Starting phenix.real_space_refine on Fri Mar 6 08:19:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vaw_31868/03_2026/7vaw_31868.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vaw_31868/03_2026/7vaw_31868.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vaw_31868/03_2026/7vaw_31868.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vaw_31868/03_2026/7vaw_31868.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vaw_31868/03_2026/7vaw_31868.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vaw_31868/03_2026/7vaw_31868.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 2 5.21 5 S 105 5.16 5 C 18735 2.51 5 N 5131 2.21 5 O 5572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29553 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "C" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "D" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3682 Classifications: {'peptide': 470} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 26, 'TRANS': 441} Chain: "E" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3668 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 441} Chain: "F" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3694 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 444} Chain: "G" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1619 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "H" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "J" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 976 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain: "K" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "L" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 980 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.62, per 1000 atoms: 0.22 Number of scatterers: 29553 At special positions: 0 Unit cell: (148.23, 145.8, 171.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 105 16.00 P 8 15.00 Mg 2 11.99 O 5572 8.00 N 5131 7.00 C 18735 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 1.4 seconds 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6918 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 25 sheets defined 47.0% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 90 through 99 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 233 through 245 Processing helix chain 'A' and resid 258 through 269 removed outlier: 3.762A pdb=" N MET A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 297 through 316 removed outlier: 4.276A pdb=" N ALA A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 342 Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 393 through 401 removed outlier: 3.628A pdb=" N ARG A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 416 Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 446 through 472 removed outlier: 3.819A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 476 removed outlier: 3.536A pdb=" N LEU A 476 " --> pdb=" O PRO A 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 473 through 476' Processing helix chain 'A' and resid 477 through 494 Processing helix chain 'A' and resid 508 through 532 Processing helix chain 'A' and resid 535 through 540 Processing helix chain 'A' and resid 542 through 551 removed outlier: 3.937A pdb=" N GLU A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 554 No H-bonds generated for 'chain 'A' and resid 552 through 554' Processing helix chain 'A' and resid 558 through 577 Processing helix chain 'B' and resid 90 through 99 removed outlier: 3.549A pdb=" N LYS B 97 " --> pdb=" O ARG B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 258 through 269 removed outlier: 3.560A pdb=" N VAL B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 295 through 315 removed outlier: 4.798A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 341 removed outlier: 3.547A pdb=" N TRP B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 363 Processing helix chain 'B' and resid 393 through 401 Processing helix chain 'B' and resid 410 through 416 removed outlier: 3.724A pdb=" N ALA B 414 " --> pdb=" O ASP B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 443 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 446 through 464 Processing helix chain 'B' and resid 464 through 471 Processing helix chain 'B' and resid 472 through 476 Processing helix chain 'B' and resid 477 through 494 Processing helix chain 'B' and resid 508 through 532 Processing helix chain 'B' and resid 535 through 540 Processing helix chain 'B' and resid 543 through 552 removed outlier: 3.642A pdb=" N ARG B 547 " --> pdb=" O PRO B 543 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ARG B 552 " --> pdb=" O ILE B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 577 Processing helix chain 'C' and resid 90 through 99 Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 233 through 245 Processing helix chain 'C' and resid 258 through 269 removed outlier: 3.880A pdb=" N MET C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 297 through 316 removed outlier: 3.940A pdb=" N ALA C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN C 316 " --> pdb=" O TYR C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 341 removed outlier: 4.008A pdb=" N TRP C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 363 Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 393 through 401 removed outlier: 3.612A pdb=" N ARG C 401 " --> pdb=" O GLN C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 416 removed outlier: 3.556A pdb=" N ARG C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 443 Processing helix chain 'C' and resid 446 through 472 removed outlier: 4.012A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 476 removed outlier: 4.035A pdb=" N LEU C 476 " --> pdb=" O PRO C 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 473 through 476' Processing helix chain 'C' and resid 477 through 495 Processing helix chain 'C' and resid 508 through 532 Processing helix chain 'C' and resid 535 through 541 removed outlier: 3.610A pdb=" N ILE C 539 " --> pdb=" O SER C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 551 removed outlier: 3.595A pdb=" N ARG C 547 " --> pdb=" O PRO C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 554 No H-bonds generated for 'chain 'C' and resid 552 through 554' Processing helix chain 'C' and resid 558 through 577 removed outlier: 3.524A pdb=" N PHE C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.640A pdb=" N LEU D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 159 through 171 Processing helix chain 'D' and resid 197 through 211 removed outlier: 3.900A pdb=" N THR D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 215 Processing helix chain 'D' and resid 227 through 250 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 259 through 274 Processing helix chain 'D' and resid 279 through 283 Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 340 through 346 Processing helix chain 'D' and resid 361 through 366 removed outlier: 3.753A pdb=" N GLY D 365 " --> pdb=" O LEU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 400 removed outlier: 3.850A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 422 Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 455 through 463 Processing helix chain 'E' and resid 85 through 89 removed outlier: 3.536A pdb=" N LEU E 89 " --> pdb=" O LYS E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 140 Processing helix chain 'E' and resid 159 through 171 Processing helix chain 'E' and resid 197 through 211 removed outlier: 3.852A pdb=" N THR E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 215 Processing helix chain 'E' and resid 227 through 250 removed outlier: 3.833A pdb=" N ARG E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE E 232 " --> pdb=" O THR E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 259 through 274 removed outlier: 3.646A pdb=" N TYR E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 Processing helix chain 'E' and resid 317 through 320 Processing helix chain 'E' and resid 323 through 333 Processing helix chain 'E' and resid 340 through 346 Processing helix chain 'E' and resid 361 through 365 Processing helix chain 'E' and resid 374 through 400 removed outlier: 3.549A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 422 removed outlier: 3.519A pdb=" N ARG E 409 " --> pdb=" O THR E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 443 Processing helix chain 'E' and resid 458 through 463 Processing helix chain 'F' and resid 85 through 90 removed outlier: 4.302A pdb=" N GLY F 90 " --> pdb=" O GLU F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 140 Processing helix chain 'F' and resid 159 through 171 Processing helix chain 'F' and resid 197 through 211 Processing helix chain 'F' and resid 213 through 215 No H-bonds generated for 'chain 'F' and resid 213 through 215' Processing helix chain 'F' and resid 229 through 250 removed outlier: 4.208A pdb=" N LEU F 233 " --> pdb=" O ILE F 229 " (cutoff:3.500A) Proline residue: F 235 - end of helix Processing helix chain 'F' and resid 259 through 274 removed outlier: 3.764A pdb=" N TYR F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 283 removed outlier: 3.835A pdb=" N GLY F 282 " --> pdb=" O GLY F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 285 No H-bonds generated for 'chain 'F' and resid 284 through 285' Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.585A pdb=" N ILE F 294 " --> pdb=" O ASP F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 333 Processing helix chain 'F' and resid 340 through 346 Processing helix chain 'F' and resid 361 through 366 removed outlier: 3.726A pdb=" N GLY F 365 " --> pdb=" O LEU F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 400 removed outlier: 3.810A pdb=" N ILE F 398 " --> pdb=" O LYS F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 404 Processing helix chain 'F' and resid 405 through 422 Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 445 through 446 No H-bonds generated for 'chain 'F' and resid 445 through 446' Processing helix chain 'F' and resid 447 through 451 Processing helix chain 'F' and resid 455 through 463 Processing helix chain 'F' and resid 466 through 471 Processing helix chain 'G' and resid 7 through 71 removed outlier: 3.758A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 83 Processing helix chain 'G' and resid 109 through 113 removed outlier: 3.647A pdb=" N ALA G 112 " --> pdb=" O PRO G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 209 removed outlier: 5.143A pdb=" N ILE G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) Proline residue: G 170 - end of helix removed outlier: 3.647A pdb=" N GLU G 208 " --> pdb=" O ARG G 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 16 removed outlier: 3.506A pdb=" N ALA H 16 " --> pdb=" O GLY H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 40 removed outlier: 3.510A pdb=" N THR H 35 " --> pdb=" O SER H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 60 removed outlier: 4.099A pdb=" N GLU H 60 " --> pdb=" O GLU H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 83 removed outlier: 3.673A pdb=" N GLN H 82 " --> pdb=" O LYS H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 98 Processing helix chain 'I' and resid 82 through 105 removed outlier: 3.990A pdb=" N ALA I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 119 Processing helix chain 'J' and resid 62 through 92 removed outlier: 4.085A pdb=" N LEU J 66 " --> pdb=" O SER J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 97 removed outlier: 3.530A pdb=" N GLN J 96 " --> pdb=" O ALA J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 115 removed outlier: 3.622A pdb=" N VAL J 103 " --> pdb=" O GLU J 99 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS J 106 " --> pdb=" O GLU J 102 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA J 111 " --> pdb=" O LEU J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 130 Proline residue: J 129 - end of helix Processing helix chain 'J' and resid 131 through 139 removed outlier: 3.640A pdb=" N ALA J 135 " --> pdb=" O LEU J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 187 removed outlier: 4.502A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN J 184 " --> pdb=" O SER J 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 105 removed outlier: 3.799A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 119 Processing helix chain 'L' and resid 62 through 93 removed outlier: 3.706A pdb=" N ALA L 93 " --> pdb=" O GLU L 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 97 Processing helix chain 'L' and resid 99 through 115 Processing helix chain 'L' and resid 124 through 126 No H-bonds generated for 'chain 'L' and resid 124 through 126' Processing helix chain 'L' and resid 127 through 139 removed outlier: 5.186A pdb=" N ALA L 133 " --> pdb=" O PRO L 129 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LEU L 134 " --> pdb=" O HIS L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 166 through 187 removed outlier: 4.898A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LYS L 181 " --> pdb=" O ALA L 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 10 removed outlier: 6.560A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ALA A 13 " --> pdb=" O ILE A 9 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 13 through 17 current: chain 'A' and resid 35 through 43 removed outlier: 5.779A pdb=" N ILE A 39 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLN A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG A 41 " --> pdb=" O PHE A 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 46 through 51 current: chain 'B' and resid 13 through 17 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 13 through 17 current: chain 'B' and resid 35 through 43 removed outlier: 5.810A pdb=" N ILE B 39 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLN B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG B 41 " --> pdb=" O PHE B 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 46 through 51 current: chain 'C' and resid 13 through 17 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 13 through 17 current: chain 'C' and resid 35 through 43 removed outlier: 5.670A pdb=" N ILE C 39 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLN C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG C 41 " --> pdb=" O PHE C 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 46 through 51 current: chain 'D' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 18 through 22 current: chain 'D' and resid 42 through 51 removed outlier: 5.695A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR D 54 " --> pdb=" O SER D 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 54 through 59 current: chain 'E' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 22 current: chain 'E' and resid 42 through 51 removed outlier: 5.792A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR E 54 " --> pdb=" O SER E 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 54 through 59 current: chain 'F' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 18 through 22 current: chain 'F' and resid 42 through 51 removed outlier: 5.746A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR F 54 " --> pdb=" O SER F 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 54 through 59 current: chain 'J' and resid 141 through 144 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 141 through 144 current: chain 'J' and resid 161 through 164 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 161 through 164 current: chain 'L' and resid 141 through 144 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 141 through 144 current: chain 'L' and resid 161 through 164 Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 75 Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 83 through 84 current: chain 'A' and resid 285 through 291 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 285 through 291 current: chain 'A' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 375 through 384 current: chain 'A' and resid 428 through 429 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 144 through 148 removed outlier: 6.577A pdb=" N HIS A 145 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR A 137 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE A 147 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ALA A 118 " --> pdb=" O PRO A 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 129 Processing sheet with id=AA6, first strand: chain 'B' and resid 72 through 75 Processing sheet with id=AA7, first strand: chain 'B' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 83 through 84 current: chain 'B' and resid 285 through 291 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 285 through 291 current: chain 'B' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 375 through 384 current: chain 'B' and resid 428 through 429 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 144 through 148 removed outlier: 6.425A pdb=" N HIS B 145 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N THR B 137 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ALA B 118 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 129 removed outlier: 6.831A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 204 through 205 removed outlier: 4.655A pdb=" N VAL B 218 " --> pdb=" O PHE B 205 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 72 through 75 Processing sheet with id=AB3, first strand: chain 'C' and resid 82 through 84 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 82 through 84 current: chain 'C' and resid 285 through 290 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 285 through 290 current: chain 'C' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 375 through 384 current: chain 'C' and resid 428 through 429 No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 144 through 148 removed outlier: 6.541A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ALA C 118 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY C 164 " --> pdb=" O TRP C 119 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 128 through 129 removed outlier: 6.649A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 81 through 84 Processing sheet with id=AB7, first strand: chain 'D' and resid 91 through 93 removed outlier: 6.642A pdb=" N ARG D 91 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU D 221 " --> pdb=" O ARG D 91 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N PHE D 93 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N LYS D 223 " --> pdb=" O PHE D 93 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 130 through 131 removed outlier: 4.637A pdb=" N LEU D 144 " --> pdb=" O ILE D 131 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 81 through 84 Processing sheet with id=AC1, first strand: chain 'E' and resid 92 through 93 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 92 through 93 current: chain 'E' and resid 217 through 223 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 217 through 223 current: chain 'E' and resid 307 through 315 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 307 through 315 current: chain 'E' and resid 358 through 359 No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.333A pdb=" N LEU E 144 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 81 through 84 Processing sheet with id=AC4, first strand: chain 'F' and resid 92 through 94 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 92 through 94 current: chain 'F' and resid 217 through 223 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 217 through 223 current: chain 'F' and resid 307 through 315 No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'F' and resid 144 through 145 removed outlier: 4.604A pdb=" N LEU F 144 " --> pdb=" O ILE F 131 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 89 through 96 Processing sheet with id=AC7, first strand: chain 'H' and resid 19 through 22 removed outlier: 6.617A pdb=" N VAL H 45 " --> pdb=" O LEU H 72 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ILE H 74 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N VAL H 47 " --> pdb=" O ILE H 74 " (cutoff:3.500A) 1293 hydrogen bonds defined for protein. 3711 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: 7.12 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.34: 9891 1.34 - 1.49: 7177 1.49 - 1.64: 12846 1.64 - 1.80: 102 1.80 - 1.95: 94 Bond restraints: 30110 Sorted by residual: bond pdb=" C4 ADP A 602 " pdb=" C5 ADP A 602 " ideal model delta sigma weight residual 1.490 1.384 0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" C PRO B 345 " pdb=" O PRO B 345 " ideal model delta sigma weight residual 1.236 1.184 0.052 1.23e-02 6.61e+03 1.81e+01 bond pdb=" C5 ADP A 602 " pdb=" C6 ADP A 602 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" C ILE B 226 " pdb=" O ILE B 226 " ideal model delta sigma weight residual 1.240 1.196 0.044 1.26e-02 6.30e+03 1.20e+01 bond pdb=" O3B ADP A 602 " pdb=" PB ADP A 602 " ideal model delta sigma weight residual 1.510 1.576 -0.066 2.00e-02 2.50e+03 1.08e+01 ... (remaining 30105 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 40584 2.95 - 5.90: 203 5.90 - 8.84: 15 8.84 - 11.79: 4 11.79 - 14.74: 1 Bond angle restraints: 40807 Sorted by residual: angle pdb=" N PRO B 345 " pdb=" CA PRO B 345 " pdb=" C PRO B 345 " ideal model delta sigma weight residual 114.35 122.73 -8.38 1.25e+00 6.40e-01 4.49e+01 angle pdb=" C PRO B 345 " pdb=" CA PRO B 345 " pdb=" CB PRO B 345 " ideal model delta sigma weight residual 110.88 103.43 7.45 1.41e+00 5.03e-01 2.79e+01 angle pdb=" O2B ADP A 602 " pdb=" PB ADP A 602 " pdb=" O3B ADP A 602 " ideal model delta sigma weight residual 119.90 105.16 14.74 3.00e+00 1.11e-01 2.41e+01 angle pdb=" C ALA B 346 " pdb=" CA ALA B 346 " pdb=" CB ALA B 346 " ideal model delta sigma weight residual 116.54 110.89 5.65 1.15e+00 7.56e-01 2.41e+01 angle pdb=" N ILE F 100 " pdb=" CA ILE F 100 " pdb=" C ILE F 100 " ideal model delta sigma weight residual 113.20 109.13 4.07 9.60e-01 1.09e+00 1.80e+01 ... (remaining 40802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.14: 17466 23.14 - 46.28: 748 46.28 - 69.42: 97 69.42 - 92.56: 43 92.56 - 115.70: 1 Dihedral angle restraints: 18355 sinusoidal: 7533 harmonic: 10822 Sorted by residual: dihedral pdb=" C5' ADP A 602 " pdb=" O5' ADP A 602 " pdb=" PA ADP A 602 " pdb=" O2A ADP A 602 " ideal model delta sinusoidal sigma weight residual -60.00 55.71 -115.70 1 2.00e+01 2.50e-03 3.44e+01 dihedral pdb=" CA LEU F 257 " pdb=" C LEU F 257 " pdb=" N THR F 258 " pdb=" CA THR F 258 " ideal model delta harmonic sigma weight residual -180.00 -157.49 -22.51 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA ARG B 532 " pdb=" C ARG B 532 " pdb=" N GLY B 533 " pdb=" CA GLY B 533 " ideal model delta harmonic sigma weight residual 180.00 157.78 22.22 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 18352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3889 0.063 - 0.125: 658 0.125 - 0.188: 25 0.188 - 0.251: 2 0.251 - 0.314: 2 Chirality restraints: 4576 Sorted by residual: chirality pdb=" CB ILE B 226 " pdb=" CA ILE B 226 " pdb=" CG1 ILE B 226 " pdb=" CG2 ILE B 226 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA LYS E 370 " pdb=" N LYS E 370 " pdb=" C LYS E 370 " pdb=" CB LYS E 370 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CB THR E 371 " pdb=" CA THR E 371 " pdb=" OG1 THR E 371 " pdb=" CG2 THR E 371 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 4573 not shown) Planarity restraints: 5333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 345 " 0.013 2.00e-02 2.50e+03 2.66e-02 7.10e+00 pdb=" C PRO B 345 " -0.046 2.00e-02 2.50e+03 pdb=" O PRO B 345 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA B 346 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 225 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.87e+00 pdb=" C ALA B 225 " 0.038 2.00e-02 2.50e+03 pdb=" O ALA B 225 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE B 226 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 226 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.84e+00 pdb=" C ILE B 226 " -0.038 2.00e-02 2.50e+03 pdb=" O ILE B 226 " 0.014 2.00e-02 2.50e+03 pdb=" N PRO B 227 " 0.013 2.00e-02 2.50e+03 ... (remaining 5330 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 170 2.55 - 3.14: 23209 3.14 - 3.72: 47673 3.72 - 4.31: 67961 4.31 - 4.90: 113307 Nonbonded interactions: 252320 Sorted by model distance: nonbonded pdb=" OG SER C 235 " pdb="MG MG C 601 " model vdw 1.960 2.170 nonbonded pdb=" O MET C 220 " pdb=" OG1 THR C 379 " model vdw 2.062 3.040 nonbonded pdb=" O MET A 220 " pdb=" OG1 THR A 379 " model vdw 2.165 3.040 nonbonded pdb=" OH TYR D 263 " pdb=" OD2 ASP D 290 " model vdw 2.200 3.040 nonbonded pdb=" OH TYR F 263 " pdb=" OD2 ASP F 290 " model vdw 2.212 3.040 ... (remaining 252315 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 578) selection = (chain 'B' and resid 1 through 578) selection = (chain 'C' and resid 1 through 578) } ncs_group { reference = (chain 'D' and resid 5 through 470) selection = (chain 'E' and resid 5 through 470) selection = (chain 'F' and resid 5 through 470) } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = (chain 'L' and resid 61 through 187) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.060 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: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 28.340 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 30112 Z= 0.174 Angle : 0.580 14.741 40807 Z= 0.308 Chirality : 0.044 0.314 4576 Planarity : 0.004 0.044 5333 Dihedral : 13.298 115.702 11437 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.03 % Allowed : 0.16 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.14), residues: 3764 helix: 1.18 (0.13), residues: 1571 sheet: -0.19 (0.21), residues: 593 loop : 0.43 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 364 TYR 0.013 0.001 TYR D 463 PHE 0.038 0.001 PHE B 269 TRP 0.009 0.001 TRP A 119 HIS 0.007 0.001 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00374 (30110) covalent geometry : angle 0.58045 (40807) hydrogen bonds : bond 0.13778 ( 1293) hydrogen bonds : angle 5.78290 ( 3711) Misc. bond : bond 0.00030 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 589 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8075 (ttmt) cc_final: 0.7576 (tttm) REVERT: A 33 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6715 (mt-10) REVERT: A 114 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6780 (mt-10) REVERT: A 124 LYS cc_start: 0.7084 (mtmm) cc_final: 0.6666 (mttm) REVERT: A 128 GLU cc_start: 0.5704 (mt-10) cc_final: 0.5489 (mt-10) REVERT: A 158 LYS cc_start: 0.7191 (ttmt) cc_final: 0.6604 (tmtt) REVERT: A 169 GLU cc_start: 0.6911 (tp30) cc_final: 0.6688 (mm-30) REVERT: A 184 TYR cc_start: 0.8425 (p90) cc_final: 0.7955 (p90) REVERT: A 197 ARG cc_start: 0.7834 (ptm-80) cc_final: 0.7080 (ptp90) REVERT: A 209 MET cc_start: 0.7456 (mtp) cc_final: 0.7088 (mtp) REVERT: A 239 GLN cc_start: 0.7555 (mt0) cc_final: 0.7172 (mp10) REVERT: A 248 ASP cc_start: 0.7471 (m-30) cc_final: 0.7251 (m-30) REVERT: A 257 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7121 (mm-30) REVERT: A 271 GLU cc_start: 0.6927 (mm-30) cc_final: 0.6470 (mm-30) REVERT: A 337 ILE cc_start: 0.7104 (mm) cc_final: 0.6897 (mm) REVERT: A 342 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6316 (mt-10) REVERT: A 343 GLU cc_start: 0.6596 (mt-10) cc_final: 0.5903 (mm-30) REVERT: A 393 GLU cc_start: 0.7042 (tm-30) cc_final: 0.6452 (pp20) REVERT: A 460 ARG cc_start: 0.7046 (mtp180) cc_final: 0.6836 (mtp-110) REVERT: A 461 GLU cc_start: 0.7096 (tt0) cc_final: 0.6735 (pt0) REVERT: A 466 GLU cc_start: 0.6321 (mt-10) cc_final: 0.5404 (tp30) REVERT: A 485 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6311 (mm-30) REVERT: A 541 GLN cc_start: 0.5786 (mm110) cc_final: 0.5518 (mm110) REVERT: A 546 GLU cc_start: 0.6052 (mm-30) cc_final: 0.5370 (mt-10) REVERT: A 564 GLU cc_start: 0.5544 (mm-30) cc_final: 0.5124 (mm-30) REVERT: B 45 ASP cc_start: 0.7672 (t0) cc_final: 0.7326 (t0) REVERT: B 53 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6322 (mt-10) REVERT: B 114 GLU cc_start: 0.6506 (mp0) cc_final: 0.5830 (pt0) REVERT: B 128 GLU cc_start: 0.6123 (mm-30) cc_final: 0.5741 (mm-30) REVERT: B 156 ARG cc_start: 0.6613 (mtp180) cc_final: 0.6108 (ttt-90) REVERT: B 166 TYR cc_start: 0.7612 (m-80) cc_final: 0.7395 (m-80) REVERT: B 209 MET cc_start: 0.6450 (mtp) cc_final: 0.6241 (mtm) REVERT: B 257 GLU cc_start: 0.6358 (mm-30) cc_final: 0.6111 (mp0) REVERT: B 262 MET cc_start: 0.8026 (tpt) cc_final: 0.7811 (tpt) REVERT: B 271 GLU cc_start: 0.6673 (mm-30) cc_final: 0.6287 (mp0) REVERT: B 397 GLN cc_start: 0.7321 (mm-40) cc_final: 0.7073 (tp40) REVERT: B 460 ARG cc_start: 0.6094 (mtp85) cc_final: 0.5105 (mmm160) REVERT: B 516 MET cc_start: 0.6317 (mtp) cc_final: 0.5918 (mtp) REVERT: B 517 LYS cc_start: 0.6535 (tttt) cc_final: 0.6128 (tppp) REVERT: B 520 LEU cc_start: 0.6274 (mm) cc_final: 0.5496 (pp) REVERT: B 547 ARG cc_start: 0.4702 (tpp-160) cc_final: 0.4445 (tpp-160) REVERT: B 567 MET cc_start: 0.5736 (mmm) cc_final: 0.5355 (mtp) REVERT: C 43 ASP cc_start: 0.7075 (t0) cc_final: 0.6842 (t0) REVERT: C 89 ARG cc_start: 0.7793 (mtm180) cc_final: 0.7339 (mtm-85) REVERT: C 114 GLU cc_start: 0.6889 (pt0) cc_final: 0.6592 (pp20) REVERT: C 127 ASP cc_start: 0.6758 (m-30) cc_final: 0.6297 (m-30) REVERT: C 130 ARG cc_start: 0.7142 (mmt-90) cc_final: 0.6917 (mmt180) REVERT: C 146 LYS cc_start: 0.8170 (mttt) cc_final: 0.7900 (mttp) REVERT: C 159 GLU cc_start: 0.6537 (mt-10) cc_final: 0.6140 (mt-10) REVERT: C 294 MET cc_start: 0.7715 (mtt) cc_final: 0.7441 (mtp) REVERT: C 323 MET cc_start: 0.8403 (mmp) cc_final: 0.8062 (mmt) REVERT: C 337 ILE cc_start: 0.7583 (mm) cc_final: 0.7331 (mp) REVERT: C 342 GLU cc_start: 0.7298 (mm-30) cc_final: 0.7029 (mm-30) REVERT: C 424 TRP cc_start: 0.7642 (p90) cc_final: 0.7385 (p90) REVERT: C 441 GLU cc_start: 0.6930 (tt0) cc_final: 0.6458 (tp30) REVERT: C 461 GLU cc_start: 0.6109 (tm-30) cc_final: 0.5803 (tm-30) REVERT: C 485 GLU cc_start: 0.6352 (mm-30) cc_final: 0.6077 (tp30) REVERT: C 489 ILE cc_start: 0.7641 (mt) cc_final: 0.7301 (mt) REVERT: C 491 ARG cc_start: 0.6610 (mtm110) cc_final: 0.6208 (mtp180) REVERT: C 544 VAL cc_start: 0.7689 (t) cc_final: 0.7447 (p) REVERT: C 546 GLU cc_start: 0.6471 (mm-30) cc_final: 0.5267 (mt-10) REVERT: C 558 GLU cc_start: 0.6924 (mt-10) cc_final: 0.6369 (mt-10) REVERT: D 7 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6765 (mm-30) REVERT: D 46 GLN cc_start: 0.8432 (tt0) cc_final: 0.8095 (tt0) REVERT: D 49 GLU cc_start: 0.7542 (tt0) cc_final: 0.7291 (tt0) REVERT: D 230 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7316 (mt-10) REVERT: D 274 ARG cc_start: 0.7221 (mtt180) cc_final: 0.6813 (mtt180) REVERT: D 353 ASP cc_start: 0.7264 (t0) cc_final: 0.7013 (t0) REVERT: D 407 ASN cc_start: 0.6289 (p0) cc_final: 0.4997 (m110) REVERT: D 409 ARG cc_start: 0.6660 (mtm-85) cc_final: 0.6415 (mtm-85) REVERT: D 410 ARG cc_start: 0.6498 (mtp180) cc_final: 0.6078 (mtt90) REVERT: D 420 ARG cc_start: 0.6670 (mtm-85) cc_final: 0.6466 (mtm-85) REVERT: D 428 GLN cc_start: 0.7493 (mt0) cc_final: 0.7174 (mt0) REVERT: D 452 LYS cc_start: 0.6659 (mttp) cc_final: 0.6260 (mtpt) REVERT: D 466 LYS cc_start: 0.5716 (ptpp) cc_final: 0.5385 (ptmt) REVERT: E 6 LYS cc_start: 0.7072 (tttt) cc_final: 0.6868 (ttpp) REVERT: E 26 ASP cc_start: 0.6543 (m-30) cc_final: 0.6065 (t70) REVERT: E 162 GLU cc_start: 0.6242 (mp0) cc_final: 0.5897 (mp0) REVERT: E 206 GLN cc_start: 0.6133 (tm-30) cc_final: 0.5931 (tp40) REVERT: E 209 GLU cc_start: 0.5859 (mt-10) cc_final: 0.5262 (pt0) REVERT: E 210 ARG cc_start: 0.6856 (ptt90) cc_final: 0.6609 (ppt-90) REVERT: E 243 GLU cc_start: 0.6820 (mt-10) cc_final: 0.6416 (mt-10) REVERT: E 265 GLU cc_start: 0.6395 (mt-10) cc_final: 0.6142 (mm-30) REVERT: E 318 ASP cc_start: 0.6760 (m-30) cc_final: 0.6490 (m-30) REVERT: E 345 ARG cc_start: 0.6436 (mmt90) cc_final: 0.6170 (mmm-85) REVERT: E 364 ASN cc_start: 0.7108 (p0) cc_final: 0.6082 (t0) REVERT: E 377 GLN cc_start: 0.6071 (mp10) cc_final: 0.5301 (mt0) REVERT: E 409 ARG cc_start: 0.4404 (mpp80) cc_final: 0.4188 (mmp80) REVERT: E 434 GLU cc_start: 0.5655 (tt0) cc_final: 0.4759 (tp30) REVERT: E 437 GLN cc_start: 0.7089 (tt0) cc_final: 0.6872 (tt0) REVERT: E 461 LYS cc_start: 0.5699 (tttt) cc_final: 0.5054 (mptp) REVERT: F 61 GLU cc_start: 0.6893 (mp0) cc_final: 0.6631 (mp0) REVERT: F 103 LEU cc_start: 0.6919 (mm) cc_final: 0.6598 (mt) REVERT: F 380 ASP cc_start: 0.7325 (m-30) cc_final: 0.6842 (m-30) REVERT: F 395 LEU cc_start: 0.7316 (tp) cc_final: 0.7093 (tp) REVERT: F 409 ARG cc_start: 0.6796 (ttm110) cc_final: 0.6286 (ttm110) REVERT: F 421 PHE cc_start: 0.7751 (m-80) cc_final: 0.7430 (m-80) REVERT: F 447 PRO cc_start: 0.7995 (Cg_exo) cc_final: 0.7773 (Cg_endo) REVERT: G 19 ARG cc_start: 0.6848 (mtm-85) cc_final: 0.6065 (ttp-110) REVERT: G 23 LYS cc_start: 0.6221 (mttp) cc_final: 0.5946 (mtpp) REVERT: G 38 GLU cc_start: 0.6430 (tt0) cc_final: 0.6156 (tt0) REVERT: G 152 GLU cc_start: 0.6474 (tt0) cc_final: 0.5775 (tp30) REVERT: G 156 LYS cc_start: 0.6233 (tptp) cc_final: 0.5768 (mtmt) REVERT: G 196 ARG cc_start: 0.6078 (mtp-110) cc_final: 0.5646 (tpp80) REVERT: H 8 GLU cc_start: 0.3311 (mt-10) cc_final: 0.3076 (pt0) REVERT: J 92 GLU cc_start: 0.2555 (tp30) cc_final: 0.2282 (tt0) REVERT: J 164 GLU cc_start: 0.5049 (tt0) cc_final: 0.4628 (mp0) REVERT: L 76 ARG cc_start: 0.4871 (mtp85) cc_final: 0.4619 (ttt90) REVERT: L 78 GLU cc_start: 0.4814 (tt0) cc_final: 0.4097 (tt0) REVERT: L 86 ARG cc_start: 0.4877 (mtp85) cc_final: 0.4261 (mtp180) REVERT: L 88 ARG cc_start: 0.4815 (mtp-110) cc_final: 0.4141 (ptm160) REVERT: L 89 GLU cc_start: 0.4040 (mm-30) cc_final: 0.3685 (pt0) REVERT: L 140 VAL cc_start: 0.3913 (m) cc_final: 0.3702 (p) REVERT: L 141 GLU cc_start: 0.4827 (tt0) cc_final: 0.4436 (mp0) REVERT: L 170 ARG cc_start: 0.5370 (mtp85) cc_final: 0.4922 (mtp85) outliers start: 1 outliers final: 3 residues processed: 590 average time/residue: 0.8728 time to fit residues: 580.4125 Evaluate side-chains 391 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 388 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain E residue 53 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 1.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 GLN ** A 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 HIS B 498 ASN C 283 HIS D 129 GLN D 363 ASN E 166 GLN F 364 ASN F 388 ASN G 162 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.155758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.122912 restraints weight = 36569.010| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.60 r_work: 0.3230 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 30112 Z= 0.158 Angle : 0.595 10.007 40807 Z= 0.303 Chirality : 0.046 0.167 4576 Planarity : 0.005 0.054 5333 Dihedral : 6.351 106.949 4238 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.65 % Allowed : 7.78 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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: 0.77 (0.14), residues: 3764 helix: 1.15 (0.13), residues: 1588 sheet: -0.22 (0.22), residues: 565 loop : 0.32 (0.16), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 93 TYR 0.012 0.002 TYR B 25 PHE 0.014 0.002 PHE C 406 TRP 0.014 0.002 TRP A 119 HIS 0.011 0.001 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00361 (30110) covalent geometry : angle 0.59478 (40807) hydrogen bonds : bond 0.04692 ( 1293) hydrogen bonds : angle 4.85089 ( 3711) Misc. bond : bond 0.00148 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 401 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7092 (mt-10) REVERT: A 124 LYS cc_start: 0.7283 (mtmm) cc_final: 0.6960 (mttm) REVERT: A 128 GLU cc_start: 0.6101 (mt-10) cc_final: 0.5892 (mt-10) REVERT: A 158 LYS cc_start: 0.7177 (ttmt) cc_final: 0.6716 (tmtt) REVERT: A 166 TYR cc_start: 0.7822 (m-80) cc_final: 0.7615 (m-80) REVERT: A 197 ARG cc_start: 0.8321 (ptm-80) cc_final: 0.7818 (ptp90) REVERT: A 209 MET cc_start: 0.8400 (mtp) cc_final: 0.8117 (mtp) REVERT: A 248 ASP cc_start: 0.7929 (m-30) cc_final: 0.7720 (m-30) REVERT: A 257 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7435 (mm-30) REVERT: A 271 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7296 (mp0) REVERT: A 343 GLU cc_start: 0.7022 (mt-10) cc_final: 0.6602 (mm-30) REVERT: A 347 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6761 (tp30) REVERT: A 461 GLU cc_start: 0.7893 (tt0) cc_final: 0.7626 (pt0) REVERT: A 466 GLU cc_start: 0.6615 (mt-10) cc_final: 0.6129 (tp30) REVERT: A 485 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7226 (mm-30) REVERT: A 491 ARG cc_start: 0.7800 (mtm110) cc_final: 0.7542 (mtm110) REVERT: A 546 GLU cc_start: 0.6127 (mm-30) cc_final: 0.5741 (mt-10) REVERT: B 114 GLU cc_start: 0.6913 (mp0) cc_final: 0.6312 (pt0) REVERT: B 128 GLU cc_start: 0.6476 (mm-30) cc_final: 0.6172 (mm-30) REVERT: B 156 ARG cc_start: 0.7020 (mtp180) cc_final: 0.6694 (ttt180) REVERT: B 209 MET cc_start: 0.7456 (mtp) cc_final: 0.7161 (mtm) REVERT: B 257 GLU cc_start: 0.7068 (mm-30) cc_final: 0.6763 (tp30) REVERT: B 271 GLU cc_start: 0.6861 (mm-30) cc_final: 0.6594 (mp0) REVERT: B 460 ARG cc_start: 0.6597 (mtp85) cc_final: 0.5850 (mmm160) REVERT: B 516 MET cc_start: 0.7111 (mtp) cc_final: 0.6736 (mtp) REVERT: B 547 ARG cc_start: 0.5268 (tpp-160) cc_final: 0.5004 (tpp-160) REVERT: B 567 MET cc_start: 0.5617 (mmm) cc_final: 0.5252 (mtp) REVERT: B 569 GLU cc_start: 0.6105 (mt-10) cc_final: 0.5589 (tm-30) REVERT: C 114 GLU cc_start: 0.7350 (pt0) cc_final: 0.7118 (pp20) REVERT: C 159 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6911 (mt-10) REVERT: C 201 PRO cc_start: 0.7952 (Cg_endo) cc_final: 0.7630 (Cg_exo) REVERT: C 257 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7284 (mp0) REVERT: C 323 MET cc_start: 0.8815 (mmp) cc_final: 0.8603 (mmt) REVERT: C 342 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7483 (mt-10) REVERT: C 441 GLU cc_start: 0.7466 (tt0) cc_final: 0.7199 (tp30) REVERT: C 461 GLU cc_start: 0.6687 (tm-30) cc_final: 0.6473 (tm-30) REVERT: C 485 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6687 (mm-30) REVERT: C 491 ARG cc_start: 0.7429 (mtm110) cc_final: 0.7121 (mtp180) REVERT: C 546 GLU cc_start: 0.6841 (mm-30) cc_final: 0.5776 (mt-10) REVERT: C 550 ARG cc_start: 0.7408 (mmm160) cc_final: 0.7152 (mmm160) REVERT: C 557 GLU cc_start: 0.6462 (mm-30) cc_final: 0.5931 (mm-30) REVERT: C 558 GLU cc_start: 0.7412 (mt-10) cc_final: 0.6919 (mt-10) REVERT: D 7 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7360 (mm-30) REVERT: D 46 GLN cc_start: 0.8660 (tt0) cc_final: 0.8455 (tt0) REVERT: D 209 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7555 (tt0) REVERT: D 316 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8242 (mtp) REVERT: D 407 ASN cc_start: 0.6571 (p0) cc_final: 0.5197 (m-40) REVERT: D 410 ARG cc_start: 0.7070 (mtp180) cc_final: 0.6811 (mtt90) REVERT: D 452 LYS cc_start: 0.7024 (mttp) cc_final: 0.6757 (mtpt) REVERT: D 466 LYS cc_start: 0.6048 (ptpp) cc_final: 0.5758 (ptmt) REVERT: E 26 ASP cc_start: 0.7280 (m-30) cc_final: 0.6956 (t70) REVERT: E 130 PHE cc_start: 0.7806 (OUTLIER) cc_final: 0.6714 (p90) REVERT: E 209 GLU cc_start: 0.6570 (mt-10) cc_final: 0.5915 (pt0) REVERT: E 243 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7265 (mt-10) REVERT: E 259 ASP cc_start: 0.7193 (OUTLIER) cc_final: 0.6822 (t70) REVERT: E 318 ASP cc_start: 0.7082 (m-30) cc_final: 0.6849 (m-30) REVERT: E 345 ARG cc_start: 0.6790 (mmt90) cc_final: 0.6560 (mmm-85) REVERT: E 364 ASN cc_start: 0.7112 (p0) cc_final: 0.6466 (t0) REVERT: E 377 GLN cc_start: 0.6605 (mp10) cc_final: 0.6017 (mt0) REVERT: E 434 GLU cc_start: 0.6436 (tt0) cc_final: 0.5813 (tp30) REVERT: E 461 LYS cc_start: 0.6161 (tttt) cc_final: 0.5476 (mtmt) REVERT: F 103 LEU cc_start: 0.7723 (mm) cc_final: 0.7442 (mp) REVERT: F 259 ASP cc_start: 0.6812 (OUTLIER) cc_final: 0.6567 (t70) REVERT: F 409 ARG cc_start: 0.7121 (ttm110) cc_final: 0.6721 (ttm110) REVERT: G 19 ARG cc_start: 0.7562 (mtm-85) cc_final: 0.7112 (ttp-110) REVERT: G 38 GLU cc_start: 0.7107 (tt0) cc_final: 0.6814 (tt0) REVERT: G 152 GLU cc_start: 0.6929 (tt0) cc_final: 0.6362 (tp30) REVERT: G 156 LYS cc_start: 0.6952 (tptp) cc_final: 0.6565 (mtmt) REVERT: G 196 ARG cc_start: 0.6526 (mtp-110) cc_final: 0.6087 (tpp80) REVERT: H 1 MET cc_start: 0.4073 (OUTLIER) cc_final: 0.3517 (mmt) REVERT: J 164 GLU cc_start: 0.5363 (tt0) cc_final: 0.4926 (mp0) REVERT: L 78 GLU cc_start: 0.5245 (tt0) cc_final: 0.4520 (tt0) REVERT: L 86 ARG cc_start: 0.5269 (mtp85) cc_final: 0.4754 (mtp180) REVERT: L 88 ARG cc_start: 0.4809 (mtp-110) cc_final: 0.4193 (ptm160) outliers start: 51 outliers final: 17 residues processed: 435 average time/residue: 0.8686 time to fit residues: 427.1348 Evaluate side-chains 379 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 354 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain L residue 92 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 281 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 139 optimal weight: 6.9990 chunk 297 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 118 optimal weight: 0.5980 chunk 270 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 307 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN F 437 GLN G 162 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.155268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.122113 restraints weight = 36648.096| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.52 r_work: 0.3214 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 30112 Z= 0.183 Angle : 0.604 8.831 40807 Z= 0.310 Chirality : 0.047 0.166 4576 Planarity : 0.005 0.054 5333 Dihedral : 6.426 107.890 4234 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.08 % Allowed : 10.51 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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: 0.58 (0.14), residues: 3764 helix: 1.07 (0.13), residues: 1575 sheet: -0.34 (0.21), residues: 578 loop : 0.14 (0.16), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 93 TYR 0.016 0.002 TYR C 562 PHE 0.018 0.002 PHE B 494 TRP 0.013 0.002 TRP J 187 HIS 0.006 0.001 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00431 (30110) covalent geometry : angle 0.60448 (40807) hydrogen bonds : bond 0.04860 ( 1293) hydrogen bonds : angle 4.89769 ( 3711) Misc. bond : bond 0.00152 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 380 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7109 (mt-10) REVERT: A 124 LYS cc_start: 0.7255 (mtmm) cc_final: 0.6909 (mttm) REVERT: A 158 LYS cc_start: 0.7188 (ttmt) cc_final: 0.6712 (tmtt) REVERT: A 166 TYR cc_start: 0.7798 (m-80) cc_final: 0.7559 (m-80) REVERT: A 197 ARG cc_start: 0.8361 (ptm-80) cc_final: 0.7820 (ptp90) REVERT: A 209 MET cc_start: 0.8394 (mtp) cc_final: 0.8082 (mtp) REVERT: A 271 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7353 (mp0) REVERT: A 343 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6558 (mm-30) REVERT: A 347 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6840 (tp30) REVERT: A 450 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8385 (tp) REVERT: A 461 GLU cc_start: 0.7950 (tt0) cc_final: 0.7645 (pt0) REVERT: A 466 GLU cc_start: 0.6748 (mt-10) cc_final: 0.6218 (tp30) REVERT: A 485 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7245 (mm-30) REVERT: A 546 GLU cc_start: 0.6152 (mm-30) cc_final: 0.5776 (mt-10) REVERT: A 559 PHE cc_start: 0.7517 (t80) cc_final: 0.7317 (t80) REVERT: B 33 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6711 (mt-10) REVERT: B 114 GLU cc_start: 0.6933 (mp0) cc_final: 0.6544 (mp0) REVERT: B 128 GLU cc_start: 0.6540 (mm-30) cc_final: 0.6238 (mm-30) REVERT: B 156 ARG cc_start: 0.6996 (mtp180) cc_final: 0.6700 (ttt-90) REVERT: B 159 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6920 (pt0) REVERT: B 209 MET cc_start: 0.7529 (mtp) cc_final: 0.7203 (mtm) REVERT: B 241 LEU cc_start: 0.7881 (mp) cc_final: 0.7645 (mt) REVERT: B 257 GLU cc_start: 0.7139 (mm-30) cc_final: 0.6912 (tp30) REVERT: B 271 GLU cc_start: 0.6856 (mm-30) cc_final: 0.6603 (mp0) REVERT: B 348 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7541 (tt0) REVERT: B 460 ARG cc_start: 0.6696 (mtp85) cc_final: 0.5895 (mmm160) REVERT: B 547 ARG cc_start: 0.4976 (tpp-160) cc_final: 0.4454 (tpp-160) REVERT: B 567 MET cc_start: 0.5608 (mmm) cc_final: 0.5332 (mtp) REVERT: B 569 GLU cc_start: 0.6120 (mt-10) cc_final: 0.5461 (tm-30) REVERT: C 114 GLU cc_start: 0.7399 (pt0) cc_final: 0.7185 (pp20) REVERT: C 159 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6905 (mt-10) REVERT: C 201 PRO cc_start: 0.7911 (Cg_endo) cc_final: 0.7592 (Cg_exo) REVERT: C 342 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7490 (mt-10) REVERT: C 344 MET cc_start: 0.7919 (ttp) cc_final: 0.7654 (tpp) REVERT: C 441 GLU cc_start: 0.7482 (tt0) cc_final: 0.7216 (tp30) REVERT: C 461 GLU cc_start: 0.6676 (tm-30) cc_final: 0.6354 (tm-30) REVERT: C 485 GLU cc_start: 0.7030 (mm-30) cc_final: 0.6785 (mm-30) REVERT: C 491 ARG cc_start: 0.7515 (mtm110) cc_final: 0.7093 (mtp180) REVERT: C 546 GLU cc_start: 0.6888 (mm-30) cc_final: 0.5851 (mt-10) REVERT: C 558 GLU cc_start: 0.7429 (mt-10) cc_final: 0.6940 (mt-10) REVERT: D 7 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7399 (mm-30) REVERT: D 209 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7659 (tt0) REVERT: D 407 ASN cc_start: 0.6597 (p0) cc_final: 0.5370 (m110) REVERT: D 452 LYS cc_start: 0.7110 (mttp) cc_final: 0.6840 (mtpt) REVERT: D 466 LYS cc_start: 0.6014 (ptpp) cc_final: 0.5709 (ptmt) REVERT: E 26 ASP cc_start: 0.7250 (m-30) cc_final: 0.6950 (t70) REVERT: E 130 PHE cc_start: 0.7746 (OUTLIER) cc_final: 0.6715 (p90) REVERT: E 209 GLU cc_start: 0.6808 (mt-10) cc_final: 0.6234 (pt0) REVERT: E 259 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.6890 (t70) REVERT: E 318 ASP cc_start: 0.7063 (m-30) cc_final: 0.6804 (m-30) REVERT: E 321 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.7100 (ttt90) REVERT: E 345 ARG cc_start: 0.6901 (mmt90) cc_final: 0.6648 (mmm-85) REVERT: E 364 ASN cc_start: 0.7090 (p0) cc_final: 0.6489 (t0) REVERT: E 377 GLN cc_start: 0.6656 (mp10) cc_final: 0.6003 (mt0) REVERT: E 434 GLU cc_start: 0.6478 (tt0) cc_final: 0.5821 (tp30) REVERT: E 446 LEU cc_start: 0.6295 (mm) cc_final: 0.5970 (mm) REVERT: E 461 LYS cc_start: 0.6301 (tttt) cc_final: 0.5435 (mtmt) REVERT: F 103 LEU cc_start: 0.7769 (mm) cc_final: 0.7471 (mp) REVERT: F 395 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7955 (tp) REVERT: F 406 GLU cc_start: 0.6651 (OUTLIER) cc_final: 0.5941 (mt-10) REVERT: F 409 ARG cc_start: 0.7177 (ttm110) cc_final: 0.6791 (ttm110) REVERT: G 19 ARG cc_start: 0.7539 (mtm-85) cc_final: 0.7100 (ttp-110) REVERT: G 38 GLU cc_start: 0.7123 (tt0) cc_final: 0.6850 (tt0) REVERT: G 156 LYS cc_start: 0.6966 (tptp) cc_final: 0.6551 (mtmt) REVERT: G 196 ARG cc_start: 0.6637 (mtp-110) cc_final: 0.6056 (tpp80) REVERT: H 1 MET cc_start: 0.4016 (OUTLIER) cc_final: 0.3543 (mmt) REVERT: J 86 ARG cc_start: 0.3383 (mmp80) cc_final: 0.3157 (mmm160) REVERT: J 121 LEU cc_start: 0.4458 (mp) cc_final: 0.4086 (mm) REVERT: J 186 LEU cc_start: 0.3675 (tt) cc_final: 0.2945 (mp) REVERT: L 86 ARG cc_start: 0.5241 (mtp85) cc_final: 0.4518 (mtp180) REVERT: L 88 ARG cc_start: 0.4840 (mtp-110) cc_final: 0.4271 (ptm160) outliers start: 64 outliers final: 21 residues processed: 422 average time/residue: 0.8788 time to fit residues: 418.4985 Evaluate side-chains 386 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 354 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 417 ARG Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain L residue 92 GLU Chi-restraints excluded: chain L residue 140 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 280 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 294 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 233 optimal weight: 10.0000 chunk 325 optimal weight: 10.0000 chunk 202 optimal weight: 0.9980 chunk 224 optimal weight: 0.9980 chunk 260 optimal weight: 10.0000 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 428 GLN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.154654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.121159 restraints weight = 36435.720| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.48 r_work: 0.3210 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 30112 Z= 0.207 Angle : 0.635 8.384 40807 Z= 0.326 Chirality : 0.047 0.169 4576 Planarity : 0.006 0.052 5333 Dihedral : 6.549 105.578 4234 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.43 % Allowed : 12.16 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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: 0.31 (0.14), residues: 3764 helix: 0.87 (0.13), residues: 1578 sheet: -0.52 (0.21), residues: 582 loop : -0.02 (0.16), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 156 TYR 0.017 0.002 TYR C 562 PHE 0.019 0.002 PHE C 559 TRP 0.014 0.002 TRP C 187 HIS 0.006 0.001 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00491 (30110) covalent geometry : angle 0.63512 (40807) hydrogen bonds : bond 0.04940 ( 1293) hydrogen bonds : angle 4.98710 ( 3711) Misc. bond : bond 0.00160 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 366 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7253 (mt-10) REVERT: A 124 LYS cc_start: 0.7372 (mtmm) cc_final: 0.6976 (mttm) REVERT: A 133 MET cc_start: 0.7800 (mtm) cc_final: 0.7531 (mtt) REVERT: A 158 LYS cc_start: 0.7200 (ttmt) cc_final: 0.6838 (tttm) REVERT: A 166 TYR cc_start: 0.7776 (m-80) cc_final: 0.7522 (m-80) REVERT: A 197 ARG cc_start: 0.8379 (ptm-80) cc_final: 0.7795 (ptp90) REVERT: A 209 MET cc_start: 0.8364 (mtp) cc_final: 0.8033 (mtp) REVERT: A 343 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6441 (mm-30) REVERT: A 347 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6784 (tp30) REVERT: A 348 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7800 (mt-10) REVERT: A 450 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8401 (tp) REVERT: A 461 GLU cc_start: 0.7898 (tt0) cc_final: 0.7592 (pt0) REVERT: A 466 GLU cc_start: 0.6701 (mt-10) cc_final: 0.6054 (tp30) REVERT: A 485 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7239 (mm-30) REVERT: A 546 GLU cc_start: 0.6178 (mm-30) cc_final: 0.5775 (mt-10) REVERT: B 33 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6758 (mt-10) REVERT: B 114 GLU cc_start: 0.6998 (mp0) cc_final: 0.6641 (mp0) REVERT: B 128 GLU cc_start: 0.6558 (mm-30) cc_final: 0.6229 (mm-30) REVERT: B 156 ARG cc_start: 0.7072 (mtp180) cc_final: 0.6802 (ttt-90) REVERT: B 159 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6921 (pt0) REVERT: B 209 MET cc_start: 0.7522 (mtp) cc_final: 0.7295 (mtm) REVERT: B 241 LEU cc_start: 0.7891 (mp) cc_final: 0.7629 (mt) REVERT: B 257 GLU cc_start: 0.7266 (mm-30) cc_final: 0.7044 (tp30) REVERT: B 271 GLU cc_start: 0.6848 (mm-30) cc_final: 0.6560 (mp0) REVERT: B 348 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7736 (tt0) REVERT: B 393 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6643 (pp20) REVERT: B 417 ARG cc_start: 0.6989 (OUTLIER) cc_final: 0.6716 (mpt180) REVERT: B 460 ARG cc_start: 0.6695 (mtp85) cc_final: 0.5866 (mmm160) REVERT: B 516 MET cc_start: 0.7089 (mtp) cc_final: 0.6754 (mtp) REVERT: B 547 ARG cc_start: 0.5072 (tpp-160) cc_final: 0.4682 (tpp80) REVERT: B 567 MET cc_start: 0.5558 (mmm) cc_final: 0.5294 (mtp) REVERT: C 114 GLU cc_start: 0.7469 (pt0) cc_final: 0.7237 (pp20) REVERT: C 159 GLU cc_start: 0.7190 (mt-10) cc_final: 0.6854 (mt-10) REVERT: C 201 PRO cc_start: 0.7933 (Cg_endo) cc_final: 0.7552 (Cg_exo) REVERT: C 342 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7496 (mt-10) REVERT: C 344 MET cc_start: 0.7938 (ttp) cc_final: 0.7721 (tpp) REVERT: C 441 GLU cc_start: 0.7409 (tt0) cc_final: 0.7142 (tp30) REVERT: C 485 GLU cc_start: 0.7070 (mm-30) cc_final: 0.6822 (mm-30) REVERT: C 546 GLU cc_start: 0.7041 (mm-30) cc_final: 0.5978 (mt-10) REVERT: C 557 GLU cc_start: 0.6423 (mm-30) cc_final: 0.5910 (mm-30) REVERT: C 558 GLU cc_start: 0.7364 (mt-10) cc_final: 0.6930 (mt-10) REVERT: D 7 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7340 (mm-30) REVERT: D 209 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7680 (tt0) REVERT: D 275 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7125 (mp0) REVERT: D 407 ASN cc_start: 0.6617 (p0) cc_final: 0.5372 (m-40) REVERT: D 452 LYS cc_start: 0.7073 (mttp) cc_final: 0.6808 (mtpt) REVERT: D 466 LYS cc_start: 0.6015 (ptpp) cc_final: 0.5716 (ptmt) REVERT: E 130 PHE cc_start: 0.7745 (OUTLIER) cc_final: 0.6747 (p90) REVERT: E 209 GLU cc_start: 0.6824 (mt-10) cc_final: 0.6158 (pt0) REVERT: E 210 ARG cc_start: 0.7154 (ptt90) cc_final: 0.6797 (ptt-90) REVERT: E 236 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.5971 (mpt180) REVERT: E 259 ASP cc_start: 0.7252 (OUTLIER) cc_final: 0.6862 (t70) REVERT: E 318 ASP cc_start: 0.7004 (m-30) cc_final: 0.6793 (m-30) REVERT: E 321 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.7062 (ttt90) REVERT: E 345 ARG cc_start: 0.6941 (mmt90) cc_final: 0.6639 (mmm-85) REVERT: E 364 ASN cc_start: 0.7054 (p0) cc_final: 0.6473 (t0) REVERT: E 377 GLN cc_start: 0.6703 (mp10) cc_final: 0.6039 (mt0) REVERT: E 461 LYS cc_start: 0.6239 (tttt) cc_final: 0.5216 (mppt) REVERT: F 103 LEU cc_start: 0.7755 (mm) cc_final: 0.7455 (mp) REVERT: F 395 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7936 (tp) REVERT: F 406 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.6018 (mt-10) REVERT: F 409 ARG cc_start: 0.7232 (ttm110) cc_final: 0.6874 (ttm110) REVERT: G 19 ARG cc_start: 0.7442 (mtm-85) cc_final: 0.6989 (ttp-110) REVERT: G 38 GLU cc_start: 0.7050 (tt0) cc_final: 0.6774 (tt0) REVERT: G 156 LYS cc_start: 0.6936 (tptp) cc_final: 0.6550 (tptp) REVERT: G 196 ARG cc_start: 0.6602 (mtp-110) cc_final: 0.6067 (tpp80) REVERT: H 1 MET cc_start: 0.4036 (OUTLIER) cc_final: 0.3514 (mmt) REVERT: J 86 ARG cc_start: 0.3404 (mmp80) cc_final: 0.3133 (mmm160) REVERT: J 121 LEU cc_start: 0.4474 (mp) cc_final: 0.4096 (mm) REVERT: J 186 LEU cc_start: 0.3536 (tt) cc_final: 0.2704 (mp) outliers start: 75 outliers final: 28 residues processed: 418 average time/residue: 0.8760 time to fit residues: 414.3119 Evaluate side-chains 393 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 350 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 417 ARG Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 236 ARG Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain L residue 92 GLU Chi-restraints excluded: chain L residue 140 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 39 optimal weight: 1.9990 chunk 117 optimal weight: 8.9990 chunk 126 optimal weight: 0.0050 chunk 330 optimal weight: 4.9990 chunk 274 optimal weight: 7.9990 chunk 175 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 348 optimal weight: 10.0000 chunk 230 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 overall best weight: 3.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 7 GLN ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 GLN D 170 GLN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.155027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.121519 restraints weight = 36523.473| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.52 r_work: 0.3218 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 30112 Z= 0.184 Angle : 0.607 8.722 40807 Z= 0.310 Chirality : 0.046 0.165 4576 Planarity : 0.005 0.058 5333 Dihedral : 6.467 103.865 4234 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.63 % Allowed : 12.84 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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: 0.28 (0.14), residues: 3764 helix: 0.89 (0.13), residues: 1582 sheet: -0.56 (0.21), residues: 576 loop : -0.09 (0.16), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 88 TYR 0.017 0.002 TYR C 562 PHE 0.018 0.002 PHE C 559 TRP 0.012 0.002 TRP A 119 HIS 0.004 0.001 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00431 (30110) covalent geometry : angle 0.60693 (40807) hydrogen bonds : bond 0.04708 ( 1293) hydrogen bonds : angle 4.92745 ( 3711) Misc. bond : bond 0.00148 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 356 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.7379 (mtmm) cc_final: 0.7014 (mttm) REVERT: A 156 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6734 (ttm-80) REVERT: A 158 LYS cc_start: 0.7223 (ttmt) cc_final: 0.6877 (tttm) REVERT: A 166 TYR cc_start: 0.7774 (m-80) cc_final: 0.7528 (m-80) REVERT: A 197 ARG cc_start: 0.8380 (ptm-80) cc_final: 0.7806 (ptp90) REVERT: A 209 MET cc_start: 0.8387 (mtp) cc_final: 0.8041 (mtp) REVERT: A 239 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8014 (mt0) REVERT: A 343 GLU cc_start: 0.6957 (mt-10) cc_final: 0.6396 (mm-30) REVERT: A 347 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6778 (tp30) REVERT: A 348 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7798 (mt-10) REVERT: A 450 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8402 (tp) REVERT: A 461 GLU cc_start: 0.7899 (tt0) cc_final: 0.7606 (pt0) REVERT: A 466 GLU cc_start: 0.6701 (mt-10) cc_final: 0.6065 (tp30) REVERT: A 485 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7255 (mm-30) REVERT: A 546 GLU cc_start: 0.6262 (mm-30) cc_final: 0.5863 (mt-10) REVERT: A 559 PHE cc_start: 0.7569 (t80) cc_final: 0.7331 (t80) REVERT: B 33 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6761 (mt-10) REVERT: B 114 GLU cc_start: 0.7041 (mp0) cc_final: 0.6705 (mp0) REVERT: B 128 GLU cc_start: 0.6618 (mm-30) cc_final: 0.6310 (mm-30) REVERT: B 156 ARG cc_start: 0.7059 (mtp180) cc_final: 0.6700 (ttt180) REVERT: B 159 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6873 (pt0) REVERT: B 209 MET cc_start: 0.7545 (mtp) cc_final: 0.7298 (mtm) REVERT: B 241 LEU cc_start: 0.7851 (mp) cc_final: 0.7592 (mt) REVERT: B 257 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6993 (tp30) REVERT: B 271 GLU cc_start: 0.6851 (mm-30) cc_final: 0.6538 (mp0) REVERT: B 348 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7764 (tt0) REVERT: B 393 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6501 (pp20) REVERT: B 417 ARG cc_start: 0.6986 (OUTLIER) cc_final: 0.6693 (mpt180) REVERT: B 458 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7135 (mt) REVERT: B 460 ARG cc_start: 0.6758 (mtp85) cc_final: 0.5936 (mmm160) REVERT: B 481 ARG cc_start: 0.6796 (mmm-85) cc_final: 0.6459 (mmm-85) REVERT: B 547 ARG cc_start: 0.5048 (tpp-160) cc_final: 0.4685 (tpp80) REVERT: B 567 MET cc_start: 0.5548 (mmm) cc_final: 0.5274 (mtp) REVERT: C 114 GLU cc_start: 0.7562 (pt0) cc_final: 0.7308 (pp20) REVERT: C 159 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6875 (mt-10) REVERT: C 201 PRO cc_start: 0.7922 (Cg_endo) cc_final: 0.7485 (Cg_exo) REVERT: C 257 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7429 (mp0) REVERT: C 342 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7572 (mt-10) REVERT: C 441 GLU cc_start: 0.7419 (tt0) cc_final: 0.7156 (tp30) REVERT: C 485 GLU cc_start: 0.7089 (mm-30) cc_final: 0.6817 (mm-30) REVERT: C 546 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6035 (mt-10) REVERT: C 558 GLU cc_start: 0.7373 (mt-10) cc_final: 0.6910 (mt-10) REVERT: D 7 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7381 (mm-30) REVERT: D 209 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7698 (tt0) REVERT: D 275 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: D 342 GLU cc_start: 0.7578 (pm20) cc_final: 0.7278 (mp0) REVERT: D 407 ASN cc_start: 0.6609 (p0) cc_final: 0.5386 (m110) REVERT: D 452 LYS cc_start: 0.7100 (mttp) cc_final: 0.6840 (mtpt) REVERT: D 466 LYS cc_start: 0.5993 (ptpp) cc_final: 0.5733 (ptmt) REVERT: E 128 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7394 (pt0) REVERT: E 130 PHE cc_start: 0.7712 (OUTLIER) cc_final: 0.6747 (p90) REVERT: E 209 GLU cc_start: 0.6843 (mt-10) cc_final: 0.6144 (pt0) REVERT: E 210 ARG cc_start: 0.7151 (ptt90) cc_final: 0.6801 (ptt-90) REVERT: E 236 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.5981 (mpt180) REVERT: E 259 ASP cc_start: 0.7206 (OUTLIER) cc_final: 0.6824 (t70) REVERT: E 318 ASP cc_start: 0.6969 (m-30) cc_final: 0.6767 (m-30) REVERT: E 321 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7063 (ttt90) REVERT: E 345 ARG cc_start: 0.6925 (mmt90) cc_final: 0.6630 (mmm-85) REVERT: E 364 ASN cc_start: 0.6953 (p0) cc_final: 0.6408 (t0) REVERT: E 377 GLN cc_start: 0.6724 (mp10) cc_final: 0.6094 (mt0) REVERT: E 461 LYS cc_start: 0.6242 (tttt) cc_final: 0.5265 (mppt) REVERT: F 103 LEU cc_start: 0.7675 (mm) cc_final: 0.7385 (mp) REVERT: F 395 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7965 (tp) REVERT: F 406 GLU cc_start: 0.6678 (OUTLIER) cc_final: 0.5952 (mt-10) REVERT: F 409 ARG cc_start: 0.7207 (ttm110) cc_final: 0.6858 (ttm110) REVERT: G 19 ARG cc_start: 0.7446 (mtm-85) cc_final: 0.6973 (ttp-110) REVERT: G 38 GLU cc_start: 0.7062 (tt0) cc_final: 0.6802 (tt0) REVERT: G 156 LYS cc_start: 0.6924 (tptp) cc_final: 0.6544 (tptp) REVERT: G 196 ARG cc_start: 0.6659 (mtp-110) cc_final: 0.6092 (tpp80) REVERT: H 1 MET cc_start: 0.4027 (OUTLIER) cc_final: 0.3513 (mmt) REVERT: J 86 ARG cc_start: 0.3388 (mmp80) cc_final: 0.3129 (mmm160) REVERT: J 121 LEU cc_start: 0.4527 (mp) cc_final: 0.4159 (mm) REVERT: J 186 LEU cc_start: 0.3562 (tt) cc_final: 0.2757 (mp) REVERT: L 81 GLU cc_start: 0.5432 (pp20) cc_final: 0.5180 (pt0) REVERT: L 88 ARG cc_start: 0.5017 (mtp85) cc_final: 0.4200 (ptm160) outliers start: 81 outliers final: 34 residues processed: 416 average time/residue: 0.8602 time to fit residues: 405.1597 Evaluate side-chains 397 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 344 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 417 ARG Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 236 ARG Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain G residue 50 ARG Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain L residue 92 GLU Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 150 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 119 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 240 optimal weight: 2.9990 chunk 236 optimal weight: 9.9990 chunk 283 optimal weight: 5.9990 chunk 238 optimal weight: 4.9990 chunk 349 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 353 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 340 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 GLN D 170 GLN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.153778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.120155 restraints weight = 36280.081| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.50 r_work: 0.3187 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 30112 Z= 0.279 Angle : 0.731 9.339 40807 Z= 0.374 Chirality : 0.051 0.193 4576 Planarity : 0.007 0.067 5333 Dihedral : 6.866 107.553 4234 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.08 % Allowed : 13.66 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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: -0.19 (0.14), residues: 3764 helix: 0.43 (0.13), residues: 1590 sheet: -0.72 (0.21), residues: 570 loop : -0.30 (0.16), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 93 TYR 0.024 0.003 TYR C 562 PHE 0.023 0.003 PHE B 494 TRP 0.016 0.003 TRP C 187 HIS 0.006 0.002 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00665 (30110) covalent geometry : angle 0.73131 (40807) hydrogen bonds : bond 0.05564 ( 1293) hydrogen bonds : angle 5.23144 ( 3711) Misc. bond : bond 0.00208 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 352 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.7352 (mtmm) cc_final: 0.6952 (mttm) REVERT: A 156 ARG cc_start: 0.7272 (OUTLIER) cc_final: 0.6775 (ttm-80) REVERT: A 158 LYS cc_start: 0.7234 (ttmt) cc_final: 0.6895 (tttm) REVERT: A 166 TYR cc_start: 0.7808 (m-80) cc_final: 0.7565 (m-80) REVERT: A 197 ARG cc_start: 0.8388 (ptm-80) cc_final: 0.7765 (ptp90) REVERT: A 209 MET cc_start: 0.8384 (mtp) cc_final: 0.8067 (mtp) REVERT: A 239 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8065 (mt0) REVERT: A 343 GLU cc_start: 0.7049 (mt-10) cc_final: 0.6480 (mm-30) REVERT: A 347 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6806 (tp30) REVERT: A 348 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7845 (mt-10) REVERT: A 450 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8418 (tp) REVERT: A 461 GLU cc_start: 0.7911 (tt0) cc_final: 0.7609 (pt0) REVERT: A 466 GLU cc_start: 0.6725 (mt-10) cc_final: 0.6110 (tp30) REVERT: A 546 GLU cc_start: 0.6300 (mm-30) cc_final: 0.5862 (mt-10) REVERT: B 114 GLU cc_start: 0.7112 (mp0) cc_final: 0.6845 (mp0) REVERT: B 128 GLU cc_start: 0.6599 (mm-30) cc_final: 0.6330 (mm-30) REVERT: B 156 ARG cc_start: 0.7060 (mtp180) cc_final: 0.6729 (ttt180) REVERT: B 170 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7382 (mm-30) REVERT: B 241 LEU cc_start: 0.7900 (mp) cc_final: 0.7633 (mt) REVERT: B 257 GLU cc_start: 0.7353 (mm-30) cc_final: 0.7142 (tp30) REVERT: B 417 ARG cc_start: 0.7015 (OUTLIER) cc_final: 0.6759 (mpt180) REVERT: B 458 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7154 (mt) REVERT: B 481 ARG cc_start: 0.6681 (mmm-85) cc_final: 0.6372 (mmm-85) REVERT: B 547 ARG cc_start: 0.4933 (tpp-160) cc_final: 0.4535 (mmt90) REVERT: C 159 GLU cc_start: 0.7288 (mt-10) cc_final: 0.6911 (mt-10) REVERT: C 342 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7546 (mt-10) REVERT: C 441 GLU cc_start: 0.7511 (tt0) cc_final: 0.7220 (tp30) REVERT: C 544 VAL cc_start: 0.8034 (t) cc_final: 0.7799 (p) REVERT: C 546 GLU cc_start: 0.7016 (mm-30) cc_final: 0.6043 (mt-10) REVERT: C 558 GLU cc_start: 0.7386 (mt-10) cc_final: 0.6817 (mt-10) REVERT: D 7 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7412 (mm-30) REVERT: D 209 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7734 (tt0) REVERT: D 275 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7205 (mp0) REVERT: D 407 ASN cc_start: 0.6738 (p0) cc_final: 0.5450 (m-40) REVERT: D 452 LYS cc_start: 0.7124 (mttp) cc_final: 0.6876 (mtpt) REVERT: D 466 LYS cc_start: 0.5979 (ptpp) cc_final: 0.5683 (ptmt) REVERT: E 128 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7387 (pt0) REVERT: E 130 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.6845 (p90) REVERT: E 209 GLU cc_start: 0.6809 (mt-10) cc_final: 0.6113 (pt0) REVERT: E 210 ARG cc_start: 0.7218 (ptt90) cc_final: 0.6890 (ptt-90) REVERT: E 236 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.6104 (mpt180) REVERT: E 259 ASP cc_start: 0.7330 (OUTLIER) cc_final: 0.7001 (t70) REVERT: E 321 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.7134 (ttt90) REVERT: E 345 ARG cc_start: 0.6963 (mmt90) cc_final: 0.6699 (mmm-85) REVERT: E 364 ASN cc_start: 0.6973 (p0) cc_final: 0.6377 (t0) REVERT: E 377 GLN cc_start: 0.6713 (mp10) cc_final: 0.6035 (mt0) REVERT: E 461 LYS cc_start: 0.6248 (tttt) cc_final: 0.5708 (ttmt) REVERT: F 11 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8155 (mm) REVERT: F 103 LEU cc_start: 0.7691 (mm) cc_final: 0.7414 (mp) REVERT: F 206 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7665 (mt0) REVERT: F 380 ASP cc_start: 0.8142 (m-30) cc_final: 0.7811 (m-30) REVERT: F 395 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8004 (tp) REVERT: F 406 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.6055 (mt-10) REVERT: F 409 ARG cc_start: 0.7357 (ttm110) cc_final: 0.6978 (ttm110) REVERT: G 19 ARG cc_start: 0.7437 (mtm-85) cc_final: 0.6962 (ttp-110) REVERT: G 38 GLU cc_start: 0.7068 (tt0) cc_final: 0.6814 (tt0) REVERT: G 156 LYS cc_start: 0.6857 (tptp) cc_final: 0.6473 (tptp) REVERT: G 196 ARG cc_start: 0.6854 (mtp-110) cc_final: 0.6270 (tpp80) REVERT: J 86 ARG cc_start: 0.3568 (mmp80) cc_final: 0.3257 (mmm160) REVERT: J 121 LEU cc_start: 0.4530 (mp) cc_final: 0.4175 (mm) REVERT: L 81 GLU cc_start: 0.5495 (pp20) cc_final: 0.5229 (pt0) REVERT: L 88 ARG cc_start: 0.4993 (mtp85) cc_final: 0.4230 (ptm160) REVERT: L 176 ASP cc_start: 0.5359 (OUTLIER) cc_final: 0.5020 (t0) outliers start: 95 outliers final: 44 residues processed: 428 average time/residue: 0.8277 time to fit residues: 401.8142 Evaluate side-chains 405 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 344 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 417 ARG Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 236 ARG Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 321 ARG Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain G residue 50 ARG Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain L residue 92 GLU Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 150 LEU Chi-restraints excluded: chain L residue 176 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 276 optimal weight: 0.9990 chunk 209 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 144 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 228 optimal weight: 3.9990 chunk 213 optimal weight: 3.9990 chunk 168 optimal weight: 6.9990 chunk 68 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 248 optimal weight: 8.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 GLN D 170 GLN D 428 GLN E 129 GLN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.157005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.123696 restraints weight = 36463.729| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.49 r_work: 0.3244 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30112 Z= 0.119 Angle : 0.544 8.603 40807 Z= 0.276 Chirality : 0.044 0.168 4576 Planarity : 0.005 0.053 5333 Dihedral : 6.174 99.521 4234 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.14 % Allowed : 15.08 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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 (0.14), residues: 3764 helix: 1.06 (0.13), residues: 1581 sheet: -0.65 (0.21), residues: 554 loop : -0.10 (0.16), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 460 TYR 0.014 0.001 TYR E 263 PHE 0.014 0.001 PHE C 559 TRP 0.021 0.001 TRP B 424 HIS 0.003 0.001 HIS E 323 Details of bonding type rmsd covalent geometry : bond 0.00267 (30110) covalent geometry : angle 0.54409 (40807) hydrogen bonds : bond 0.03983 ( 1293) hydrogen bonds : angle 4.75455 ( 3711) Misc. bond : bond 0.00079 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 377 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.7367 (mtmm) cc_final: 0.6954 (mttm) REVERT: A 158 LYS cc_start: 0.7205 (ttmt) cc_final: 0.6857 (tttm) REVERT: A 166 TYR cc_start: 0.7751 (m-80) cc_final: 0.7448 (m-80) REVERT: A 184 TYR cc_start: 0.8611 (p90) cc_final: 0.8283 (p90) REVERT: A 197 ARG cc_start: 0.8369 (ptm-80) cc_final: 0.7750 (ptp90) REVERT: A 209 MET cc_start: 0.8380 (mtp) cc_final: 0.8095 (mtp) REVERT: A 343 GLU cc_start: 0.6885 (mt-10) cc_final: 0.6328 (mm-30) REVERT: A 348 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7769 (mt-10) REVERT: A 450 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8358 (tp) REVERT: A 461 GLU cc_start: 0.7950 (tt0) cc_final: 0.7664 (pt0) REVERT: A 466 GLU cc_start: 0.6719 (mt-10) cc_final: 0.6028 (tp30) REVERT: A 485 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7186 (mm-30) REVERT: A 546 GLU cc_start: 0.6240 (mm-30) cc_final: 0.5848 (mt-10) REVERT: A 559 PHE cc_start: 0.7473 (t80) cc_final: 0.7088 (t80) REVERT: B 114 GLU cc_start: 0.7024 (mp0) cc_final: 0.6728 (mp0) REVERT: B 128 GLU cc_start: 0.6457 (mm-30) cc_final: 0.6226 (mm-30) REVERT: B 156 ARG cc_start: 0.7009 (mtp180) cc_final: 0.6733 (ttt180) REVERT: B 159 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6749 (pt0) REVERT: B 209 MET cc_start: 0.7461 (mtp) cc_final: 0.7226 (mtm) REVERT: B 241 LEU cc_start: 0.7865 (mp) cc_final: 0.7513 (tt) REVERT: B 271 GLU cc_start: 0.6927 (mm-30) cc_final: 0.6693 (mp0) REVERT: B 393 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6503 (pp20) REVERT: B 417 ARG cc_start: 0.7034 (OUTLIER) cc_final: 0.6542 (mpt180) REVERT: B 458 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7137 (mt) REVERT: B 460 ARG cc_start: 0.6720 (mtp85) cc_final: 0.5904 (mmm160) REVERT: B 481 ARG cc_start: 0.6599 (mmm-85) cc_final: 0.6260 (mmm-85) REVERT: B 494 PHE cc_start: 0.7548 (t80) cc_final: 0.7323 (t80) REVERT: B 516 MET cc_start: 0.7132 (mtp) cc_final: 0.6718 (mtp) REVERT: B 547 ARG cc_start: 0.4858 (tpp-160) cc_final: 0.4645 (mmt90) REVERT: C 159 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6844 (mt-10) REVERT: C 257 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: C 342 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7587 (mt-10) REVERT: C 441 GLU cc_start: 0.7392 (tt0) cc_final: 0.7143 (tp30) REVERT: C 546 GLU cc_start: 0.6944 (mm-30) cc_final: 0.5926 (mt-10) REVERT: C 558 GLU cc_start: 0.7256 (mt-10) cc_final: 0.7045 (pt0) REVERT: D 7 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7342 (mm-30) REVERT: D 209 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7724 (tt0) REVERT: D 275 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7157 (mp0) REVERT: D 407 ASN cc_start: 0.6657 (p0) cc_final: 0.5373 (m110) REVERT: D 452 LYS cc_start: 0.7147 (mttp) cc_final: 0.6874 (mtpt) REVERT: D 466 LYS cc_start: 0.5921 (ptpp) cc_final: 0.5670 (ptmt) REVERT: E 128 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7303 (pt0) REVERT: E 130 PHE cc_start: 0.7640 (OUTLIER) cc_final: 0.6632 (p90) REVERT: E 209 GLU cc_start: 0.6777 (mt-10) cc_final: 0.6112 (pt0) REVERT: E 210 ARG cc_start: 0.7108 (ptt90) cc_final: 0.6847 (ppt-90) REVERT: E 236 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.5915 (mpt180) REVERT: E 345 ARG cc_start: 0.6923 (mmt90) cc_final: 0.6683 (mmm-85) REVERT: E 364 ASN cc_start: 0.6970 (p0) cc_final: 0.6472 (t0) REVERT: E 377 GLN cc_start: 0.6586 (mp10) cc_final: 0.5981 (mt0) REVERT: E 461 LYS cc_start: 0.6179 (tttt) cc_final: 0.5716 (ttmt) REVERT: F 103 LEU cc_start: 0.7575 (mm) cc_final: 0.7289 (mp) REVERT: F 406 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6217 (mm-30) REVERT: F 409 ARG cc_start: 0.7151 (ttm110) cc_final: 0.6852 (ttm110) REVERT: G 19 ARG cc_start: 0.7399 (mtm-85) cc_final: 0.6959 (ttp-110) REVERT: G 38 GLU cc_start: 0.6977 (tt0) cc_final: 0.6745 (tt0) REVERT: G 156 LYS cc_start: 0.6890 (tptp) cc_final: 0.6533 (tptp) REVERT: G 196 ARG cc_start: 0.6717 (mtp-110) cc_final: 0.6176 (tpp80) REVERT: H 1 MET cc_start: 0.4094 (OUTLIER) cc_final: 0.3477 (mmt) REVERT: J 122 VAL cc_start: 0.2906 (t) cc_final: 0.2680 (t) REVERT: J 164 GLU cc_start: 0.5280 (tt0) cc_final: 0.4708 (mp0) REVERT: J 186 LEU cc_start: 0.3395 (tt) cc_final: 0.2642 (mp) REVERT: L 81 GLU cc_start: 0.5541 (pp20) cc_final: 0.5252 (pt0) REVERT: L 88 ARG cc_start: 0.4928 (mtp85) cc_final: 0.4261 (ptm160) outliers start: 66 outliers final: 24 residues processed: 425 average time/residue: 0.8373 time to fit residues: 403.6179 Evaluate side-chains 381 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 345 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 417 ARG Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 236 ARG Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 140 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 260 optimal weight: 10.0000 chunk 359 optimal weight: 10.0000 chunk 244 optimal weight: 0.7980 chunk 182 optimal weight: 1.9990 chunk 265 optimal weight: 7.9990 chunk 348 optimal weight: 5.9990 chunk 237 optimal weight: 4.9990 chunk 240 optimal weight: 0.9990 chunk 333 optimal weight: 20.0000 chunk 295 optimal weight: 7.9990 chunk 350 optimal weight: 20.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 GLN D 166 GLN D 428 GLN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 381 GLN G 162 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.155678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.122328 restraints weight = 36431.921| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.52 r_work: 0.3226 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 30112 Z= 0.169 Angle : 0.599 8.371 40807 Z= 0.305 Chirality : 0.046 0.211 4576 Planarity : 0.005 0.052 5333 Dihedral : 6.314 100.570 4234 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.17 % Allowed : 15.57 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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: 0.23 (0.14), residues: 3764 helix: 0.92 (0.13), residues: 1604 sheet: -0.71 (0.21), residues: 547 loop : -0.16 (0.16), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 491 TYR 0.017 0.002 TYR C 562 PHE 0.018 0.002 PHE C 559 TRP 0.020 0.002 TRP B 424 HIS 0.003 0.001 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00396 (30110) covalent geometry : angle 0.59923 (40807) hydrogen bonds : bond 0.04479 ( 1293) hydrogen bonds : angle 4.83439 ( 3711) Misc. bond : bond 0.00124 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 342 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.7351 (mtmm) cc_final: 0.6946 (mttm) REVERT: A 158 LYS cc_start: 0.7226 (ttmt) cc_final: 0.6862 (tttm) REVERT: A 166 TYR cc_start: 0.7731 (m-80) cc_final: 0.7476 (m-80) REVERT: A 197 ARG cc_start: 0.8361 (ptm-80) cc_final: 0.7739 (ptp90) REVERT: A 209 MET cc_start: 0.8384 (mtp) cc_final: 0.8058 (mtp) REVERT: A 343 GLU cc_start: 0.6917 (mt-10) cc_final: 0.6358 (mm-30) REVERT: A 348 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7751 (mt-10) REVERT: A 450 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8405 (tp) REVERT: A 461 GLU cc_start: 0.7935 (tt0) cc_final: 0.7662 (pt0) REVERT: A 466 GLU cc_start: 0.6750 (mt-10) cc_final: 0.6026 (tp30) REVERT: A 546 GLU cc_start: 0.6260 (mm-30) cc_final: 0.5860 (mt-10) REVERT: A 559 PHE cc_start: 0.7564 (t80) cc_final: 0.7048 (t80) REVERT: A 564 GLU cc_start: 0.6175 (mm-30) cc_final: 0.5819 (mm-30) REVERT: A 567 MET cc_start: 0.7017 (mmm) cc_final: 0.6791 (mmp) REVERT: B 114 GLU cc_start: 0.7061 (mp0) cc_final: 0.6797 (mp0) REVERT: B 128 GLU cc_start: 0.6547 (mm-30) cc_final: 0.6327 (mm-30) REVERT: B 156 ARG cc_start: 0.7017 (mtp180) cc_final: 0.6726 (ttt180) REVERT: B 209 MET cc_start: 0.7494 (mtp) cc_final: 0.7199 (mtm) REVERT: B 241 LEU cc_start: 0.7894 (mp) cc_final: 0.7485 (tt) REVERT: B 271 GLU cc_start: 0.6839 (mm-30) cc_final: 0.6540 (mp0) REVERT: B 417 ARG cc_start: 0.7036 (OUTLIER) cc_final: 0.6566 (mpt180) REVERT: B 458 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7117 (mt) REVERT: B 460 ARG cc_start: 0.6699 (mtp85) cc_final: 0.5891 (mmm160) REVERT: B 481 ARG cc_start: 0.6612 (mmm-85) cc_final: 0.6266 (mmm-85) REVERT: B 516 MET cc_start: 0.7134 (mtp) cc_final: 0.6753 (mtp) REVERT: B 547 ARG cc_start: 0.4873 (tpp-160) cc_final: 0.4639 (mmt90) REVERT: C 159 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6844 (mt-10) REVERT: C 257 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7345 (mp0) REVERT: C 342 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7589 (mt-10) REVERT: C 441 GLU cc_start: 0.7433 (tt0) cc_final: 0.7130 (tp30) REVERT: C 546 GLU cc_start: 0.6917 (mm-30) cc_final: 0.5924 (mt-10) REVERT: C 558 GLU cc_start: 0.7276 (mt-10) cc_final: 0.7074 (pt0) REVERT: D 7 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7361 (mm-30) REVERT: D 209 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7760 (tt0) REVERT: D 275 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7151 (mp0) REVERT: D 407 ASN cc_start: 0.6720 (p0) cc_final: 0.5446 (m110) REVERT: D 452 LYS cc_start: 0.7181 (mttp) cc_final: 0.6901 (mtpt) REVERT: D 466 LYS cc_start: 0.5874 (ptpp) cc_final: 0.5631 (ptmt) REVERT: E 128 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7392 (pt0) REVERT: E 130 PHE cc_start: 0.7675 (OUTLIER) cc_final: 0.6699 (p90) REVERT: E 156 SER cc_start: 0.6507 (p) cc_final: 0.6244 (m) REVERT: E 209 GLU cc_start: 0.6766 (mt-10) cc_final: 0.6113 (pt0) REVERT: E 210 ARG cc_start: 0.7171 (ptt90) cc_final: 0.6904 (ppt-90) REVERT: E 236 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.5904 (mpt180) REVERT: E 259 ASP cc_start: 0.7103 (OUTLIER) cc_final: 0.6786 (t70) REVERT: E 345 ARG cc_start: 0.6910 (mmt90) cc_final: 0.6612 (mmm-85) REVERT: E 364 ASN cc_start: 0.6972 (p0) cc_final: 0.6492 (t0) REVERT: E 377 GLN cc_start: 0.6690 (mp10) cc_final: 0.6065 (mt0) REVERT: E 461 LYS cc_start: 0.6182 (tttt) cc_final: 0.5708 (ttmt) REVERT: F 103 LEU cc_start: 0.7653 (mm) cc_final: 0.7355 (mp) REVERT: F 199 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.6918 (ttp80) REVERT: F 206 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7512 (mt0) REVERT: F 259 ASP cc_start: 0.6738 (OUTLIER) cc_final: 0.6331 (t70) REVERT: F 406 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.6225 (mm-30) REVERT: F 409 ARG cc_start: 0.7241 (ttm110) cc_final: 0.6960 (ttm110) REVERT: G 19 ARG cc_start: 0.7433 (mtm-85) cc_final: 0.6966 (ttp-110) REVERT: G 38 GLU cc_start: 0.7020 (tt0) cc_final: 0.6789 (tt0) REVERT: G 156 LYS cc_start: 0.6857 (tptp) cc_final: 0.6510 (tptp) REVERT: G 196 ARG cc_start: 0.6710 (mtp-110) cc_final: 0.6158 (tpp80) REVERT: H 1 MET cc_start: 0.4054 (OUTLIER) cc_final: 0.3431 (mmt) REVERT: J 122 VAL cc_start: 0.2887 (t) cc_final: 0.2664 (t) REVERT: J 164 GLU cc_start: 0.5309 (tt0) cc_final: 0.5023 (tp30) REVERT: J 186 LEU cc_start: 0.3417 (tt) cc_final: 0.2664 (mp) REVERT: L 81 GLU cc_start: 0.5555 (pp20) cc_final: 0.5278 (pt0) REVERT: L 88 ARG cc_start: 0.4958 (mtp85) cc_final: 0.4301 (ptm160) outliers start: 67 outliers final: 36 residues processed: 395 average time/residue: 0.8462 time to fit residues: 378.6480 Evaluate side-chains 387 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 337 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 417 ARG Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 236 ARG Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 199 ARG Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 140 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 175 optimal weight: 6.9990 chunk 364 optimal weight: 20.0000 chunk 153 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 chunk 305 optimal weight: 7.9990 chunk 190 optimal weight: 7.9990 chunk 150 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 chunk 341 optimal weight: 10.0000 chunk 301 optimal weight: 5.9990 chunk 197 optimal weight: 9.9990 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.155000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.121400 restraints weight = 36322.339| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.49 r_work: 0.3220 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 30112 Z= 0.207 Angle : 0.647 8.416 40807 Z= 0.330 Chirality : 0.048 0.211 4576 Planarity : 0.005 0.055 5333 Dihedral : 6.519 103.436 4234 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.40 % Allowed : 15.50 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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: 0.03 (0.14), residues: 3764 helix: 0.73 (0.13), residues: 1604 sheet: -0.81 (0.21), residues: 544 loop : -0.25 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 93 TYR 0.020 0.002 TYR C 562 PHE 0.023 0.002 PHE B 494 TRP 0.020 0.002 TRP B 424 HIS 0.004 0.001 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00491 (30110) covalent geometry : angle 0.64693 (40807) hydrogen bonds : bond 0.04866 ( 1293) hydrogen bonds : angle 4.98725 ( 3711) Misc. bond : bond 0.00154 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 341 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.7308 (mtmm) cc_final: 0.6924 (mtmm) REVERT: A 158 LYS cc_start: 0.7207 (ttmt) cc_final: 0.6868 (tttm) REVERT: A 166 TYR cc_start: 0.7736 (m-80) cc_final: 0.7468 (m-80) REVERT: A 197 ARG cc_start: 0.8382 (ptm-80) cc_final: 0.7744 (ptp90) REVERT: A 209 MET cc_start: 0.8363 (mtp) cc_final: 0.8053 (mtp) REVERT: A 257 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7623 (mm-30) REVERT: A 343 GLU cc_start: 0.6947 (mt-10) cc_final: 0.6356 (mm-30) REVERT: A 348 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7797 (mt-10) REVERT: A 450 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8409 (tp) REVERT: A 461 GLU cc_start: 0.7925 (tt0) cc_final: 0.7636 (pt0) REVERT: A 466 GLU cc_start: 0.6734 (mt-10) cc_final: 0.6019 (tp30) REVERT: A 546 GLU cc_start: 0.6301 (mm-30) cc_final: 0.5879 (mt-10) REVERT: A 564 GLU cc_start: 0.6147 (mm-30) cc_final: 0.5833 (mm-30) REVERT: B 114 GLU cc_start: 0.7066 (mp0) cc_final: 0.6790 (mp0) REVERT: B 128 GLU cc_start: 0.6534 (mm-30) cc_final: 0.6307 (mm-30) REVERT: B 156 ARG cc_start: 0.7035 (mtp180) cc_final: 0.6739 (ttt180) REVERT: B 209 MET cc_start: 0.7512 (mtp) cc_final: 0.7266 (mtm) REVERT: B 241 LEU cc_start: 0.7849 (mp) cc_final: 0.7573 (mt) REVERT: B 271 GLU cc_start: 0.6853 (mm-30) cc_final: 0.6569 (mp0) REVERT: B 417 ARG cc_start: 0.6972 (OUTLIER) cc_final: 0.6623 (mpt180) REVERT: B 458 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7115 (mt) REVERT: B 481 ARG cc_start: 0.6679 (mmm-85) cc_final: 0.6329 (mmm-85) REVERT: B 516 MET cc_start: 0.7120 (mtp) cc_final: 0.6729 (mtp) REVERT: B 547 ARG cc_start: 0.4870 (tpp-160) cc_final: 0.4643 (mmt90) REVERT: C 159 GLU cc_start: 0.7225 (mt-10) cc_final: 0.6859 (mt-10) REVERT: C 257 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7350 (mp0) REVERT: C 342 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7593 (mt-10) REVERT: C 441 GLU cc_start: 0.7448 (tt0) cc_final: 0.7136 (tp30) REVERT: C 546 GLU cc_start: 0.6902 (mm-30) cc_final: 0.5955 (mt-10) REVERT: C 558 GLU cc_start: 0.7338 (mt-10) cc_final: 0.6869 (mt-10) REVERT: D 7 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7371 (mm-30) REVERT: D 209 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7770 (tt0) REVERT: D 275 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: D 407 ASN cc_start: 0.6647 (p0) cc_final: 0.5427 (m110) REVERT: D 452 LYS cc_start: 0.7138 (mttp) cc_final: 0.6883 (mtpt) REVERT: D 466 LYS cc_start: 0.5916 (ptpp) cc_final: 0.5680 (ptmt) REVERT: E 88 MET cc_start: 0.8038 (mtt) cc_final: 0.7741 (mtt) REVERT: E 128 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7293 (pt0) REVERT: E 130 PHE cc_start: 0.7703 (OUTLIER) cc_final: 0.6740 (p90) REVERT: E 156 SER cc_start: 0.6677 (p) cc_final: 0.6369 (m) REVERT: E 209 GLU cc_start: 0.6781 (mt-10) cc_final: 0.6128 (pt0) REVERT: E 210 ARG cc_start: 0.7186 (ptt90) cc_final: 0.6929 (ppt-90) REVERT: E 236 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.6026 (mpt180) REVERT: E 259 ASP cc_start: 0.7162 (OUTLIER) cc_final: 0.6810 (t70) REVERT: E 345 ARG cc_start: 0.6953 (mmt90) cc_final: 0.6686 (mmm-85) REVERT: E 364 ASN cc_start: 0.7038 (p0) cc_final: 0.6479 (t0) REVERT: E 377 GLN cc_start: 0.6749 (mp10) cc_final: 0.6053 (mt0) REVERT: E 461 LYS cc_start: 0.6230 (tttt) cc_final: 0.5704 (ttmt) REVERT: F 103 LEU cc_start: 0.7662 (mm) cc_final: 0.7376 (mp) REVERT: F 199 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.6946 (ttp80) REVERT: F 206 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7556 (mt0) REVERT: F 380 ASP cc_start: 0.8110 (m-30) cc_final: 0.7862 (m-30) REVERT: F 406 GLU cc_start: 0.6708 (OUTLIER) cc_final: 0.6263 (mm-30) REVERT: F 409 ARG cc_start: 0.7263 (ttm110) cc_final: 0.6985 (ttm110) REVERT: G 19 ARG cc_start: 0.7436 (mtm-85) cc_final: 0.6964 (ttp-110) REVERT: G 38 GLU cc_start: 0.7013 (tt0) cc_final: 0.6779 (tt0) REVERT: G 156 LYS cc_start: 0.6863 (tptp) cc_final: 0.6509 (tptp) REVERT: G 196 ARG cc_start: 0.6810 (mtp-110) cc_final: 0.6211 (tpp80) REVERT: H 15 LEU cc_start: 0.4141 (OUTLIER) cc_final: 0.3410 (tp) REVERT: J 164 GLU cc_start: 0.5275 (tt0) cc_final: 0.5049 (tp30) REVERT: J 186 LEU cc_start: 0.3637 (tt) cc_final: 0.2855 (mp) REVERT: L 81 GLU cc_start: 0.5531 (pp20) cc_final: 0.5259 (pt0) REVERT: L 88 ARG cc_start: 0.4997 (mtp85) cc_final: 0.4311 (ptm160) REVERT: L 92 GLU cc_start: 0.3520 (OUTLIER) cc_final: 0.3227 (tp30) outliers start: 74 outliers final: 39 residues processed: 401 average time/residue: 0.8236 time to fit residues: 374.7453 Evaluate side-chains 388 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 335 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 417 ARG Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 236 ARG Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 319 ASP Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 199 ARG Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain L residue 92 GLU Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 140 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 270 optimal weight: 8.9990 chunk 240 optimal weight: 7.9990 chunk 150 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 chunk 271 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 216 optimal weight: 10.0000 chunk 252 optimal weight: 0.3980 chunk 140 optimal weight: 2.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.156192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.122587 restraints weight = 36334.902| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.48 r_work: 0.3231 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30112 Z= 0.146 Angle : 0.579 8.504 40807 Z= 0.294 Chirality : 0.045 0.218 4576 Planarity : 0.005 0.053 5333 Dihedral : 6.268 100.520 4234 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.88 % Allowed : 16.02 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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: 0.30 (0.14), residues: 3764 helix: 1.00 (0.13), residues: 1590 sheet: -0.69 (0.20), residues: 591 loop : -0.11 (0.16), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 93 TYR 0.016 0.001 TYR D 29 PHE 0.026 0.002 PHE B 494 TRP 0.022 0.002 TRP B 424 HIS 0.003 0.001 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00338 (30110) covalent geometry : angle 0.57889 (40807) hydrogen bonds : bond 0.04275 ( 1293) hydrogen bonds : angle 4.80901 ( 3711) Misc. bond : bond 0.00112 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 340 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.7260 (mtmm) cc_final: 0.6875 (mtmm) REVERT: A 158 LYS cc_start: 0.7186 (ttmt) cc_final: 0.6858 (tttm) REVERT: A 166 TYR cc_start: 0.7710 (m-80) cc_final: 0.7462 (m-80) REVERT: A 197 ARG cc_start: 0.8388 (ptm-80) cc_final: 0.7757 (ptp90) REVERT: A 209 MET cc_start: 0.8374 (mtp) cc_final: 0.8054 (mtp) REVERT: A 343 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6317 (mm-30) REVERT: A 348 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7734 (mt-10) REVERT: A 450 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8405 (tp) REVERT: A 461 GLU cc_start: 0.7931 (tt0) cc_final: 0.7647 (pt0) REVERT: A 466 GLU cc_start: 0.6764 (mt-10) cc_final: 0.6056 (tp30) REVERT: A 546 GLU cc_start: 0.6288 (mm-30) cc_final: 0.5883 (mt-10) REVERT: A 559 PHE cc_start: 0.7282 (t80) cc_final: 0.6907 (t80) REVERT: B 114 GLU cc_start: 0.7063 (mp0) cc_final: 0.6798 (mp0) REVERT: B 128 GLU cc_start: 0.6499 (mm-30) cc_final: 0.6298 (mm-30) REVERT: B 156 ARG cc_start: 0.7009 (mtp180) cc_final: 0.6752 (ttt180) REVERT: B 209 MET cc_start: 0.7477 (mtp) cc_final: 0.7159 (mtm) REVERT: B 241 LEU cc_start: 0.7901 (mp) cc_final: 0.7523 (tt) REVERT: B 271 GLU cc_start: 0.6811 (mm-30) cc_final: 0.6530 (mp0) REVERT: B 393 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6459 (pp20) REVERT: B 417 ARG cc_start: 0.7022 (OUTLIER) cc_final: 0.6650 (mpt180) REVERT: B 458 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7109 (mt) REVERT: B 481 ARG cc_start: 0.6676 (mmm-85) cc_final: 0.6307 (mmm-85) REVERT: B 547 ARG cc_start: 0.4845 (tpp-160) cc_final: 0.4551 (mmt90) REVERT: B 568 LYS cc_start: 0.4925 (mmpt) cc_final: 0.4633 (mmtt) REVERT: C 159 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6896 (mt-10) REVERT: C 257 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7340 (mp0) REVERT: C 342 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7619 (mt-10) REVERT: C 441 GLU cc_start: 0.7421 (tt0) cc_final: 0.7120 (tp30) REVERT: C 546 GLU cc_start: 0.6827 (mm-30) cc_final: 0.5836 (mt-10) REVERT: C 558 GLU cc_start: 0.7298 (mt-10) cc_final: 0.7092 (pt0) REVERT: D 7 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7365 (mm-30) REVERT: D 209 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7733 (tt0) REVERT: D 275 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7199 (mp0) REVERT: D 407 ASN cc_start: 0.6587 (p0) cc_final: 0.5452 (m110) REVERT: D 452 LYS cc_start: 0.7160 (mttp) cc_final: 0.6893 (mtpt) REVERT: D 466 LYS cc_start: 0.5930 (ptpp) cc_final: 0.5713 (ptmt) REVERT: E 88 MET cc_start: 0.8058 (mtt) cc_final: 0.7745 (mtt) REVERT: E 128 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7344 (pt0) REVERT: E 130 PHE cc_start: 0.7658 (OUTLIER) cc_final: 0.6688 (p90) REVERT: E 156 SER cc_start: 0.6576 (p) cc_final: 0.6292 (m) REVERT: E 209 GLU cc_start: 0.6800 (mt-10) cc_final: 0.6139 (pt0) REVERT: E 210 ARG cc_start: 0.7134 (ptt90) cc_final: 0.6891 (ppt-90) REVERT: E 236 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.6013 (mpt180) REVERT: E 259 ASP cc_start: 0.7044 (OUTLIER) cc_final: 0.6742 (t70) REVERT: E 345 ARG cc_start: 0.6969 (mmt90) cc_final: 0.6722 (mmm-85) REVERT: E 364 ASN cc_start: 0.7006 (p0) cc_final: 0.6522 (t0) REVERT: E 377 GLN cc_start: 0.6676 (mp10) cc_final: 0.6038 (mt0) REVERT: E 461 LYS cc_start: 0.6146 (tttt) cc_final: 0.5669 (ttmt) REVERT: F 103 LEU cc_start: 0.7677 (mm) cc_final: 0.7377 (mp) REVERT: F 206 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7540 (mt0) REVERT: F 406 GLU cc_start: 0.6648 (OUTLIER) cc_final: 0.6219 (mm-30) REVERT: F 409 ARG cc_start: 0.7231 (ttm110) cc_final: 0.6950 (ttm110) REVERT: G 19 ARG cc_start: 0.7430 (mtm-85) cc_final: 0.6982 (ttp-110) REVERT: G 38 GLU cc_start: 0.7023 (tt0) cc_final: 0.6792 (tt0) REVERT: G 156 LYS cc_start: 0.6853 (tptp) cc_final: 0.6508 (tptp) REVERT: G 196 ARG cc_start: 0.6753 (mtp-110) cc_final: 0.6217 (tpp80) REVERT: H 1 MET cc_start: 0.3579 (mtm) cc_final: 0.3038 (mmt) REVERT: J 122 VAL cc_start: 0.2881 (t) cc_final: 0.2674 (t) REVERT: J 164 GLU cc_start: 0.5299 (tt0) cc_final: 0.5033 (tp30) REVERT: J 186 LEU cc_start: 0.3449 (tt) cc_final: 0.2680 (mp) REVERT: L 81 GLU cc_start: 0.5561 (pp20) cc_final: 0.5282 (pt0) REVERT: L 88 ARG cc_start: 0.5075 (mtp85) cc_final: 0.4326 (ptm160) outliers start: 58 outliers final: 37 residues processed: 385 average time/residue: 0.8177 time to fit residues: 357.7856 Evaluate side-chains 379 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 330 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 417 ARG Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 257 GLU Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 236 ARG Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 406 GLU Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 140 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 267 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 157 optimal weight: 0.0870 chunk 107 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 128 optimal weight: 8.9990 chunk 362 optimal weight: 8.9990 chunk 225 optimal weight: 0.5980 chunk 356 optimal weight: 10.0000 chunk 15 optimal weight: 0.0010 chunk 358 optimal weight: 6.9990 overall best weight: 2.3368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.156266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.122669 restraints weight = 36438.820| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.50 r_work: 0.3237 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 30112 Z= 0.148 Angle : 0.583 8.273 40807 Z= 0.296 Chirality : 0.045 0.208 4576 Planarity : 0.005 0.054 5333 Dihedral : 6.231 99.379 4234 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.85 % Allowed : 16.41 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % 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 (0.14), residues: 3764 helix: 0.96 (0.13), residues: 1606 sheet: -0.74 (0.21), residues: 561 loop : -0.14 (0.16), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 410 TYR 0.017 0.001 TYR D 29 PHE 0.017 0.002 PHE C 559 TRP 0.023 0.002 TRP B 424 HIS 0.003 0.001 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00345 (30110) covalent geometry : angle 0.58304 (40807) hydrogen bonds : bond 0.04277 ( 1293) hydrogen bonds : angle 4.78522 ( 3711) Misc. bond : bond 0.00122 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11959.86 seconds wall clock time: 203 minutes 28.81 seconds (12208.81 seconds total)