Starting phenix.real_space_refine on Fri Mar 6 08:06:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7van_31853/03_2026/7van_31853.cif Found real_map, /net/cci-nas-00/data/ceres_data/7van_31853/03_2026/7van_31853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7van_31853/03_2026/7van_31853.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7van_31853/03_2026/7van_31853.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7van_31853/03_2026/7van_31853.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7van_31853/03_2026/7van_31853.map" } resolution = 3.0 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= 0.009 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 9 5.49 5 Mg 2 5.21 5 S 103 5.16 5 C 18735 2.51 5 N 5131 2.21 5 O 5578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s 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: 29558 Number of models: 1 Model: "" Number of chains: 15 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: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 442} 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.05, per 1000 atoms: 0.24 Number of scatterers: 29558 At special positions: 0 Unit cell: (147.84, 139.92, 177.76, 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 103 16.00 P 9 15.00 Mg 2 11.99 O 5578 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=0, symmetry=0 Time building additional restraints: 2.60 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: 147 helices and 25 sheets defined 48.1% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 90 through 98 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: 3.948A pdb=" N MET A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 297 through 316 removed outlier: 3.959A pdb=" N ALA A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR A 304 " --> pdb=" O GLU A 300 " (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: 3.769A 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: 3.911A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix 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 543 through 551 removed outlier: 4.258A pdb=" N ARG A 547 " --> pdb=" O PRO A 543 " (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 576 removed outlier: 3.881A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 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: 3.569A pdb=" N PHE B 269 " --> pdb=" O VAL B 265 " (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 316 removed outlier: 4.969A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 341 removed outlier: 3.713A 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: 3.969A 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 550 removed outlier: 3.653A pdb=" N ARG B 547 " --> pdb=" O PRO B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 577 removed outlier: 3.608A pdb=" N TYR B 562 " --> pdb=" O GLU B 558 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) 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: 3.974A pdb=" N MET C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 272 No H-bonds generated for 'chain 'C' and resid 270 through 272' Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 297 through 316 removed outlier: 4.181A pdb=" N ALA C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 342 removed outlier: 4.208A pdb=" N TRP C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 350 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: 3.572A pdb=" N ARG C 401 " --> pdb=" O GLN C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 416 removed outlier: 3.576A pdb=" N ARG C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 434 No H-bonds generated for 'chain 'C' and resid 432 through 434' Processing helix chain 'C' and resid 435 through 443 removed outlier: 3.552A pdb=" N GLU C 441 " --> pdb=" O PRO C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 471 removed outlier: 4.119A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 476 Processing helix chain 'C' and resid 477 through 494 Processing helix chain 'C' and resid 508 through 532 Processing helix chain 'C' and resid 535 through 541 removed outlier: 3.709A pdb=" N ILE C 539 " --> pdb=" O SER C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 550 removed outlier: 3.760A pdb=" N ARG C 547 " --> pdb=" O PRO C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 554 Processing helix chain 'C' and resid 558 through 578 removed outlier: 3.554A pdb=" N TYR C 562 " --> pdb=" O GLU C 558 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN C 571 " --> pdb=" O MET C 567 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA C 578 " --> pdb=" O PHE C 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.583A pdb=" N MET D 88 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 85 through 89' 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 174 through 178 Processing helix chain 'D' and resid 197 through 211 removed outlier: 4.098A 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 removed outlier: 3.501A pdb=" N ARG D 231 " --> pdb=" O PRO D 227 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 259 through 274 removed outlier: 3.713A pdb=" N TYR D 263 " --> pdb=" O ASP D 259 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG D 274 " --> pdb=" O ILE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 283 removed outlier: 3.552A pdb=" N GLY D 282 " --> pdb=" O GLY D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 323 through 333 removed outlier: 3.741A pdb=" N ILE D 332 " --> pdb=" O LEU D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 346 Processing helix chain 'D' and resid 361 through 366 removed outlier: 3.820A pdb=" N GLY D 365 " --> pdb=" O LEU D 361 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL D 366 " --> pdb=" O MET D 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 361 through 366' Processing helix chain 'D' and resid 374 through 400 removed outlier: 4.031A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.326A 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 'D' and resid 467 through 472 Processing helix chain 'E' and resid 85 through 89 removed outlier: 3.817A pdb=" N LEU E 89 " --> pdb=" O LYS E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 122 No H-bonds generated for 'chain 'E' and resid 120 through 122' Processing helix chain 'E' and resid 135 through 142 Processing helix chain 'E' and resid 159 through 171 Processing helix chain 'E' and resid 175 through 179 removed outlier: 3.649A pdb=" N GLY E 179 " --> pdb=" O ASP E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 211 removed outlier: 4.045A 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: 3.888A pdb=" N ARG E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) removed outlier: 3.797A 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 275 removed outlier: 3.915A pdb=" N TYR E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 removed outlier: 3.622A pdb=" N ILE E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 320 Processing helix chain 'E' and resid 323 through 331 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: 3.963A pdb=" N ALA E 397 " --> pdb=" O ARG E 393 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE E 399 " --> pdb=" O LEU E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 404 Processing helix chain 'E' and resid 405 through 422 Processing helix chain 'E' and resid 431 through 444 Processing helix chain 'E' and resid 455 through 463 Processing helix chain 'F' and resid 85 through 89 removed outlier: 3.880A pdb=" N LEU F 89 " --> pdb=" O LYS F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 124 Processing helix chain 'F' and resid 135 through 140 Processing helix chain 'F' and resid 159 through 171 Processing helix chain 'F' and resid 174 through 179 removed outlier: 3.541A pdb=" N SER F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 212 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 228 through 232 Processing helix chain 'F' and resid 233 through 250 Processing helix chain 'F' and resid 259 through 274 removed outlier: 3.875A pdb=" N TYR F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 283 removed outlier: 4.339A pdb=" N GLY F 282 " --> pdb=" O GLY F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.680A 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: 3.951A pdb=" N GLY F 365 " --> pdb=" O LEU F 361 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL F 366 " --> pdb=" O MET F 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 361 through 366' Processing helix chain 'F' and resid 374 through 400 removed outlier: 3.529A pdb=" N ALA F 397 " --> pdb=" O ARG F 393 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE F 398 " --> pdb=" O LYS F 394 " (cutoff:3.500A) 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 removed outlier: 3.672A pdb=" N LEU F 451 " --> pdb=" O GLN F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 463 Processing helix chain 'G' and resid 7 through 71 removed outlier: 3.811A pdb=" N GLY G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLN G 68 " --> pdb=" O LEU G 64 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 83 removed outlier: 3.541A pdb=" N VAL G 83 " --> pdb=" O ALA G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 113 removed outlier: 3.672A pdb=" N ALA G 112 " --> pdb=" O PRO G 109 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU G 113 " --> pdb=" O ASP G 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 109 through 113' Processing helix chain 'G' and resid 122 through 209 removed outlier: 3.731A pdb=" N ALA G 126 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG G 128 " --> pdb=" O LEU G 124 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA G 129 " --> pdb=" O GLU G 125 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG G 146 " --> pdb=" O ASN G 142 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ILE G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) Proline residue: G 170 - end of helix Processing helix chain 'H' and resid 6 through 16 Processing helix chain 'H' and resid 25 through 39 removed outlier: 3.823A pdb=" N LEU H 33 " --> pdb=" O ALA H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 64 removed outlier: 5.878A pdb=" N ARG H 61 " --> pdb=" O ARG H 57 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 83 removed outlier: 4.271A pdb=" N PHE H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) removed outlier: 4.269A 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 Processing helix chain 'I' and resid 106 through 119 Processing helix chain 'J' and resid 62 through 93 Processing helix chain 'J' and resid 94 through 97 Processing helix chain 'J' and resid 99 through 115 removed outlier: 3.823A pdb=" N VAL J 103 " --> pdb=" O GLU J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 126 No H-bonds generated for 'chain 'J' and resid 124 through 126' Processing helix chain 'J' and resid 127 through 139 removed outlier: 4.758A pdb=" N ALA J 133 " --> pdb=" O PRO J 129 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU J 134 " --> pdb=" O HIS J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 187 removed outlier: 4.797A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN J 184 " --> pdb=" O SER J 180 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA J 185 " --> pdb=" O LYS J 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 119 removed outlier: 3.847A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ARG K 106 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ASP K 108 " --> pdb=" O MET K 104 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N GLU K 109 " --> pdb=" O ALA K 105 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU K 119 " --> pdb=" O LEU K 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 92 removed outlier: 3.549A pdb=" N GLU L 92 " --> pdb=" O ARG L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 93 through 97 Processing helix chain 'L' and resid 99 through 115 Processing helix chain 'L' and resid 127 through 130 Processing helix chain 'L' and resid 131 through 139 removed outlier: 3.584A pdb=" N ARG L 136 " --> pdb=" O GLU L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 166 through 188 removed outlier: 4.916A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LYS L 181 " --> pdb=" O ALA L 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 10 removed outlier: 6.625A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.178A 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: 6.538A pdb=" N PHE A 48 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU A 42 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR A 46 " --> pdb=" O LEU A 42 " (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: 5.970A pdb=" N ILE B 39 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLN B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 3.629A 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: 5.833A pdb=" N ILE C 39 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLN C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 3.734A 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: 5.615A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU D 49 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 3.872A 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 21 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 21 current: chain 'E' and resid 42 through 51 removed outlier: 5.869A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU E 49 " --> pdb=" O VAL E 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 55 through 59 current: chain 'F' and resid 18 through 21 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 18 through 21 current: chain 'F' and resid 42 through 51 removed outlier: 5.914A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 55 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 82 through 84 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 82 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 143 through 148 removed outlier: 3.871A pdb=" N GLY A 136 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 5.705A 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 removed outlier: 3.527A pdb=" N GLY A 155 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) 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 143 through 148 removed outlier: 3.870A pdb=" N GLY B 136 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 5.812A 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: 6.938A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 72 through 75 Processing sheet with id=AB2, 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=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 144 through 148 removed outlier: 3.875A pdb=" N GLY C 136 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ALA C 118 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY C 164 " --> pdb=" O TRP C 119 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 128 through 129 removed outlier: 3.536A pdb=" N GLY C 155 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.758A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 91 through 93 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 91 through 93 current: chain 'D' and resid 217 through 223 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 217 through 223 current: chain 'D' and resid 307 through 315 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 307 through 315 current: chain 'D' and resid 358 through 359 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 130 through 131 removed outlier: 4.719A pdb=" N LEU D 144 " --> pdb=" O ILE D 131 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 81 through 84 Processing sheet with id=AB9, first strand: chain 'E' and resid 91 through 93 removed outlier: 6.689A pdb=" N ARG E 91 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N LEU E 221 " --> pdb=" O ARG E 91 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N PHE E 93 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N LYS E 223 " --> pdb=" O PHE E 93 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET E 194 " --> pdb=" O THR E 258 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 124 through 125 removed outlier: 4.794A pdb=" N VAL E 300 " --> pdb=" O ARG E 125 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.608A 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 removed outlier: 6.542A pdb=" N PHE F 93 " --> pdb=" O LEU F 221 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N LYS F 223 " --> pdb=" O PHE F 93 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ALA F 188 " --> pdb=" O LEU F 254 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ILE F 256 " --> pdb=" O ALA F 188 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL F 190 " --> pdb=" O ILE F 256 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU F 257 " --> pdb=" O ILE F 311 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 144 through 145 removed outlier: 4.718A pdb=" N LEU F 144 " --> pdb=" O ILE F 131 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 91 through 96 Processing sheet with id=AC7, first strand: chain 'H' and resid 19 through 22 removed outlier: 3.624A pdb=" N ASP H 48 " --> pdb=" O ILE H 4 " (cutoff:3.500A) 1305 hydrogen bonds defined for protein. 3723 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: 6.59 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9958 1.34 - 1.46: 4411 1.46 - 1.57: 15542 1.57 - 1.69: 9 1.69 - 1.81: 194 Bond restraints: 30114 Sorted by residual: bond pdb=" O1 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.565 1.444 0.121 2.00e-02 2.50e+03 3.63e+01 bond pdb=" O2 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.567 1.467 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" O4 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.568 1.482 0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" O3 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.569 1.485 0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" O3B ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sigma weight residual 1.510 1.432 0.078 2.00e-02 2.50e+03 1.54e+01 ... (remaining 30109 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 40639 3.11 - 6.22: 161 6.22 - 9.33: 12 9.33 - 12.44: 0 12.44 - 15.55: 1 Bond angle restraints: 40813 Sorted by residual: angle pdb=" O3A ADP A 601 " pdb=" PB ADP A 601 " pdb=" O3B ADP A 601 " ideal model delta sigma weight residual 108.20 92.65 15.55 3.00e+00 1.11e-01 2.69e+01 angle pdb=" C THR E 371 " pdb=" CA THR E 371 " pdb=" CB THR E 371 " ideal model delta sigma weight residual 117.23 110.24 6.99 1.36e+00 5.41e-01 2.64e+01 angle pdb=" CA THR E 371 " pdb=" C THR E 371 " pdb=" N ARG E 372 " ideal model delta sigma weight residual 119.98 117.47 2.51 8.50e-01 1.38e+00 8.73e+00 angle pdb=" N GLY C 82 " pdb=" CA GLY C 82 " pdb=" C GLY C 82 " ideal model delta sigma weight residual 111.18 115.67 -4.49 1.54e+00 4.22e-01 8.50e+00 angle pdb=" C2' ADP A 601 " pdb=" C1' ADP A 601 " pdb=" N9 ADP A 601 " ideal model delta sigma weight residual 109.47 100.90 8.57 3.00e+00 1.11e-01 8.16e+00 ... (remaining 40808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.16: 17549 25.16 - 50.31: 733 50.31 - 75.47: 75 75.47 - 100.63: 24 100.63 - 125.78: 2 Dihedral angle restraints: 18383 sinusoidal: 7561 harmonic: 10822 Sorted by residual: dihedral pdb=" O1B ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PB ADP A 601 " pdb=" PA ADP A 601 " ideal model delta sinusoidal sigma weight residual 300.00 174.22 125.78 1 2.00e+01 2.50e-03 3.80e+01 dihedral pdb=" C5' ADP A 601 " pdb=" O5' ADP A 601 " pdb=" PA ADP A 601 " pdb=" O2A ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 -167.00 107.00 1 2.00e+01 2.50e-03 3.10e+01 dihedral pdb=" O2A ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PA ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 29.56 -89.56 1 2.00e+01 2.50e-03 2.38e+01 ... (remaining 18380 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 3425 0.048 - 0.095: 882 0.095 - 0.143: 256 0.143 - 0.191: 7 0.191 - 0.238: 2 Chirality restraints: 4572 Sorted by residual: chirality pdb=" CB ILE C 83 " pdb=" CA ILE C 83 " pdb=" CG1 ILE C 83 " pdb=" CG2 ILE C 83 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C1' ADP A 601 " pdb=" C2' ADP A 601 " pdb=" N9 ADP A 601 " pdb=" O4' ADP A 601 " both_signs ideal model delta sigma weight residual False 2.48 2.69 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C2' ADP A 601 " pdb=" C1' ADP A 601 " pdb=" C3' ADP A 601 " pdb=" O2' ADP A 601 " both_signs ideal model delta sigma weight residual False -2.51 -2.33 -0.18 2.00e-01 2.50e+01 8.31e-01 ... (remaining 4569 not shown) Planarity restraints: 5333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ADP A 601 " 0.023 2.00e-02 2.50e+03 1.06e-02 3.08e+00 pdb=" C2 ADP A 601 " -0.006 2.00e-02 2.50e+03 pdb=" C4 ADP A 601 " -0.001 2.00e-02 2.50e+03 pdb=" C5 ADP A 601 " 0.004 2.00e-02 2.50e+03 pdb=" C6 ADP A 601 " 0.012 2.00e-02 2.50e+03 pdb=" C8 ADP A 601 " -0.010 2.00e-02 2.50e+03 pdb=" N1 ADP A 601 " -0.004 2.00e-02 2.50e+03 pdb=" N3 ADP A 601 " -0.002 2.00e-02 2.50e+03 pdb=" N6 ADP A 601 " 0.004 2.00e-02 2.50e+03 pdb=" N7 ADP A 601 " -0.002 2.00e-02 2.50e+03 pdb=" N9 ADP A 601 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS D 323 " -0.029 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO D 324 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO D 324 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 324 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 393 " 0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO C 394 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 394 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 394 " 0.021 5.00e-02 4.00e+02 ... (remaining 5330 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 91 2.51 - 3.11: 21197 3.11 - 3.70: 44143 3.70 - 4.30: 63785 4.30 - 4.90: 110091 Nonbonded interactions: 239307 Sorted by model distance: nonbonded pdb="MG MG A 602 " pdb=" O4 PO4 A 603 " model vdw 1.909 2.170 nonbonded pdb=" OG SER C 235 " pdb="MG MG C 602 " model vdw 1.966 2.170 nonbonded pdb=" O2G ATP C 601 " pdb="MG MG C 602 " model vdw 1.969 2.170 nonbonded pdb=" O1B ATP C 601 " pdb="MG MG C 602 " model vdw 2.062 2.170 nonbonded pdb=" O MET A 220 " pdb=" OG1 THR A 379 " model vdw 2.077 3.040 ... (remaining 239302 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: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.980 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.121 30114 Z= 0.229 Angle : 0.585 15.546 40813 Z= 0.307 Chirality : 0.045 0.238 4572 Planarity : 0.004 0.043 5333 Dihedral : 13.652 125.781 11465 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.14), residues: 3764 helix: 1.95 (0.14), residues: 1544 sheet: 0.19 (0.23), residues: 561 loop : 0.18 (0.16), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 401 TYR 0.010 0.001 TYR B 304 PHE 0.025 0.002 PHE G 40 TRP 0.012 0.001 TRP L 175 HIS 0.004 0.001 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00534 (30114) covalent geometry : angle 0.58549 (40813) hydrogen bonds : bond 0.15324 ( 1305) hydrogen bonds : angle 6.08223 ( 3723) *********************** 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 557 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 557 time to evaluate : 1.120 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5130 (mmt) cc_final: 0.4629 (mtp) REVERT: A 3 GLN cc_start: 0.7368 (mt0) cc_final: 0.6981 (tt0) REVERT: A 32 GLU cc_start: 0.6359 (mm-30) cc_final: 0.6019 (mt-10) REVERT: A 33 GLU cc_start: 0.7060 (tt0) cc_final: 0.6419 (mp0) REVERT: A 109 HIS cc_start: 0.6946 (m-70) cc_final: 0.6673 (m-70) REVERT: A 114 GLU cc_start: 0.6941 (mm-30) cc_final: 0.6492 (mm-30) REVERT: A 122 MET cc_start: 0.6686 (mtp) cc_final: 0.6271 (mtt) REVERT: A 124 LYS cc_start: 0.6344 (mtmm) cc_final: 0.5902 (mttm) REVERT: A 128 GLU cc_start: 0.6170 (tp30) cc_final: 0.5435 (pt0) REVERT: A 137 THR cc_start: 0.8173 (m) cc_final: 0.7862 (p) REVERT: A 154 ARG cc_start: 0.6354 (mtp85) cc_final: 0.6035 (mtt90) REVERT: A 197 ARG cc_start: 0.7098 (ttp-110) cc_final: 0.6640 (ttp80) REVERT: A 209 MET cc_start: 0.6752 (mtp) cc_final: 0.6345 (mtp) REVERT: A 220 MET cc_start: 0.6962 (tpt) cc_final: 0.6579 (tpt) REVERT: A 276 LYS cc_start: 0.4794 (ptmt) cc_final: 0.4208 (ttpt) REVERT: A 277 THR cc_start: 0.7523 (m) cc_final: 0.7220 (p) REVERT: A 332 GLU cc_start: 0.6564 (mt-10) cc_final: 0.6300 (mt-10) REVERT: A 410 ASP cc_start: 0.6068 (t0) cc_final: 0.5644 (t0) REVERT: A 441 GLU cc_start: 0.6485 (mm-30) cc_final: 0.6147 (mm-30) REVERT: A 469 GLN cc_start: 0.6122 (mt0) cc_final: 0.5615 (mm110) REVERT: A 476 LEU cc_start: 0.7559 (mt) cc_final: 0.7294 (mm) REVERT: A 491 ARG cc_start: 0.6049 (mmt180) cc_final: 0.5096 (mtm110) REVERT: A 493 ASP cc_start: 0.6889 (m-30) cc_final: 0.6450 (t70) REVERT: A 496 GLN cc_start: 0.7541 (tt0) cc_final: 0.7055 (tt0) REVERT: A 507 CYS cc_start: 0.7243 (t) cc_final: 0.6967 (p) REVERT: A 508 SER cc_start: 0.7993 (t) cc_final: 0.7406 (p) REVERT: A 524 LYS cc_start: 0.6643 (mtpp) cc_final: 0.6315 (ttpp) REVERT: A 527 GLU cc_start: 0.6276 (tt0) cc_final: 0.5542 (tp30) REVERT: A 546 GLU cc_start: 0.5654 (pp20) cc_final: 0.5407 (mm-30) REVERT: B 1 MET cc_start: 0.5883 (mtp) cc_final: 0.5642 (mtm) REVERT: B 2 ILE cc_start: 0.8134 (mm) cc_final: 0.7707 (mm) REVERT: B 33 GLU cc_start: 0.6806 (mt-10) cc_final: 0.6420 (mt-10) REVERT: B 41 ARG cc_start: 0.7882 (ttp-110) cc_final: 0.7588 (ttp80) REVERT: B 53 GLU cc_start: 0.6557 (mp0) cc_final: 0.6331 (mp0) REVERT: B 79 MET cc_start: 0.8590 (mtm) cc_final: 0.8277 (mtm) REVERT: B 92 GLU cc_start: 0.6837 (mm-30) cc_final: 0.6261 (mm-30) REVERT: B 106 VAL cc_start: 0.6982 (p) cc_final: 0.6610 (m) REVERT: B 114 GLU cc_start: 0.6633 (mm-30) cc_final: 0.6303 (mt-10) REVERT: B 137 THR cc_start: 0.8124 (p) cc_final: 0.7794 (t) REVERT: B 154 ARG cc_start: 0.6385 (mtp-110) cc_final: 0.5988 (mtp85) REVERT: B 156 ARG cc_start: 0.6717 (ttm170) cc_final: 0.6304 (mtp85) REVERT: B 159 GLU cc_start: 0.6200 (tm-30) cc_final: 0.5861 (tm-30) REVERT: B 180 GLU cc_start: 0.6369 (mt-10) cc_final: 0.6069 (pt0) REVERT: B 243 LYS cc_start: 0.5634 (mtmt) cc_final: 0.5231 (tttm) REVERT: B 273 THR cc_start: 0.7210 (p) cc_final: 0.6979 (t) REVERT: B 348 GLU cc_start: 0.7305 (mt-10) cc_final: 0.7075 (mt-10) REVERT: B 408 ARG cc_start: 0.6641 (ttm170) cc_final: 0.6313 (tpp80) REVERT: B 516 MET cc_start: 0.4678 (mtm) cc_final: 0.4340 (mtp) REVERT: B 565 GLU cc_start: 0.5062 (mm-30) cc_final: 0.4712 (tp30) REVERT: C 122 MET cc_start: 0.7502 (mtm) cc_final: 0.7143 (mtp) REVERT: C 124 LYS cc_start: 0.7464 (mtmm) cc_final: 0.6509 (mptt) REVERT: C 128 GLU cc_start: 0.7319 (mm-30) cc_final: 0.7075 (mm-30) REVERT: C 138 VAL cc_start: 0.7291 (t) cc_final: 0.7008 (m) REVERT: C 158 LYS cc_start: 0.7471 (ttpp) cc_final: 0.7183 (ttmm) REVERT: C 169 GLU cc_start: 0.7368 (mm-30) cc_final: 0.6968 (tp30) REVERT: C 170 GLU cc_start: 0.6845 (tp30) cc_final: 0.6367 (mm-30) REVERT: C 182 LYS cc_start: 0.7134 (mtmt) cc_final: 0.6813 (mtmt) REVERT: C 197 ARG cc_start: 0.7169 (ttp-110) cc_final: 0.6605 (ttp-170) REVERT: C 209 MET cc_start: 0.7654 (mtp) cc_final: 0.7107 (mtp) REVERT: C 336 GLU cc_start: 0.5756 (tp30) cc_final: 0.5355 (tp30) REVERT: C 339 SER cc_start: 0.7848 (t) cc_final: 0.7496 (p) REVERT: C 347 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6860 (mt-10) REVERT: C 449 GLU cc_start: 0.6858 (mp0) cc_final: 0.6341 (mp0) REVERT: C 456 GLU cc_start: 0.6449 (mm-30) cc_final: 0.6060 (tm-30) REVERT: C 461 GLU cc_start: 0.6957 (tm-30) cc_final: 0.6480 (tm-30) REVERT: C 480 GLU cc_start: 0.6653 (mp0) cc_final: 0.6180 (mp0) REVERT: C 488 ARG cc_start: 0.7101 (ttp-110) cc_final: 0.6745 (ttp-170) REVERT: C 527 GLU cc_start: 0.5858 (tt0) cc_final: 0.5495 (mm-30) REVERT: C 558 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6288 (tm-30) REVERT: C 565 GLU cc_start: 0.6133 (mm-30) cc_final: 0.5919 (mt-10) REVERT: D 6 LYS cc_start: 0.7155 (tttp) cc_final: 0.6837 (tppt) REVERT: D 34 ASP cc_start: 0.6552 (m-30) cc_final: 0.6324 (t0) REVERT: D 46 GLN cc_start: 0.8522 (tt0) cc_final: 0.8232 (tt0) REVERT: D 210 ARG cc_start: 0.7286 (ptt90) cc_final: 0.6970 (ptt90) REVERT: D 274 ARG cc_start: 0.7119 (mtt180) cc_final: 0.6833 (mtt180) REVERT: D 302 GLU cc_start: 0.7072 (tt0) cc_final: 0.6358 (tp30) REVERT: D 316 MET cc_start: 0.7433 (mtm) cc_final: 0.7143 (mtm) REVERT: D 342 GLU cc_start: 0.6531 (tt0) cc_final: 0.6298 (mp0) REVERT: D 373 GLU cc_start: 0.6728 (pm20) cc_final: 0.6477 (pm20) REVERT: D 380 ASP cc_start: 0.6896 (m-30) cc_final: 0.6638 (m-30) REVERT: D 410 ARG cc_start: 0.6401 (ttm170) cc_final: 0.5803 (ttt90) REVERT: D 413 GLN cc_start: 0.6231 (mt0) cc_final: 0.5904 (mm-40) REVERT: D 416 ASP cc_start: 0.6496 (m-30) cc_final: 0.5804 (t70) REVERT: D 420 ARG cc_start: 0.6960 (mtp180) cc_final: 0.6313 (mmt180) REVERT: D 452 LYS cc_start: 0.5851 (mmtp) cc_final: 0.5491 (mmmt) REVERT: D 456 LYS cc_start: 0.6084 (tppt) cc_final: 0.5633 (mmpt) REVERT: E 6 LYS cc_start: 0.6156 (tttt) cc_final: 0.5722 (ttpt) REVERT: E 25 LYS cc_start: 0.6837 (mtmt) cc_final: 0.6622 (mppt) REVERT: E 41 ARG cc_start: 0.6705 (ttt180) cc_final: 0.6474 (ttt-90) REVERT: E 49 GLU cc_start: 0.7456 (tt0) cc_final: 0.7211 (tt0) REVERT: E 88 MET cc_start: 0.7600 (mtp) cc_final: 0.7207 (mtp) REVERT: E 98 LYS cc_start: 0.6691 (mmmt) cc_final: 0.5443 (ttpp) REVERT: E 129 GLN cc_start: 0.7268 (mm110) cc_final: 0.7028 (mm-40) REVERT: E 194 MET cc_start: 0.8410 (mtm) cc_final: 0.8157 (mtm) REVERT: E 206 GLN cc_start: 0.6205 (pt0) cc_final: 0.5651 (mt0) REVERT: E 228 THR cc_start: 0.8514 (t) cc_final: 0.8175 (m) REVERT: E 260 MET cc_start: 0.6662 (mmm) cc_final: 0.6437 (mmm) REVERT: E 302 GLU cc_start: 0.7415 (tt0) cc_final: 0.7128 (tp30) REVERT: E 410 ARG cc_start: 0.6824 (tpp80) cc_final: 0.6485 (tpp80) REVERT: E 413 GLN cc_start: 0.6923 (mt0) cc_final: 0.6316 (mp-120) REVERT: E 420 ARG cc_start: 0.6917 (mtm110) cc_final: 0.6672 (mtp-110) REVERT: E 427 GLN cc_start: 0.7782 (mm-40) cc_final: 0.7231 (mm110) REVERT: E 428 GLN cc_start: 0.6837 (tt0) cc_final: 0.6562 (mt0) REVERT: F 5 LYS cc_start: 0.5310 (ttpt) cc_final: 0.4785 (tttt) REVERT: F 8 TYR cc_start: 0.7118 (m-80) cc_final: 0.6856 (m-80) REVERT: F 23 ASN cc_start: 0.7416 (m110) cc_final: 0.7116 (t0) REVERT: F 26 ASP cc_start: 0.6473 (m-30) cc_final: 0.6216 (m-30) REVERT: F 52 GLU cc_start: 0.7238 (mt-10) cc_final: 0.7024 (mt-10) REVERT: F 53 GLU cc_start: 0.7057 (mt-10) cc_final: 0.6854 (mt-10) REVERT: F 79 VAL cc_start: 0.6695 (t) cc_final: 0.6454 (p) REVERT: F 98 LYS cc_start: 0.7202 (mmtt) cc_final: 0.6398 (mmmt) REVERT: F 206 GLN cc_start: 0.6486 (mt0) cc_final: 0.5955 (tm-30) REVERT: F 280 ARG cc_start: 0.7190 (mtt180) cc_final: 0.6889 (mmt90) REVERT: F 305 LYS cc_start: 0.7527 (mmtm) cc_final: 0.7220 (mmmt) REVERT: F 316 MET cc_start: 0.8145 (mtm) cc_final: 0.7896 (mtm) REVERT: F 368 LYS cc_start: 0.7173 (ttpt) cc_final: 0.6914 (ttpp) REVERT: F 376 LYS cc_start: 0.6529 (tptm) cc_final: 0.6309 (mttt) REVERT: F 380 ASP cc_start: 0.6184 (m-30) cc_final: 0.5962 (m-30) REVERT: F 394 LYS cc_start: 0.6739 (mmtm) cc_final: 0.6437 (mttp) REVERT: F 398 ILE cc_start: 0.6746 (mt) cc_final: 0.6144 (tp) REVERT: F 452 LYS cc_start: 0.7314 (mmtp) cc_final: 0.6764 (mtpt) REVERT: F 456 LYS cc_start: 0.6181 (mttt) cc_final: 0.5942 (mmtp) REVERT: G 19 ARG cc_start: 0.5454 (mtm-85) cc_final: 0.5026 (ttp-110) REVERT: G 181 GLN cc_start: 0.6787 (mm-40) cc_final: 0.5627 (mt0) REVERT: G 196 ARG cc_start: 0.6235 (mtp-110) cc_final: 0.5829 (mtt180) REVERT: G 202 GLU cc_start: 0.5541 (mm-30) cc_final: 0.4823 (tm-30) REVERT: L 102 GLU cc_start: 0.3850 (tp30) cc_final: 0.3584 (tm-30) REVERT: L 167 LEU cc_start: 0.4400 (mt) cc_final: 0.4168 (tt) outliers start: 0 outliers final: 1 residues processed: 557 average time/residue: 0.9494 time to fit residues: 594.1620 Evaluate side-chains 363 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 362 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 484 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.0970 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 4.9990 overall best weight: 2.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN B 316 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 GLN E 364 ASN E 458 HIS ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN F 437 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.153682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.115166 restraints weight = 36831.019| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.46 r_work: 0.3035 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 30114 Z= 0.150 Angle : 0.564 8.909 40813 Z= 0.292 Chirality : 0.045 0.154 4572 Planarity : 0.005 0.043 5333 Dihedral : 6.691 122.977 4261 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.08 % Allowed : 7.88 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.14), residues: 3764 helix: 1.81 (0.13), residues: 1567 sheet: 0.22 (0.22), residues: 570 loop : 0.09 (0.16), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 335 TYR 0.013 0.001 TYR B 101 PHE 0.018 0.002 PHE A 230 TRP 0.012 0.001 TRP L 175 HIS 0.004 0.001 HIS F 458 Details of bonding type rmsd covalent geometry : bond 0.00346 (30114) covalent geometry : angle 0.56362 (40813) hydrogen bonds : bond 0.04950 ( 1305) hydrogen bonds : angle 4.79666 ( 3723) *********************** 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 473 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 409 time to evaluate : 1.216 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5372 (mmt) cc_final: 0.4886 (mtp) REVERT: A 3 GLN cc_start: 0.8017 (mt0) cc_final: 0.7734 (tt0) REVERT: A 32 GLU cc_start: 0.7125 (mm-30) cc_final: 0.6857 (mt-10) REVERT: A 33 GLU cc_start: 0.7742 (tt0) cc_final: 0.7515 (mp0) REVERT: A 56 SER cc_start: 0.8596 (p) cc_final: 0.8384 (m) REVERT: A 112 ASP cc_start: 0.8230 (t0) cc_final: 0.8028 (t70) REVERT: A 114 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7170 (mm-30) REVERT: A 122 MET cc_start: 0.7318 (mtp) cc_final: 0.6976 (mtt) REVERT: A 124 LYS cc_start: 0.6992 (mtmm) cc_final: 0.6571 (mttm) REVERT: A 128 GLU cc_start: 0.6754 (tp30) cc_final: 0.6200 (pt0) REVERT: A 154 ARG cc_start: 0.6887 (mtp85) cc_final: 0.6568 (mtt90) REVERT: A 276 LYS cc_start: 0.5395 (ptmt) cc_final: 0.4679 (pptt) REVERT: A 277 THR cc_start: 0.8017 (m) cc_final: 0.7711 (p) REVERT: A 410 ASP cc_start: 0.6618 (t0) cc_final: 0.6389 (t0) REVERT: A 441 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7326 (mm-30) REVERT: A 469 GLN cc_start: 0.6540 (mt0) cc_final: 0.6164 (mm110) REVERT: A 491 ARG cc_start: 0.7441 (mmt180) cc_final: 0.6745 (mtm110) REVERT: A 493 ASP cc_start: 0.7838 (m-30) cc_final: 0.7575 (t70) REVERT: A 496 GLN cc_start: 0.8101 (tt0) cc_final: 0.7877 (tt0) REVERT: A 516 MET cc_start: 0.8259 (mtm) cc_final: 0.7874 (mtp) REVERT: A 527 GLU cc_start: 0.6858 (tt0) cc_final: 0.6333 (tp30) REVERT: A 546 GLU cc_start: 0.6588 (pp20) cc_final: 0.6381 (mm-30) REVERT: B 2 ILE cc_start: 0.8679 (mm) cc_final: 0.8364 (mm) REVERT: B 106 VAL cc_start: 0.7485 (p) cc_final: 0.7103 (m) REVERT: B 159 GLU cc_start: 0.6877 (tm-30) cc_final: 0.6596 (tm-30) REVERT: B 408 ARG cc_start: 0.7781 (ttm170) cc_final: 0.7579 (tpp80) REVERT: B 516 MET cc_start: 0.5511 (mtm) cc_final: 0.5199 (mtp) REVERT: B 565 GLU cc_start: 0.5665 (mm-30) cc_final: 0.5168 (tp30) REVERT: C 122 MET cc_start: 0.8272 (mtm) cc_final: 0.8021 (mtp) REVERT: C 124 LYS cc_start: 0.7937 (mtmm) cc_final: 0.7185 (mptt) REVERT: C 156 ARG cc_start: 0.7841 (ttm110) cc_final: 0.7500 (ttp-110) REVERT: C 169 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7573 (tp30) REVERT: C 197 ARG cc_start: 0.7859 (ttp-110) cc_final: 0.7596 (ttp-170) REVERT: C 209 MET cc_start: 0.8536 (mtp) cc_final: 0.8132 (mtp) REVERT: C 336 GLU cc_start: 0.7581 (tp30) cc_final: 0.7301 (tp30) REVERT: C 347 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7380 (mt-10) REVERT: C 449 GLU cc_start: 0.8018 (mp0) cc_final: 0.7588 (mp0) REVERT: C 461 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7321 (tm-30) REVERT: C 480 GLU cc_start: 0.7741 (mp0) cc_final: 0.7182 (mp0) REVERT: C 488 ARG cc_start: 0.8229 (ttp-110) cc_final: 0.7973 (ttp-170) REVERT: C 547 ARG cc_start: 0.7901 (ttm110) cc_final: 0.7556 (ttm110) REVERT: C 558 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7199 (tm-30) REVERT: D 162 GLU cc_start: 0.8060 (mp0) cc_final: 0.7708 (tt0) REVERT: D 210 ARG cc_start: 0.8076 (ptt90) cc_final: 0.7874 (ptt90) REVERT: D 274 ARG cc_start: 0.8133 (mtt180) cc_final: 0.7821 (mtt180) REVERT: D 302 GLU cc_start: 0.7871 (tt0) cc_final: 0.7571 (tp30) REVERT: D 327 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7520 (m-30) REVERT: D 404 LEU cc_start: 0.6414 (mt) cc_final: 0.5743 (mp) REVERT: D 410 ARG cc_start: 0.6837 (ttm170) cc_final: 0.6501 (ttt90) REVERT: D 413 GLN cc_start: 0.7175 (mt0) cc_final: 0.6855 (mm-40) REVERT: D 420 ARG cc_start: 0.8040 (mtp180) cc_final: 0.7761 (mmt180) REVERT: D 456 LYS cc_start: 0.6609 (tppt) cc_final: 0.6188 (mmpt) REVERT: E 6 LYS cc_start: 0.6921 (tttt) cc_final: 0.6576 (ttpt) REVERT: E 62 GLU cc_start: 0.7414 (pm20) cc_final: 0.7192 (pm20) REVERT: E 98 LYS cc_start: 0.7908 (mmmt) cc_final: 0.6807 (ttpp) REVERT: E 206 GLN cc_start: 0.7322 (pt0) cc_final: 0.6998 (mt0) REVERT: E 228 THR cc_start: 0.8501 (t) cc_final: 0.8268 (m) REVERT: E 410 ARG cc_start: 0.7531 (tpp80) cc_final: 0.7013 (tpp80) REVERT: E 413 GLN cc_start: 0.7692 (mt0) cc_final: 0.7333 (mp-120) REVERT: E 427 GLN cc_start: 0.8167 (mm-40) cc_final: 0.7762 (mm110) REVERT: E 453 ARG cc_start: 0.7623 (mmt180) cc_final: 0.7120 (mmm160) REVERT: F 5 LYS cc_start: 0.6485 (ttpt) cc_final: 0.5972 (tttt) REVERT: F 26 ASP cc_start: 0.6439 (m-30) cc_final: 0.6231 (m-30) REVERT: F 103 LEU cc_start: 0.7827 (mt) cc_final: 0.7618 (mp) REVERT: F 398 ILE cc_start: 0.7316 (mt) cc_final: 0.6780 (tp) REVERT: G 19 ARG cc_start: 0.6230 (mtm-85) cc_final: 0.5923 (ttp-110) REVERT: G 74 GLU cc_start: 0.2622 (mp0) cc_final: 0.1944 (pt0) REVERT: G 177 ARG cc_start: 0.6515 (ttp80) cc_final: 0.6298 (mtp180) REVERT: L 80 LEU cc_start: 0.3339 (OUTLIER) cc_final: 0.2799 (tm) REVERT: L 85 ARG cc_start: 0.2310 (ttp80) cc_final: 0.1518 (ttp80) REVERT: L 162 GLN cc_start: 0.6476 (pt0) cc_final: 0.6108 (pt0) outliers start: 64 outliers final: 19 residues processed: 443 average time/residue: 0.9345 time to fit residues: 466.9903 Evaluate side-chains 343 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 322 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 165 GLU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain L residue 80 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 49 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 270 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 307 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 95 optimal weight: 20.0000 chunk 169 optimal weight: 10.0000 chunk 251 optimal weight: 10.0000 chunk 170 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 316 GLN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 GLN E 58 GLN E 364 ASN F 388 ASN H 84 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.154098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.116509 restraints weight = 36791.953| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.45 r_work: 0.3040 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 30114 Z= 0.126 Angle : 0.516 9.259 40813 Z= 0.265 Chirality : 0.043 0.151 4572 Planarity : 0.005 0.041 5333 Dihedral : 6.449 119.048 4259 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.37 % Allowed : 11.00 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.14), residues: 3764 helix: 1.93 (0.13), residues: 1571 sheet: 0.32 (0.23), residues: 567 loop : 0.05 (0.16), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 197 TYR 0.012 0.001 TYR C 562 PHE 0.013 0.001 PHE C 574 TRP 0.011 0.001 TRP C 119 HIS 0.004 0.001 HIS E 252 Details of bonding type rmsd covalent geometry : bond 0.00287 (30114) covalent geometry : angle 0.51614 (40813) hydrogen bonds : bond 0.04473 ( 1305) hydrogen bonds : angle 4.56786 ( 3723) *********************** 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 417 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 344 time to evaluate : 1.114 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5418 (mmt) cc_final: 0.4988 (mtp) REVERT: A 3 GLN cc_start: 0.8061 (mt0) cc_final: 0.7737 (tt0) REVERT: A 32 GLU cc_start: 0.7235 (mm-30) cc_final: 0.6835 (mt-10) REVERT: A 114 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7179 (mm-30) REVERT: A 122 MET cc_start: 0.7274 (mtp) cc_final: 0.6923 (mtt) REVERT: A 124 LYS cc_start: 0.6857 (mtmm) cc_final: 0.6558 (mttm) REVERT: A 128 GLU cc_start: 0.6805 (tp30) cc_final: 0.6288 (pt0) REVERT: A 239 GLN cc_start: 0.8403 (mt0) cc_final: 0.8159 (mt0) REVERT: A 276 LYS cc_start: 0.5271 (ptmt) cc_final: 0.4580 (pptt) REVERT: A 277 THR cc_start: 0.7963 (m) cc_final: 0.7687 (p) REVERT: A 410 ASP cc_start: 0.6512 (t0) cc_final: 0.6278 (t0) REVERT: A 441 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7299 (mm-30) REVERT: A 469 GLN cc_start: 0.6554 (mt0) cc_final: 0.6122 (mm-40) REVERT: A 491 ARG cc_start: 0.7444 (mmt180) cc_final: 0.6790 (mtm110) REVERT: A 493 ASP cc_start: 0.7823 (m-30) cc_final: 0.7508 (t70) REVERT: A 496 GLN cc_start: 0.8103 (tt0) cc_final: 0.7883 (tt0) REVERT: A 527 GLU cc_start: 0.6885 (tt0) cc_final: 0.6400 (tp30) REVERT: B 2 ILE cc_start: 0.8683 (mm) cc_final: 0.8382 (mm) REVERT: B 104 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.6915 (ptp-170) REVERT: B 106 VAL cc_start: 0.7423 (p) cc_final: 0.6998 (m) REVERT: B 159 GLU cc_start: 0.6779 (tm-30) cc_final: 0.6549 (tm-30) REVERT: B 516 MET cc_start: 0.5486 (mtm) cc_final: 0.5182 (mtp) REVERT: B 565 GLU cc_start: 0.5829 (mm-30) cc_final: 0.5299 (tp30) REVERT: C 29 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8294 (mtpp) REVERT: C 122 MET cc_start: 0.8359 (mtm) cc_final: 0.7963 (mtp) REVERT: C 156 ARG cc_start: 0.7804 (ttm110) cc_final: 0.7535 (ttp-110) REVERT: C 159 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7695 (pt0) REVERT: C 197 ARG cc_start: 0.7887 (ttp-110) cc_final: 0.7560 (ttp-170) REVERT: C 209 MET cc_start: 0.8477 (mtp) cc_final: 0.8074 (mtp) REVERT: C 347 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7435 (mt-10) REVERT: C 461 GLU cc_start: 0.7543 (tm-30) cc_final: 0.7249 (tm-30) REVERT: C 480 GLU cc_start: 0.7725 (mp0) cc_final: 0.7175 (mp0) REVERT: C 488 ARG cc_start: 0.8201 (ttp-110) cc_final: 0.7964 (ttp-170) REVERT: C 547 ARG cc_start: 0.7946 (ttm110) cc_final: 0.7513 (ttm110) REVERT: C 558 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7216 (tm-30) REVERT: D 53 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.7175 (mm-30) REVERT: D 162 GLU cc_start: 0.8039 (mp0) cc_final: 0.7776 (mm-30) REVERT: D 302 GLU cc_start: 0.7878 (tt0) cc_final: 0.7541 (tp30) REVERT: D 404 LEU cc_start: 0.6309 (mt) cc_final: 0.5658 (mp) REVERT: D 410 ARG cc_start: 0.6866 (ttm170) cc_final: 0.6480 (ttt90) REVERT: D 413 GLN cc_start: 0.7142 (mt0) cc_final: 0.6819 (mm-40) REVERT: D 420 ARG cc_start: 0.8017 (mtp180) cc_final: 0.7762 (mmt180) REVERT: D 456 LYS cc_start: 0.6592 (tppt) cc_final: 0.6133 (mmpt) REVERT: E 62 GLU cc_start: 0.7430 (pm20) cc_final: 0.7152 (pm20) REVERT: E 98 LYS cc_start: 0.7847 (mmmt) cc_final: 0.6810 (ttpp) REVERT: E 206 GLN cc_start: 0.7301 (pt0) cc_final: 0.6975 (mt0) REVERT: E 287 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8416 (ttp) REVERT: E 410 ARG cc_start: 0.7560 (tpp80) cc_final: 0.7173 (tpp80) REVERT: E 413 GLN cc_start: 0.7697 (mt0) cc_final: 0.7349 (mp-120) REVERT: E 453 ARG cc_start: 0.7621 (mmt180) cc_final: 0.7152 (mmm160) REVERT: F 5 LYS cc_start: 0.6477 (ttpt) cc_final: 0.5982 (tttt) REVERT: F 52 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7405 (mt-10) REVERT: F 103 LEU cc_start: 0.7755 (mt) cc_final: 0.7523 (mp) REVERT: F 398 ILE cc_start: 0.7275 (mt) cc_final: 0.6805 (tp) REVERT: F 413 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7871 (mp10) REVERT: G 19 ARG cc_start: 0.6275 (mtm-85) cc_final: 0.5966 (ttp-110) REVERT: J 89 GLU cc_start: 0.3929 (tm-30) cc_final: 0.3284 (pp20) REVERT: J 92 GLU cc_start: 0.3405 (pt0) cc_final: 0.3202 (pt0) REVERT: J 173 ARG cc_start: 0.4952 (mtp-110) cc_final: 0.4110 (mtp85) REVERT: K 104 MET cc_start: 0.3539 (tmm) cc_final: 0.3298 (tmt) REVERT: L 85 ARG cc_start: 0.2284 (ttp80) cc_final: 0.1509 (ttp80) REVERT: L 162 GLN cc_start: 0.6673 (pt0) cc_final: 0.6242 (pt0) outliers start: 73 outliers final: 26 residues processed: 393 average time/residue: 0.9412 time to fit residues: 416.3208 Evaluate side-chains 344 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 311 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain B residue 104 ARG Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 413 GLN Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 165 GLU Chi-restraints excluded: chain G residue 168 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 260 optimal weight: 10.0000 chunk 206 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 293 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 311 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 118 optimal weight: 8.9990 chunk 342 optimal weight: 5.9990 chunk 239 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 316 GLN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 HIS D 338 GLN E 364 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.152300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.114336 restraints weight = 36411.541| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.48 r_work: 0.3007 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 30114 Z= 0.204 Angle : 0.629 8.421 40813 Z= 0.325 Chirality : 0.047 0.203 4572 Planarity : 0.006 0.044 5333 Dihedral : 6.701 117.109 4259 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.54 % Allowed : 12.49 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.14), residues: 3764 helix: 1.47 (0.13), residues: 1568 sheet: 0.22 (0.23), residues: 541 loop : -0.26 (0.15), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 124 TYR 0.015 0.002 TYR B 304 PHE 0.023 0.002 PHE A 230 TRP 0.017 0.002 TRP L 175 HIS 0.007 0.002 HIS E 252 Details of bonding type rmsd covalent geometry : bond 0.00491 (30114) covalent geometry : angle 0.62909 (40813) hydrogen bonds : bond 0.05504 ( 1305) hydrogen bonds : angle 4.81480 ( 3723) *********************** 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 435 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 326 time to evaluate : 1.142 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5341 (mmt) cc_final: 0.5003 (mtp) REVERT: A 3 GLN cc_start: 0.7919 (mt0) cc_final: 0.7643 (tt0) REVERT: A 32 GLU cc_start: 0.7250 (mm-30) cc_final: 0.6992 (mt-10) REVERT: A 114 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7214 (mm-30) REVERT: A 122 MET cc_start: 0.7432 (mtp) cc_final: 0.7121 (mtt) REVERT: A 124 LYS cc_start: 0.7043 (mtmm) cc_final: 0.6672 (mttp) REVERT: A 128 GLU cc_start: 0.6707 (tp30) cc_final: 0.6336 (pt0) REVERT: A 239 GLN cc_start: 0.8466 (mt0) cc_final: 0.8247 (mt0) REVERT: A 276 LYS cc_start: 0.5346 (ptmt) cc_final: 0.4649 (pptt) REVERT: A 277 THR cc_start: 0.8016 (m) cc_final: 0.7768 (p) REVERT: A 410 ASP cc_start: 0.6578 (t0) cc_final: 0.6336 (t0) REVERT: A 441 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7253 (mm-30) REVERT: A 469 GLN cc_start: 0.6590 (mt0) cc_final: 0.6178 (mm110) REVERT: A 471 VAL cc_start: 0.6889 (m) cc_final: 0.6656 (t) REVERT: A 491 ARG cc_start: 0.7547 (mmt180) cc_final: 0.6870 (mtm110) REVERT: A 496 GLN cc_start: 0.8086 (tt0) cc_final: 0.7869 (tt0) REVERT: A 527 GLU cc_start: 0.6917 (tt0) cc_final: 0.6463 (tp30) REVERT: B 2 ILE cc_start: 0.8679 (mm) cc_final: 0.8442 (mm) REVERT: B 104 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.6532 (ptp-170) REVERT: B 197 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.7063 (ptp90) REVERT: B 565 GLU cc_start: 0.5852 (mm-30) cc_final: 0.5323 (tp30) REVERT: C 122 MET cc_start: 0.8406 (mtm) cc_final: 0.8137 (mpp) REVERT: C 156 ARG cc_start: 0.7818 (ttm110) cc_final: 0.7617 (ttp-110) REVERT: C 159 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7820 (pt0) REVERT: C 182 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7644 (mtmt) REVERT: C 197 ARG cc_start: 0.7933 (ttp-110) cc_final: 0.7657 (ttp-170) REVERT: C 209 MET cc_start: 0.8558 (mtp) cc_final: 0.8166 (mtp) REVERT: C 347 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7464 (mt-10) REVERT: C 450 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8055 (tp) REVERT: C 461 GLU cc_start: 0.7512 (tm-30) cc_final: 0.7239 (tm-30) REVERT: C 480 GLU cc_start: 0.7760 (mp0) cc_final: 0.7242 (mp0) REVERT: C 488 ARG cc_start: 0.8290 (ttp-110) cc_final: 0.8017 (ttp-170) REVERT: C 547 ARG cc_start: 0.8035 (ttm110) cc_final: 0.7636 (ttm110) REVERT: C 558 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7125 (tm-30) REVERT: D 49 GLU cc_start: 0.8688 (tt0) cc_final: 0.8402 (tt0) REVERT: D 53 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7268 (mm-30) REVERT: D 87 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7711 (mp0) REVERT: D 162 GLU cc_start: 0.8072 (mp0) cc_final: 0.7639 (tt0) REVERT: D 302 GLU cc_start: 0.7917 (tt0) cc_final: 0.7579 (tp30) REVERT: D 327 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7730 (m-30) REVERT: D 373 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.6765 (pm20) REVERT: D 410 ARG cc_start: 0.6891 (ttm170) cc_final: 0.6555 (ttt90) REVERT: D 413 GLN cc_start: 0.7176 (mt0) cc_final: 0.6873 (mm-40) REVERT: D 445 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7913 (mtt) REVERT: D 465 GLN cc_start: 0.5909 (mm-40) cc_final: 0.5527 (pt0) REVERT: E 25 LYS cc_start: 0.7676 (OUTLIER) cc_final: 0.7292 (mmtm) REVERT: E 62 GLU cc_start: 0.7506 (pm20) cc_final: 0.7176 (pm20) REVERT: E 98 LYS cc_start: 0.7896 (mmmt) cc_final: 0.6901 (ttpt) REVERT: E 128 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7029 (pp20) REVERT: E 206 GLN cc_start: 0.7306 (pt0) cc_final: 0.6953 (mt0) REVERT: E 237 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8113 (mtp) REVERT: E 287 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8341 (ttp) REVERT: E 334 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8056 (mt-10) REVERT: E 373 GLU cc_start: 0.7670 (pm20) cc_final: 0.7400 (pt0) REVERT: E 405 THR cc_start: 0.5481 (OUTLIER) cc_final: 0.4766 (t) REVERT: E 410 ARG cc_start: 0.7607 (tpp80) cc_final: 0.7245 (tpp80) REVERT: E 413 GLN cc_start: 0.7756 (mt0) cc_final: 0.7411 (mp10) REVERT: E 453 ARG cc_start: 0.7652 (mmt180) cc_final: 0.7180 (mmm160) REVERT: F 5 LYS cc_start: 0.6543 (ttpt) cc_final: 0.6051 (tttt) REVERT: F 52 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7395 (mt-10) REVERT: F 206 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7893 (mp10) REVERT: F 368 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.7679 (ttpp) REVERT: F 398 ILE cc_start: 0.7163 (mt) cc_final: 0.6749 (tp) REVERT: F 409 ARG cc_start: 0.7629 (ttm-80) cc_final: 0.7418 (ttm170) REVERT: I 115 LEU cc_start: 0.2370 (OUTLIER) cc_final: 0.2087 (mt) REVERT: J 89 GLU cc_start: 0.4059 (OUTLIER) cc_final: 0.3374 (pp20) REVERT: K 104 MET cc_start: 0.3344 (tmm) cc_final: 0.3080 (tmt) REVERT: L 85 ARG cc_start: 0.2500 (ttp80) cc_final: 0.1777 (ttp-170) REVERT: L 86 ARG cc_start: 0.2388 (ttt180) cc_final: 0.1895 (tpt170) REVERT: L 162 GLN cc_start: 0.6809 (pt0) cc_final: 0.6324 (pt0) outliers start: 109 outliers final: 40 residues processed: 407 average time/residue: 0.9074 time to fit residues: 416.7976 Evaluate side-chains 362 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 301 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain B residue 104 ARG Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain D residue 445 MET Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain E residue 25 LYS Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 206 GLN Chi-restraints excluded: chain F residue 368 LYS Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 165 GLU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 84 HIS Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain J residue 89 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 44 optimal weight: 5.9990 chunk 189 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 chunk 178 optimal weight: 10.0000 chunk 211 optimal weight: 10.0000 chunk 348 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 273 optimal weight: 0.6980 chunk 54 optimal weight: 9.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN B 316 GLN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 GLN E 364 ASN G 181 GLN J 96 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.153034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.115105 restraints weight = 36570.371| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.48 r_work: 0.3014 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 30114 Z= 0.161 Angle : 0.564 9.809 40813 Z= 0.292 Chirality : 0.045 0.177 4572 Planarity : 0.005 0.045 5333 Dihedral : 6.470 118.289 4259 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.67 % Allowed : 13.46 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.14), residues: 3764 helix: 1.53 (0.13), residues: 1585 sheet: 0.30 (0.23), residues: 531 loop : -0.31 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 297 TYR 0.013 0.001 TYR C 562 PHE 0.016 0.002 PHE C 574 TRP 0.015 0.001 TRP L 175 HIS 0.004 0.001 HIS J 130 Details of bonding type rmsd covalent geometry : bond 0.00382 (30114) covalent geometry : angle 0.56439 (40813) hydrogen bonds : bond 0.04856 ( 1305) hydrogen bonds : angle 4.66880 ( 3723) *********************** 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 420 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 307 time to evaluate : 1.139 Fit side-chains revert: symmetry clash REVERT: A 3 GLN cc_start: 0.7910 (mt0) cc_final: 0.7671 (tt0) REVERT: A 32 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6997 (mt-10) REVERT: A 114 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7199 (mm-30) REVERT: A 122 MET cc_start: 0.7459 (mtp) cc_final: 0.7146 (mtt) REVERT: A 124 LYS cc_start: 0.6995 (mtmm) cc_final: 0.6597 (mttp) REVERT: A 128 GLU cc_start: 0.6708 (tp30) cc_final: 0.6324 (pt0) REVERT: A 276 LYS cc_start: 0.5335 (ptmt) cc_final: 0.4682 (pptt) REVERT: A 277 THR cc_start: 0.8041 (m) cc_final: 0.7808 (p) REVERT: A 410 ASP cc_start: 0.6616 (t0) cc_final: 0.6400 (t0) REVERT: A 441 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7164 (mm-30) REVERT: A 465 GLN cc_start: 0.6749 (mm-40) cc_final: 0.6548 (tp40) REVERT: A 469 GLN cc_start: 0.6569 (mt0) cc_final: 0.6176 (mm110) REVERT: A 491 ARG cc_start: 0.7488 (mmt180) cc_final: 0.6832 (mtm110) REVERT: A 496 GLN cc_start: 0.8065 (tt0) cc_final: 0.7832 (tt0) REVERT: A 527 GLU cc_start: 0.6886 (tt0) cc_final: 0.6447 (tp30) REVERT: B 1 MET cc_start: 0.6518 (mtm) cc_final: 0.6194 (mtp) REVERT: B 2 ILE cc_start: 0.8687 (mm) cc_final: 0.8462 (mm) REVERT: B 104 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.6451 (ptp-170) REVERT: B 197 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.7055 (ptp90) REVERT: B 220 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7746 (tpp) REVERT: B 425 ASN cc_start: 0.5930 (m110) cc_final: 0.5663 (t0) REVERT: B 565 GLU cc_start: 0.5876 (mm-30) cc_final: 0.5308 (tp30) REVERT: C 122 MET cc_start: 0.8391 (mtm) cc_final: 0.8142 (mpp) REVERT: C 156 ARG cc_start: 0.7858 (ttm110) cc_final: 0.7482 (ttm110) REVERT: C 159 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7848 (pt0) REVERT: C 182 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7550 (mtmt) REVERT: C 197 ARG cc_start: 0.7951 (ttp-110) cc_final: 0.7715 (ttp-170) REVERT: C 209 MET cc_start: 0.8497 (mtp) cc_final: 0.8209 (mtp) REVERT: C 347 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7492 (mt-10) REVERT: C 461 GLU cc_start: 0.7451 (tm-30) cc_final: 0.7185 (tm-30) REVERT: C 480 GLU cc_start: 0.7756 (mp0) cc_final: 0.7230 (mp0) REVERT: C 488 ARG cc_start: 0.8209 (ttp-110) cc_final: 0.7904 (ttp-170) REVERT: C 492 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7549 (mp0) REVERT: C 547 ARG cc_start: 0.8027 (ttm110) cc_final: 0.7574 (ttm110) REVERT: C 558 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7152 (tm-30) REVERT: D 49 GLU cc_start: 0.8695 (tt0) cc_final: 0.8450 (tt0) REVERT: D 87 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: D 162 GLU cc_start: 0.8044 (mp0) cc_final: 0.7779 (mm-30) REVERT: D 237 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8375 (mtt) REVERT: D 302 GLU cc_start: 0.7928 (tt0) cc_final: 0.7607 (tp30) REVERT: D 398 ILE cc_start: 0.6734 (OUTLIER) cc_final: 0.6467 (tp) REVERT: D 410 ARG cc_start: 0.6897 (ttm170) cc_final: 0.6546 (ttt90) REVERT: D 413 GLN cc_start: 0.7184 (mt0) cc_final: 0.6879 (mm-40) REVERT: D 445 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7924 (mtt) REVERT: D 465 GLN cc_start: 0.5923 (mm-40) cc_final: 0.5405 (pt0) REVERT: E 62 GLU cc_start: 0.7508 (pm20) cc_final: 0.7207 (pm20) REVERT: E 98 LYS cc_start: 0.7878 (mmmt) cc_final: 0.6861 (ttpt) REVERT: E 128 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7035 (pp20) REVERT: E 206 GLN cc_start: 0.7295 (pt0) cc_final: 0.6920 (mt0) REVERT: E 237 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8087 (mtp) REVERT: E 287 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8417 (ttp) REVERT: E 334 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8008 (mt-10) REVERT: E 410 ARG cc_start: 0.7621 (tpp80) cc_final: 0.7224 (tpp80) REVERT: E 453 ARG cc_start: 0.7559 (mmt180) cc_final: 0.7093 (mmm160) REVERT: F 5 LYS cc_start: 0.6586 (ttpt) cc_final: 0.6082 (tttt) REVERT: F 103 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7756 (mm) REVERT: F 130 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.8198 (t80) REVERT: F 368 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.7816 (ttpp) REVERT: F 398 ILE cc_start: 0.7124 (mt) cc_final: 0.6728 (tp) REVERT: G 89 VAL cc_start: 0.0709 (OUTLIER) cc_final: 0.0435 (t) REVERT: I 115 LEU cc_start: 0.2187 (OUTLIER) cc_final: 0.1955 (mt) REVERT: J 89 GLU cc_start: 0.4028 (tm-30) cc_final: 0.3340 (pp20) REVERT: L 80 LEU cc_start: 0.3530 (OUTLIER) cc_final: 0.3191 (tm) REVERT: L 85 ARG cc_start: 0.2594 (ttp80) cc_final: 0.1785 (ttp80) REVERT: L 162 GLN cc_start: 0.6766 (pt0) cc_final: 0.6376 (pt0) outliers start: 113 outliers final: 45 residues processed: 389 average time/residue: 0.8806 time to fit residues: 386.7618 Evaluate side-chains 358 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 293 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 104 ARG Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 570 ILE Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain D residue 445 MET Chi-restraints excluded: chain E residue 25 LYS Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 368 LYS Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 165 GLU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 84 HIS Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain L residue 80 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 158 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 253 optimal weight: 0.5980 chunk 41 optimal weight: 9.9990 chunk 296 optimal weight: 2.9990 chunk 242 optimal weight: 7.9990 chunk 240 optimal weight: 6.9990 chunk 257 optimal weight: 6.9990 chunk 361 optimal weight: 8.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN B 316 GLN B 465 GLN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 GLN E 364 ASN F 413 GLN G 180 GLN G 181 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.153131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.115261 restraints weight = 36531.132| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.49 r_work: 0.3018 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 30114 Z= 0.169 Angle : 0.578 8.295 40813 Z= 0.298 Chirality : 0.045 0.197 4572 Planarity : 0.005 0.045 5333 Dihedral : 6.455 115.331 4259 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.89 % Allowed : 14.27 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.14), residues: 3764 helix: 1.49 (0.13), residues: 1575 sheet: 0.21 (0.23), residues: 541 loop : -0.38 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 88 TYR 0.012 0.002 TYR C 562 PHE 0.017 0.002 PHE A 230 TRP 0.016 0.001 TRP L 175 HIS 0.004 0.001 HIS J 130 Details of bonding type rmsd covalent geometry : bond 0.00402 (30114) covalent geometry : angle 0.57764 (40813) hydrogen bonds : bond 0.05013 ( 1305) hydrogen bonds : angle 4.69300 ( 3723) *********************** 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 420 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 300 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: A 3 GLN cc_start: 0.7915 (mt0) cc_final: 0.7683 (tt0) REVERT: A 32 GLU cc_start: 0.7243 (mm-30) cc_final: 0.7014 (mt-10) REVERT: A 114 GLU cc_start: 0.7441 (mm-30) cc_final: 0.7193 (mm-30) REVERT: A 122 MET cc_start: 0.7461 (mtp) cc_final: 0.7136 (mtt) REVERT: A 124 LYS cc_start: 0.7004 (mtmm) cc_final: 0.6605 (mttp) REVERT: A 128 GLU cc_start: 0.6646 (tp30) cc_final: 0.6311 (pt0) REVERT: A 276 LYS cc_start: 0.5428 (ptmt) cc_final: 0.4823 (pptt) REVERT: A 277 THR cc_start: 0.8066 (m) cc_final: 0.7778 (p) REVERT: A 410 ASP cc_start: 0.6649 (t0) cc_final: 0.6430 (t0) REVERT: A 441 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7128 (mm-30) REVERT: A 465 GLN cc_start: 0.6816 (mm-40) cc_final: 0.6578 (tp40) REVERT: A 469 GLN cc_start: 0.6564 (mt0) cc_final: 0.6194 (mm-40) REVERT: A 491 ARG cc_start: 0.7446 (mmt180) cc_final: 0.6818 (mtm110) REVERT: A 496 GLN cc_start: 0.8079 (tt0) cc_final: 0.7845 (tt0) REVERT: A 527 GLU cc_start: 0.6842 (tt0) cc_final: 0.6389 (tp30) REVERT: B 2 ILE cc_start: 0.8777 (mm) cc_final: 0.8554 (mm) REVERT: B 53 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7407 (mt-10) REVERT: B 104 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.6370 (ptp-170) REVERT: B 154 ARG cc_start: 0.6595 (OUTLIER) cc_final: 0.6161 (mtp85) REVERT: B 197 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.7028 (ptp90) REVERT: B 220 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7661 (tpp) REVERT: B 565 GLU cc_start: 0.5890 (mm-30) cc_final: 0.5325 (tp30) REVERT: C 83 ILE cc_start: 0.9077 (OUTLIER) cc_final: 0.8666 (tp) REVERT: C 156 ARG cc_start: 0.7857 (ttm110) cc_final: 0.7463 (ttm110) REVERT: C 182 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7555 (mtmt) REVERT: C 197 ARG cc_start: 0.7931 (ttp-110) cc_final: 0.7692 (ttp-170) REVERT: C 209 MET cc_start: 0.8501 (mtp) cc_final: 0.8244 (mtp) REVERT: C 347 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7532 (mt-10) REVERT: C 461 GLU cc_start: 0.7409 (tm-30) cc_final: 0.7137 (tm-30) REVERT: C 480 GLU cc_start: 0.7773 (mp0) cc_final: 0.7245 (mp0) REVERT: C 547 ARG cc_start: 0.8018 (ttm110) cc_final: 0.7558 (ttm110) REVERT: C 558 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7111 (tm-30) REVERT: D 49 GLU cc_start: 0.8698 (tt0) cc_final: 0.8434 (tt0) REVERT: D 87 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7542 (mp0) REVERT: D 162 GLU cc_start: 0.8060 (mp0) cc_final: 0.7796 (mm-30) REVERT: D 237 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8367 (mtt) REVERT: D 302 GLU cc_start: 0.7938 (tt0) cc_final: 0.7662 (tp30) REVERT: D 314 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8554 (pt) REVERT: D 318 ASP cc_start: 0.6151 (t0) cc_final: 0.5950 (t0) REVERT: D 353 ASP cc_start: 0.7136 (t0) cc_final: 0.6927 (t0) REVERT: D 398 ILE cc_start: 0.6806 (OUTLIER) cc_final: 0.6533 (tp) REVERT: D 410 ARG cc_start: 0.6933 (ttm170) cc_final: 0.6570 (ttt90) REVERT: D 413 GLN cc_start: 0.7152 (mt0) cc_final: 0.6872 (mm-40) REVERT: D 445 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7913 (mtt) REVERT: D 465 GLN cc_start: 0.5866 (mm-40) cc_final: 0.5422 (pt0) REVERT: E 62 GLU cc_start: 0.7493 (pm20) cc_final: 0.7192 (pm20) REVERT: E 98 LYS cc_start: 0.7887 (mmmt) cc_final: 0.6854 (ttpt) REVERT: E 128 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7049 (pp20) REVERT: E 206 GLN cc_start: 0.7312 (pt0) cc_final: 0.6928 (mt0) REVERT: E 237 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8082 (mtp) REVERT: E 287 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8419 (ttp) REVERT: E 334 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8022 (mt-10) REVERT: E 373 GLU cc_start: 0.7624 (pm20) cc_final: 0.7358 (pt0) REVERT: E 405 THR cc_start: 0.5342 (OUTLIER) cc_final: 0.4647 (t) REVERT: E 410 ARG cc_start: 0.7627 (tpp80) cc_final: 0.7263 (tpp80) REVERT: E 453 ARG cc_start: 0.7511 (mmt180) cc_final: 0.7090 (mmm160) REVERT: F 5 LYS cc_start: 0.6595 (ttpt) cc_final: 0.6088 (tttt) REVERT: F 103 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7744 (mm) REVERT: F 130 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.8190 (t80) REVERT: F 368 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.7814 (ttpp) REVERT: F 398 ILE cc_start: 0.7120 (mt) cc_final: 0.6722 (tp) REVERT: G 87 GLU cc_start: 0.1298 (OUTLIER) cc_final: 0.1015 (mm-30) REVERT: G 89 VAL cc_start: 0.0906 (OUTLIER) cc_final: 0.0618 (t) REVERT: G 181 GLN cc_start: 0.7691 (mm-40) cc_final: 0.6946 (mt0) REVERT: H 90 MET cc_start: 0.1802 (tpp) cc_final: 0.0604 (tpp) REVERT: I 115 LEU cc_start: 0.2205 (OUTLIER) cc_final: 0.1966 (mt) REVERT: J 158 GLU cc_start: 0.4262 (OUTLIER) cc_final: 0.3312 (tt0) REVERT: L 80 LEU cc_start: 0.3514 (OUTLIER) cc_final: 0.3196 (tm) REVERT: L 85 ARG cc_start: 0.2611 (ttp80) cc_final: 0.1890 (ttp-170) REVERT: L 162 GLN cc_start: 0.6822 (pt0) cc_final: 0.6400 (pt0) outliers start: 120 outliers final: 56 residues processed: 385 average time/residue: 0.8847 time to fit residues: 385.8981 Evaluate side-chains 371 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 290 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 104 ARG Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 46 GLN Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain D residue 445 MET Chi-restraints excluded: chain E residue 25 LYS Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 368 LYS Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 413 GLN Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 165 GLU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain J residue 158 GLU Chi-restraints excluded: chain L residue 80 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 303 optimal weight: 0.7980 chunk 24 optimal weight: 8.9990 chunk 87 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 99 optimal weight: 3.9990 chunk 223 optimal weight: 10.0000 chunk 272 optimal weight: 7.9990 chunk 208 optimal weight: 10.0000 chunk 371 optimal weight: 30.0000 chunk 324 optimal weight: 0.9990 chunk 313 optimal weight: 10.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 425 ASN B 316 GLN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 364 ASN F 413 GLN G 180 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.152788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.114741 restraints weight = 36386.309| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.48 r_work: 0.3018 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30114 Z= 0.186 Angle : 0.599 8.361 40813 Z= 0.309 Chirality : 0.046 0.212 4572 Planarity : 0.005 0.046 5333 Dihedral : 6.511 113.108 4259 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.63 % Allowed : 15.24 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.14), residues: 3764 helix: 1.42 (0.13), residues: 1571 sheet: 0.16 (0.23), residues: 545 loop : -0.45 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 297 TYR 0.013 0.002 TYR C 562 PHE 0.018 0.002 PHE A 230 TRP 0.016 0.002 TRP L 175 HIS 0.004 0.001 HIS E 323 Details of bonding type rmsd covalent geometry : bond 0.00449 (30114) covalent geometry : angle 0.59902 (40813) hydrogen bonds : bond 0.05192 ( 1305) hydrogen bonds : angle 4.74538 ( 3723) *********************** 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 411 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 299 time to evaluate : 1.142 Fit side-chains revert: symmetry clash REVERT: A 3 GLN cc_start: 0.7882 (mt0) cc_final: 0.7628 (tt0) REVERT: A 32 GLU cc_start: 0.7226 (mm-30) cc_final: 0.7010 (mt-10) REVERT: A 114 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7253 (mm-30) REVERT: A 122 MET cc_start: 0.7481 (mtp) cc_final: 0.7112 (mtt) REVERT: A 124 LYS cc_start: 0.6945 (mtmm) cc_final: 0.6567 (mttp) REVERT: A 128 GLU cc_start: 0.6648 (tp30) cc_final: 0.6310 (pt0) REVERT: A 276 LYS cc_start: 0.5433 (ptmt) cc_final: 0.4814 (pptt) REVERT: A 277 THR cc_start: 0.8058 (m) cc_final: 0.7763 (p) REVERT: A 410 ASP cc_start: 0.6593 (t0) cc_final: 0.6385 (t0) REVERT: A 441 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7073 (mm-30) REVERT: A 465 GLN cc_start: 0.6770 (mm-40) cc_final: 0.6529 (tp40) REVERT: A 469 GLN cc_start: 0.6559 (mt0) cc_final: 0.6179 (mm-40) REVERT: A 491 ARG cc_start: 0.7447 (mmt180) cc_final: 0.6806 (mtm110) REVERT: A 496 GLN cc_start: 0.8081 (tt0) cc_final: 0.7838 (tt0) REVERT: A 527 GLU cc_start: 0.6822 (tt0) cc_final: 0.6375 (tp30) REVERT: B 2 ILE cc_start: 0.8772 (mm) cc_final: 0.8559 (mm) REVERT: B 53 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7405 (mt-10) REVERT: B 104 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.6438 (ptp-170) REVERT: B 197 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7051 (ptp90) REVERT: B 220 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.7655 (tpp) REVERT: B 565 GLU cc_start: 0.5854 (mm-30) cc_final: 0.5261 (tp30) REVERT: C 83 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8673 (tp) REVERT: C 156 ARG cc_start: 0.7842 (ttm110) cc_final: 0.7431 (ttm110) REVERT: C 182 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7538 (mtmt) REVERT: C 197 ARG cc_start: 0.7915 (ttp-110) cc_final: 0.7674 (ttp-170) REVERT: C 209 MET cc_start: 0.8518 (mtp) cc_final: 0.8206 (mtp) REVERT: C 461 GLU cc_start: 0.7365 (tm-30) cc_final: 0.7083 (tm-30) REVERT: C 480 GLU cc_start: 0.7751 (mp0) cc_final: 0.7228 (mp0) REVERT: C 492 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7507 (mp0) REVERT: C 547 ARG cc_start: 0.8007 (ttm110) cc_final: 0.7747 (tpp-160) REVERT: C 558 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7079 (tm-30) REVERT: D 49 GLU cc_start: 0.8681 (tt0) cc_final: 0.8415 (tt0) REVERT: D 87 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7523 (mp0) REVERT: D 162 GLU cc_start: 0.8040 (mp0) cc_final: 0.7795 (mm-30) REVERT: D 237 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8328 (mtt) REVERT: D 280 ARG cc_start: 0.7872 (mtm110) cc_final: 0.7417 (ttp-170) REVERT: D 302 GLU cc_start: 0.7912 (tt0) cc_final: 0.7619 (tp30) REVERT: D 314 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8535 (pt) REVERT: D 318 ASP cc_start: 0.6175 (t0) cc_final: 0.5966 (t0) REVERT: D 398 ILE cc_start: 0.6855 (OUTLIER) cc_final: 0.6575 (tp) REVERT: D 410 ARG cc_start: 0.6957 (ttm170) cc_final: 0.6587 (ttt90) REVERT: D 413 GLN cc_start: 0.7145 (mt0) cc_final: 0.6876 (mm-40) REVERT: D 445 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7910 (mtt) REVERT: D 465 GLN cc_start: 0.5916 (mm-40) cc_final: 0.5458 (pt0) REVERT: E 62 GLU cc_start: 0.7527 (pm20) cc_final: 0.7199 (pm20) REVERT: E 98 LYS cc_start: 0.7918 (mmmt) cc_final: 0.6842 (ttpt) REVERT: E 128 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.6983 (pp20) REVERT: E 206 GLN cc_start: 0.7277 (pt0) cc_final: 0.6877 (mt0) REVERT: E 237 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8060 (mtp) REVERT: E 287 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8412 (ttp) REVERT: E 334 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8020 (mt-10) REVERT: E 405 THR cc_start: 0.5555 (OUTLIER) cc_final: 0.4925 (t) REVERT: E 410 ARG cc_start: 0.7596 (tpp80) cc_final: 0.7246 (tpp80) REVERT: E 413 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7334 (mt0) REVERT: E 453 ARG cc_start: 0.7507 (mmt180) cc_final: 0.7068 (mmm160) REVERT: F 5 LYS cc_start: 0.6546 (ttpt) cc_final: 0.6033 (tttt) REVERT: F 103 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7723 (mm) REVERT: F 130 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.8176 (t80) REVERT: F 368 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.7801 (ttpp) REVERT: F 398 ILE cc_start: 0.7168 (mt) cc_final: 0.6751 (tp) REVERT: I 115 LEU cc_start: 0.2223 (OUTLIER) cc_final: 0.1975 (mt) REVERT: J 158 GLU cc_start: 0.4354 (OUTLIER) cc_final: 0.3211 (tt0) REVERT: L 80 LEU cc_start: 0.3429 (OUTLIER) cc_final: 0.3214 (tm) REVERT: L 85 ARG cc_start: 0.2909 (ttp80) cc_final: 0.2161 (ttp-170) REVERT: L 86 ARG cc_start: 0.2358 (ttp80) cc_final: 0.1697 (tpt170) REVERT: L 145 GLU cc_start: 0.2925 (OUTLIER) cc_final: 0.2713 (tm-30) REVERT: L 162 GLN cc_start: 0.6824 (pt0) cc_final: 0.6375 (pt0) outliers start: 112 outliers final: 52 residues processed: 384 average time/residue: 0.8946 time to fit residues: 389.3653 Evaluate side-chains 368 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 291 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 104 ARG Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 392 SER Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 46 GLN Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain D residue 445 MET Chi-restraints excluded: chain E residue 25 LYS Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 413 GLN Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 368 LYS Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 165 GLU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain J residue 158 GLU Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 145 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 316 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 327 optimal weight: 4.9990 chunk 310 optimal weight: 7.9990 chunk 140 optimal weight: 0.7980 chunk 176 optimal weight: 6.9990 chunk 330 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 199 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 347 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN B 316 GLN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 364 ASN G 13 GLN G 180 GLN G 181 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.153899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.116140 restraints weight = 36616.311| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.42 r_work: 0.3033 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30114 Z= 0.135 Angle : 0.539 9.501 40813 Z= 0.278 Chirality : 0.044 0.195 4572 Planarity : 0.005 0.046 5333 Dihedral : 6.276 112.121 4259 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.31 % Allowed : 15.93 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.14), residues: 3764 helix: 1.65 (0.13), residues: 1562 sheet: 0.14 (0.23), residues: 555 loop : -0.37 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 91 TYR 0.012 0.001 TYR C 562 PHE 0.015 0.001 PHE C 574 TRP 0.014 0.001 TRP L 175 HIS 0.003 0.001 HIS H 84 Details of bonding type rmsd covalent geometry : bond 0.00313 (30114) covalent geometry : angle 0.53909 (40813) hydrogen bonds : bond 0.04529 ( 1305) hydrogen bonds : angle 4.57857 ( 3723) *********************** 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 397 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 295 time to evaluate : 1.121 Fit side-chains revert: symmetry clash REVERT: A 3 GLN cc_start: 0.7916 (mt0) cc_final: 0.7637 (tt0) REVERT: A 32 GLU cc_start: 0.7279 (mm-30) cc_final: 0.7032 (mt-10) REVERT: A 114 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7207 (mm-30) REVERT: A 122 MET cc_start: 0.7422 (mtp) cc_final: 0.7091 (mtt) REVERT: A 124 LYS cc_start: 0.7007 (mtmm) cc_final: 0.6631 (mttp) REVERT: A 128 GLU cc_start: 0.6677 (tp30) cc_final: 0.6336 (pt0) REVERT: A 276 LYS cc_start: 0.5376 (ptmt) cc_final: 0.4743 (pptt) REVERT: A 277 THR cc_start: 0.8047 (m) cc_final: 0.7728 (p) REVERT: A 410 ASP cc_start: 0.6739 (t0) cc_final: 0.6530 (t0) REVERT: A 441 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7044 (mm-30) REVERT: A 465 GLN cc_start: 0.6814 (mm-40) cc_final: 0.6458 (tp40) REVERT: A 469 GLN cc_start: 0.6440 (mt0) cc_final: 0.6097 (mm-40) REVERT: A 491 ARG cc_start: 0.7454 (mmt180) cc_final: 0.6800 (mtm110) REVERT: A 496 GLN cc_start: 0.8077 (tt0) cc_final: 0.7861 (tt0) REVERT: A 527 GLU cc_start: 0.6807 (tt0) cc_final: 0.6395 (tp30) REVERT: B 2 ILE cc_start: 0.8774 (mm) cc_final: 0.8573 (mm) REVERT: B 53 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7382 (mt-10) REVERT: B 104 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.6524 (ptp-170) REVERT: B 154 ARG cc_start: 0.6551 (OUTLIER) cc_final: 0.6143 (mtp85) REVERT: B 197 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7160 (ptp90) REVERT: B 565 GLU cc_start: 0.5907 (mm-30) cc_final: 0.5328 (tp30) REVERT: C 156 ARG cc_start: 0.7871 (ttm110) cc_final: 0.7476 (ttm110) REVERT: C 159 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7841 (pt0) REVERT: C 182 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7512 (mtmt) REVERT: C 197 ARG cc_start: 0.7917 (ttp-110) cc_final: 0.7602 (ttp-170) REVERT: C 209 MET cc_start: 0.8464 (mtp) cc_final: 0.8236 (mtp) REVERT: C 461 GLU cc_start: 0.7418 (tm-30) cc_final: 0.7145 (tm-30) REVERT: C 480 GLU cc_start: 0.7804 (mp0) cc_final: 0.7290 (mp0) REVERT: C 492 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7578 (mp0) REVERT: C 547 ARG cc_start: 0.8009 (ttm110) cc_final: 0.7766 (tpp-160) REVERT: D 49 GLU cc_start: 0.8684 (tt0) cc_final: 0.8426 (tt0) REVERT: D 87 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7578 (mp0) REVERT: D 162 GLU cc_start: 0.8023 (mp0) cc_final: 0.7761 (mm-30) REVERT: D 280 ARG cc_start: 0.7861 (mtm110) cc_final: 0.7412 (ttp-170) REVERT: D 302 GLU cc_start: 0.7934 (tt0) cc_final: 0.7655 (tp30) REVERT: D 410 ARG cc_start: 0.6958 (ttm170) cc_final: 0.6591 (ttt90) REVERT: D 413 GLN cc_start: 0.7174 (mt0) cc_final: 0.6913 (mm-40) REVERT: D 445 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7919 (mtt) REVERT: D 465 GLN cc_start: 0.5917 (mm-40) cc_final: 0.5484 (pt0) REVERT: E 62 GLU cc_start: 0.7542 (pm20) cc_final: 0.7287 (pm20) REVERT: E 98 LYS cc_start: 0.7933 (mmmt) cc_final: 0.6861 (ttpt) REVERT: E 128 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7021 (pp20) REVERT: E 206 GLN cc_start: 0.7291 (pt0) cc_final: 0.6886 (mt0) REVERT: E 237 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8052 (mtp) REVERT: E 287 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8348 (ttt) REVERT: E 334 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7932 (mt-10) REVERT: E 405 THR cc_start: 0.5554 (OUTLIER) cc_final: 0.4899 (t) REVERT: E 410 ARG cc_start: 0.7596 (tpp80) cc_final: 0.7222 (tpp80) REVERT: E 453 ARG cc_start: 0.7532 (mmt180) cc_final: 0.7119 (mmm160) REVERT: F 5 LYS cc_start: 0.6606 (ttpt) cc_final: 0.6101 (tttt) REVERT: F 103 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7762 (mm) REVERT: F 130 PHE cc_start: 0.8780 (OUTLIER) cc_final: 0.8202 (t80) REVERT: F 368 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.7665 (ttpp) REVERT: F 398 ILE cc_start: 0.7153 (mt) cc_final: 0.6757 (tp) REVERT: I 115 LEU cc_start: 0.2433 (OUTLIER) cc_final: 0.2232 (mt) REVERT: J 86 ARG cc_start: 0.2941 (OUTLIER) cc_final: 0.2639 (mmt180) REVERT: J 89 GLU cc_start: 0.3953 (tm-30) cc_final: 0.3258 (pp20) REVERT: J 158 GLU cc_start: 0.4280 (OUTLIER) cc_final: 0.3132 (tt0) REVERT: L 85 ARG cc_start: 0.2940 (ttp80) cc_final: 0.2255 (ttp-170) REVERT: L 86 ARG cc_start: 0.2569 (ttp80) cc_final: 0.1883 (ttm-80) REVERT: L 162 GLN cc_start: 0.6823 (pt0) cc_final: 0.6389 (pt0) outliers start: 102 outliers final: 46 residues processed: 370 average time/residue: 0.8872 time to fit residues: 372.1820 Evaluate side-chains 357 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 291 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 104 ARG Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 46 GLN Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 445 MET Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 368 LYS Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 165 GLU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain J residue 86 ARG Chi-restraints excluded: chain J residue 158 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 371 optimal weight: 20.0000 chunk 370 optimal weight: 9.9990 chunk 203 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 141 optimal weight: 0.0370 chunk 65 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 294 optimal weight: 5.9990 chunk 289 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 overall best weight: 4.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 425 ASN B 316 GLN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 364 ASN G 13 GLN G 180 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.153111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.115449 restraints weight = 36475.072| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.42 r_work: 0.3021 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 30114 Z= 0.170 Angle : 0.589 12.148 40813 Z= 0.303 Chirality : 0.045 0.208 4572 Planarity : 0.005 0.045 5333 Dihedral : 6.393 108.673 4259 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.05 % Allowed : 16.38 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.14), residues: 3764 helix: 1.49 (0.13), residues: 1562 sheet: 0.18 (0.23), residues: 548 loop : -0.43 (0.15), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 154 TYR 0.019 0.002 TYR H 89 PHE 0.018 0.002 PHE A 230 TRP 0.011 0.001 TRP C 424 HIS 0.004 0.001 HIS H 84 Details of bonding type rmsd covalent geometry : bond 0.00406 (30114) covalent geometry : angle 0.58923 (40813) hydrogen bonds : bond 0.04992 ( 1305) hydrogen bonds : angle 4.68595 ( 3723) *********************** 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 386 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 292 time to evaluate : 1.169 Fit side-chains revert: symmetry clash REVERT: A 3 GLN cc_start: 0.7891 (mt0) cc_final: 0.7602 (tt0) REVERT: A 32 GLU cc_start: 0.7299 (mm-30) cc_final: 0.7070 (mt-10) REVERT: A 114 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7188 (mm-30) REVERT: A 122 MET cc_start: 0.7454 (mtp) cc_final: 0.7131 (mtt) REVERT: A 124 LYS cc_start: 0.6943 (mtmm) cc_final: 0.6578 (mttp) REVERT: A 128 GLU cc_start: 0.6706 (tp30) cc_final: 0.6331 (pt0) REVERT: A 276 LYS cc_start: 0.5424 (ptmt) cc_final: 0.4778 (pptt) REVERT: A 277 THR cc_start: 0.8046 (m) cc_final: 0.7722 (p) REVERT: A 410 ASP cc_start: 0.6670 (t0) cc_final: 0.6469 (t0) REVERT: A 441 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7069 (mm-30) REVERT: A 465 GLN cc_start: 0.6858 (mm-40) cc_final: 0.6356 (tp40) REVERT: A 469 GLN cc_start: 0.6425 (mt0) cc_final: 0.6131 (mm-40) REVERT: A 491 ARG cc_start: 0.7441 (mmt180) cc_final: 0.6805 (mtm110) REVERT: A 527 GLU cc_start: 0.6801 (tt0) cc_final: 0.6365 (tp30) REVERT: B 53 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7403 (mt-10) REVERT: B 104 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.6446 (ptp-170) REVERT: B 154 ARG cc_start: 0.6524 (OUTLIER) cc_final: 0.6113 (mtp85) REVERT: B 197 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.7009 (ptp90) REVERT: B 565 GLU cc_start: 0.5887 (mm-30) cc_final: 0.5291 (tp30) REVERT: C 83 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8639 (tp) REVERT: C 156 ARG cc_start: 0.7877 (ttm110) cc_final: 0.7347 (ttm110) REVERT: C 159 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7830 (pt0) REVERT: C 182 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7535 (mtmt) REVERT: C 197 ARG cc_start: 0.7927 (ttp-110) cc_final: 0.7697 (ttp-170) REVERT: C 209 MET cc_start: 0.8494 (mtp) cc_final: 0.8271 (mtp) REVERT: C 461 GLU cc_start: 0.7363 (tm-30) cc_final: 0.7084 (tm-30) REVERT: C 480 GLU cc_start: 0.7781 (mp0) cc_final: 0.7197 (mp0) REVERT: C 492 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7524 (mp0) REVERT: C 547 ARG cc_start: 0.7993 (ttm110) cc_final: 0.7770 (tpp-160) REVERT: D 49 GLU cc_start: 0.8701 (tt0) cc_final: 0.8436 (tt0) REVERT: D 87 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7535 (mp0) REVERT: D 162 GLU cc_start: 0.8041 (mp0) cc_final: 0.7796 (mm-30) REVERT: D 237 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8370 (mtt) REVERT: D 280 ARG cc_start: 0.7898 (mtm110) cc_final: 0.7452 (ttp-170) REVERT: D 302 GLU cc_start: 0.7927 (tt0) cc_final: 0.7666 (tp30) REVERT: D 410 ARG cc_start: 0.6975 (ttm170) cc_final: 0.6607 (ttt90) REVERT: D 413 GLN cc_start: 0.7135 (mt0) cc_final: 0.6884 (mm-40) REVERT: D 445 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7918 (mtt) REVERT: D 465 GLN cc_start: 0.5897 (mm-40) cc_final: 0.5470 (pt0) REVERT: E 62 GLU cc_start: 0.7525 (pm20) cc_final: 0.7255 (pm20) REVERT: E 98 LYS cc_start: 0.7929 (mmmt) cc_final: 0.6832 (ttpt) REVERT: E 128 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7024 (pp20) REVERT: E 206 GLN cc_start: 0.7295 (pt0) cc_final: 0.6894 (mt0) REVERT: E 237 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8070 (mtp) REVERT: E 287 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8423 (ttp) REVERT: E 334 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8024 (mt-10) REVERT: E 405 THR cc_start: 0.5588 (OUTLIER) cc_final: 0.4975 (t) REVERT: E 410 ARG cc_start: 0.7589 (tpp80) cc_final: 0.7244 (tpp80) REVERT: E 413 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7338 (mt0) REVERT: E 453 ARG cc_start: 0.7507 (mmt180) cc_final: 0.7070 (mmm160) REVERT: F 5 LYS cc_start: 0.6568 (ttpt) cc_final: 0.6057 (tttt) REVERT: F 103 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7743 (mm) REVERT: F 130 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.8182 (t80) REVERT: F 368 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.7660 (ttpp) REVERT: F 398 ILE cc_start: 0.7170 (mt) cc_final: 0.6767 (tp) REVERT: I 115 LEU cc_start: 0.2204 (OUTLIER) cc_final: 0.1977 (mt) REVERT: J 158 GLU cc_start: 0.4327 (OUTLIER) cc_final: 0.3116 (tt0) REVERT: L 85 ARG cc_start: 0.2816 (ttp80) cc_final: 0.2190 (ttp-170) REVERT: L 86 ARG cc_start: 0.2527 (ttp80) cc_final: 0.1858 (ttm-80) REVERT: L 162 GLN cc_start: 0.6862 (pt0) cc_final: 0.6380 (pt0) outliers start: 94 outliers final: 50 residues processed: 361 average time/residue: 0.9058 time to fit residues: 369.7499 Evaluate side-chains 358 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 287 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 104 ARG Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 46 GLN Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 445 MET Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 413 GLN Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 368 LYS Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 165 GLU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain J residue 158 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 295 optimal weight: 3.9990 chunk 339 optimal weight: 1.9990 chunk 288 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 chunk 325 optimal weight: 9.9990 chunk 258 optimal weight: 10.0000 chunk 284 optimal weight: 3.9990 chunk 272 optimal weight: 0.9990 chunk 286 optimal weight: 4.9990 chunk 250 optimal weight: 0.8980 chunk 219 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN B 316 GLN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 364 ASN F 413 GLN G 13 GLN G 180 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.154332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.116699 restraints weight = 36455.276| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.43 r_work: 0.3043 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30114 Z= 0.127 Angle : 0.532 10.720 40813 Z= 0.273 Chirality : 0.044 0.203 4572 Planarity : 0.005 0.046 5333 Dihedral : 6.122 106.754 4259 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.59 % Allowed : 16.90 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.14), residues: 3764 helix: 1.72 (0.13), residues: 1562 sheet: 0.18 (0.23), residues: 558 loop : -0.33 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 154 TYR 0.011 0.001 TYR C 562 PHE 0.013 0.001 PHE C 574 TRP 0.010 0.001 TRP C 424 HIS 0.003 0.001 HIS H 84 Details of bonding type rmsd covalent geometry : bond 0.00293 (30114) covalent geometry : angle 0.53249 (40813) hydrogen bonds : bond 0.04320 ( 1305) hydrogen bonds : angle 4.51146 ( 3723) ********************** 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 377 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 297 time to evaluate : 1.050 Fit side-chains revert: symmetry clash REVERT: A 3 GLN cc_start: 0.7896 (mt0) cc_final: 0.7661 (tt0) REVERT: A 114 GLU cc_start: 0.7380 (mm-30) cc_final: 0.7119 (mm-30) REVERT: A 122 MET cc_start: 0.7372 (mtp) cc_final: 0.7030 (mtt) REVERT: A 124 LYS cc_start: 0.6885 (mtmm) cc_final: 0.6527 (mttp) REVERT: A 128 GLU cc_start: 0.6713 (tp30) cc_final: 0.6331 (pt0) REVERT: A 276 LYS cc_start: 0.5394 (ptmt) cc_final: 0.4745 (pptt) REVERT: A 277 THR cc_start: 0.8030 (m) cc_final: 0.7708 (p) REVERT: A 410 ASP cc_start: 0.6695 (t0) cc_final: 0.6485 (t0) REVERT: A 441 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7073 (mm-30) REVERT: A 465 GLN cc_start: 0.6800 (mm-40) cc_final: 0.6321 (tp40) REVERT: A 469 GLN cc_start: 0.6267 (mt0) cc_final: 0.6045 (mm-40) REVERT: A 491 ARG cc_start: 0.7392 (mmt180) cc_final: 0.6751 (mtm110) REVERT: A 527 GLU cc_start: 0.6799 (tt0) cc_final: 0.6344 (tp30) REVERT: B 33 GLU cc_start: 0.7600 (tt0) cc_final: 0.7310 (tt0) REVERT: B 53 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7241 (mt-10) REVERT: B 104 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.7072 (ptt180) REVERT: B 565 GLU cc_start: 0.5908 (mm-30) cc_final: 0.5312 (tp30) REVERT: C 156 ARG cc_start: 0.7804 (ttm110) cc_final: 0.7419 (ttm110) REVERT: C 159 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7777 (pt0) REVERT: C 182 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7455 (mtmt) REVERT: C 197 ARG cc_start: 0.7901 (ttp-110) cc_final: 0.7597 (ttp-170) REVERT: C 209 MET cc_start: 0.8436 (mtp) cc_final: 0.8221 (mtp) REVERT: C 461 GLU cc_start: 0.7379 (tm-30) cc_final: 0.7099 (tm-30) REVERT: C 480 GLU cc_start: 0.7758 (mp0) cc_final: 0.7232 (mp0) REVERT: C 492 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7578 (mp0) REVERT: C 536 ILE cc_start: 0.6523 (OUTLIER) cc_final: 0.5951 (pt) REVERT: C 547 ARG cc_start: 0.7975 (ttm110) cc_final: 0.7729 (tpp-160) REVERT: D 49 GLU cc_start: 0.8687 (tt0) cc_final: 0.8422 (tt0) REVERT: D 87 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7529 (mp0) REVERT: D 162 GLU cc_start: 0.7978 (mp0) cc_final: 0.7746 (mm-30) REVERT: D 237 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8346 (mtt) REVERT: D 280 ARG cc_start: 0.7881 (mtm110) cc_final: 0.7446 (ttp-170) REVERT: D 302 GLU cc_start: 0.7929 (tt0) cc_final: 0.7652 (tp30) REVERT: D 410 ARG cc_start: 0.6973 (ttm170) cc_final: 0.6569 (ttt90) REVERT: D 413 GLN cc_start: 0.7126 (mt0) cc_final: 0.6860 (mm-40) REVERT: D 465 GLN cc_start: 0.5874 (mm-40) cc_final: 0.5452 (pt0) REVERT: E 62 GLU cc_start: 0.7496 (pm20) cc_final: 0.7252 (pm20) REVERT: E 98 LYS cc_start: 0.7889 (mmmt) cc_final: 0.6776 (ttpt) REVERT: E 206 GLN cc_start: 0.7248 (pt0) cc_final: 0.6832 (mt0) REVERT: E 237 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8045 (mtp) REVERT: E 287 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8353 (ttt) REVERT: E 334 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7915 (mt-10) REVERT: E 405 THR cc_start: 0.5450 (OUTLIER) cc_final: 0.4831 (t) REVERT: E 453 ARG cc_start: 0.7509 (mmt180) cc_final: 0.7078 (mmm160) REVERT: F 5 LYS cc_start: 0.6535 (ttpt) cc_final: 0.6032 (tttt) REVERT: F 103 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7782 (mm) REVERT: F 130 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.8204 (t80) REVERT: F 368 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.7659 (ttpp) REVERT: F 398 ILE cc_start: 0.7171 (mt) cc_final: 0.6744 (tp) REVERT: L 85 ARG cc_start: 0.2796 (ttp80) cc_final: 0.2049 (ttp-170) REVERT: L 162 GLN cc_start: 0.6799 (pt0) cc_final: 0.6337 (pt0) outliers start: 80 outliers final: 51 residues processed: 355 average time/residue: 0.8913 time to fit residues: 357.5419 Evaluate side-chains 353 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 287 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 567 MET Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 104 ARG Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 159 GLU Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain C residue 339 SER Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 46 GLN Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain E residue 25 LYS Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 384 SER Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 368 LYS Chi-restraints excluded: chain F residue 380 ASP Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 413 GLN Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 165 GLU Chi-restraints excluded: chain G residue 168 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 31 optimal weight: 9.9990 chunk 361 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 367 optimal weight: 10.0000 chunk 210 optimal weight: 1.9990 chunk 254 optimal weight: 20.0000 chunk 181 optimal weight: 6.9990 chunk 226 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 425 ASN B 316 GLN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 364 ASN G 13 GLN G 180 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.153953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.116096 restraints weight = 36471.987| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.45 r_work: 0.3049 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.133 30114 Z= 0.161 Angle : 0.656 59.200 40813 Z= 0.364 Chirality : 0.045 0.539 4572 Planarity : 0.005 0.045 5333 Dihedral : 6.140 106.664 4259 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.63 % Allowed : 17.00 % Favored : 80.38 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.14), residues: 3764 helix: 1.71 (0.13), residues: 1562 sheet: 0.19 (0.23), residues: 558 loop : -0.33 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 174 TYR 0.011 0.001 TYR C 562 PHE 0.014 0.002 PHE C 574 TRP 0.009 0.001 TRP B 119 HIS 0.003 0.001 HIS H 84 Details of bonding type rmsd covalent geometry : bond 0.00369 (30114) covalent geometry : angle 0.65576 (40813) hydrogen bonds : bond 0.04416 ( 1305) hydrogen bonds : angle 4.51854 ( 3723) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11237.97 seconds wall clock time: 191 minutes 26.77 seconds (11486.77 seconds total)