Starting phenix.real_space_refine on Fri Mar 6 08:56:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vay_31871/03_2026/7vay_31871.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vay_31871/03_2026/7vay_31871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vay_31871/03_2026/7vay_31871.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vay_31871/03_2026/7vay_31871.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vay_31871/03_2026/7vay_31871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vay_31871/03_2026/7vay_31871.map" } resolution = 3.3 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 2 5.21 5 S 105 5.16 5 C 18735 2.51 5 N 5131 2.21 5 O 5572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29553 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "C" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "D" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3682 Classifications: {'peptide': 470} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 26, 'TRANS': 441} Chain: "E" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3668 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 441} Chain: "F" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3694 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 444} Chain: "G" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1619 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "H" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "J" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 976 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain: "K" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "L" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 980 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.74, per 1000 atoms: 0.23 Number of scatterers: 29553 At special positions: 0 Unit cell: (149.04, 144.18, 171.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 105 16.00 P 8 15.00 Mg 2 11.99 O 5572 8.00 N 5131 7.00 C 18735 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.69 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: 140 helices and 24 sheets defined 47.7% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 90 through 99 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 233 through 245 Processing helix chain 'A' and resid 258 through 272 removed outlier: 3.882A pdb=" N MET A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 297 through 316 removed outlier: 4.242A pdb=" N ALA A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 342 Processing helix chain 'A' and resid 353 through 364 removed outlier: 3.713A pdb=" N ARG A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 393 through 401 removed outlier: 3.580A pdb=" N ARG A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 416 removed outlier: 3.557A pdb=" N ALA A 414 " --> pdb=" O ASP A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 443 removed outlier: 3.592A pdb=" N ASP A 436 " --> pdb=" O THR A 432 " (cutoff:3.500A) Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 446 through 472 removed outlier: 3.833A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 494 Processing helix chain 'A' and resid 508 through 533 Processing helix chain 'A' and resid 535 through 541 removed outlier: 3.600A pdb=" N GLN A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 552 removed outlier: 3.947A pdb=" N GLU A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ARG A 552 " --> pdb=" O ILE A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 577 removed outlier: 3.541A pdb=" N TYR A 562 " --> pdb=" O GLU A 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 removed outlier: 3.599A pdb=" N LYS B 97 " --> pdb=" O ARG B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 258 through 269 Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 295 through 315 removed outlier: 4.631A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 341 removed outlier: 3.559A 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: 4.207A 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 477 through 494 Processing helix chain 'B' and resid 508 through 532 Processing helix chain 'B' and resid 535 through 540 Processing helix chain 'B' and resid 543 through 552 removed outlier: 3.540A pdb=" N ARG B 547 " --> pdb=" O PRO B 543 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG B 552 " --> pdb=" O ILE B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 577 Processing helix chain 'C' and resid 90 through 99 Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 233 through 245 Processing helix chain 'C' and resid 258 through 269 removed outlier: 3.912A pdb=" N MET C 262 " --> pdb=" O ARG C 258 " (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 281 through 283 No H-bonds generated for 'chain 'C' and resid 281 through 283' Processing helix chain 'C' and resid 297 through 316 removed outlier: 4.307A pdb=" N ALA C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN C 316 " --> pdb=" O TYR C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 341 removed outlier: 4.099A pdb=" N TRP C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 363 Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 393 through 401 removed outlier: 3.561A pdb=" N ARG C 401 " --> pdb=" O GLN C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 416 Processing helix chain 'C' and resid 435 through 443 Processing helix chain 'C' and resid 446 through 472 removed outlier: 4.154A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 476 removed outlier: 3.957A pdb=" N LEU C 476 " --> pdb=" O PRO C 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 473 through 476' Processing helix chain 'C' and resid 477 through 495 Processing helix chain 'C' and resid 508 through 532 Processing helix chain 'C' and resid 535 through 540 Processing helix chain 'C' and resid 543 through 551 removed outlier: 3.588A pdb=" N ARG C 547 " --> pdb=" O PRO C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 554 No H-bonds generated for 'chain 'C' and resid 552 through 554' Processing helix chain 'C' and resid 558 through 578 removed outlier: 3.641A pdb=" N PHE C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA C 578 " --> pdb=" O PHE C 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.607A pdb=" N LEU D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 159 through 171 Processing helix chain 'D' and resid 175 through 179 Processing helix chain 'D' and resid 197 through 211 removed outlier: 3.855A pdb=" N THR D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 215 Processing helix chain 'D' and resid 227 through 250 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 259 through 274 Processing helix chain 'D' and resid 279 through 283 removed outlier: 3.531A 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 Processing helix chain 'D' and resid 340 through 346 Processing helix chain 'D' and resid 361 through 366 removed outlier: 3.729A pdb=" N GLY D 365 " --> pdb=" O LEU D 361 " (cutoff:3.500A) removed outlier: 3.540A 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: 3.837A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.465A 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 446 removed outlier: 3.825A pdb=" N MET D 445 " --> pdb=" O ALA D 441 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU D 446 " --> pdb=" O LEU D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 463 Processing helix chain 'E' and resid 85 through 89 removed outlier: 3.764A pdb=" N LEU E 89 " --> pdb=" O LYS E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 124 Processing helix chain 'E' and resid 135 through 140 Processing helix chain 'E' and resid 159 through 171 Processing helix chain 'E' and resid 197 through 210 Processing helix chain 'E' and resid 212 through 215 Processing helix chain 'E' and resid 227 through 250 removed outlier: 3.772A pdb=" N ARG E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) removed outlier: 3.808A 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: 3.676A pdb=" N TYR E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 Processing helix chain 'E' and resid 317 through 320 Processing helix chain 'E' and resid 323 through 333 Processing helix chain 'E' and resid 340 through 346 Processing helix chain 'E' and resid 361 through 365 removed outlier: 3.697A pdb=" N ASN E 364 " --> pdb=" O LEU E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 400 removed outlier: 3.682A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 422 removed outlier: 3.532A pdb=" N ARG E 409 " --> pdb=" O THR E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 443 Processing helix chain 'E' and resid 458 through 463 Processing helix chain 'F' and resid 85 through 90 removed outlier: 3.588A pdb=" N MET F 88 " --> pdb=" O SER F 85 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU F 89 " --> pdb=" O LYS F 86 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLY F 90 " --> pdb=" O GLU F 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 85 through 90' 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 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 229 through 250 removed outlier: 3.955A pdb=" N LEU F 233 " --> pdb=" O ILE F 229 " (cutoff:3.500A) Proline residue: F 235 - end of helix Processing helix chain 'F' and resid 259 through 275 removed outlier: 3.712A pdb=" N TYR F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 283 removed outlier: 3.583A pdb=" N GLY F 282 " --> pdb=" O GLY F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 285 No H-bonds generated for 'chain 'F' and resid 284 through 285' Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.502A 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: 3.757A pdb=" N GLY F 365 " --> pdb=" O LEU F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 400 removed outlier: 3.802A pdb=" N ILE F 398 " --> pdb=" O LYS F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 404 Processing helix chain 'F' and resid 405 through 422 Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 445 through 446 No H-bonds generated for 'chain 'F' and resid 445 through 446' Processing helix chain 'F' and resid 447 through 451 Processing helix chain 'F' and resid 455 through 463 Processing helix chain 'F' and resid 466 through 471 removed outlier: 3.561A pdb=" N ILE F 470 " --> pdb=" O LYS F 466 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 71 removed outlier: 3.601A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 83 Processing helix chain 'G' and resid 109 through 113 removed outlier: 4.029A pdb=" N ALA G 112 " --> pdb=" O PRO G 109 " (cutoff:3.500A) removed outlier: 3.621A 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: 3.715A pdb=" N ALA G 126 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 4.860A 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 15 Processing helix chain 'H' and resid 25 through 40 Processing helix chain 'H' and resid 55 through 60 removed outlier: 3.927A pdb=" N GLU H 60 " --> pdb=" O GLU H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 83 removed outlier: 3.979A 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 119 removed outlier: 4.029A pdb=" N ALA I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ARG I 106 " --> pdb=" O LYS I 102 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASP I 108 " --> pdb=" O MET I 104 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N GLU I 109 " --> pdb=" O ALA I 105 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU I 119 " --> pdb=" O LEU I 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 92 Processing helix chain 'J' and resid 93 through 97 Processing helix chain 'J' and resid 99 through 115 removed outlier: 3.577A pdb=" N VAL J 103 " --> pdb=" O GLU J 99 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU J 115 " --> pdb=" O ALA J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 131 Proline residue: J 129 - end of helix Processing helix chain 'J' and resid 132 through 139 Processing helix chain 'J' and resid 166 through 187 removed outlier: 4.394A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN J 184 " --> pdb=" O SER J 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 105 removed outlier: 3.664A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 119 Processing helix chain 'L' and resid 62 through 93 removed outlier: 3.784A pdb=" N LEU L 66 " --> pdb=" O SER L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 97 Processing helix chain 'L' and resid 99 through 115 Processing helix chain 'L' and resid 124 through 126 No H-bonds generated for 'chain 'L' and resid 124 through 126' Processing helix chain 'L' and resid 127 through 139 removed outlier: 5.023A pdb=" N ALA L 133 " --> pdb=" O PRO L 129 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LEU L 134 " --> pdb=" O HIS L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 166 through 187 removed outlier: 5.540A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS L 181 " --> pdb=" O ALA L 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 10 removed outlier: 6.577A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ALA A 13 " --> pdb=" O ILE A 9 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 13 through 17 current: chain 'A' and resid 35 through 43 removed outlier: 5.790A pdb=" N ILE A 39 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLN A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A 41 " --> pdb=" O PHE A 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 46 through 51 current: chain 'B' and resid 13 through 17 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 13 through 17 current: chain 'B' and resid 35 through 43 removed outlier: 6.098A pdb=" N ILE B 39 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLN B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 3.922A 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: 5.710A pdb=" N ILE C 39 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLN C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 3.724A 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: 5.678A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU D 49 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR D 54 " --> pdb=" O SER D 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 54 through 59 current: chain 'E' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 22 current: chain 'E' and resid 42 through 50 removed outlier: 5.917A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 54 through 59 current: chain 'F' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 18 through 22 current: chain 'F' and resid 42 through 51 removed outlier: 5.792A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 3.516A 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 54 through 59 current: chain 'J' and resid 141 through 144 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 141 through 144 current: chain 'J' and resid 161 through 164 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 161 through 164 current: chain 'L' and resid 143 through 144 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 143 through 144 current: chain 'L' and resid 161 through 164 Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 75 Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 83 through 84 current: chain 'A' and resid 285 through 291 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 285 through 291 current: chain 'A' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 375 through 384 current: chain 'A' and resid 428 through 429 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 144 through 148 removed outlier: 6.654A pdb=" N HIS A 145 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N THR A 137 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE A 147 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ALA A 118 " --> pdb=" O PRO A 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 129 Processing sheet with id=AA6, first strand: chain 'B' and resid 72 through 75 Processing sheet with id=AA7, first strand: chain 'B' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 83 through 84 current: chain 'B' and resid 285 through 291 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 285 through 291 current: chain 'B' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 375 through 384 current: chain 'B' and resid 428 through 429 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 144 through 148 removed outlier: 3.648A pdb=" N GLY B 136 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 5.382A 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: 6.821A 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 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 83 through 84 current: chain 'C' and resid 285 through 291 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 285 through 291 current: chain 'C' and resid 375 through 382 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 375 through 382 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: 3.641A pdb=" N GLY C 136 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ALA C 118 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.818A 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: 6.661A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL C 160 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL C 172 " --> pdb=" O VAL C 160 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.599A 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 removed outlier: 3.868A pdb=" N ARG D 91 " --> pdb=" O SER D 217 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 130 through 131 removed outlier: 4.708A 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 92 through 93 removed outlier: 8.749A pdb=" N VAL E 218 " --> pdb=" O PHE E 187 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL E 189 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N PHE E 220 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE E 191 " --> pdb=" O PHE E 220 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.539A pdb=" N LEU E 144 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 81 through 84 Processing sheet with id=AC3, first strand: chain 'F' and resid 92 through 94 removed outlier: 3.727A pdb=" N LEU F 257 " --> pdb=" O ILE F 311 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 131 through 132 Processing sheet with id=AC5, first strand: chain 'G' and resid 89 through 96 Processing sheet with id=AC6, first strand: chain 'H' and resid 19 through 22 removed outlier: 6.708A pdb=" N VAL H 45 " --> pdb=" O LEU H 72 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ILE H 74 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N VAL H 47 " --> pdb=" O ILE H 74 " (cutoff:3.500A) 1339 hydrogen bonds defined for protein. 3846 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: 5.93 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 - 1.37: 10094 1.37 - 1.51: 9463 1.51 - 1.66: 10357 1.66 - 1.80: 188 1.80 - 1.95: 8 Bond restraints: 30110 Sorted by residual: bond pdb=" C4 ADP A 602 " pdb=" C5 ADP A 602 " ideal model delta sigma weight residual 1.490 1.384 0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" C5 ADP A 602 " pdb=" C6 ADP A 602 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C HIS C 418 " pdb=" N PHE C 419 " ideal model delta sigma weight residual 1.327 1.273 0.054 1.71e-02 3.42e+03 9.87e+00 bond pdb=" O3B ADP A 602 " pdb=" PB ADP A 602 " ideal model delta sigma weight residual 1.510 1.572 -0.062 2.00e-02 2.50e+03 9.75e+00 bond pdb=" CA GLU D 296 " pdb=" C GLU D 296 " ideal model delta sigma weight residual 1.522 1.489 0.033 1.38e-02 5.25e+03 5.76e+00 ... (remaining 30105 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 40581 2.86 - 5.73: 208 5.73 - 8.59: 10 8.59 - 11.45: 7 11.45 - 14.32: 1 Bond angle restraints: 40807 Sorted by residual: angle pdb=" O2B ADP A 602 " pdb=" PB ADP A 602 " pdb=" O3B ADP A 602 " ideal model delta sigma weight residual 119.90 105.58 14.32 3.00e+00 1.11e-01 2.28e+01 angle pdb=" N ILE D 100 " pdb=" CA ILE D 100 " pdb=" C ILE D 100 " ideal model delta sigma weight residual 113.20 109.54 3.66 9.60e-01 1.09e+00 1.45e+01 angle pdb=" N ILE E 100 " pdb=" CA ILE E 100 " pdb=" C ILE E 100 " ideal model delta sigma weight residual 113.20 109.96 3.24 9.60e-01 1.09e+00 1.14e+01 angle pdb=" N ILE D 96 " pdb=" CA ILE D 96 " pdb=" C ILE D 96 " ideal model delta sigma weight residual 111.88 108.45 3.43 1.06e+00 8.90e-01 1.05e+01 angle pdb=" CA LEU L 148 " pdb=" CB LEU L 148 " pdb=" CG LEU L 148 " ideal model delta sigma weight residual 116.30 127.27 -10.97 3.50e+00 8.16e-02 9.82e+00 ... (remaining 40802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.88: 17532 24.88 - 49.76: 701 49.76 - 74.63: 85 74.63 - 99.51: 36 99.51 - 124.39: 1 Dihedral angle restraints: 18355 sinusoidal: 7533 harmonic: 10822 Sorted by residual: dihedral pdb=" C5' ADP A 602 " pdb=" O5' ADP A 602 " pdb=" PA ADP A 602 " pdb=" O2A ADP A 602 " ideal model delta sinusoidal sigma weight residual -60.00 64.39 -124.39 1 2.00e+01 2.50e-03 3.76e+01 dihedral pdb=" CA ARG K 87 " pdb=" C ARG K 87 " pdb=" N TYR K 88 " pdb=" CA TYR K 88 " ideal model delta harmonic sigma weight residual 180.00 158.30 21.70 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" O2A ADP A 602 " pdb=" O3A ADP A 602 " pdb=" PA ADP A 602 " pdb=" PB ADP A 602 " ideal model delta sinusoidal sigma weight residual -60.00 -129.64 69.64 1 2.00e+01 2.50e-03 1.57e+01 ... (remaining 18352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2991 0.035 - 0.071: 1027 0.071 - 0.106: 432 0.106 - 0.142: 119 0.142 - 0.177: 7 Chirality restraints: 4576 Sorted by residual: chirality pdb=" C2' ADP A 602 " pdb=" C1' ADP A 602 " pdb=" C3' ADP A 602 " pdb=" O2' ADP A 602 " both_signs ideal model delta sigma weight residual False -2.51 -2.69 0.18 2.00e-01 2.50e+01 7.86e-01 chirality pdb=" CA ARG K 87 " pdb=" N ARG K 87 " pdb=" C ARG K 87 " pdb=" CB ARG K 87 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.64e-01 chirality pdb=" CA PHE B 269 " pdb=" N PHE B 269 " pdb=" C PHE B 269 " pdb=" CB PHE B 269 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.09e-01 ... (remaining 4573 not shown) Planarity restraints: 5333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS E 323 " -0.030 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO E 324 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO E 324 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 324 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 277 " 0.028 5.00e-02 4.00e+02 4.24e-02 2.88e+00 pdb=" N PRO E 278 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO E 278 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 278 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS F 323 " 0.028 5.00e-02 4.00e+02 4.23e-02 2.86e+00 pdb=" N PRO F 324 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO F 324 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 324 " 0.024 5.00e-02 4.00e+02 ... (remaining 5330 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 195 2.54 - 3.13: 23076 3.13 - 3.72: 47409 3.72 - 4.31: 66105 4.31 - 4.90: 111974 Nonbonded interactions: 248759 Sorted by model distance: nonbonded pdb=" OG SER C 235 " pdb="MG MG C 601 " model vdw 1.949 2.170 nonbonded pdb=" OE2 GLU G 59 " pdb=" NH2 ARG G 132 " model vdw 2.062 3.120 nonbonded pdb=" OH TYR E 411 " pdb=" OE1 GLU E 450 " model vdw 2.107 3.040 nonbonded pdb=" OH TYR F 263 " pdb=" OD2 ASP F 290 " model vdw 2.110 3.040 nonbonded pdb=" O MET C 220 " pdb=" OG1 THR C 379 " model vdw 2.140 3.040 ... (remaining 248754 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: 4.160 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: 0.040 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 27.310 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 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 0.106 30112 Z= 0.204 Angle : 0.585 14.315 40807 Z= 0.309 Chirality : 0.044 0.177 4576 Planarity : 0.004 0.045 5333 Dihedral : 13.655 124.388 11437 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.14), residues: 3764 helix: 1.53 (0.14), residues: 1545 sheet: -0.29 (0.23), residues: 534 loop : 0.43 (0.16), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 132 TYR 0.015 0.001 TYR D 463 PHE 0.021 0.001 PHE B 269 TRP 0.013 0.001 TRP F 471 HIS 0.003 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00450 (30110) covalent geometry : angle 0.58522 (40807) hydrogen bonds : bond 0.13634 ( 1339) hydrogen bonds : angle 5.93153 ( 3846) Misc. bond : bond 0.00059 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 639 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8146 (mm) cc_final: 0.7872 (mt) REVERT: A 8 LYS cc_start: 0.7634 (ttmt) cc_final: 0.7273 (tttt) REVERT: A 124 LYS cc_start: 0.7447 (mtmm) cc_final: 0.7084 (mmtt) REVERT: A 180 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7635 (mt-10) REVERT: A 311 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7681 (mt-10) REVERT: A 323 MET cc_start: 0.7563 (mpp) cc_final: 0.7271 (mmt) REVERT: A 340 ARG cc_start: 0.7231 (mmt180) cc_final: 0.6927 (mmm160) REVERT: A 408 ARG cc_start: 0.7433 (ttt180) cc_final: 0.7219 (ttm-80) REVERT: A 452 ASP cc_start: 0.7000 (m-30) cc_final: 0.6272 (m-30) REVERT: A 491 ARG cc_start: 0.7384 (mtm110) cc_final: 0.7183 (mtm110) REVERT: A 492 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7396 (mt-10) REVERT: A 527 GLU cc_start: 0.6926 (tt0) cc_final: 0.6690 (tt0) REVERT: A 537 ASP cc_start: 0.6948 (m-30) cc_final: 0.6673 (t70) REVERT: B 7 GLN cc_start: 0.7852 (tm-30) cc_final: 0.7485 (tt0) REVERT: B 43 ASP cc_start: 0.7152 (t0) cc_final: 0.6892 (t70) REVERT: B 152 ASP cc_start: 0.6600 (p0) cc_final: 0.6303 (t70) REVERT: B 176 GLU cc_start: 0.6362 (mm-30) cc_final: 0.6006 (pm20) REVERT: B 271 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7450 (mt-10) REVERT: B 311 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6864 (mt-10) REVERT: B 348 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7491 (mm-30) REVERT: B 424 TRP cc_start: 0.6738 (p90) cc_final: 0.5883 (p90) REVERT: B 459 GLN cc_start: 0.6721 (tp-100) cc_final: 0.6355 (mm-40) REVERT: B 480 GLU cc_start: 0.6282 (mp0) cc_final: 0.5932 (mt-10) REVERT: B 509 MET cc_start: 0.5869 (mmm) cc_final: 0.5338 (mmm) REVERT: B 547 ARG cc_start: 0.4691 (tpp-160) cc_final: 0.4387 (tpp80) REVERT: B 550 ARG cc_start: 0.6385 (mmm160) cc_final: 0.5775 (mmp80) REVERT: B 558 GLU cc_start: 0.6446 (mt-10) cc_final: 0.6226 (tp30) REVERT: C 112 ASP cc_start: 0.8002 (t0) cc_final: 0.7737 (t70) REVERT: C 124 LYS cc_start: 0.8302 (mppt) cc_final: 0.7699 (mmtt) REVERT: C 161 LYS cc_start: 0.7789 (mmtp) cc_final: 0.7551 (mmtt) REVERT: C 267 VAL cc_start: 0.7584 (t) cc_final: 0.7073 (m) REVERT: C 343 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7814 (mt-10) REVERT: C 344 MET cc_start: 0.7974 (ttp) cc_final: 0.7297 (tpp) REVERT: C 408 ARG cc_start: 0.7115 (ttt180) cc_final: 0.6866 (ttt-90) REVERT: C 488 ARG cc_start: 0.7312 (tmm160) cc_final: 0.6471 (ttt90) REVERT: D 6 LYS cc_start: 0.8051 (tptp) cc_final: 0.7628 (tttm) REVERT: D 34 ASP cc_start: 0.7519 (m-30) cc_final: 0.7104 (p0) REVERT: D 74 SER cc_start: 0.8113 (p) cc_final: 0.7756 (t) REVERT: D 86 LYS cc_start: 0.7405 (mtpt) cc_final: 0.7171 (ttmt) REVERT: D 194 MET cc_start: 0.8777 (mtm) cc_final: 0.8573 (mtm) REVERT: D 203 TYR cc_start: 0.7851 (t80) cc_final: 0.7600 (t80) REVERT: D 264 CYS cc_start: 0.7686 (m) cc_final: 0.7123 (m) REVERT: D 338 GLN cc_start: 0.7967 (tt0) cc_final: 0.7641 (tt0) REVERT: D 368 LYS cc_start: 0.8043 (mtmt) cc_final: 0.7591 (mtmm) REVERT: D 377 GLN cc_start: 0.7181 (mt0) cc_final: 0.6777 (mm-40) REVERT: D 398 ILE cc_start: 0.7738 (pt) cc_final: 0.7502 (mt) REVERT: D 416 ASP cc_start: 0.7648 (t0) cc_final: 0.6872 (m-30) REVERT: D 428 GLN cc_start: 0.7457 (mt0) cc_final: 0.7114 (mt0) REVERT: E 79 VAL cc_start: 0.7888 (t) cc_final: 0.7686 (p) REVERT: E 186 PRO cc_start: 0.7081 (Cg_exo) cc_final: 0.6832 (Cg_endo) REVERT: E 206 GLN cc_start: 0.7289 (tm-30) cc_final: 0.6823 (pt0) REVERT: E 207 GLU cc_start: 0.6837 (mm-30) cc_final: 0.6578 (mm-30) REVERT: E 250 ASP cc_start: 0.7692 (m-30) cc_final: 0.6700 (t0) REVERT: E 260 MET cc_start: 0.8317 (mmm) cc_final: 0.7706 (mmm) REVERT: E 315 SER cc_start: 0.8027 (m) cc_final: 0.7788 (p) REVERT: E 362 MET cc_start: 0.7763 (ttt) cc_final: 0.7464 (ttp) REVERT: E 376 LYS cc_start: 0.6835 (ttpt) cc_final: 0.6582 (ttmm) REVERT: E 393 ARG cc_start: 0.5729 (ptp-170) cc_final: 0.5402 (ptp-170) REVERT: E 421 PHE cc_start: 0.6745 (m-80) cc_final: 0.6143 (m-80) REVERT: E 440 TRP cc_start: 0.6539 (m100) cc_final: 0.6270 (m100) REVERT: E 450 GLU cc_start: 0.6050 (mm-30) cc_final: 0.5336 (mt-10) REVERT: F 22 GLU cc_start: 0.7952 (pt0) cc_final: 0.7670 (pt0) REVERT: F 25 LYS cc_start: 0.8246 (ptmm) cc_final: 0.7852 (ptmt) REVERT: F 52 GLU cc_start: 0.7539 (pt0) cc_final: 0.7219 (mt-10) REVERT: F 128 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6955 (mt-10) REVERT: F 264 CYS cc_start: 0.8098 (m) cc_final: 0.7704 (m) REVERT: F 318 ASP cc_start: 0.6354 (p0) cc_final: 0.5807 (t0) REVERT: F 340 SER cc_start: 0.8389 (t) cc_final: 0.7762 (p) REVERT: F 406 GLU cc_start: 0.7165 (tp30) cc_final: 0.6553 (mm-30) REVERT: G 6 PRO cc_start: 0.8161 (Cg_endo) cc_final: 0.7904 (Cg_exo) REVERT: G 13 GLN cc_start: 0.7173 (tm-30) cc_final: 0.6493 (tm-30) REVERT: G 44 ARG cc_start: 0.7350 (mtp180) cc_final: 0.6940 (ttm170) REVERT: G 145 THR cc_start: 0.7834 (t) cc_final: 0.7587 (p) REVERT: G 184 GLU cc_start: 0.7096 (tt0) cc_final: 0.6771 (tp30) REVERT: G 187 GLU cc_start: 0.6816 (tt0) cc_final: 0.6602 (tt0) REVERT: H 18 LEU cc_start: 0.3588 (mm) cc_final: 0.2868 (tt) REVERT: H 71 LEU cc_start: 0.6443 (pp) cc_final: 0.6099 (pt) REVERT: H 90 MET cc_start: 0.6084 (tpp) cc_final: 0.5422 (tpp) REVERT: J 65 GLU cc_start: 0.3383 (tp30) cc_final: 0.3103 (tp30) REVERT: J 70 THR cc_start: 0.5159 (m) cc_final: 0.4956 (m) REVERT: J 78 GLU cc_start: 0.6113 (tp30) cc_final: 0.5626 (mt-10) REVERT: J 82 GLU cc_start: 0.5756 (mm-30) cc_final: 0.5298 (mt-10) REVERT: J 103 VAL cc_start: 0.5950 (m) cc_final: 0.5726 (p) REVERT: J 113 GLU cc_start: 0.6754 (tm-30) cc_final: 0.6427 (pt0) REVERT: L 65 GLU cc_start: 0.5057 (pp20) cc_final: 0.3997 (tp30) REVERT: L 67 LEU cc_start: 0.6106 (pp) cc_final: 0.5398 (tp) REVERT: L 81 GLU cc_start: 0.7153 (pp20) cc_final: 0.5878 (mm-30) REVERT: L 82 GLU cc_start: 0.5948 (tp30) cc_final: 0.4990 (tt0) REVERT: L 88 ARG cc_start: 0.6419 (mtp-110) cc_final: 0.5914 (tmm-80) REVERT: L 109 LEU cc_start: 0.7083 (pp) cc_final: 0.6276 (mt) REVERT: L 141 GLU cc_start: 0.5950 (tt0) cc_final: 0.5565 (tp30) REVERT: L 173 ARG cc_start: 0.6339 (mmm-85) cc_final: 0.4976 (ttt180) outliers start: 0 outliers final: 0 residues processed: 639 average time/residue: 0.2493 time to fit residues: 234.5983 Evaluate side-chains 375 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.0770 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 6.9990 overall best weight: 3.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN C 571 GLN D 170 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 58 GLN E 129 GLN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 GLN F 206 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.129922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.104080 restraints weight = 46512.418| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.55 r_work: 0.3166 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 30112 Z= 0.243 Angle : 0.630 8.271 40807 Z= 0.321 Chirality : 0.048 0.215 4576 Planarity : 0.005 0.052 5333 Dihedral : 6.238 104.912 4231 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.97 % Allowed : 7.88 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.14), residues: 3764 helix: 1.26 (0.13), residues: 1567 sheet: -0.48 (0.21), residues: 599 loop : 0.23 (0.16), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 139 TYR 0.019 0.002 TYR E 54 PHE 0.018 0.002 PHE A 559 TRP 0.012 0.002 TRP B 119 HIS 0.005 0.001 HIS E 375 Details of bonding type rmsd covalent geometry : bond 0.00585 (30110) covalent geometry : angle 0.63050 (40807) hydrogen bonds : bond 0.04786 ( 1339) hydrogen bonds : angle 4.96303 ( 3846) Misc. bond : bond 0.01311 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 377 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8047 (t0) cc_final: 0.7804 (t70) REVERT: A 340 ARG cc_start: 0.7900 (mmt180) cc_final: 0.7633 (mmm160) REVERT: A 452 ASP cc_start: 0.7800 (m-30) cc_final: 0.7399 (m-30) REVERT: A 469 GLN cc_start: 0.7071 (OUTLIER) cc_final: 0.5958 (mp10) REVERT: B 7 GLN cc_start: 0.8445 (tm-30) cc_final: 0.8069 (tt0) REVERT: B 152 ASP cc_start: 0.6990 (p0) cc_final: 0.6739 (t70) REVERT: B 271 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7835 (mt-10) REVERT: B 424 TRP cc_start: 0.7478 (p90) cc_final: 0.7261 (p-90) REVERT: B 447 TYR cc_start: 0.6679 (t80) cc_final: 0.6416 (t80) REVERT: B 459 GLN cc_start: 0.7467 (tp-100) cc_final: 0.7234 (mm-40) REVERT: B 493 ASP cc_start: 0.6491 (m-30) cc_final: 0.5932 (t0) REVERT: B 547 ARG cc_start: 0.5533 (tpp-160) cc_final: 0.5188 (tpp80) REVERT: B 550 ARG cc_start: 0.7006 (mmm160) cc_final: 0.6438 (mmp80) REVERT: C 124 LYS cc_start: 0.8515 (mppt) cc_final: 0.8232 (mmtt) REVERT: C 197 ARG cc_start: 0.8312 (ttp-110) cc_final: 0.8105 (mtm110) REVERT: C 267 VAL cc_start: 0.8626 (t) cc_final: 0.8242 (m) REVERT: C 343 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7859 (mt-10) REVERT: D 74 SER cc_start: 0.8638 (p) cc_final: 0.8403 (t) REVERT: D 264 CYS cc_start: 0.8653 (m) cc_final: 0.8358 (m) REVERT: D 377 GLN cc_start: 0.7722 (mt0) cc_final: 0.7520 (mm-40) REVERT: D 394 LYS cc_start: 0.8228 (ttmm) cc_final: 0.7957 (mtpt) REVERT: D 398 ILE cc_start: 0.8664 (pt) cc_final: 0.8175 (mt) REVERT: D 434 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7779 (mm-30) REVERT: E 133 THR cc_start: 0.8507 (OUTLIER) cc_final: 0.8238 (t) REVERT: E 250 ASP cc_start: 0.8397 (m-30) cc_final: 0.8024 (t0) REVERT: E 421 PHE cc_start: 0.7945 (m-80) cc_final: 0.7710 (m-80) REVERT: E 440 TRP cc_start: 0.7022 (m100) cc_final: 0.6741 (m100) REVERT: G 6 PRO cc_start: 0.8572 (Cg_endo) cc_final: 0.8120 (Cg_exo) REVERT: G 202 GLU cc_start: 0.5651 (tp30) cc_final: 0.5410 (tm-30) REVERT: H 1 MET cc_start: 0.5069 (mmt) cc_final: 0.4782 (mtt) REVERT: H 71 LEU cc_start: 0.6148 (pp) cc_final: 0.5458 (mp) REVERT: H 90 MET cc_start: 0.6141 (tpp) cc_final: 0.5853 (tpp) REVERT: J 65 GLU cc_start: 0.4187 (tp30) cc_final: 0.3843 (tp30) REVERT: L 65 GLU cc_start: 0.5321 (pp20) cc_final: 0.4031 (tp30) REVERT: L 67 LEU cc_start: 0.6046 (pp) cc_final: 0.5119 (tp) REVERT: L 74 GLN cc_start: 0.7176 (mm-40) cc_final: 0.6797 (mm-40) REVERT: L 81 GLU cc_start: 0.7194 (pp20) cc_final: 0.5768 (mm-30) REVERT: L 82 GLU cc_start: 0.5905 (tp30) cc_final: 0.4857 (tt0) REVERT: L 141 GLU cc_start: 0.5860 (tt0) cc_final: 0.5543 (tp30) outliers start: 30 outliers final: 20 residues processed: 401 average time/residue: 0.2276 time to fit residues: 139.4122 Evaluate side-chains 313 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 290 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 434 GLU Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain E residue 336 GLN Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain L residue 103 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 281 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 139 optimal weight: 7.9990 chunk 297 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 270 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 307 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 571 GLN E 170 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.131679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.106885 restraints weight = 46280.556| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.50 r_work: 0.3209 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30112 Z= 0.121 Angle : 0.524 8.999 40807 Z= 0.265 Chirality : 0.044 0.159 4576 Planarity : 0.004 0.064 5333 Dihedral : 5.957 110.725 4231 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.17 % Allowed : 10.09 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.14), residues: 3764 helix: 1.37 (0.13), residues: 1570 sheet: -0.45 (0.21), residues: 592 loop : 0.27 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 547 TYR 0.015 0.001 TYR E 54 PHE 0.012 0.001 PHE B 559 TRP 0.011 0.001 TRP F 471 HIS 0.006 0.001 HIS E 375 Details of bonding type rmsd covalent geometry : bond 0.00273 (30110) covalent geometry : angle 0.52443 (40807) hydrogen bonds : bond 0.03905 ( 1339) hydrogen bonds : angle 4.66360 ( 3846) Misc. bond : bond 0.00036 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 324 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.7940 (t0) cc_final: 0.7727 (t70) REVERT: A 264 ASP cc_start: 0.6891 (m-30) cc_final: 0.6646 (m-30) REVERT: A 340 ARG cc_start: 0.7828 (mmt180) cc_final: 0.7537 (mmm160) REVERT: A 452 ASP cc_start: 0.7743 (m-30) cc_final: 0.7318 (m-30) REVERT: A 469 GLN cc_start: 0.7105 (OUTLIER) cc_final: 0.5867 (mp10) REVERT: B 7 GLN cc_start: 0.8366 (tm-30) cc_final: 0.7994 (tt0) REVERT: B 152 ASP cc_start: 0.6859 (p0) cc_final: 0.6588 (t70) REVERT: B 156 ARG cc_start: 0.7738 (ttm-80) cc_final: 0.7449 (mtm180) REVERT: B 424 TRP cc_start: 0.7445 (p90) cc_final: 0.7195 (p-90) REVERT: B 459 GLN cc_start: 0.7402 (tp-100) cc_final: 0.7177 (mm-40) REVERT: B 482 LEU cc_start: 0.7430 (tp) cc_final: 0.7210 (tt) REVERT: B 488 ARG cc_start: 0.7571 (ttp80) cc_final: 0.6539 (mtp180) REVERT: B 489 ILE cc_start: 0.6918 (OUTLIER) cc_final: 0.6557 (mt) REVERT: B 493 ASP cc_start: 0.6313 (m-30) cc_final: 0.5846 (t0) REVERT: B 547 ARG cc_start: 0.5625 (tpp-160) cc_final: 0.5285 (tpp80) REVERT: B 550 ARG cc_start: 0.7028 (mmm160) cc_final: 0.6416 (mmp80) REVERT: C 124 LYS cc_start: 0.8444 (mppt) cc_final: 0.8165 (mmtt) REVERT: C 156 ARG cc_start: 0.7866 (ptp-110) cc_final: 0.7588 (ptp-110) REVERT: C 267 VAL cc_start: 0.8566 (t) cc_final: 0.8212 (m) REVERT: C 343 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7819 (mt-10) REVERT: C 567 MET cc_start: 0.7645 (mmm) cc_final: 0.7279 (mmm) REVERT: D 9 THR cc_start: 0.7564 (OUTLIER) cc_final: 0.7026 (p) REVERT: D 264 CYS cc_start: 0.8528 (m) cc_final: 0.8099 (m) REVERT: D 377 GLN cc_start: 0.7679 (mt0) cc_final: 0.7422 (mm-40) REVERT: D 394 LYS cc_start: 0.8154 (ttmm) cc_final: 0.7915 (mtpt) REVERT: D 398 ILE cc_start: 0.8602 (pt) cc_final: 0.8184 (mt) REVERT: D 456 LYS cc_start: 0.7926 (tptp) cc_final: 0.7680 (mmmt) REVERT: E 250 ASP cc_start: 0.8337 (m-30) cc_final: 0.8032 (t0) REVERT: E 411 TYR cc_start: 0.6264 (m-80) cc_final: 0.6031 (m-80) REVERT: E 421 PHE cc_start: 0.7859 (m-80) cc_final: 0.7649 (m-80) REVERT: E 440 TRP cc_start: 0.6938 (m100) cc_final: 0.6713 (m100) REVERT: G 6 PRO cc_start: 0.8516 (Cg_endo) cc_final: 0.8095 (Cg_exo) REVERT: G 197 ILE cc_start: 0.7351 (pt) cc_final: 0.7005 (mm) REVERT: H 90 MET cc_start: 0.6101 (tpp) cc_final: 0.5868 (tpp) REVERT: J 65 GLU cc_start: 0.4213 (tp30) cc_final: 0.3949 (tp30) REVERT: J 162 GLN cc_start: 0.7650 (pm20) cc_final: 0.7381 (pm20) REVERT: L 65 GLU cc_start: 0.5520 (pp20) cc_final: 0.4298 (mt-10) REVERT: L 67 LEU cc_start: 0.6114 (pp) cc_final: 0.5133 (tp) REVERT: L 74 GLN cc_start: 0.7252 (mm-40) cc_final: 0.6828 (mm-40) REVERT: L 81 GLU cc_start: 0.7170 (pp20) cc_final: 0.5881 (mm-30) REVERT: L 82 GLU cc_start: 0.5811 (tp30) cc_final: 0.4887 (tt0) REVERT: L 141 GLU cc_start: 0.5817 (tt0) cc_final: 0.5518 (tp30) REVERT: L 145 GLU cc_start: 0.2845 (tp30) cc_final: 0.2276 (mm-30) outliers start: 36 outliers final: 21 residues processed: 352 average time/residue: 0.2242 time to fit residues: 120.7783 Evaluate side-chains 318 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 294 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 280 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 88 optimal weight: 7.9990 chunk 294 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 233 optimal weight: 8.9990 chunk 325 optimal weight: 0.9990 chunk 202 optimal weight: 9.9990 chunk 224 optimal weight: 6.9990 chunk 260 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 HIS B 81 ASN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.127191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.102167 restraints weight = 46679.315| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.53 r_work: 0.3130 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.068 30112 Z= 0.352 Angle : 0.724 13.140 40807 Z= 0.366 Chirality : 0.051 0.221 4576 Planarity : 0.006 0.069 5333 Dihedral : 6.371 102.984 4231 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.08 % Favored : 96.89 % Rotamer: Outliers : 2.27 % Allowed : 12.49 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.14), residues: 3764 helix: 0.75 (0.13), residues: 1572 sheet: -0.78 (0.21), residues: 591 loop : -0.25 (0.16), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 193 TYR 0.019 0.002 TYR E 54 PHE 0.021 0.003 PHE B 230 TRP 0.014 0.002 TRP F 471 HIS 0.006 0.002 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00855 (30110) covalent geometry : angle 0.72441 (40807) hydrogen bonds : bond 0.05234 ( 1339) hydrogen bonds : angle 5.03737 ( 3846) Misc. bond : bond 0.00273 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 288 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 ASP cc_start: 0.8168 (t0) cc_final: 0.7899 (t0) REVERT: A 122 MET cc_start: 0.8082 (mtp) cc_final: 0.7732 (ttm) REVERT: A 452 ASP cc_start: 0.7755 (m-30) cc_final: 0.7360 (m-30) REVERT: A 469 GLN cc_start: 0.7136 (OUTLIER) cc_final: 0.6407 (mp10) REVERT: B 269 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8625 (m-80) REVERT: B 493 ASP cc_start: 0.6396 (m-30) cc_final: 0.5952 (t0) REVERT: B 547 ARG cc_start: 0.5846 (tpp-160) cc_final: 0.5363 (tpp80) REVERT: B 550 ARG cc_start: 0.7030 (mmm160) cc_final: 0.6392 (mmp80) REVERT: C 124 LYS cc_start: 0.8544 (mppt) cc_final: 0.8304 (mmtt) REVERT: C 476 LEU cc_start: 0.6563 (OUTLIER) cc_final: 0.6067 (mt) REVERT: C 488 ARG cc_start: 0.8600 (ttp-170) cc_final: 0.8113 (ttt90) REVERT: D 106 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8121 (pt) REVERT: D 264 CYS cc_start: 0.8726 (m) cc_final: 0.8287 (m) REVERT: D 377 GLN cc_start: 0.7775 (mt0) cc_final: 0.7532 (mm-40) REVERT: D 394 LYS cc_start: 0.8354 (ttmm) cc_final: 0.8043 (mtpt) REVERT: D 398 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8228 (mt) REVERT: D 434 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7709 (mm-30) REVERT: E 57 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8925 (mt) REVERT: E 133 THR cc_start: 0.8588 (OUTLIER) cc_final: 0.8304 (t) REVERT: E 250 ASP cc_start: 0.8390 (m-30) cc_final: 0.8005 (t0) REVERT: E 421 PHE cc_start: 0.8173 (m-80) cc_final: 0.7807 (m-80) REVERT: E 440 TRP cc_start: 0.7046 (m100) cc_final: 0.6812 (m100) REVERT: G 6 PRO cc_start: 0.8637 (Cg_endo) cc_final: 0.8133 (Cg_exo) REVERT: H 19 GLU cc_start: 0.4141 (tp30) cc_final: 0.3572 (mp0) REVERT: H 44 LEU cc_start: 0.6106 (OUTLIER) cc_final: 0.5800 (mp) REVERT: H 90 MET cc_start: 0.6292 (tpp) cc_final: 0.5866 (tpp) REVERT: L 65 GLU cc_start: 0.5554 (pp20) cc_final: 0.4264 (tp30) REVERT: L 81 GLU cc_start: 0.7209 (pp20) cc_final: 0.5818 (mm-30) REVERT: L 141 GLU cc_start: 0.6091 (tt0) cc_final: 0.5547 (tp30) outliers start: 70 outliers final: 47 residues processed: 346 average time/residue: 0.2052 time to fit residues: 110.9072 Evaluate side-chains 320 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 264 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain D residue 434 GLU Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 336 GLN Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 126 LYS Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 394 LYS Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 179 SER Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 161 THR Chi-restraints excluded: chain L residue 182 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 39 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 330 optimal weight: 10.0000 chunk 274 optimal weight: 9.9990 chunk 175 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 348 optimal weight: 1.9990 chunk 230 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN F 437 GLN J 162 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.130597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.104828 restraints weight = 46346.254| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.55 r_work: 0.3183 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30112 Z= 0.142 Angle : 0.545 15.608 40807 Z= 0.275 Chirality : 0.044 0.158 4576 Planarity : 0.005 0.048 5333 Dihedral : 6.000 114.601 4231 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.75 % Allowed : 13.79 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.14), residues: 3764 helix: 1.08 (0.13), residues: 1572 sheet: -0.83 (0.20), residues: 607 loop : -0.03 (0.16), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 488 TYR 0.020 0.001 TYR B 513 PHE 0.012 0.001 PHE B 230 TRP 0.011 0.001 TRP B 119 HIS 0.005 0.001 HIS E 375 Details of bonding type rmsd covalent geometry : bond 0.00331 (30110) covalent geometry : angle 0.54515 (40807) hydrogen bonds : bond 0.04012 ( 1339) hydrogen bonds : angle 4.69746 ( 3846) Misc. bond : bond 0.00121 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 288 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8048 (mtp) cc_final: 0.7686 (ttm) REVERT: A 340 ARG cc_start: 0.7851 (mmt-90) cc_final: 0.7646 (mmm160) REVERT: A 452 ASP cc_start: 0.7748 (m-30) cc_final: 0.7334 (m-30) REVERT: A 469 GLN cc_start: 0.7036 (OUTLIER) cc_final: 0.5806 (mp10) REVERT: B 488 ARG cc_start: 0.7560 (ttp80) cc_final: 0.6430 (mtp180) REVERT: B 489 ILE cc_start: 0.6974 (OUTLIER) cc_final: 0.6584 (mt) REVERT: B 493 ASP cc_start: 0.6352 (m-30) cc_final: 0.5988 (t0) REVERT: B 547 ARG cc_start: 0.5802 (tpp-160) cc_final: 0.5338 (tpp80) REVERT: B 550 ARG cc_start: 0.6952 (mmm160) cc_final: 0.6318 (mmp80) REVERT: C 124 LYS cc_start: 0.8475 (mppt) cc_final: 0.8232 (mmtt) REVERT: C 476 LEU cc_start: 0.6541 (OUTLIER) cc_final: 0.6045 (mt) REVERT: C 488 ARG cc_start: 0.8562 (ttp-170) cc_final: 0.8066 (ttt90) REVERT: C 567 MET cc_start: 0.7642 (mmm) cc_final: 0.7329 (mmm) REVERT: D 264 CYS cc_start: 0.8575 (m) cc_final: 0.8119 (m) REVERT: D 377 GLN cc_start: 0.7691 (mt0) cc_final: 0.7449 (mm-40) REVERT: D 394 LYS cc_start: 0.8199 (ttmm) cc_final: 0.7909 (mtpt) REVERT: D 398 ILE cc_start: 0.8653 (pt) cc_final: 0.8270 (mt) REVERT: E 250 ASP cc_start: 0.8363 (m-30) cc_final: 0.7944 (t0) REVERT: E 421 PHE cc_start: 0.8095 (m-80) cc_final: 0.7803 (m-80) REVERT: E 440 TRP cc_start: 0.6954 (m100) cc_final: 0.6743 (m100) REVERT: G 6 PRO cc_start: 0.8502 (Cg_endo) cc_final: 0.8042 (Cg_exo) REVERT: H 19 GLU cc_start: 0.4189 (tp30) cc_final: 0.3655 (mp0) REVERT: H 90 MET cc_start: 0.6161 (tpp) cc_final: 0.5928 (tpp) REVERT: J 148 LEU cc_start: 0.6604 (OUTLIER) cc_final: 0.5971 (tt) REVERT: L 65 GLU cc_start: 0.5469 (pp20) cc_final: 0.4157 (tp30) REVERT: L 81 GLU cc_start: 0.7199 (pp20) cc_final: 0.5946 (mm-30) REVERT: L 141 GLU cc_start: 0.6016 (tt0) cc_final: 0.5518 (tp30) outliers start: 54 outliers final: 35 residues processed: 336 average time/residue: 0.2062 time to fit residues: 107.1451 Evaluate side-chains 308 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 269 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 394 LYS Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 162 GLN Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 119 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 240 optimal weight: 0.8980 chunk 236 optimal weight: 10.0000 chunk 283 optimal weight: 2.9990 chunk 238 optimal weight: 3.9990 chunk 349 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 353 optimal weight: 0.0470 chunk 26 optimal weight: 1.9990 chunk 340 optimal weight: 10.0000 overall best weight: 1.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 ASN F 206 GLN F 437 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.130784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.105202 restraints weight = 46098.046| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.55 r_work: 0.3192 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30112 Z= 0.139 Angle : 0.531 10.359 40807 Z= 0.267 Chirality : 0.044 0.205 4576 Planarity : 0.004 0.049 5333 Dihedral : 5.824 117.816 4231 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.95 % Allowed : 14.14 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.14), residues: 3764 helix: 1.26 (0.13), residues: 1559 sheet: -0.91 (0.20), residues: 638 loop : 0.07 (0.16), residues: 1567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 93 TYR 0.013 0.001 TYR E 286 PHE 0.014 0.001 PHE B 559 TRP 0.011 0.001 TRP B 119 HIS 0.005 0.001 HIS E 375 Details of bonding type rmsd covalent geometry : bond 0.00324 (30110) covalent geometry : angle 0.53070 (40807) hydrogen bonds : bond 0.03836 ( 1339) hydrogen bonds : angle 4.59251 ( 3846) Misc. bond : bond 0.00112 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 282 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8007 (mtp) cc_final: 0.7674 (ttm) REVERT: A 452 ASP cc_start: 0.7712 (m-30) cc_final: 0.7296 (m-30) REVERT: A 469 GLN cc_start: 0.7057 (OUTLIER) cc_final: 0.5777 (mp10) REVERT: B 488 ARG cc_start: 0.7514 (ttp80) cc_final: 0.6347 (mtp180) REVERT: B 489 ILE cc_start: 0.6923 (OUTLIER) cc_final: 0.6563 (mt) REVERT: B 493 ASP cc_start: 0.6132 (m-30) cc_final: 0.5802 (t0) REVERT: B 520 LEU cc_start: 0.6947 (OUTLIER) cc_final: 0.6594 (tt) REVERT: B 547 ARG cc_start: 0.5867 (tpp-160) cc_final: 0.5396 (tpp80) REVERT: B 550 ARG cc_start: 0.7040 (mmm160) cc_final: 0.6410 (mmp80) REVERT: C 124 LYS cc_start: 0.8469 (mppt) cc_final: 0.8227 (mmtt) REVERT: C 476 LEU cc_start: 0.6518 (OUTLIER) cc_final: 0.6035 (mt) REVERT: C 488 ARG cc_start: 0.8565 (ttp-170) cc_final: 0.8042 (ttt90) REVERT: C 567 MET cc_start: 0.7648 (mmm) cc_final: 0.7357 (mmm) REVERT: D 9 THR cc_start: 0.7607 (OUTLIER) cc_final: 0.7100 (p) REVERT: D 106 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.7972 (pt) REVERT: D 264 CYS cc_start: 0.8540 (m) cc_final: 0.8080 (m) REVERT: D 268 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.8227 (ttt180) REVERT: D 377 GLN cc_start: 0.7692 (mt0) cc_final: 0.7455 (mm-40) REVERT: D 394 LYS cc_start: 0.8149 (ttmm) cc_final: 0.7860 (mtpt) REVERT: D 398 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8307 (mt) REVERT: E 236 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7547 (mmt-90) REVERT: E 411 TYR cc_start: 0.6271 (m-80) cc_final: 0.6015 (m-80) REVERT: E 421 PHE cc_start: 0.8052 (m-80) cc_final: 0.7794 (m-80) REVERT: E 440 TRP cc_start: 0.6933 (m100) cc_final: 0.6722 (m100) REVERT: G 6 PRO cc_start: 0.8560 (Cg_endo) cc_final: 0.8112 (Cg_exo) REVERT: J 148 LEU cc_start: 0.6559 (OUTLIER) cc_final: 0.5987 (tt) REVERT: L 81 GLU cc_start: 0.7210 (pp20) cc_final: 0.5980 (mm-30) REVERT: L 82 GLU cc_start: 0.5918 (tp30) cc_final: 0.4738 (tt0) REVERT: L 109 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.6471 (mt) REVERT: L 141 GLU cc_start: 0.5934 (tt0) cc_final: 0.5477 (tp30) outliers start: 60 outliers final: 42 residues processed: 336 average time/residue: 0.2067 time to fit residues: 108.2353 Evaluate side-chains 325 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 272 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 236 ARG Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 394 LYS Chi-restraints excluded: chain F residue 437 GLN Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 182 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 276 optimal weight: 1.9990 chunk 209 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 76 optimal weight: 0.2980 chunk 228 optimal weight: 0.6980 chunk 213 optimal weight: 6.9990 chunk 168 optimal weight: 8.9990 chunk 68 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 GLN A 501 HIS B 81 ASN J 162 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.131173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.105443 restraints weight = 46266.043| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.49 r_work: 0.3202 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30112 Z= 0.128 Angle : 0.516 8.852 40807 Z= 0.260 Chirality : 0.043 0.208 4576 Planarity : 0.004 0.048 5333 Dihedral : 5.719 120.128 4231 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.17 % Allowed : 14.66 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.14), residues: 3764 helix: 1.31 (0.13), residues: 1554 sheet: -0.88 (0.20), residues: 614 loop : 0.07 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 174 TYR 0.011 0.001 TYR E 286 PHE 0.032 0.001 PHE G 108 TRP 0.010 0.001 TRP C 119 HIS 0.004 0.001 HIS E 375 Details of bonding type rmsd covalent geometry : bond 0.00299 (30110) covalent geometry : angle 0.51604 (40807) hydrogen bonds : bond 0.03687 ( 1339) hydrogen bonds : angle 4.53408 ( 3846) Misc. bond : bond 0.00100 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 287 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.7970 (mtp) cc_final: 0.7677 (ttm) REVERT: A 452 ASP cc_start: 0.7724 (m-30) cc_final: 0.7305 (m-30) REVERT: A 469 GLN cc_start: 0.7051 (OUTLIER) cc_final: 0.6590 (mp10) REVERT: B 488 ARG cc_start: 0.7505 (ttp80) cc_final: 0.6341 (mtp180) REVERT: B 489 ILE cc_start: 0.6991 (OUTLIER) cc_final: 0.6660 (mt) REVERT: B 493 ASP cc_start: 0.6130 (m-30) cc_final: 0.5817 (t0) REVERT: B 520 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6580 (tt) REVERT: B 547 ARG cc_start: 0.5886 (tpp-160) cc_final: 0.5407 (tpp80) REVERT: B 550 ARG cc_start: 0.7009 (mmm160) cc_final: 0.6333 (mmp80) REVERT: C 124 LYS cc_start: 0.8448 (mppt) cc_final: 0.8215 (mmtt) REVERT: C 476 LEU cc_start: 0.6517 (OUTLIER) cc_final: 0.6034 (mt) REVERT: C 488 ARG cc_start: 0.8528 (ttp-170) cc_final: 0.8005 (ttt90) REVERT: D 9 THR cc_start: 0.7570 (OUTLIER) cc_final: 0.7024 (p) REVERT: D 106 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.7957 (pt) REVERT: D 236 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7904 (mpt180) REVERT: D 264 CYS cc_start: 0.8503 (m) cc_final: 0.8067 (m) REVERT: D 268 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8194 (ttt180) REVERT: D 377 GLN cc_start: 0.7666 (mt0) cc_final: 0.7427 (mm-40) REVERT: D 394 LYS cc_start: 0.8113 (ttmm) cc_final: 0.7827 (mtpt) REVERT: D 398 ILE cc_start: 0.8651 (pt) cc_final: 0.8316 (mt) REVERT: E 236 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7557 (mmt-90) REVERT: E 250 ASP cc_start: 0.8318 (m-30) cc_final: 0.7901 (t0) REVERT: E 421 PHE cc_start: 0.7988 (m-80) cc_final: 0.7741 (m-80) REVERT: E 440 TRP cc_start: 0.6925 (m100) cc_final: 0.6716 (m100) REVERT: E 446 LEU cc_start: 0.6204 (mp) cc_final: 0.5478 (tp) REVERT: G 6 PRO cc_start: 0.8515 (Cg_endo) cc_final: 0.8078 (Cg_exo) REVERT: J 148 LEU cc_start: 0.6512 (OUTLIER) cc_final: 0.6031 (tt) REVERT: L 65 GLU cc_start: 0.5527 (pp20) cc_final: 0.3964 (mt-10) REVERT: L 81 GLU cc_start: 0.7185 (pp20) cc_final: 0.6052 (mm-30) REVERT: L 82 GLU cc_start: 0.5876 (tp30) cc_final: 0.4735 (tt0) REVERT: L 109 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.6519 (mt) REVERT: L 141 GLU cc_start: 0.5837 (tt0) cc_final: 0.5418 (tp30) outliers start: 67 outliers final: 49 residues processed: 346 average time/residue: 0.2150 time to fit residues: 114.6402 Evaluate side-chains 330 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 270 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 236 ARG Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 236 ARG Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 394 LYS Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 182 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 260 optimal weight: 7.9990 chunk 359 optimal weight: 20.0000 chunk 244 optimal weight: 5.9990 chunk 182 optimal weight: 0.0770 chunk 265 optimal weight: 6.9990 chunk 348 optimal weight: 9.9990 chunk 237 optimal weight: 3.9990 chunk 240 optimal weight: 2.9990 chunk 333 optimal weight: 30.0000 chunk 295 optimal weight: 0.9990 chunk 350 optimal weight: 9.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 GLN F 437 GLN J 162 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.130323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.104989 restraints weight = 46344.524| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.52 r_work: 0.3177 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 30112 Z= 0.183 Angle : 0.559 8.338 40807 Z= 0.283 Chirality : 0.045 0.217 4576 Planarity : 0.005 0.049 5333 Dihedral : 5.748 116.961 4231 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.43 % Allowed : 14.82 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.14), residues: 3764 helix: 1.23 (0.13), residues: 1554 sheet: -0.91 (0.20), residues: 614 loop : -0.03 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 340 TYR 0.014 0.001 TYR E 286 PHE 0.019 0.002 PHE G 108 TRP 0.010 0.001 TRP F 471 HIS 0.005 0.001 HIS A 501 Details of bonding type rmsd covalent geometry : bond 0.00440 (30110) covalent geometry : angle 0.55876 (40807) hydrogen bonds : bond 0.04037 ( 1339) hydrogen bonds : angle 4.62694 ( 3846) Misc. bond : bond 0.00146 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 271 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8090 (mtp) cc_final: 0.7809 (ttm) REVERT: A 452 ASP cc_start: 0.7724 (m-30) cc_final: 0.7323 (m-30) REVERT: A 469 GLN cc_start: 0.7029 (OUTLIER) cc_final: 0.5806 (mp10) REVERT: B 488 ARG cc_start: 0.7532 (ttp80) cc_final: 0.6335 (mtp180) REVERT: B 489 ILE cc_start: 0.6998 (OUTLIER) cc_final: 0.6685 (mt) REVERT: B 493 ASP cc_start: 0.6208 (m-30) cc_final: 0.5923 (t0) REVERT: B 520 LEU cc_start: 0.6913 (OUTLIER) cc_final: 0.6564 (tt) REVERT: B 547 ARG cc_start: 0.5928 (tpp-160) cc_final: 0.5416 (tpp80) REVERT: B 550 ARG cc_start: 0.7012 (mmm160) cc_final: 0.6340 (mmp80) REVERT: C 124 LYS cc_start: 0.8483 (mppt) cc_final: 0.8251 (mmtt) REVERT: C 238 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8131 (mt0) REVERT: C 476 LEU cc_start: 0.6534 (OUTLIER) cc_final: 0.6036 (mt) REVERT: C 488 ARG cc_start: 0.8574 (ttp-170) cc_final: 0.8043 (ttt90) REVERT: D 9 THR cc_start: 0.7664 (OUTLIER) cc_final: 0.7132 (p) REVERT: D 106 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.8008 (pt) REVERT: D 236 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7931 (mpt180) REVERT: D 264 CYS cc_start: 0.8565 (m) cc_final: 0.8136 (m) REVERT: D 268 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8258 (ttt180) REVERT: D 377 GLN cc_start: 0.7711 (mt0) cc_final: 0.7462 (mm-40) REVERT: D 394 LYS cc_start: 0.8162 (ttmm) cc_final: 0.7856 (mtpt) REVERT: D 398 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8316 (mt) REVERT: E 4 LEU cc_start: 0.0934 (OUTLIER) cc_final: 0.0382 (tp) REVERT: E 236 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7414 (mmt-90) REVERT: E 250 ASP cc_start: 0.8372 (m-30) cc_final: 0.7924 (t0) REVERT: E 411 TYR cc_start: 0.6247 (m-80) cc_final: 0.6007 (m-80) REVERT: E 440 TRP cc_start: 0.6992 (m100) cc_final: 0.6774 (m100) REVERT: E 446 LEU cc_start: 0.6290 (mp) cc_final: 0.5592 (tp) REVERT: G 6 PRO cc_start: 0.8603 (Cg_endo) cc_final: 0.8150 (Cg_exo) REVERT: H 19 GLU cc_start: 0.4126 (tp30) cc_final: 0.3697 (mp0) REVERT: J 131 LEU cc_start: 0.5177 (mt) cc_final: 0.4823 (mm) REVERT: J 148 LEU cc_start: 0.6492 (OUTLIER) cc_final: 0.6058 (tt) REVERT: L 65 GLU cc_start: 0.5533 (pp20) cc_final: 0.3971 (mt-10) REVERT: L 81 GLU cc_start: 0.7180 (pp20) cc_final: 0.6078 (mm-30) REVERT: L 82 GLU cc_start: 0.5946 (tp30) cc_final: 0.4737 (tt0) REVERT: L 109 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.6532 (mt) REVERT: L 141 GLU cc_start: 0.5756 (tt0) cc_final: 0.5344 (tp30) outliers start: 75 outliers final: 48 residues processed: 339 average time/residue: 0.2136 time to fit residues: 111.8320 Evaluate side-chains 337 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 275 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain B residue 79 MET Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 238 GLN Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 375 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 236 ARG Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 236 ARG Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 394 LYS Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 182 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 175 optimal weight: 1.9990 chunk 364 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 305 optimal weight: 2.9990 chunk 190 optimal weight: 0.0040 chunk 150 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 341 optimal weight: 10.0000 chunk 301 optimal weight: 3.9990 chunk 197 optimal weight: 0.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN F 161 ASN F 437 GLN J 162 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.132276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.106946 restraints weight = 46065.395| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.51 r_work: 0.3219 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30112 Z= 0.113 Angle : 0.504 7.874 40807 Z= 0.255 Chirality : 0.043 0.215 4576 Planarity : 0.004 0.048 5333 Dihedral : 5.525 122.838 4231 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.98 % Allowed : 15.50 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.14), residues: 3764 helix: 1.40 (0.13), residues: 1552 sheet: -0.89 (0.20), residues: 594 loop : 0.10 (0.16), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 93 TYR 0.013 0.001 TYR E 286 PHE 0.015 0.001 PHE B 559 TRP 0.011 0.001 TRP C 119 HIS 0.004 0.001 HIS E 375 Details of bonding type rmsd covalent geometry : bond 0.00261 (30110) covalent geometry : angle 0.50374 (40807) hydrogen bonds : bond 0.03509 ( 1339) hydrogen bonds : angle 4.46660 ( 3846) Misc. bond : bond 0.00080 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 295 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.7999 (mtp) cc_final: 0.7751 (ttm) REVERT: A 452 ASP cc_start: 0.7695 (m-30) cc_final: 0.7285 (m-30) REVERT: A 469 GLN cc_start: 0.7014 (OUTLIER) cc_final: 0.6563 (mp10) REVERT: B 488 ARG cc_start: 0.7421 (ttp80) cc_final: 0.6260 (mtp180) REVERT: B 489 ILE cc_start: 0.7008 (OUTLIER) cc_final: 0.6730 (mt) REVERT: B 520 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.6543 (tt) REVERT: B 547 ARG cc_start: 0.5950 (tpp-160) cc_final: 0.5480 (tpp80) REVERT: B 550 ARG cc_start: 0.6980 (mmm160) cc_final: 0.6330 (mmp80) REVERT: C 124 LYS cc_start: 0.8384 (mppt) cc_final: 0.8182 (mmtt) REVERT: C 476 LEU cc_start: 0.6469 (OUTLIER) cc_final: 0.5989 (mt) REVERT: C 488 ARG cc_start: 0.8522 (ttp-170) cc_final: 0.8019 (ttt90) REVERT: D 9 THR cc_start: 0.7592 (OUTLIER) cc_final: 0.7072 (p) REVERT: D 236 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7808 (mpt180) REVERT: D 264 CYS cc_start: 0.8414 (m) cc_final: 0.8021 (m) REVERT: D 268 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8222 (ttt180) REVERT: D 377 GLN cc_start: 0.7610 (mt0) cc_final: 0.7380 (mm-40) REVERT: D 394 LYS cc_start: 0.8074 (ttmm) cc_final: 0.7791 (mtpt) REVERT: D 398 ILE cc_start: 0.8644 (pt) cc_final: 0.8332 (mt) REVERT: E 4 LEU cc_start: 0.0972 (OUTLIER) cc_final: 0.0429 (tp) REVERT: E 250 ASP cc_start: 0.8311 (m-30) cc_final: 0.7929 (t0) REVERT: E 411 TYR cc_start: 0.6169 (m-80) cc_final: 0.5921 (m-80) REVERT: E 440 TRP cc_start: 0.6866 (m100) cc_final: 0.6647 (m100) REVERT: E 446 LEU cc_start: 0.6100 (mp) cc_final: 0.5618 (tp) REVERT: F 420 ARG cc_start: 0.7740 (mtp-110) cc_final: 0.7477 (mtp-110) REVERT: G 6 PRO cc_start: 0.8531 (Cg_endo) cc_final: 0.8086 (Cg_exo) REVERT: H 14 ARG cc_start: 0.6024 (tpp80) cc_final: 0.5660 (mtp85) REVERT: H 19 GLU cc_start: 0.4139 (tp30) cc_final: 0.3764 (mp0) REVERT: J 102 GLU cc_start: 0.5886 (mm-30) cc_final: 0.4849 (tp30) REVERT: J 131 LEU cc_start: 0.5217 (mt) cc_final: 0.4883 (mm) REVERT: J 148 LEU cc_start: 0.6384 (OUTLIER) cc_final: 0.6070 (tt) REVERT: J 162 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7515 (pt0) REVERT: L 65 GLU cc_start: 0.5684 (pp20) cc_final: 0.4127 (mt-10) REVERT: L 81 GLU cc_start: 0.7139 (pp20) cc_final: 0.6236 (mm-30) REVERT: L 82 GLU cc_start: 0.5793 (tp30) cc_final: 0.4742 (tt0) REVERT: L 109 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.6531 (mt) REVERT: L 141 GLU cc_start: 0.5672 (tt0) cc_final: 0.5361 (tp30) outliers start: 61 outliers final: 41 residues processed: 350 average time/residue: 0.2171 time to fit residues: 116.7703 Evaluate side-chains 324 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 272 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 236 ARG Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 394 LYS Chi-restraints excluded: chain F residue 437 GLN Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 162 GLN Chi-restraints excluded: chain J residue 179 SER Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 182 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 270 optimal weight: 10.0000 chunk 240 optimal weight: 9.9990 chunk 150 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 192 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 271 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 216 optimal weight: 2.9990 chunk 252 optimal weight: 0.0980 chunk 140 optimal weight: 7.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 GLN F 437 GLN J 162 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.130775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.105360 restraints weight = 46302.287| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.52 r_work: 0.3187 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 30112 Z= 0.174 Angle : 0.549 7.636 40807 Z= 0.278 Chirality : 0.045 0.213 4576 Planarity : 0.005 0.058 5333 Dihedral : 5.605 119.173 4231 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.91 % Allowed : 15.83 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.14), residues: 3764 helix: 1.32 (0.13), residues: 1554 sheet: -0.89 (0.20), residues: 614 loop : 0.01 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 174 TYR 0.014 0.001 TYR E 286 PHE 0.015 0.001 PHE B 559 TRP 0.010 0.001 TRP F 471 HIS 0.004 0.001 HIS E 375 Details of bonding type rmsd covalent geometry : bond 0.00418 (30110) covalent geometry : angle 0.54943 (40807) hydrogen bonds : bond 0.03890 ( 1339) hydrogen bonds : angle 4.56059 ( 3846) Misc. bond : bond 0.00123 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 273 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 MET cc_start: 0.8016 (mtp) cc_final: 0.7772 (ttm) REVERT: A 452 ASP cc_start: 0.7697 (m-30) cc_final: 0.7305 (m-30) REVERT: A 469 GLN cc_start: 0.7058 (OUTLIER) cc_final: 0.5787 (mp10) REVERT: B 488 ARG cc_start: 0.7413 (ttp80) cc_final: 0.6282 (mtp180) REVERT: B 489 ILE cc_start: 0.7025 (OUTLIER) cc_final: 0.6766 (mt) REVERT: B 520 LEU cc_start: 0.6872 (OUTLIER) cc_final: 0.6540 (tt) REVERT: B 547 ARG cc_start: 0.5983 (tpp-160) cc_final: 0.5514 (tpp80) REVERT: B 550 ARG cc_start: 0.6909 (mmm160) cc_final: 0.6236 (mmp80) REVERT: C 476 LEU cc_start: 0.6547 (OUTLIER) cc_final: 0.6046 (mt) REVERT: C 488 ARG cc_start: 0.8560 (ttp-170) cc_final: 0.8043 (ttt90) REVERT: D 9 THR cc_start: 0.7646 (OUTLIER) cc_final: 0.7124 (p) REVERT: D 106 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.7992 (pt) REVERT: D 236 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7925 (mpt180) REVERT: D 264 CYS cc_start: 0.8467 (m) cc_final: 0.8038 (m) REVERT: D 268 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8213 (ttt180) REVERT: D 377 GLN cc_start: 0.7660 (mt0) cc_final: 0.7446 (mm-40) REVERT: D 394 LYS cc_start: 0.8098 (ttmm) cc_final: 0.7813 (mtpt) REVERT: D 398 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8319 (mt) REVERT: E 4 LEU cc_start: 0.0997 (OUTLIER) cc_final: 0.0418 (tp) REVERT: E 176 ASP cc_start: 0.7599 (p0) cc_final: 0.6372 (t0) REVERT: E 250 ASP cc_start: 0.8345 (m-30) cc_final: 0.7917 (t0) REVERT: E 440 TRP cc_start: 0.6938 (m100) cc_final: 0.6713 (m100) REVERT: E 446 LEU cc_start: 0.6208 (mp) cc_final: 0.5719 (tp) REVERT: G 6 PRO cc_start: 0.8597 (Cg_endo) cc_final: 0.8146 (Cg_exo) REVERT: H 14 ARG cc_start: 0.6029 (tpp80) cc_final: 0.5640 (mtp85) REVERT: H 19 GLU cc_start: 0.4089 (tp30) cc_final: 0.3682 (mp0) REVERT: J 102 GLU cc_start: 0.5874 (mm-30) cc_final: 0.4818 (tp30) REVERT: J 131 LEU cc_start: 0.5273 (mt) cc_final: 0.4928 (mm) REVERT: J 148 LEU cc_start: 0.6435 (OUTLIER) cc_final: 0.6130 (tt) REVERT: L 65 GLU cc_start: 0.5573 (pp20) cc_final: 0.3968 (mt-10) REVERT: L 81 GLU cc_start: 0.7112 (pp20) cc_final: 0.6213 (mm-30) REVERT: L 82 GLU cc_start: 0.5902 (tp30) cc_final: 0.4747 (tt0) REVERT: L 109 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.6596 (mt) outliers start: 59 outliers final: 41 residues processed: 326 average time/residue: 0.2194 time to fit residues: 110.1327 Evaluate side-chains 323 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 270 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 236 ARG Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 268 ARG Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 315 SER Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain E residue 4 LEU Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 206 GLN Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 394 LYS Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 44 ARG Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 179 SER Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 182 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 267 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 362 optimal weight: 9.9990 chunk 225 optimal weight: 0.0040 chunk 356 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 358 optimal weight: 7.9990 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 465 GLN F 23 ASN F 437 GLN J 162 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.130793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.105304 restraints weight = 46130.607| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.54 r_work: 0.3188 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 30112 Z= 0.172 Angle : 0.551 7.530 40807 Z= 0.279 Chirality : 0.045 0.210 4576 Planarity : 0.005 0.066 5333 Dihedral : 5.648 118.191 4231 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.08 % Allowed : 15.60 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.14), residues: 3764 helix: 1.24 (0.13), residues: 1555 sheet: -0.91 (0.20), residues: 614 loop : -0.01 (0.16), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 130 TYR 0.014 0.001 TYR G 133 PHE 0.015 0.001 PHE B 559 TRP 0.009 0.001 TRP F 471 HIS 0.004 0.001 HIS E 375 Details of bonding type rmsd covalent geometry : bond 0.00411 (30110) covalent geometry : angle 0.55104 (40807) hydrogen bonds : bond 0.03937 ( 1339) hydrogen bonds : angle 4.59174 ( 3846) Misc. bond : bond 0.00130 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7671.57 seconds wall clock time: 131 minutes 58.49 seconds (7918.49 seconds total)