chain 'D' and resid 66 through 76 Processing helix chain 'D' and resid 77 through 82 Processing helix chain 'D' and resid 98 through 115 removed outlier: 3.685A pdb=" N GLN D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 151 removed outlier: 3.599A pdb=" N ARG D 137 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASP D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU D 139 " --> pdb=" O ASP D 135 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS D 142 " --> pdb=" O ASP D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 181 Processing helix chain 'D' and resid 183 through 198 removed outlier: 4.324A pdb=" N MET D 189 " --> pdb=" O GLN D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 243 Processing helix chain 'D' and resid 244 through 246 No H-bonds generated for 'chain 'D' and resid 244 through 246' Processing helix chain 'D' and resid 282 through 298 removed outlier: 4.233A pdb=" N THR D 286 " --> pdb=" O PRO D 282 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE D 288 " --> pdb=" O ALA D 284 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYS D 295 " --> pdb=" O ARG D 291 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N HIS D 296 " --> pdb=" O ASN D 292 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 100 through 102 Processing sheet with id=AA2, first strand: chain 'E' and resid 139 through 144 removed outlier: 3.915A pdb=" N SER E 214 " --> pdb=" O PHE E 173 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 258 through 262 removed outlier: 3.929A pdb=" N SER D 251 " --> pdb=" O LYS E 319 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N GLN D 250 " --> pdb=" O ILE D 265 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU D 202 " --> pdb=" O VAL D 275 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER D 215 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N GLU D 207 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL D 213 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 9 through 13 removed outlier: 3.771A pdb=" N CYS B 9 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU B 85 " --> pdb=" O CYS B 67 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS B 67 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL B 57 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 144 through 148 Processing sheet with id=AA6, first strand: chain 'B' and resid 174 through 177 Processing sheet with id=AA7, first strand: chain 'B' and resid 245 through 247 Processing sheet with id=AA8, first strand: chain 'B' and resid 327 through 329 Processing sheet with id=AA9, first strand: chain 'A' and resid 8 through 12 removed outlier: 6.966A pdb=" N LYS A 8 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N VAL A 69 " --> pdb=" O LYS A 8 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL A 10 " --> pdb=" O VAL A 69 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 51 through 54 removed outlier: 4.433A pdb=" N ILE A 38 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 131 through 134 removed outlier: 5.407A pdb=" N ALA A 141 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N THR A 103 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N GLU A 143 " --> pdb=" O GLU A 101 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 125 through 127 Processing sheet with id=AB4, first strand: chain 'A' and resid 364 through 367 removed outlier: 6.741A pdb=" N VAL A 171 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N VAL A 219 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE A 173 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N PHE A 221 " --> pdb=" O ILE A 173 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ILE A 175 " --> pdb=" O PHE A 221 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N ARG A 223 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N TYR A 251 " --> pdb=" O THR A 889 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N SER A 891 " --> pdb=" O TYR A 251 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ASP A 253 " --> pdb=" O SER A 891 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N CYS A 893 " --> pdb=" O ASP A 253 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TYR A 255 " --> pdb=" O CYS A 893 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 380 through 381 Processing sheet with id=AB6, first strand: chain 'A' and resid 773 through 777 removed outlier: 3.696A pdb=" N PHE A 860 " --> pdb=" O TYR A 875 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1351 through 1357 removed outlier: 6.394A pdb=" N GLU A1385 " --> pdb=" O HIS A1375 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TRP A 942 " --> pdb=" O TRP A1390 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG A 945 " --> pdb=" O VAL A1419 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1204 through 1206 Processing sheet with id=AB9, first strand: chain 'A' and resid 1254 through 1255 Processing sheet with id=AC1, first strand: chain 'A' and resid 1439 through 1442 removed outlier: 5.471A pdb=" N VAL A1509 " --> pdb=" O HIS A1504 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLN A1501 " --> pdb=" O ASP A1485 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 31 through 36 removed outlier: 6.657A pdb=" N VAL H 24 " --> pdb=" O VAL H 32 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N LYS H 34 " --> pdb=" O ILE H 22 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE H 22 " --> pdb=" O LYS H 34 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ALA H 36 " --> pdb=" O HIS H 20 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N HIS H 20 " --> pdb=" O ALA H 36 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE H 93 " --> pdb=" O HIS H 20 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ILE H 22 " --> pdb=" O SER H 91 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N SER H 91 " --> pdb=" O ILE H 22 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL H 24 " --> pdb=" O VAL H 89 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL H 89 " --> pdb=" O VAL H 24 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG H 85 " --> pdb=" O LEU H 88 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N TYR H 78 " --> pdb=" O TYR H 75 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER H 70 " --> pdb=" O ASP G 75 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP G 75 " --> pdb=" O SER H 70 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N PHE G 71 " --> pdb=" O TYR H 74 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N LYS G 70 " --> pdb=" O ARG G 85 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ARG G 85 " --> pdb=" O LYS G 70 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG G 80 " --> pdb=" O ALA G 95 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU G 90 " --> pdb=" O LEU G 24 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU G 24 " --> pdb=" O LEU G 90 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N CYS G 92 " --> pdb=" O THR G 22 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N THR G 22 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TYR G 94 " --> pdb=" O GLN G 20 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N GLN G 20 " --> pdb=" O GLY G 36 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N GLY G 36 " --> pdb=" O GLN G 20 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N THR G 22 " --> pdb=" O TYR G 34 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N TYR G 34 " --> pdb=" O THR G 22 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU G 24 " --> pdb=" O LEU G 32 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 30 through 35 removed outlier: 3.619A pdb=" N GLY J 32 " --> pdb=" O ACYS J 23 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLY J 20 " --> pdb=" O HIS J 87 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL I 86 " --> pdb=" O LEU I 19 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU I 19 " --> pdb=" O VAL I 86 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 21 through 22 removed outlier: 3.591A pdb=" N SER I 22 " --> pdb=" O ALA I 25 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA I 25 " --> pdb=" O SER I 22 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 20 through 26 removed outlier: 6.422A pdb=" N LEU C 12 " --> pdb=" O LEU C 23 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ARG C 25 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL C 10 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL C 126 " --> pdb=" O HIS C 96 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS C 96 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG C 92 " --> pdb=" O LEU C 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 260 through 263 Processing sheet with id=AC7, first strand: chain 'C' and resid 372 through 373 removed outlier: 4.428A pdb=" N VAL C 372 " --> pdb=" O TYR C 334 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR C 334 " --> pdb=" O VAL C 372 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N VAL C 333 " --> pdb=" O LEU C 406 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 47 through 52 removed outlier: 3.569A pdb=" N VAL D 87 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU D 88 " --> pdb=" O LYS D 121 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 91 through 93 removed outlier: 6.178A pdb=" N PHE D 92 " --> pdb=" O HIS D 127 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL D 126 " --> pdb=" O THR D 162 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 991 hydrogen bonds defined for protein. 2794 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: 4.44 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7529 1.34 - 1.46: 5471 1.46 - 1.59: 10579 1.59 - 1.71: 8 1.71 - 1.83: 203 Bond restraints: 23790 Sorted by residual: bond pdb=" F2 AF3 E 502 " pdb="AL AF3 E 502 " ideal model delta sigma weight residual 1.637 1.711 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" F2 AF3 D 601 " pdb="AL AF3 D 601 " ideal model delta sigma weight residual 1.637 1.708 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" F3 AF3 E 502 " pdb="AL AF3 E 502 " ideal model delta sigma weight residual 1.637 1.708 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" F1 AF3 E 502 " pdb="AL AF3 E 502 " ideal model delta sigma weight residual 1.637 1.707 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" F1 AF3 D 601 " pdb="AL AF3 D 601 " ideal model delta sigma weight residual 1.637 1.706 -0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 23785 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.17: 31591 3.17 - 6.34: 506 6.34 - 9.51: 102 9.51 - 12.68: 24 12.68 - 15.85: 8 Bond angle restraints: 32231 Sorted by residual: angle pdb=" CA GLU C 226 " pdb=" CB GLU C 226 " pdb=" CG GLU C 226 " ideal model delta sigma weight residual 114.10 125.20 -11.10 2.00e+00 2.50e-01 3.08e+01 angle pdb=" N ILE C 88 " pdb=" CA ILE C 88 " pdb=" C ILE C 88 " ideal model delta sigma weight residual 110.05 104.02 6.03 1.09e+00 8.42e-01 3.06e+01 angle pdb=" C ALA C 302 " pdb=" N ASP C 303 " pdb=" CA ASP C 303 " ideal model delta sigma weight residual 122.46 130.08 -7.62 1.41e+00 5.03e-01 2.92e+01 angle pdb=" CB ARG B 78 " pdb=" CG ARG B 78 " pdb=" CD ARG B 78 " ideal model delta sigma weight residual 111.30 123.71 -12.41 2.30e+00 1.89e-01 2.91e+01 angle pdb=" C PRO B 17 " pdb=" N THR B 18 " pdb=" CA THR B 18 " ideal model delta sigma weight residual 121.54 131.63 -10.09 1.91e+00 2.74e-01 2.79e+01 ... (remaining 32226 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.51: 13510 26.51 - 53.03: 742 53.03 - 79.54: 60 79.54 - 106.05: 1 106.05 - 132.57: 1 Dihedral angle restraints: 14314 sinusoidal: 5793 harmonic: 8521 Sorted by residual: dihedral pdb=" CA ILE B 200 " pdb=" C ILE B 200 " pdb=" N ASP B 201 " pdb=" CA ASP B 201 " ideal model delta harmonic sigma weight residual -180.00 -147.65 -32.35 0 5.00e+00 4.00e-02 4.19e+01 dihedral pdb=" O2B GDP B 501 " pdb=" O3A GDP B 501 " pdb=" PB GDP B 501 " pdb=" PA GDP B 501 " ideal model delta sinusoidal sigma weight residual 180.00 47.43 132.57 1 2.00e+01 2.50e-03 4.02e+01 dihedral pdb=" CA LEU E 66 " pdb=" C LEU E 66 " pdb=" N MET E 67 " pdb=" CA MET E 67 " ideal model delta harmonic sigma weight residual -180.00 -148.45 -31.55 0 5.00e+00 4.00e-02 3.98e+01 ... (remaining 14311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 3192 0.091 - 0.182: 410 0.182 - 0.273: 34 0.273 - 0.364: 7 0.364 - 0.455: 3 Chirality restraints: 3646 Sorted by residual: chirality pdb=" CB ILE D 265 " pdb=" CA ILE D 265 " pdb=" CG1 ILE D 265 " pdb=" CG2 ILE D 265 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.17e+00 chirality pdb=" CB ILE E 318 " pdb=" CA ILE E 318 " pdb=" CG1 ILE E 318 " pdb=" CG2 ILE E 318 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" CB ILE D 122 " pdb=" CA ILE D 122 " pdb=" CG1 ILE D 122 " pdb=" CG2 ILE D 122 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.79e+00 ... (remaining 3643 not shown) Planarity restraints: 4103 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 142 " -0.040 2.00e-02 2.50e+03 2.64e-02 1.39e+01 pdb=" CG TYR E 142 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR E 142 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR E 142 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR E 142 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR E 142 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR E 142 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 142 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 248 " -0.054 5.00e-02 4.00e+02 8.14e-02 1.06e+01 pdb=" N PRO B 249 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO B 249 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 249 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 306 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C TYR A 306 " 0.055 2.00e-02 2.50e+03 pdb=" O TYR A 306 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU A 307 " -0.019 2.00e-02 2.50e+03 ... (remaining 4100 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 6001 2.80 - 3.32: 20701 3.32 - 3.85: 40678 3.85 - 4.37: 44644 4.37 - 4.90: 75501 Nonbonded interactions: 187525 Sorted by model distance: nonbonded pdb=" O VAL I 68 " pdb=" OG1 THR I 74 " model vdw 2.270 3.040 nonbonded pdb=" O1B GDP E 501 " pdb=" F2 AF3 E 502 " model vdw 2.278 2.990 nonbonded pdb=" OG SER A 222 " pdb=" OH TYR A 281 " model vdw 2.280 3.040 nonbonded pdb=" O2B GDP B 501 " pdb=" F3 AF3 D 601 " model vdw 2.281 2.990 nonbonded pdb=" OG1 THR D 42 " pdb=" F1 AF3 D 601 " model vdw 2.286 2.990 ... (remaining 187520 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.180 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.720 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 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 : 0.005 0.075 23791 Z= 0.239 Angle : 1.048 15.850 32231 Z= 0.541 Chirality : 0.060 0.455 3646 Planarity : 0.007 0.101 4103 Dihedral : 15.360 132.568 8770 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.04 % Allowed : 0.39 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.74 (0.14), residues: 2849 helix: -2.01 (0.12), residues: 1029 sheet: -1.01 (0.22), residues: 539 loop : -1.89 (0.16), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG B 78 TYR 0.062 0.002 TYR E 142 PHE 0.034 0.002 PHE B 31 TRP 0.019 0.002 TRP A1548 HIS 0.011 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00511 (23790) covalent geometry : angle 1.04779 (32231) hydrogen bonds : bond 0.12676 ( 991) hydrogen bonds : angle 7.08800 ( 2794) Misc. bond : bond 0.00263 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 234 GLN cc_start: 0.9361 (pt0) cc_final: 0.9012 (pt0) REVERT: E 310 TYR cc_start: 0.8625 (p90) cc_final: 0.8174 (p90) REVERT: E 315 MET cc_start: 0.8229 (tmm) cc_final: 0.7907 (tmm) REVERT: B 132 MET cc_start: 0.8980 (ptm) cc_final: 0.8609 (ptm) REVERT: B 319 MET cc_start: 0.9048 (mpp) cc_final: 0.8715 (mpp) REVERT: A 369 MET cc_start: 0.7980 (tmm) cc_final: 0.7703 (tmm) REVERT: A 808 MET cc_start: 0.9129 (mmm) cc_final: 0.8710 (mmt) REVERT: A 856 MET cc_start: 0.8258 (ppp) cc_final: 0.8049 (ppp) REVERT: A 1184 MET cc_start: 0.9105 (mpp) cc_final: 0.8874 (mpp) REVERT: H 17 GLU cc_start: 0.8998 (tp30) cc_final: 0.8611 (tp30) REVERT: H 46 ARG cc_start: 0.8766 (mmp80) cc_final: 0.8468 (mmp80) REVERT: H 68 ASN cc_start: 0.8309 (t0) cc_final: 0.6754 (m110) REVERT: H 71 ILE cc_start: 0.8721 (mm) cc_final: 0.8483 (mm) REVERT: H 108 LYS cc_start: 0.9182 (pptt) cc_final: 0.8824 (pptt) REVERT: H 109 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8681 (mm-30) REVERT: G 20 GLN cc_start: 0.9042 (mt0) cc_final: 0.8678 (mm-40) REVERT: G 96 LYS cc_start: 0.8818 (mptt) cc_final: 0.8204 (mptt) REVERT: J 6 GLU cc_start: 0.9114 (pp20) cc_final: 0.8747 (pp20) REVERT: J 7 GLN cc_start: 0.9356 (mm-40) cc_final: 0.9101 (tm-30) REVERT: J 10 GLU cc_start: 0.9385 (mm-30) cc_final: 0.9079 (mm-30) REVERT: J 11 ASP cc_start: 0.9082 (p0) cc_final: 0.8706 (p0) REVERT: J 55 LEU cc_start: 0.6915 (tt) cc_final: 0.6662 (tt) REVERT: J 75 MET cc_start: 0.8804 (mmp) cc_final: 0.7806 (tpp) REVERT: J 76 ILE cc_start: 0.9251 (mm) cc_final: 0.9032 (mp) REVERT: F 76 MET cc_start: 0.7907 (tpp) cc_final: 0.7608 (tpt) REVERT: F 82 MET cc_start: 0.8836 (mpp) cc_final: 0.8479 (mpp) REVERT: C 397 MET cc_start: 0.9179 (ppp) cc_final: 0.8835 (ppp) REVERT: C 530 MET cc_start: 0.9350 (pmm) cc_final: 0.9093 (pmm) REVERT: D 189 MET cc_start: 0.9157 (tmm) cc_final: 0.8905 (tmm) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.1732 time to fit residues: 40.7819 Evaluate side-chains 123 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.0470 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 8.9990 overall best weight: 2.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 172 ASN B 153 ASN B 315 GLN A 311 ASN ** H 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 GLN D 84 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.042720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.033354 restraints weight = 250776.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.034226 restraints weight = 129713.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.034810 restraints weight = 84809.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.035188 restraints weight = 63928.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.035454 restraints weight = 52865.043| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23791 Z= 0.164 Angle : 0.633 8.504 32231 Z= 0.330 Chirality : 0.044 0.244 3646 Planarity : 0.004 0.065 4103 Dihedral : 6.482 135.541 3143 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.08 % Allowed : 6.23 % Favored : 93.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -1.50 (0.15), residues: 2849 helix: -0.36 (0.15), residues: 1035 sheet: -0.94 (0.22), residues: 538 loop : -1.47 (0.18), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 78 TYR 0.027 0.001 TYR F 81 PHE 0.024 0.001 PHE B 31 TRP 0.016 0.001 TRP A1548 HIS 0.005 0.001 HIS A 405 Details of bonding type rmsd covalent geometry : bond 0.00353 (23790) covalent geometry : angle 0.63266 (32231) hydrogen bonds : bond 0.03607 ( 991) hydrogen bonds : angle 5.59794 ( 2794) Misc. bond : bond 0.00221 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 151 MET cc_start: 0.8985 (mmm) cc_final: 0.8753 (mmm) REVERT: E 234 GLN cc_start: 0.9429 (pt0) cc_final: 0.9081 (pt0) REVERT: E 315 MET cc_start: 0.8252 (tmm) cc_final: 0.7992 (tmm) REVERT: A 369 MET cc_start: 0.8245 (tmm) cc_final: 0.7845 (tmm) REVERT: H 17 GLU cc_start: 0.9064 (tp30) cc_final: 0.8612 (tp30) REVERT: H 42 GLU cc_start: 0.8582 (mp0) cc_final: 0.8380 (mp0) REVERT: H 46 ARG cc_start: 0.8721 (mmp80) cc_final: 0.8505 (mmp80) REVERT: H 68 ASN cc_start: 0.8178 (t0) cc_final: 0.7672 (t0) REVERT: H 108 LYS cc_start: 0.9289 (pptt) cc_final: 0.8857 (pptt) REVERT: H 118 ARG cc_start: 0.8896 (tpp-160) cc_final: 0.8449 (tpp-160) REVERT: G 20 GLN cc_start: 0.9203 (mt0) cc_final: 0.8720 (mm-40) REVERT: J 7 GLN cc_start: 0.9325 (mm-40) cc_final: 0.8968 (tm-30) REVERT: J 11 ASP cc_start: 0.9036 (p0) cc_final: 0.8665 (p0) REVERT: J 75 MET cc_start: 0.8386 (mmp) cc_final: 0.7582 (tpp) REVERT: J 76 ILE cc_start: 0.9183 (mm) cc_final: 0.8855 (mp) REVERT: F 82 MET cc_start: 0.8990 (mpp) cc_final: 0.8647 (mpp) REVERT: D 6 MET cc_start: 0.8848 (tmm) cc_final: 0.8578 (tmm) outliers start: 1 outliers final: 1 residues processed: 136 average time/residue: 0.1779 time to fit residues: 37.8906 Evaluate side-chains 119 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 98 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 110 optimal weight: 3.9990 chunk 251 optimal weight: 0.8980 chunk 77 optimal weight: 0.0050 chunk 257 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 229 optimal weight: 0.6980 chunk 235 optimal weight: 10.0000 chunk 93 optimal weight: 0.5980 chunk 41 optimal weight: 9.9990 chunk 114 optimal weight: 0.8980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 301 HIS B 349 HIS H 79 GLN G 109 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.043418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.033805 restraints weight = 320222.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.034817 restraints weight = 149146.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.035488 restraints weight = 91934.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.035938 restraints weight = 66556.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.036235 restraints weight = 53488.623| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 23791 Z= 0.100 Angle : 0.585 8.721 32231 Z= 0.299 Chirality : 0.044 0.206 3646 Planarity : 0.004 0.060 4103 Dihedral : 5.991 131.556 3143 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.31 % Allowed : 9.09 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -1.02 (0.16), residues: 2849 helix: 0.20 (0.16), residues: 1049 sheet: -0.76 (0.22), residues: 539 loop : -1.32 (0.18), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 78 TYR 0.017 0.001 TYR E 269 PHE 0.020 0.001 PHE B 31 TRP 0.010 0.001 TRP A1548 HIS 0.004 0.001 HIS E 196 Details of bonding type rmsd covalent geometry : bond 0.00211 (23790) covalent geometry : angle 0.58465 (32231) hydrogen bonds : bond 0.03154 ( 991) hydrogen bonds : angle 5.21696 ( 2794) Misc. bond : bond 0.00100 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 135 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 234 GLN cc_start: 0.9386 (pt0) cc_final: 0.9071 (pt0) REVERT: A 114 MET cc_start: 0.8976 (pmm) cc_final: 0.8504 (pmm) REVERT: A 369 MET cc_start: 0.8109 (tmm) cc_final: 0.7723 (tmm) REVERT: H 17 GLU cc_start: 0.9082 (tp30) cc_final: 0.8604 (tp30) REVERT: H 108 LYS cc_start: 0.9221 (pptt) cc_final: 0.8884 (pptt) REVERT: G 103 MET cc_start: 0.8922 (mmm) cc_final: 0.8614 (mpp) REVERT: J 7 GLN cc_start: 0.9256 (mm-40) cc_final: 0.9000 (tm-30) REVERT: J 75 MET cc_start: 0.8311 (mmp) cc_final: 0.7583 (tpp) REVERT: J 76 ILE cc_start: 0.9143 (mm) cc_final: 0.8740 (mm) REVERT: F 76 MET cc_start: 0.7115 (tpp) cc_final: 0.6637 (tpp) REVERT: F 82 MET cc_start: 0.9001 (mpp) cc_final: 0.8647 (mpp) REVERT: C 393 MET cc_start: 0.9363 (mmp) cc_final: 0.8943 (mmm) outliers start: 7 outliers final: 4 residues processed: 138 average time/residue: 0.1596 time to fit residues: 35.4313 Evaluate side-chains 117 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 113 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain H residue 28 ASP Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain J residue 47 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 254 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 136 optimal weight: 0.6980 chunk 277 optimal weight: 6.9990 chunk 154 optimal weight: 9.9990 chunk 167 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 268 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 chunk 266 optimal weight: 6.9990 chunk 230 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.043431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.033919 restraints weight = 298819.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.034903 restraints weight = 143259.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.035550 restraints weight = 89599.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.035978 restraints weight = 65515.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.036253 restraints weight = 53133.704| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 23791 Z= 0.101 Angle : 0.569 9.386 32231 Z= 0.290 Chirality : 0.043 0.221 3646 Planarity : 0.004 0.059 4103 Dihedral : 5.711 130.894 3143 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.81 % Allowed : 10.87 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.16), residues: 2849 helix: 0.58 (0.16), residues: 1046 sheet: -0.73 (0.22), residues: 564 loop : -1.13 (0.19), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 118 TYR 0.014 0.001 TYR E 269 PHE 0.020 0.001 PHE B 31 TRP 0.010 0.001 TRP A1548 HIS 0.005 0.001 HIS H 43 Details of bonding type rmsd covalent geometry : bond 0.00220 (23790) covalent geometry : angle 0.56932 (32231) hydrogen bonds : bond 0.02948 ( 991) hydrogen bonds : angle 5.07742 ( 2794) Misc. bond : bond 0.00101 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.969 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: E 234 GLN cc_start: 0.9376 (pt0) cc_final: 0.9020 (pt0) REVERT: E 315 MET cc_start: 0.8121 (tmm) cc_final: 0.7733 (tmm) REVERT: A 114 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8638 (pmm) REVERT: A 369 MET cc_start: 0.8062 (tmm) cc_final: 0.7788 (tmm) REVERT: H 17 GLU cc_start: 0.9092 (tp30) cc_final: 0.8593 (tp30) REVERT: H 108 LYS cc_start: 0.9230 (pptt) cc_final: 0.8885 (pptt) REVERT: G 103 MET cc_start: 0.8954 (mmm) cc_final: 0.8678 (mpp) REVERT: J 7 GLN cc_start: 0.9258 (mm-40) cc_final: 0.9009 (tm-30) REVERT: J 75 MET cc_start: 0.8276 (mmp) cc_final: 0.7416 (tpp) REVERT: J 76 ILE cc_start: 0.9164 (mm) cc_final: 0.8634 (mp) REVERT: F 76 MET cc_start: 0.7310 (tpp) cc_final: 0.6864 (tpp) REVERT: F 82 MET cc_start: 0.8986 (mpp) cc_final: 0.8670 (mpp) REVERT: D 6 MET cc_start: 0.8764 (tmm) cc_final: 0.8357 (tmm) outliers start: 20 outliers final: 9 residues processed: 135 average time/residue: 0.1616 time to fit residues: 35.4149 Evaluate side-chains 126 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 142 TYR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain H residue 28 ASP Chi-restraints excluded: chain G residue 109 GLN Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain D residue 213 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 195 optimal weight: 20.0000 chunk 162 optimal weight: 10.0000 chunk 283 optimal weight: 0.0270 chunk 105 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 251 optimal weight: 3.9990 chunk 218 optimal weight: 6.9990 chunk 188 optimal weight: 7.9990 chunk 229 optimal weight: 0.4980 chunk 158 optimal weight: 3.9990 overall best weight: 2.5044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 280 GLN ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.042748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.032949 restraints weight = 349793.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.033976 restraints weight = 159461.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.034649 restraints weight = 97036.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.035082 restraints weight = 69918.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.035384 restraints weight = 56285.380| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23791 Z= 0.143 Angle : 0.584 10.112 32231 Z= 0.298 Chirality : 0.043 0.216 3646 Planarity : 0.003 0.061 4103 Dihedral : 5.667 131.447 3143 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.93 % Allowed : 12.81 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.17), residues: 2849 helix: 0.85 (0.17), residues: 1047 sheet: -0.72 (0.22), residues: 575 loop : -0.99 (0.19), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 78 TYR 0.013 0.001 TYR B 25 PHE 0.021 0.001 PHE B 31 TRP 0.014 0.001 TRP A1548 HIS 0.005 0.001 HIS J 87 Details of bonding type rmsd covalent geometry : bond 0.00313 (23790) covalent geometry : angle 0.58448 (32231) hydrogen bonds : bond 0.02971 ( 991) hydrogen bonds : angle 5.04126 ( 2794) Misc. bond : bond 0.00141 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 234 GLN cc_start: 0.9420 (pt0) cc_final: 0.9055 (pt0) REVERT: B 319 MET cc_start: 0.9188 (mpp) cc_final: 0.8885 (mpp) REVERT: A 114 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.8593 (pmm) REVERT: A 211 ASN cc_start: 0.9142 (t0) cc_final: 0.8924 (p0) REVERT: H 17 GLU cc_start: 0.9136 (tp30) cc_final: 0.8635 (tp30) REVERT: H 108 LYS cc_start: 0.9249 (pptt) cc_final: 0.8903 (pptt) REVERT: J 7 GLN cc_start: 0.9245 (mm-40) cc_final: 0.9013 (tm-30) REVERT: F 76 MET cc_start: 0.7350 (tpp) cc_final: 0.6941 (tpp) REVERT: F 82 MET cc_start: 0.9000 (mpp) cc_final: 0.8692 (mpp) REVERT: D 6 MET cc_start: 0.8770 (tmm) cc_final: 0.8545 (tmm) outliers start: 23 outliers final: 16 residues processed: 137 average time/residue: 0.1559 time to fit residues: 34.9258 Evaluate side-chains 127 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 142 TYR Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain H residue 28 ASP Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 109 GLN Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 213 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 35 optimal weight: 8.9990 chunk 193 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 182 optimal weight: 20.0000 chunk 143 optimal weight: 2.9990 chunk 253 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 197 optimal weight: 0.0470 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 797 GLN ** H 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 GLN C 399 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.042805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.033260 restraints weight = 284756.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.034190 restraints weight = 141166.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.034807 restraints weight = 90106.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.035205 restraints weight = 66827.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.035483 restraints weight = 54816.657| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23791 Z= 0.125 Angle : 0.577 9.811 32231 Z= 0.294 Chirality : 0.043 0.341 3646 Planarity : 0.003 0.062 4103 Dihedral : 5.623 132.329 3143 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.01 % Allowed : 14.05 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.17), residues: 2849 helix: 0.93 (0.17), residues: 1057 sheet: -0.66 (0.22), residues: 568 loop : -0.98 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 78 TYR 0.013 0.001 TYR E 269 PHE 0.022 0.001 PHE B 31 TRP 0.012 0.001 TRP A1548 HIS 0.004 0.001 HIS C 315 Details of bonding type rmsd covalent geometry : bond 0.00275 (23790) covalent geometry : angle 0.57741 (32231) hydrogen bonds : bond 0.02892 ( 991) hydrogen bonds : angle 4.97946 ( 2794) Misc. bond : bond 0.00132 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 234 GLN cc_start: 0.9423 (pt0) cc_final: 0.9086 (pt0) REVERT: B 319 MET cc_start: 0.9167 (mpp) cc_final: 0.8906 (mpp) REVERT: A 114 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8605 (pmm) REVERT: A 211 ASN cc_start: 0.9160 (t0) cc_final: 0.8908 (p0) REVERT: H 17 GLU cc_start: 0.9145 (tp30) cc_final: 0.8646 (tp30) REVERT: H 108 LYS cc_start: 0.9252 (pptt) cc_final: 0.8900 (pptt) REVERT: G 103 MET cc_start: 0.9004 (mmm) cc_final: 0.8627 (mpp) REVERT: J 7 GLN cc_start: 0.9228 (mm-40) cc_final: 0.9016 (tm-30) REVERT: J 75 MET cc_start: 0.8363 (mmp) cc_final: 0.7098 (tpp) REVERT: F 76 MET cc_start: 0.7327 (tpp) cc_final: 0.6928 (tpp) REVERT: F 82 MET cc_start: 0.8989 (mpp) cc_final: 0.8650 (mpp) REVERT: C 121 MET cc_start: 0.8940 (tmm) cc_final: 0.8732 (tmm) REVERT: D 6 MET cc_start: 0.8763 (tmm) cc_final: 0.8520 (tmm) REVERT: D 249 PHE cc_start: 0.9240 (OUTLIER) cc_final: 0.8885 (t80) outliers start: 25 outliers final: 16 residues processed: 131 average time/residue: 0.1627 time to fit residues: 34.8537 Evaluate side-chains 130 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 142 TYR Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain H residue 28 ASP Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 109 GLN Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 249 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 181 optimal weight: 5.9990 chunk 95 optimal weight: 0.0050 chunk 153 optimal weight: 0.0020 chunk 77 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 31 optimal weight: 0.0470 chunk 14 optimal weight: 4.9990 chunk 184 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.043079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.033263 restraints weight = 349334.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.034294 restraints weight = 159475.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.034974 restraints weight = 97553.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.035423 restraints weight = 70277.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.035724 restraints weight = 56368.329| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23791 Z= 0.105 Angle : 0.570 10.682 32231 Z= 0.288 Chirality : 0.043 0.340 3646 Planarity : 0.003 0.059 4103 Dihedral : 5.511 130.185 3143 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 1.20 % Allowed : 14.28 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.17), residues: 2849 helix: 1.01 (0.17), residues: 1055 sheet: -0.57 (0.22), residues: 566 loop : -0.95 (0.19), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 78 TYR 0.014 0.001 TYR E 269 PHE 0.021 0.001 PHE I 85 TRP 0.009 0.001 TRP A1548 HIS 0.003 0.001 HIS C 315 Details of bonding type rmsd covalent geometry : bond 0.00231 (23790) covalent geometry : angle 0.56980 (32231) hydrogen bonds : bond 0.02800 ( 991) hydrogen bonds : angle 4.91237 ( 2794) Misc. bond : bond 0.00101 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 234 GLN cc_start: 0.9399 (pt0) cc_final: 0.9070 (pt0) REVERT: E 315 MET cc_start: 0.8234 (tmm) cc_final: 0.7917 (tmm) REVERT: B 319 MET cc_start: 0.9154 (mpp) cc_final: 0.8905 (mpp) REVERT: A 114 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8604 (pmm) REVERT: A 211 ASN cc_start: 0.9145 (t0) cc_final: 0.8873 (p0) REVERT: H 17 GLU cc_start: 0.9125 (tp30) cc_final: 0.8611 (tp30) REVERT: H 108 LYS cc_start: 0.9259 (pptt) cc_final: 0.8897 (pptt) REVERT: G 103 MET cc_start: 0.9020 (mmm) cc_final: 0.8647 (mpp) REVERT: J 7 GLN cc_start: 0.9228 (mm-40) cc_final: 0.9009 (tm-30) REVERT: J 75 MET cc_start: 0.8300 (mmp) cc_final: 0.7045 (tpp) REVERT: F 76 MET cc_start: 0.7319 (tpp) cc_final: 0.6913 (tpp) REVERT: F 82 MET cc_start: 0.8987 (mpp) cc_final: 0.8659 (mpp) REVERT: C 225 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7793 (tt) REVERT: D 6 MET cc_start: 0.8766 (tmm) cc_final: 0.8517 (tmm) REVERT: D 249 PHE cc_start: 0.9216 (OUTLIER) cc_final: 0.8904 (t80) outliers start: 30 outliers final: 20 residues processed: 141 average time/residue: 0.1660 time to fit residues: 37.9074 Evaluate side-chains 137 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 142 TYR Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain G residue 109 GLN Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 249 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 274 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 120 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 281 optimal weight: 4.9990 chunk 263 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 chunk 176 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 GLN B 226 ASN ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 45 ASN ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 30 ASN ** J 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.041763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.032311 restraints weight = 263480.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.033175 restraints weight = 134755.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.033750 restraints weight = 87662.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.034126 restraints weight = 65818.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.034380 restraints weight = 54462.242| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 23791 Z= 0.220 Angle : 0.667 10.268 32231 Z= 0.338 Chirality : 0.045 0.403 3646 Planarity : 0.004 0.065 4103 Dihedral : 5.795 130.855 3143 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 1.28 % Allowed : 14.82 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.17), residues: 2849 helix: 0.97 (0.16), residues: 1057 sheet: -0.70 (0.22), residues: 566 loop : -1.04 (0.19), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 78 TYR 0.028 0.002 TYR A 191 PHE 0.025 0.001 PHE B 31 TRP 0.019 0.001 TRP A1548 HIS 0.005 0.001 HIS C 315 Details of bonding type rmsd covalent geometry : bond 0.00476 (23790) covalent geometry : angle 0.66716 (32231) hydrogen bonds : bond 0.03222 ( 991) hydrogen bonds : angle 5.08427 ( 2794) Misc. bond : bond 0.00195 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 114 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 315 MET cc_start: 0.8236 (tmm) cc_final: 0.7912 (tmm) REVERT: B 319 MET cc_start: 0.9185 (mpp) cc_final: 0.8972 (mpp) REVERT: A 114 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8572 (pmm) REVERT: A 211 ASN cc_start: 0.9182 (t0) cc_final: 0.8909 (p0) REVERT: H 17 GLU cc_start: 0.9163 (tp30) cc_final: 0.8675 (tp30) REVERT: H 108 LYS cc_start: 0.9229 (pptt) cc_final: 0.8880 (pptt) REVERT: J 7 GLN cc_start: 0.9255 (mm-40) cc_final: 0.9024 (tm-30) REVERT: J 75 MET cc_start: 0.8251 (mmp) cc_final: 0.7033 (tpp) REVERT: F 76 MET cc_start: 0.7627 (tpp) cc_final: 0.7252 (tpp) REVERT: F 82 MET cc_start: 0.9009 (mpp) cc_final: 0.8721 (mpp) REVERT: D 6 MET cc_start: 0.8809 (tmm) cc_final: 0.8227 (tmm) REVERT: D 211 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7562 (t80) outliers start: 32 outliers final: 22 residues processed: 139 average time/residue: 0.1620 time to fit residues: 36.9558 Evaluate side-chains 135 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 142 TYR Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain H residue 28 ASP Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 109 GLN Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 213 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 234 optimal weight: 0.0670 chunk 266 optimal weight: 0.8980 chunk 252 optimal weight: 8.9990 chunk 281 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 231 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 188 optimal weight: 6.9990 chunk 180 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 overall best weight: 2.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.042202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.032260 restraints weight = 387456.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.033303 restraints weight = 168865.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.033990 restraints weight = 101522.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.034448 restraints weight = 72484.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.034751 restraints weight = 57775.011| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23791 Z= 0.146 Angle : 0.622 11.095 32231 Z= 0.314 Chirality : 0.044 0.378 3646 Planarity : 0.004 0.063 4103 Dihedral : 5.746 132.215 3143 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.32 % Allowed : 15.05 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.17), residues: 2849 helix: 1.06 (0.17), residues: 1056 sheet: -0.66 (0.22), residues: 554 loop : -1.00 (0.19), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 78 TYR 0.026 0.001 TYR A 191 PHE 0.023 0.001 PHE B 31 TRP 0.015 0.001 TRP C 224 HIS 0.005 0.001 HIS C 315 Details of bonding type rmsd covalent geometry : bond 0.00324 (23790) covalent geometry : angle 0.62238 (32231) hydrogen bonds : bond 0.03033 ( 991) hydrogen bonds : angle 5.01192 ( 2794) Misc. bond : bond 0.00141 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 113 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 315 MET cc_start: 0.8289 (tmm) cc_final: 0.7968 (tmm) REVERT: B 319 MET cc_start: 0.9166 (mpp) cc_final: 0.8948 (mpp) REVERT: A 114 MET cc_start: 0.9078 (OUTLIER) cc_final: 0.8550 (pmm) REVERT: A 211 ASN cc_start: 0.9160 (t0) cc_final: 0.8914 (p0) REVERT: H 17 GLU cc_start: 0.9161 (tp30) cc_final: 0.8670 (tp30) REVERT: H 108 LYS cc_start: 0.9258 (pptt) cc_final: 0.8913 (pptt) REVERT: J 7 GLN cc_start: 0.9260 (mm-40) cc_final: 0.9033 (tm-30) REVERT: J 31 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8768 (mm) REVERT: J 75 MET cc_start: 0.8216 (mmp) cc_final: 0.7033 (tpp) REVERT: F 76 MET cc_start: 0.7530 (tpp) cc_final: 0.7163 (tpp) REVERT: F 82 MET cc_start: 0.9021 (mpp) cc_final: 0.8702 (mpp) REVERT: D 6 MET cc_start: 0.8803 (tmm) cc_final: 0.8524 (tmm) outliers start: 33 outliers final: 25 residues processed: 137 average time/residue: 0.1586 time to fit residues: 35.9836 Evaluate side-chains 138 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 142 TYR Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain H residue 28 ASP Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 109 GLN Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 273 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 189 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 264 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 chunk 248 optimal weight: 30.0000 chunk 176 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 150 optimal weight: 7.9990 chunk 179 optimal weight: 10.0000 chunk 258 optimal weight: 0.4980 chunk 272 optimal weight: 5.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.042180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.032570 restraints weight = 296677.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.033496 restraints weight = 144104.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.034116 restraints weight = 91348.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.034528 restraints weight = 67491.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.034807 restraints weight = 55025.539| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23791 Z= 0.151 Angle : 0.625 11.369 32231 Z= 0.313 Chirality : 0.044 0.391 3646 Planarity : 0.004 0.063 4103 Dihedral : 5.721 132.708 3143 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 1.04 % Allowed : 15.33 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.17), residues: 2849 helix: 1.09 (0.17), residues: 1057 sheet: -0.69 (0.22), residues: 555 loop : -0.98 (0.19), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 78 TYR 0.029 0.001 TYR A 191 PHE 0.023 0.001 PHE B 31 TRP 0.013 0.001 TRP C 224 HIS 0.005 0.001 HIS C 315 Details of bonding type rmsd covalent geometry : bond 0.00334 (23790) covalent geometry : angle 0.62489 (32231) hydrogen bonds : bond 0.03015 ( 991) hydrogen bonds : angle 4.99357 ( 2794) Misc. bond : bond 0.00144 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 315 MET cc_start: 0.8291 (tmm) cc_final: 0.7953 (tmm) REVERT: B 319 MET cc_start: 0.9179 (mpp) cc_final: 0.8945 (mpp) REVERT: A 114 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8581 (pmm) REVERT: A 211 ASN cc_start: 0.9161 (t0) cc_final: 0.8911 (p0) REVERT: A 369 MET cc_start: 0.8346 (tmm) cc_final: 0.7928 (tmm) REVERT: H 17 GLU cc_start: 0.9174 (tp30) cc_final: 0.8689 (tp30) REVERT: H 108 LYS cc_start: 0.9266 (pptt) cc_final: 0.8918 (pptt) REVERT: J 7 GLN cc_start: 0.9252 (mm-40) cc_final: 0.9025 (tm-30) REVERT: J 31 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8729 (mm) REVERT: J 75 MET cc_start: 0.8201 (mmp) cc_final: 0.7017 (tpp) REVERT: F 76 MET cc_start: 0.7461 (tpp) cc_final: 0.7071 (tpp) REVERT: F 82 MET cc_start: 0.9018 (mpp) cc_final: 0.8699 (mpp) REVERT: D 6 MET cc_start: 0.8776 (tmm) cc_final: 0.8497 (tmm) REVERT: D 211 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7597 (t80) outliers start: 26 outliers final: 23 residues processed: 134 average time/residue: 0.1516 time to fit residues: 33.9050 Evaluate side-chains 138 residues out of total 2584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 142 TYR Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain H residue 28 ASP Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 109 GLN Chi-restraints excluded: chain J residue 31 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 213 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 267 optimal weight: 6.9990 chunk 283 optimal weight: 0.8980 chunk 162 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 99 optimal weight: 0.3980 chunk 132 optimal weight: 0.0870 chunk 112 optimal weight: 0.9990 chunk 161 optimal weight: 6.9990 chunk 214 optimal weight: 20.0000 chunk 71 optimal weight: 0.9980 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 ASN ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.043048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.033243 restraints weight = 338186.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.034275 restraints weight = 154871.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.034950 restraints weight = 94633.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.035399 restraints weight = 68451.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.035697 restraints weight = 55037.375| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23791 Z= 0.102 Angle : 0.595 11.646 32231 Z= 0.298 Chirality : 0.044 0.332 3646 Planarity : 0.003 0.059 4103 Dihedral : 5.498 131.448 3143 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.12 % Allowed : 15.33 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.17), residues: 2849 helix: 1.17 (0.17), residues: 1059 sheet: -0.56 (0.22), residues: 541 loop : -0.95 (0.19), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 193 TYR 0.025 0.001 TYR A1487 PHE 0.019 0.001 PHE B 31 TRP 0.008 0.001 TRP A 853 HIS 0.003 0.001 HIS J 8 Details of bonding type rmsd covalent geometry : bond 0.00223 (23790) covalent geometry : angle 0.59504 (32231) hydrogen bonds : bond 0.02826 ( 991) hydrogen bonds : angle 4.86809 ( 2794) Misc. bond : bond 0.00077 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4290.60 seconds wall clock time: 75 minutes 3.79 seconds (4503.79 seconds total)