Starting phenix.real_space_refine on Mon Aug 25 16:41:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gxw_34363/08_2025/8gxw_34363.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gxw_34363/08_2025/8gxw_34363.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gxw_34363/08_2025/8gxw_34363.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gxw_34363/08_2025/8gxw_34363.map" model { file = "/net/cci-nas-00/data/ceres_data/8gxw_34363/08_2025/8gxw_34363.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gxw_34363/08_2025/8gxw_34363.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 6 5.49 5 Mg 1 5.21 5 S 104 5.16 5 C 18725 2.51 5 N 5126 2.21 5 O 5568 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29530 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "C" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "D" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3682 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 442} Chain: "E" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3668 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 441} Chain: "F" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3694 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 444} Chain: "G" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1619 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "H" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "J" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 976 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain: "K" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "L" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 980 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'SO4': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.76, per 1000 atoms: 0.30 Number of scatterers: 29530 At special positions: 0 Unit cell: (149.4, 151.06, 173.47, 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 104 16.00 P 6 15.00 Mg 1 11.99 O 5568 8.00 N 5126 7.00 C 18725 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.94 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 146 helices and 26 sheets defined 48.0% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 90 through 98 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 233 through 245 Processing helix chain 'A' and resid 258 through 269 removed outlier: 3.926A pdb=" N MET A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 296 through 316 removed outlier: 4.359A pdb=" N GLU A 300 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 341 removed outlier: 3.831A pdb=" N TRP A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 393 through 401 Processing helix chain 'A' and resid 410 through 416 Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 446 through 472 removed outlier: 4.013A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 476 Processing helix chain 'A' and resid 477 through 494 Processing helix chain 'A' and resid 508 through 532 Processing helix chain 'A' and resid 535 through 540 Processing helix chain 'A' and resid 543 through 551 removed outlier: 3.782A pdb=" N ARG A 547 " --> pdb=" O PRO A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 554 No H-bonds generated for 'chain 'A' and resid 552 through 554' Processing helix chain 'A' and resid 558 through 576 removed outlier: 3.848A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 258 through 269 Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 295 through 316 removed outlier: 4.983A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 341 Processing helix chain 'B' and resid 353 through 363 Processing helix chain 'B' and resid 393 through 403 removed outlier: 3.639A pdb=" N ILE B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 416 removed outlier: 3.639A 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 533 Processing helix chain 'B' and resid 535 through 541 removed outlier: 3.706A pdb=" N ILE B 539 " --> pdb=" O SER B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 550 removed outlier: 3.605A pdb=" N ARG B 547 " --> pdb=" O PRO B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 554 removed outlier: 3.662A pdb=" N VAL B 554 " --> pdb=" O ALA B 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 551 through 554' Processing helix chain 'B' and resid 558 through 577 removed outlier: 3.863A pdb=" N PHE B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS B 575 " --> pdb=" O GLN B 571 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU B 577 " --> pdb=" O ALA B 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 99 Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 233 through 245 Processing helix chain 'C' and resid 258 through 269 removed outlier: 4.101A 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 280 through 283 Processing helix chain 'C' and resid 297 through 316 removed outlier: 4.074A pdb=" N ALA C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 342 removed outlier: 3.858A pdb=" N TRP C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 353 through 363 Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 393 through 400 Processing helix chain 'C' and resid 410 through 416 removed outlier: 3.554A pdb=" N ARG C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 443 Processing helix chain 'C' and resid 446 through 472 removed outlier: 4.039A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 494 removed outlier: 3.533A pdb=" N ARG C 481 " --> pdb=" O GLN C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 533 Processing helix chain 'C' and resid 535 through 541 Processing helix chain 'C' and resid 543 through 550 removed outlier: 3.577A pdb=" N ARG C 547 " --> pdb=" O PRO C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 554 Processing helix chain 'C' and resid 558 through 576 removed outlier: 3.595A pdb=" N GLN C 571 " --> pdb=" O MET C 567 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA C 576 " --> pdb=" O GLY C 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.528A pdb=" N LEU D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 159 through 171 Processing helix chain 'D' and resid 197 through 211 removed outlier: 3.898A pdb=" N THR D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 215 Processing helix chain 'D' and resid 227 through 250 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 259 through 274 Processing helix chain 'D' and resid 279 through 283 Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 340 through 347 Processing helix chain 'D' and resid 361 through 366 removed outlier: 3.544A pdb=" N GLY D 365 " --> pdb=" O LEU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 400 removed outlier: 3.916A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.454A 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 445 removed outlier: 3.878A pdb=" N MET D 445 " --> pdb=" O ALA D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 463 Processing helix chain 'D' and resid 467 through 472 Processing helix chain 'E' and resid 85 through 89 Processing helix chain 'E' and resid 135 through 141 Processing helix chain 'E' and resid 159 through 171 Processing helix chain 'E' and resid 174 through 179 removed outlier: 3.633A pdb=" N LEU E 177 " --> pdb=" O ARG E 174 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY E 179 " --> pdb=" O ASP E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 211 removed outlier: 4.072A pdb=" N THR E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 215 Processing helix chain 'E' and resid 227 through 250 removed outlier: 3.729A pdb=" N ARG E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE E 232 " --> pdb=" O THR E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 259 through 274 removed outlier: 3.639A pdb=" N TYR E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 removed outlier: 3.534A pdb=" N ILE E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 320 Processing helix chain 'E' and resid 323 through 333 Processing helix chain 'E' and resid 340 through 346 Processing helix chain 'E' and resid 361 through 365 Processing helix chain 'E' and resid 374 through 400 removed outlier: 3.882A pdb=" N ALA E 397 " --> pdb=" O ARG E 393 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE E 399 " --> pdb=" O LEU E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 404 Processing helix chain 'E' and resid 405 through 422 Processing helix chain 'E' and resid 431 through 444 Processing helix chain 'E' and resid 455 through 463 Processing helix chain 'F' and resid 85 through 89 Processing helix chain 'F' and resid 135 through 142 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 228 through 232 Processing helix chain 'F' and resid 233 through 250 Processing helix chain 'F' and resid 259 through 274 removed outlier: 3.755A pdb=" N TYR F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 283 removed outlier: 4.400A pdb=" N GLY F 282 " --> pdb=" O GLY F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.606A 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 365 Processing helix chain 'F' and resid 374 through 400 removed outlier: 3.686A 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 470 Processing helix chain 'G' and resid 7 through 66 removed outlier: 3.698A pdb=" N GLY G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 71 removed outlier: 3.592A pdb=" N ASP G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 83 Processing helix chain 'G' and resid 109 through 113 removed outlier: 3.634A pdb=" N ALA G 112 " --> pdb=" O PRO G 109 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU G 113 " --> pdb=" O ASP G 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 109 through 113' Processing helix chain 'G' and resid 122 through 208 removed outlier: 4.213A pdb=" N ARG G 128 " --> pdb=" O LEU G 124 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA G 129 " --> pdb=" O GLU G 125 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ILE G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) Proline residue: G 170 - end of helix Processing helix chain 'H' and resid 6 through 16 removed outlier: 3.527A pdb=" N GLN H 11 " --> pdb=" O PRO H 7 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 39 Processing helix chain 'H' and resid 54 through 64 removed outlier: 6.787A pdb=" N ARG H 61 " --> pdb=" O ARG H 57 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N MET H 63 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG H 64 " --> pdb=" O GLU H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 83 removed outlier: 3.820A pdb=" N PHE H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN H 82 " --> pdb=" O LYS H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 98 Processing helix chain 'I' and resid 82 through 105 Processing helix chain 'I' and resid 106 through 119 Processing helix chain 'J' and resid 62 through 93 Processing helix chain 'J' and resid 94 through 97 Processing helix chain 'J' and resid 99 through 115 removed outlier: 3.863A pdb=" N VAL J 103 " --> pdb=" O GLU J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 126 No H-bonds generated for 'chain 'J' and resid 124 through 126' Processing helix chain 'J' and resid 127 through 139 removed outlier: 4.518A pdb=" N ALA J 133 " --> pdb=" O PRO J 129 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LEU J 134 " --> pdb=" O HIS J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 187 removed outlier: 4.499A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN J 184 " --> pdb=" O SER J 180 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA J 185 " --> pdb=" O LYS J 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 119 removed outlier: 3.971A pdb=" N ARG K 106 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ASP K 108 " --> pdb=" O MET K 104 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N GLU K 109 " --> pdb=" O ALA K 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 93 Processing helix chain 'L' and resid 94 through 97 Processing helix chain 'L' and resid 99 through 115 Processing helix chain 'L' and resid 127 through 130 Processing helix chain 'L' and resid 131 through 139 removed outlier: 3.642A pdb=" N ARG L 136 " --> pdb=" O GLU L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 166 through 187 removed outlier: 5.346A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LYS L 181 " --> pdb=" O ALA L 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 10 removed outlier: 6.606A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.018A 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: 5.696A pdb=" N ILE A 39 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLN A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.667A 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: 6.007A pdb=" N ILE B 39 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLN B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 3.785A 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: 5.486A pdb=" N ILE C 39 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLN C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 3.788A 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 21 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 18 through 21 current: chain 'D' and resid 42 through 51 removed outlier: 5.862A pdb=" N GLY D 45 " --> pdb=" O PHE D 60 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N PHE D 60 " --> pdb=" O GLY D 45 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU D 49 " --> pdb=" O VAL D 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 55 through 60 current: chain 'E' and resid 18 through 21 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 21 current: chain 'E' and resid 42 through 51 removed outlier: 6.858A pdb=" N VAL E 56 " --> pdb=" O ILE E 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 55 through 59 current: chain 'F' and resid 18 through 21 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 18 through 21 current: chain 'F' and resid 42 through 51 removed outlier: 6.311A pdb=" N VAL F 56 " --> pdb=" O ILE F 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 55 through 59 current: chain 'J' and resid 141 through 144 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 141 through 144 current: chain 'J' and resid 161 through 164 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 161 through 164 current: chain 'L' and resid 141 through 144 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 141 through 144 current: chain 'L' and resid 161 through 164 Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 75 Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 84 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 82 through 84 current: chain 'A' and resid 285 through 290 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 285 through 290 current: chain 'A' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 375 through 384 current: chain 'A' and resid 428 through 429 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 148 removed outlier: 3.814A pdb=" N GLY A 136 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ALA A 118 " --> pdb=" O PRO A 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 129 removed outlier: 7.132A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 72 through 75 Processing sheet with id=AA7, first strand: chain 'B' and resid 82 through 84 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 82 through 84 current: chain 'B' and resid 285 through 291 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 285 through 291 current: chain 'B' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 375 through 384 current: chain 'B' and resid 428 through 429 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 143 through 148 removed outlier: 3.589A pdb=" N GLY B 136 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 5.822A 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: 6.533A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 72 through 75 Processing sheet with id=AB2, first strand: chain 'C' and resid 82 through 84 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 82 through 84 current: chain 'C' and resid 285 through 290 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 285 through 290 current: chain 'C' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 375 through 384 current: chain 'C' and resid 428 through 429 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 144 through 148 removed outlier: 6.823A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ALA C 118 " --> pdb=" O PRO C 139 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 128 through 129 removed outlier: 6.813A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 81 through 84 Processing sheet with id=AB6, first strand: chain 'D' and resid 91 through 93 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 91 through 93 current: chain 'D' and resid 217 through 223 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 217 through 223 current: chain 'D' and resid 307 through 315 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 307 through 315 current: chain 'D' and resid 358 through 359 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 130 through 131 removed outlier: 4.634A 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 removed outlier: 3.601A pdb=" N LYS E 110 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 91 through 93 removed outlier: 3.806A pdb=" N ARG E 91 " --> pdb=" O SER E 217 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALA E 188 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ILE E 256 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL E 190 " --> pdb=" O ILE E 256 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N THR E 258 " --> pdb=" O VAL E 190 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ALA E 192 " --> pdb=" O THR E 258 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 124 through 125 removed outlier: 4.629A pdb=" N VAL E 300 " --> pdb=" O ARG E 125 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.606A pdb=" N LEU E 144 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 81 through 84 Processing sheet with id=AC4, first strand: chain 'F' and resid 92 through 94 removed outlier: 6.571A pdb=" N VAL F 189 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N PHE F 220 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE F 191 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ASN F 222 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ALA F 193 " --> pdb=" O ASN F 222 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU F 257 " --> pdb=" O ILE F 311 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 124 through 125 removed outlier: 4.375A pdb=" N VAL F 300 " --> pdb=" O ARG F 125 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 144 through 145 removed outlier: 4.641A pdb=" N LEU F 144 " --> pdb=" O ILE F 131 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 91 through 96 Processing sheet with id=AC8, first strand: chain 'H' and resid 19 through 22 removed outlier: 3.534A pdb=" N TYR H 21 " --> pdb=" O VAL H 3 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASP H 48 " --> pdb=" O ILE H 4 " (cutoff:3.500A) 1327 hydrogen bonds defined for protein. 3771 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.39 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9964 1.34 - 1.46: 4874 1.46 - 1.58: 15045 1.58 - 1.69: 8 1.69 - 1.81: 194 Bond restraints: 30085 Sorted by residual: bond pdb=" O3 SO4 A 600 " pdb=" S SO4 A 600 " ideal model delta sigma weight residual 1.499 1.450 0.049 2.00e-02 2.50e+03 5.89e+00 bond pdb=" O4 SO4 A 600 " pdb=" S SO4 A 600 " ideal model delta sigma weight residual 1.499 1.453 0.046 2.00e-02 2.50e+03 5.27e+00 bond pdb=" O2 SO4 A 600 " pdb=" S SO4 A 600 " ideal model delta sigma weight residual 1.498 1.452 0.046 2.00e-02 2.50e+03 5.19e+00 bond pdb=" O1 SO4 A 600 " pdb=" S SO4 A 600 " ideal model delta sigma weight residual 1.498 1.454 0.044 2.00e-02 2.50e+03 4.85e+00 bond pdb=" N MET H 1 " pdb=" CA MET H 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 ... (remaining 30080 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 39638 1.37 - 2.75: 868 2.75 - 4.12: 229 4.12 - 5.49: 25 5.49 - 6.87: 8 Bond angle restraints: 40768 Sorted by residual: angle pdb=" N ILE C 402 " pdb=" CA ILE C 402 " pdb=" C ILE C 402 " ideal model delta sigma weight residual 113.71 110.88 2.83 9.50e-01 1.11e+00 8.88e+00 angle pdb=" C3' ATP C 601 " pdb=" C4' ATP C 601 " pdb=" O4' ATP C 601 " ideal model delta sigma weight residual 105.22 101.58 3.64 1.30e+00 5.94e-01 7.85e+00 angle pdb=" N PRO A 420 " pdb=" CA PRO A 420 " pdb=" C PRO A 420 " ideal model delta sigma weight residual 112.10 118.97 -6.87 2.60e+00 1.48e-01 6.98e+00 angle pdb=" N ILE D 325 " pdb=" CA ILE D 325 " pdb=" C ILE D 325 " ideal model delta sigma weight residual 112.35 109.39 2.96 1.20e+00 6.94e-01 6.08e+00 angle pdb=" N VAL D 76 " pdb=" CA VAL D 76 " pdb=" C VAL D 76 " ideal model delta sigma weight residual 111.67 109.38 2.29 9.50e-01 1.11e+00 5.83e+00 ... (remaining 40763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 16628 17.85 - 35.71: 1354 35.71 - 53.56: 302 53.56 - 71.42: 58 71.42 - 89.27: 30 Dihedral angle restraints: 18372 sinusoidal: 7550 harmonic: 10822 Sorted by residual: dihedral pdb=" CA VAL A 368 " pdb=" C VAL A 368 " pdb=" N ILE A 369 " pdb=" CA ILE A 369 " ideal model delta harmonic sigma weight residual 180.00 155.70 24.30 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA LEU D 257 " pdb=" C LEU D 257 " pdb=" N THR D 258 " pdb=" CA THR D 258 " ideal model delta harmonic sigma weight residual 180.00 -158.40 -21.60 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA LEU F 257 " pdb=" C LEU F 257 " pdb=" N THR F 258 " pdb=" CA THR F 258 " ideal model delta harmonic sigma weight residual 180.00 -159.11 -20.89 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 18369 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3848 0.058 - 0.117: 653 0.117 - 0.175: 61 0.175 - 0.234: 0 0.234 - 0.292: 6 Chirality restraints: 4568 Sorted by residual: chirality pdb=" C2' ATP C 601 " pdb=" C1' ATP C 601 " pdb=" C3' ATP C 601 " pdb=" O2' ATP C 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" C2' ATP B 601 " pdb=" C1' ATP B 601 " pdb=" C3' ATP B 601 " pdb=" O2' ATP B 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C3' ATP B 601 " pdb=" C2' ATP B 601 " pdb=" C4' ATP B 601 " pdb=" O3' ATP B 601 " both_signs ideal model delta sigma weight residual False -2.63 -2.91 0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 4565 not shown) Planarity restraints: 5332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 323 " -0.038 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO D 324 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 324 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 324 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 386 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO C 387 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 387 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 387 " -0.029 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 4.17e-02 2.78e+00 pdb=" N PRO F 324 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO F 324 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 324 " -0.023 5.00e-02 4.00e+02 ... (remaining 5329 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 117 2.45 - 3.07: 20227 3.07 - 3.68: 44616 3.68 - 4.29: 67241 4.29 - 4.90: 113422 Nonbonded interactions: 245623 Sorted by model distance: nonbonded pdb=" OG SER C 235 " pdb="MG MG C 602 " model vdw 1.843 2.170 nonbonded pdb=" O2G ATP C 601 " pdb="MG MG C 602 " model vdw 1.883 2.170 nonbonded pdb=" O MET C 220 " pdb=" OG1 THR C 379 " model vdw 1.952 3.040 nonbonded pdb=" O LYS E 370 " pdb=" OG1 THR E 371 " model vdw 1.955 3.040 nonbonded pdb=" O MET A 220 " pdb=" OG1 THR A 379 " model vdw 1.983 3.040 ... (remaining 245618 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: 4.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.670 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 31.780 Find NCS groups from input model: 0.580 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:7.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 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 : 0.006 0.086 30085 Z= 0.242 Angle : 0.546 6.868 40768 Z= 0.286 Chirality : 0.044 0.292 4568 Planarity : 0.004 0.057 5332 Dihedral : 14.203 89.274 11454 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.36 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.14), residues: 3764 helix: 1.67 (0.13), residues: 1570 sheet: -0.06 (0.22), residues: 552 loop : 0.01 (0.16), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 210 TYR 0.016 0.002 TYR E 463 PHE 0.017 0.002 PHE D 60 TRP 0.009 0.001 TRP C 119 HIS 0.008 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00556 (30085) covalent geometry : angle 0.54645 (40768) hydrogen bonds : bond 0.14996 ( 1327) hydrogen bonds : angle 6.27462 ( 3771) *********************** 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 798 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 798 time to evaluate : 1.215 Fit side-chains REVERT: A 3 GLN cc_start: 0.7613 (mt0) cc_final: 0.7333 (tm-30) REVERT: A 93 ARG cc_start: 0.7595 (mmp80) cc_final: 0.7230 (mmp80) REVERT: A 133 MET cc_start: 0.7648 (mtp) cc_final: 0.7347 (mtt) REVERT: A 156 ARG cc_start: 0.6628 (mtm110) cc_final: 0.5655 (ttm-80) REVERT: A 296 VAL cc_start: 0.8746 (p) cc_final: 0.8426 (t) REVERT: A 397 GLN cc_start: 0.8469 (mm110) cc_final: 0.8232 (mm110) REVERT: A 491 ARG cc_start: 0.7530 (mmt180) cc_final: 0.6575 (mtm110) REVERT: A 502 GLU cc_start: 0.6514 (mp0) cc_final: 0.6262 (tp30) REVERT: A 524 LYS cc_start: 0.7689 (mmmt) cc_final: 0.7372 (mttm) REVERT: A 527 GLU cc_start: 0.7008 (tt0) cc_final: 0.6583 (pt0) REVERT: B 93 ARG cc_start: 0.7372 (mtm-85) cc_final: 0.7167 (mtm110) REVERT: B 282 MET cc_start: 0.8431 (mmm) cc_final: 0.8210 (tpt) REVERT: B 415 PHE cc_start: 0.7649 (t80) cc_final: 0.7035 (t80) REVERT: B 447 TYR cc_start: 0.7074 (t80) cc_final: 0.6692 (t80) REVERT: B 452 ASP cc_start: 0.6537 (m-30) cc_final: 0.5858 (t70) REVERT: B 456 GLU cc_start: 0.6833 (tp30) cc_final: 0.6299 (tm-30) REVERT: B 477 GLN cc_start: 0.4762 (mt0) cc_final: 0.4411 (pt0) REVERT: B 524 LYS cc_start: 0.5586 (mmmt) cc_final: 0.5355 (ttmt) REVERT: B 527 GLU cc_start: 0.5878 (tt0) cc_final: 0.5593 (tt0) REVERT: C 133 MET cc_start: 0.8049 (mtp) cc_final: 0.7836 (mtp) REVERT: C 152 ASP cc_start: 0.7643 (m-30) cc_final: 0.7245 (p0) REVERT: C 182 LYS cc_start: 0.8171 (mtpt) cc_final: 0.7924 (mttp) REVERT: C 424 TRP cc_start: 0.7882 (p90) cc_final: 0.7266 (p-90) REVERT: C 425 ASN cc_start: 0.8172 (m-40) cc_final: 0.7677 (t0) REVERT: C 527 GLU cc_start: 0.6580 (mm-30) cc_final: 0.6117 (pt0) REVERT: C 548 ILE cc_start: 0.6871 (mt) cc_final: 0.6523 (mt) REVERT: C 567 MET cc_start: 0.7028 (mmm) cc_final: 0.6648 (mmm) REVERT: C 568 LYS cc_start: 0.7113 (mttt) cc_final: 0.6841 (mppt) REVERT: D 34 ASP cc_start: 0.7079 (m-30) cc_final: 0.6839 (m-30) REVERT: D 70 THR cc_start: 0.7621 (p) cc_final: 0.7420 (p) REVERT: D 259 ASP cc_start: 0.6161 (t0) cc_final: 0.5796 (t0) REVERT: D 358 LEU cc_start: 0.8805 (tp) cc_final: 0.8590 (tm) REVERT: D 362 MET cc_start: 0.8712 (ttt) cc_final: 0.8345 (ttp) REVERT: D 388 ASN cc_start: 0.7403 (m-40) cc_final: 0.6941 (t0) REVERT: D 420 ARG cc_start: 0.7050 (mtm-85) cc_final: 0.6833 (mmm160) REVERT: E 5 LYS cc_start: 0.4667 (mttt) cc_final: 0.4388 (ptmt) REVERT: E 81 ARG cc_start: 0.7204 (mtm-85) cc_final: 0.6722 (mtt90) REVERT: E 133 THR cc_start: 0.8549 (p) cc_final: 0.8272 (t) REVERT: E 206 GLN cc_start: 0.7063 (tp40) cc_final: 0.6810 (tp40) REVERT: E 248 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7438 (mm-30) REVERT: E 250 ASP cc_start: 0.7994 (m-30) cc_final: 0.7768 (m-30) REVERT: E 364 ASN cc_start: 0.8192 (t0) cc_final: 0.7963 (t0) REVERT: E 393 ARG cc_start: 0.7245 (ttp-170) cc_final: 0.7015 (ttm170) REVERT: F 5 LYS cc_start: 0.6382 (tttt) cc_final: 0.6053 (ttmt) REVERT: F 36 LYS cc_start: 0.7973 (tttt) cc_final: 0.7768 (ttpp) REVERT: F 50 VAL cc_start: 0.8940 (t) cc_final: 0.8682 (m) REVERT: F 376 LYS cc_start: 0.7930 (tttp) cc_final: 0.7692 (tptt) REVERT: G 9 MET cc_start: 0.7477 (ttp) cc_final: 0.7264 (ptm) REVERT: G 31 LYS cc_start: 0.7629 (tttm) cc_final: 0.7317 (tttp) REVERT: G 44 ARG cc_start: 0.5662 (mtm180) cc_final: 0.5082 (mmp80) REVERT: G 47 MET cc_start: 0.5288 (ptp) cc_final: 0.4137 (ptm) REVERT: G 162 ASN cc_start: 0.7349 (m-40) cc_final: 0.7096 (m-40) REVERT: G 193 ARG cc_start: 0.7336 (mtm-85) cc_final: 0.6472 (mtm110) REVERT: H 68 LEU cc_start: 0.4196 (tt) cc_final: 0.3880 (mp) REVERT: H 87 GLU cc_start: 0.5490 (tm-30) cc_final: 0.5189 (mm-30) REVERT: L 78 GLU cc_start: 0.4726 (mt-10) cc_final: 0.4399 (mp0) outliers start: 0 outliers final: 0 residues processed: 798 average time/residue: 0.9005 time to fit residues: 811.5161 Evaluate side-chains 446 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 446 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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: 0.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 GLN A 496 GLN B 239 GLN B 397 GLN B 442 ASN C 238 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 23 ASN E 46 GLN E 58 GLN E 170 GLN E 338 GLN E 427 GLN E 437 GLN E 448 GLN E 458 HIS E 465 GLN F 161 ASN F 206 GLN F 262 ASN F 364 ASN F 413 GLN F 425 GLN F 465 GLN G 175 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.162522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.127096 restraints weight = 35477.132| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.33 r_work: 0.3230 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30085 Z= 0.148 Angle : 0.577 13.086 40768 Z= 0.295 Chirality : 0.045 0.212 4568 Planarity : 0.005 0.051 5332 Dihedral : 6.070 74.088 4248 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.05 % Favored : 97.93 % Rotamer: Outliers : 3.08 % Allowed : 14.08 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.14), residues: 3764 helix: 1.74 (0.13), residues: 1597 sheet: 0.04 (0.22), residues: 548 loop : 0.26 (0.16), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 210 TYR 0.014 0.001 TYR B 166 PHE 0.019 0.002 PHE A 559 TRP 0.011 0.001 TRP A 119 HIS 0.008 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00336 (30085) covalent geometry : angle 0.57673 (40768) hydrogen bonds : bond 0.04572 ( 1327) hydrogen bonds : angle 4.89515 ( 3771) *********************** 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 561 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 466 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7743 (mm) REVERT: A 133 MET cc_start: 0.8012 (mtp) cc_final: 0.7808 (mtt) REVERT: A 156 ARG cc_start: 0.6915 (mtm110) cc_final: 0.6320 (ttm-80) REVERT: A 374 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7733 (mm-30) REVERT: A 393 GLU cc_start: 0.6131 (tt0) cc_final: 0.5911 (tp30) REVERT: A 397 GLN cc_start: 0.8505 (mm110) cc_final: 0.8293 (mm110) REVERT: A 445 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7233 (mm-30) REVERT: A 491 ARG cc_start: 0.7503 (mmt180) cc_final: 0.6849 (mtm110) REVERT: A 524 LYS cc_start: 0.7799 (mmmt) cc_final: 0.7522 (mttp) REVERT: A 532 ARG cc_start: 0.6252 (ttp-110) cc_final: 0.5770 (mtp-110) REVERT: B 93 ARG cc_start: 0.7671 (mtm-85) cc_final: 0.7406 (mtm110) REVERT: B 161 LYS cc_start: 0.8006 (mmtp) cc_final: 0.7725 (mppt) REVERT: B 179 THR cc_start: 0.7767 (t) cc_final: 0.7180 (p) REVERT: B 282 MET cc_start: 0.8315 (mmm) cc_final: 0.8074 (tpt) REVERT: B 415 PHE cc_start: 0.7881 (t80) cc_final: 0.7336 (t80) REVERT: B 447 TYR cc_start: 0.7068 (t80) cc_final: 0.6814 (t80) REVERT: B 449 GLU cc_start: 0.5333 (mp0) cc_final: 0.4418 (mt-10) REVERT: B 452 ASP cc_start: 0.6709 (m-30) cc_final: 0.5750 (t70) REVERT: B 477 GLN cc_start: 0.4727 (mt0) cc_final: 0.4348 (pt0) REVERT: B 527 GLU cc_start: 0.6113 (tt0) cc_final: 0.5806 (tt0) REVERT: C 53 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7864 (mt-10) REVERT: C 133 MET cc_start: 0.8378 (mtp) cc_final: 0.8148 (mtp) REVERT: C 152 ASP cc_start: 0.7840 (m-30) cc_final: 0.7585 (p0) REVERT: C 260 ASN cc_start: 0.8064 (m-40) cc_final: 0.7846 (m110) REVERT: C 424 TRP cc_start: 0.7965 (p90) cc_final: 0.7609 (p-90) REVERT: C 425 ASN cc_start: 0.8152 (m-40) cc_final: 0.7913 (t0) REVERT: C 527 GLU cc_start: 0.6715 (mm-30) cc_final: 0.6382 (pt0) REVERT: C 567 MET cc_start: 0.7109 (mmm) cc_final: 0.6718 (mmm) REVERT: C 568 LYS cc_start: 0.6957 (mttt) cc_final: 0.6711 (mppt) REVERT: D 26 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.7839 (m-30) REVERT: D 50 VAL cc_start: 0.8901 (OUTLIER) cc_final: 0.8642 (m) REVERT: D 275 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6623 (mp0) REVERT: D 316 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7171 (mpp) REVERT: D 394 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7520 (mtpt) REVERT: D 433 GLU cc_start: 0.8142 (mp0) cc_final: 0.7936 (mp0) REVERT: D 452 LYS cc_start: 0.7224 (mmmt) cc_final: 0.6980 (mtpt) REVERT: E 5 LYS cc_start: 0.5663 (mttt) cc_final: 0.5231 (ptmt) REVERT: E 6 LYS cc_start: 0.7695 (ttmm) cc_final: 0.7485 (ttmt) REVERT: E 81 ARG cc_start: 0.7561 (mtm-85) cc_final: 0.7132 (mtt90) REVERT: E 87 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7261 (mm-30) REVERT: E 103 LEU cc_start: 0.8038 (mp) cc_final: 0.7831 (mt) REVERT: E 130 PHE cc_start: 0.8267 (OUTLIER) cc_final: 0.6415 (p90) REVERT: E 206 GLN cc_start: 0.7212 (tp40) cc_final: 0.6925 (tp40) REVERT: E 248 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7593 (mm-30) REVERT: E 265 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7645 (mt-10) REVERT: E 410 ARG cc_start: 0.7042 (mtm180) cc_final: 0.6689 (ttt180) REVERT: E 448 GLN cc_start: 0.7586 (tt0) cc_final: 0.7295 (tt0) REVERT: F 5 LYS cc_start: 0.7457 (tttt) cc_final: 0.7227 (ttmt) REVERT: G 44 ARG cc_start: 0.6094 (mtm180) cc_final: 0.5576 (mmp80) REVERT: G 48 GLU cc_start: 0.5880 (OUTLIER) cc_final: 0.5544 (mp0) REVERT: G 162 ASN cc_start: 0.7362 (m-40) cc_final: 0.7103 (m-40) REVERT: G 193 ARG cc_start: 0.7511 (mtm-85) cc_final: 0.6842 (mtm110) REVERT: H 87 GLU cc_start: 0.5533 (tm-30) cc_final: 0.5147 (mm-30) REVERT: J 164 GLU cc_start: 0.5218 (tp30) cc_final: 0.4615 (tp30) REVERT: L 78 GLU cc_start: 0.5760 (mt-10) cc_final: 0.5269 (mp0) REVERT: L 102 GLU cc_start: 0.3578 (tp30) cc_final: 0.3092 (tm-30) REVERT: L 132 GLU cc_start: 0.2839 (mm-30) cc_final: 0.2382 (tt0) outliers start: 95 outliers final: 29 residues processed: 530 average time/residue: 0.8272 time to fit residues: 494.5789 Evaluate side-chains 452 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 412 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 459 GLN Chi-restraints excluded: chain C residue 548 ILE Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain D residue 394 LYS Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 338 GLN Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 156 LYS Chi-restraints excluded: chain G residue 181 GLN Chi-restraints excluded: chain L residue 92 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 94 optimal weight: 0.0770 chunk 120 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 202 optimal weight: 0.9990 chunk 359 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 310 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN A 7 GLN A 293 ASN B 397 GLN D 166 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 ASN D 413 GLN E 338 GLN E 427 GLN F 206 GLN F 364 ASN F 413 GLN F 465 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.161622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.127183 restraints weight = 35445.199| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.49 r_work: 0.3200 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30085 Z= 0.140 Angle : 0.543 12.485 40768 Z= 0.277 Chirality : 0.044 0.218 4568 Planarity : 0.005 0.050 5332 Dihedral : 5.943 77.376 4248 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.73 % Favored : 98.25 % Rotamer: Outliers : 3.08 % Allowed : 15.60 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.14), residues: 3764 helix: 1.80 (0.13), residues: 1591 sheet: -0.06 (0.22), residues: 563 loop : 0.30 (0.16), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 547 TYR 0.016 0.001 TYR A 166 PHE 0.020 0.002 PHE A 559 TRP 0.011 0.001 TRP A 119 HIS 0.008 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00323 (30085) covalent geometry : angle 0.54275 (40768) hydrogen bonds : bond 0.04320 ( 1327) hydrogen bonds : angle 4.73557 ( 3771) *********************** 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 518 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 423 time to evaluate : 0.828 Fit side-chains REVERT: A 2 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7703 (mm) REVERT: A 8 LYS cc_start: 0.8817 (tttp) cc_final: 0.8288 (tmmt) REVERT: A 133 MET cc_start: 0.8033 (mtp) cc_final: 0.7804 (mtt) REVERT: A 374 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7716 (mm-30) REVERT: A 393 GLU cc_start: 0.6499 (tt0) cc_final: 0.6119 (tp30) REVERT: A 397 GLN cc_start: 0.8540 (mm110) cc_final: 0.8308 (mm110) REVERT: A 445 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.7182 (mm-30) REVERT: A 491 ARG cc_start: 0.7548 (mmt180) cc_final: 0.6888 (mtm110) REVERT: A 524 LYS cc_start: 0.7832 (mmmt) cc_final: 0.7566 (mttp) REVERT: B 282 MET cc_start: 0.8396 (mmm) cc_final: 0.8096 (tpt) REVERT: B 391 MET cc_start: 0.6894 (mmt) cc_final: 0.5945 (mmp) REVERT: B 415 PHE cc_start: 0.7933 (t80) cc_final: 0.7345 (t80) REVERT: B 449 GLU cc_start: 0.5277 (mp0) cc_final: 0.4445 (mt-10) REVERT: B 452 ASP cc_start: 0.6806 (m-30) cc_final: 0.5863 (t70) REVERT: B 477 GLN cc_start: 0.4602 (mt0) cc_final: 0.4199 (mt0) REVERT: B 524 LYS cc_start: 0.5962 (OUTLIER) cc_final: 0.5476 (ttmt) REVERT: B 527 GLU cc_start: 0.6267 (tt0) cc_final: 0.5959 (tt0) REVERT: B 548 ILE cc_start: 0.6863 (tt) cc_final: 0.6487 (tp) REVERT: C 53 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7894 (mt-10) REVERT: C 133 MET cc_start: 0.8397 (mtp) cc_final: 0.8171 (mtp) REVERT: C 260 ASN cc_start: 0.8139 (m-40) cc_final: 0.7880 (m110) REVERT: C 344 MET cc_start: 0.8277 (ttm) cc_final: 0.8004 (ttm) REVERT: C 424 TRP cc_start: 0.8005 (p90) cc_final: 0.7672 (p-90) REVERT: C 425 ASN cc_start: 0.8239 (m-40) cc_final: 0.7964 (t0) REVERT: C 488 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7413 (ttt-90) REVERT: C 567 MET cc_start: 0.7065 (mmm) cc_final: 0.6672 (mmm) REVERT: D 26 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7828 (m-30) REVERT: D 50 VAL cc_start: 0.8829 (OUTLIER) cc_final: 0.8594 (m) REVERT: D 130 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.8528 (p90) REVERT: D 275 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6683 (mp0) REVERT: D 316 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7189 (mpp) REVERT: D 402 ASP cc_start: 0.6441 (m-30) cc_final: 0.6166 (m-30) REVERT: D 433 GLU cc_start: 0.8205 (mp0) cc_final: 0.7993 (mp0) REVERT: E 5 LYS cc_start: 0.5541 (mttt) cc_final: 0.5120 (ptmt) REVERT: E 81 ARG cc_start: 0.7547 (mtm-85) cc_final: 0.7094 (mtt180) REVERT: E 174 ARG cc_start: 0.7858 (mmm-85) cc_final: 0.7353 (mmm-85) REVERT: E 209 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7143 (mt-10) REVERT: E 248 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7684 (mm-30) REVERT: E 265 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7652 (mt-10) REVERT: E 364 ASN cc_start: 0.8025 (t0) cc_final: 0.7780 (t0) REVERT: E 380 ASP cc_start: 0.7640 (m-30) cc_final: 0.7394 (m-30) REVERT: E 410 ARG cc_start: 0.7114 (mtm180) cc_final: 0.6748 (ttt180) REVERT: E 445 MET cc_start: 0.7419 (mtt) cc_final: 0.7103 (mtt) REVERT: F 5 LYS cc_start: 0.7462 (tttt) cc_final: 0.7194 (ttmt) REVERT: F 67 ASP cc_start: 0.7818 (p0) cc_final: 0.7511 (p0) REVERT: F 410 ARG cc_start: 0.7561 (mtt90) cc_final: 0.7183 (ttp-170) REVERT: F 465 GLN cc_start: 0.6029 (tt0) cc_final: 0.5669 (pt0) REVERT: G 5 SER cc_start: 0.7178 (p) cc_final: 0.6548 (t) REVERT: G 44 ARG cc_start: 0.6085 (mtm180) cc_final: 0.5456 (mmp80) REVERT: G 47 MET cc_start: 0.5177 (ptp) cc_final: 0.4329 (ptm) REVERT: G 48 GLU cc_start: 0.6118 (OUTLIER) cc_final: 0.5718 (mp0) REVERT: G 193 ARG cc_start: 0.7509 (mtm-85) cc_final: 0.7196 (mpt-90) REVERT: H 63 MET cc_start: 0.1819 (mpt) cc_final: 0.1582 (mpt) REVERT: J 160 LYS cc_start: 0.6753 (mmtm) cc_final: 0.6479 (mmtt) REVERT: L 78 GLU cc_start: 0.5781 (mt-10) cc_final: 0.5266 (mp0) REVERT: L 132 GLU cc_start: 0.3070 (mm-30) cc_final: 0.2440 (tt0) outliers start: 95 outliers final: 31 residues processed: 482 average time/residue: 0.7501 time to fit residues: 412.4750 Evaluate side-chains 433 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 389 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 459 GLN Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 181 GLN Chi-restraints excluded: chain L residue 171 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 289 optimal weight: 1.9990 chunk 258 optimal weight: 5.9990 chunk 238 optimal weight: 7.9990 chunk 232 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 354 optimal weight: 10.0000 chunk 263 optimal weight: 0.6980 chunk 219 optimal weight: 0.7980 chunk 303 optimal weight: 4.9990 chunk 339 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN A 316 GLN B 397 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 338 GLN E 427 GLN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 ASN F 413 GLN G 175 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.158924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.124303 restraints weight = 35219.263| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.49 r_work: 0.3145 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 30085 Z= 0.221 Angle : 0.648 13.493 40768 Z= 0.332 Chirality : 0.047 0.186 4568 Planarity : 0.006 0.063 5332 Dihedral : 6.301 89.379 4248 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.86 % Allowed : 16.02 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.14), residues: 3764 helix: 1.44 (0.13), residues: 1576 sheet: -0.13 (0.22), residues: 555 loop : 0.12 (0.16), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 410 TYR 0.020 0.002 TYR A 304 PHE 0.024 0.002 PHE A 559 TRP 0.013 0.002 TRP C 187 HIS 0.010 0.002 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00527 (30085) covalent geometry : angle 0.64794 (40768) hydrogen bonds : bond 0.05099 ( 1327) hydrogen bonds : angle 4.97060 ( 3771) *********************** 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 508 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 389 time to evaluate : 1.417 Fit side-chains revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.7822 (mm) REVERT: A 8 LYS cc_start: 0.8889 (tttp) cc_final: 0.8401 (tmmt) REVERT: A 124 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7380 (mtpt) REVERT: A 133 MET cc_start: 0.8068 (mtp) cc_final: 0.7807 (mtt) REVERT: A 156 ARG cc_start: 0.7285 (ttp80) cc_final: 0.6889 (ttm-80) REVERT: A 323 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8323 (mpt) REVERT: A 374 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7778 (mm-30) REVERT: A 393 GLU cc_start: 0.6848 (tt0) cc_final: 0.6328 (tp30) REVERT: A 397 GLN cc_start: 0.8669 (mm110) cc_final: 0.8421 (mm110) REVERT: A 423 ASN cc_start: 0.8576 (t0) cc_final: 0.8348 (t0) REVERT: A 445 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7256 (mm-30) REVERT: A 491 ARG cc_start: 0.7652 (mmt180) cc_final: 0.6967 (ttp-110) REVERT: A 520 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.7900 (mt) REVERT: A 524 LYS cc_start: 0.7815 (mmmt) cc_final: 0.7516 (mttm) REVERT: A 532 ARG cc_start: 0.6320 (ttp-110) cc_final: 0.5937 (ttm-80) REVERT: B 282 MET cc_start: 0.8579 (mmm) cc_final: 0.8105 (tpt) REVERT: B 391 MET cc_start: 0.6970 (mmt) cc_final: 0.6256 (mmp) REVERT: B 449 GLU cc_start: 0.5509 (mp0) cc_final: 0.4928 (mp0) REVERT: B 452 ASP cc_start: 0.6823 (m-30) cc_final: 0.5881 (t70) REVERT: B 477 GLN cc_start: 0.4782 (mt0) cc_final: 0.4257 (mt0) REVERT: B 524 LYS cc_start: 0.5993 (OUTLIER) cc_final: 0.5470 (ttmt) REVERT: C 53 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.7958 (mt-10) REVERT: C 133 MET cc_start: 0.8421 (mtp) cc_final: 0.8211 (mtp) REVERT: C 260 ASN cc_start: 0.8257 (m-40) cc_final: 0.7965 (m110) REVERT: C 424 TRP cc_start: 0.8104 (p90) cc_final: 0.7708 (p-90) REVERT: C 425 ASN cc_start: 0.8274 (m-40) cc_final: 0.7991 (t0) REVERT: C 488 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7436 (ttt-90) REVERT: C 567 MET cc_start: 0.7004 (mmm) cc_final: 0.6592 (mmm) REVERT: D 26 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.7886 (m-30) REVERT: D 130 PHE cc_start: 0.8871 (OUTLIER) cc_final: 0.8628 (p90) REVERT: D 275 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6778 (mp0) REVERT: D 316 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7332 (mpp) REVERT: D 402 ASP cc_start: 0.6791 (m-30) cc_final: 0.6578 (m-30) REVERT: E 5 LYS cc_start: 0.5831 (mttt) cc_final: 0.5250 (ptmt) REVERT: E 49 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8283 (tm-30) REVERT: E 81 ARG cc_start: 0.7643 (mtm-85) cc_final: 0.7200 (mtt180) REVERT: E 174 ARG cc_start: 0.7971 (mmm-85) cc_final: 0.7566 (mmm-85) REVERT: E 209 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7186 (mt-10) REVERT: E 248 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7666 (mm-30) REVERT: E 265 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7762 (mt-10) REVERT: E 364 ASN cc_start: 0.8095 (t0) cc_final: 0.7851 (t0) REVERT: E 380 ASP cc_start: 0.7710 (m-30) cc_final: 0.7481 (m-30) REVERT: E 410 ARG cc_start: 0.7198 (mtm180) cc_final: 0.6750 (ttt180) REVERT: F 5 LYS cc_start: 0.7746 (tttt) cc_final: 0.7396 (ttmt) REVERT: F 49 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8098 (tm-30) REVERT: F 206 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7684 (mt0) REVERT: G 5 SER cc_start: 0.7261 (p) cc_final: 0.6617 (t) REVERT: G 44 ARG cc_start: 0.6195 (mtm180) cc_final: 0.5538 (mmp80) REVERT: G 48 GLU cc_start: 0.6160 (OUTLIER) cc_final: 0.5783 (mp0) REVERT: H 63 MET cc_start: 0.1953 (mpt) cc_final: 0.1587 (mpt) REVERT: J 160 LYS cc_start: 0.7074 (mmtm) cc_final: 0.6778 (mmpt) REVERT: K 104 MET cc_start: 0.5141 (mmt) cc_final: 0.4860 (pp-130) REVERT: L 78 GLU cc_start: 0.6007 (mt-10) cc_final: 0.5401 (mp0) REVERT: L 102 GLU cc_start: 0.3822 (tp30) cc_final: 0.3410 (tm-30) REVERT: L 128 LEU cc_start: 0.3649 (pt) cc_final: 0.3424 (mp) REVERT: L 132 GLU cc_start: 0.2793 (mm-30) cc_final: 0.2130 (tt0) outliers start: 119 outliers final: 46 residues processed: 471 average time/residue: 0.8988 time to fit residues: 482.2592 Evaluate side-chains 428 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 365 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 459 GLN Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 126 LYS Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 156 LYS Chi-restraints excluded: chain G residue 181 GLN Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain L residue 92 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 24 optimal weight: 0.8980 chunk 326 optimal weight: 6.9990 chunk 224 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 361 optimal weight: 7.9990 chunk 129 optimal weight: 0.9980 chunk 99 optimal weight: 0.0870 chunk 273 optimal weight: 2.9990 chunk 359 optimal weight: 6.9990 chunk 299 optimal weight: 0.7980 chunk 291 optimal weight: 4.9990 overall best weight: 1.1560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN B 397 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 338 GLN E 427 GLN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 ASN F 413 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.160898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.125886 restraints weight = 35367.851| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.27 r_work: 0.3217 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30085 Z= 0.142 Angle : 0.547 11.567 40768 Z= 0.279 Chirality : 0.044 0.171 4568 Planarity : 0.005 0.059 5332 Dihedral : 5.958 88.889 4248 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.44 % Allowed : 16.74 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.14), residues: 3764 helix: 1.62 (0.13), residues: 1597 sheet: -0.12 (0.21), residues: 570 loop : 0.22 (0.16), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 410 TYR 0.015 0.001 TYR A 166 PHE 0.017 0.002 PHE A 559 TRP 0.012 0.001 TRP A 119 HIS 0.006 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00331 (30085) covalent geometry : angle 0.54664 (40768) hydrogen bonds : bond 0.04235 ( 1327) hydrogen bonds : angle 4.72481 ( 3771) *********************** 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 496 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 390 time to evaluate : 1.151 Fit side-chains REVERT: A 2 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.7727 (mm) REVERT: A 8 LYS cc_start: 0.8729 (tttp) cc_final: 0.8306 (tmmt) REVERT: A 133 MET cc_start: 0.7993 (mtp) cc_final: 0.7727 (mtt) REVERT: A 156 ARG cc_start: 0.7227 (ttp80) cc_final: 0.6875 (ttm-80) REVERT: A 323 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8118 (mpt) REVERT: A 374 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7681 (mm-30) REVERT: A 393 GLU cc_start: 0.6582 (tt0) cc_final: 0.6155 (tp30) REVERT: A 397 GLN cc_start: 0.8590 (mm110) cc_final: 0.8336 (mm110) REVERT: A 423 ASN cc_start: 0.8522 (t0) cc_final: 0.8313 (t0) REVERT: A 445 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.7109 (mm-30) REVERT: A 491 ARG cc_start: 0.7507 (mmt180) cc_final: 0.6928 (ttp-110) REVERT: A 524 LYS cc_start: 0.7785 (mmmt) cc_final: 0.7464 (ttmm) REVERT: B 282 MET cc_start: 0.8519 (mmm) cc_final: 0.8006 (tpt) REVERT: B 342 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7524 (pt0) REVERT: B 391 MET cc_start: 0.7027 (mmt) cc_final: 0.6108 (mmp) REVERT: B 449 GLU cc_start: 0.5468 (mp0) cc_final: 0.4607 (mt-10) REVERT: B 452 ASP cc_start: 0.6749 (m-30) cc_final: 0.5884 (t70) REVERT: B 471 VAL cc_start: 0.6849 (OUTLIER) cc_final: 0.6543 (m) REVERT: B 477 GLN cc_start: 0.4816 (mt0) cc_final: 0.4292 (mt0) REVERT: B 524 LYS cc_start: 0.5986 (OUTLIER) cc_final: 0.5425 (ttmt) REVERT: B 548 ILE cc_start: 0.6997 (tt) cc_final: 0.6583 (tp) REVERT: C 53 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7873 (mt-10) REVERT: C 133 MET cc_start: 0.8335 (mtp) cc_final: 0.8080 (mtp) REVERT: C 260 ASN cc_start: 0.8186 (m-40) cc_final: 0.7946 (m110) REVERT: C 424 TRP cc_start: 0.8032 (p90) cc_final: 0.7696 (p-90) REVERT: C 425 ASN cc_start: 0.8219 (m-40) cc_final: 0.7990 (t0) REVERT: C 488 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7338 (ttt-90) REVERT: C 567 MET cc_start: 0.7067 (mmm) cc_final: 0.6711 (mmm) REVERT: D 26 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7746 (m-30) REVERT: D 96 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7458 (tt) REVERT: D 275 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6718 (mp0) REVERT: D 316 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7144 (mpp) REVERT: D 402 ASP cc_start: 0.6698 (m-30) cc_final: 0.6466 (m-30) REVERT: E 5 LYS cc_start: 0.5805 (mttt) cc_final: 0.5277 (ptmt) REVERT: E 81 ARG cc_start: 0.7515 (mtm-85) cc_final: 0.7165 (mtt180) REVERT: E 174 ARG cc_start: 0.7921 (mmm-85) cc_final: 0.7602 (mmm-85) REVERT: E 248 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7589 (mm-30) REVERT: E 265 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7606 (mt-10) REVERT: E 380 ASP cc_start: 0.7688 (m-30) cc_final: 0.7458 (m-30) REVERT: E 410 ARG cc_start: 0.7113 (mtm180) cc_final: 0.6715 (ttt180) REVERT: E 445 MET cc_start: 0.7411 (mtt) cc_final: 0.7173 (mtp) REVERT: E 456 LYS cc_start: 0.5975 (mmmm) cc_final: 0.5559 (mmtm) REVERT: E 457 ASP cc_start: 0.5870 (t70) cc_final: 0.5452 (t0) REVERT: F 5 LYS cc_start: 0.7918 (tttt) cc_final: 0.7486 (ttmt) REVERT: F 49 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7920 (tm-30) REVERT: F 126 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8207 (tttp) REVERT: F 206 GLN cc_start: 0.7946 (mm-40) cc_final: 0.7662 (mt0) REVERT: G 5 SER cc_start: 0.7141 (p) cc_final: 0.6514 (t) REVERT: G 44 ARG cc_start: 0.6268 (mtm180) cc_final: 0.5651 (mmp80) REVERT: G 47 MET cc_start: 0.5078 (ptp) cc_final: 0.4361 (ptp) REVERT: G 48 GLU cc_start: 0.6172 (OUTLIER) cc_final: 0.5789 (mp0) REVERT: H 63 MET cc_start: 0.2079 (mpt) cc_final: 0.1510 (mtm) REVERT: H 104 LEU cc_start: 0.4056 (pp) cc_final: 0.3841 (mt) REVERT: J 122 VAL cc_start: 0.4469 (OUTLIER) cc_final: 0.4097 (t) REVERT: J 160 LYS cc_start: 0.7136 (mmtm) cc_final: 0.6781 (mmpt) REVERT: L 78 GLU cc_start: 0.6090 (mt-10) cc_final: 0.5427 (mp0) REVERT: L 102 GLU cc_start: 0.3833 (tp30) cc_final: 0.3400 (tm-30) REVERT: L 128 LEU cc_start: 0.3448 (pt) cc_final: 0.3196 (mp) outliers start: 106 outliers final: 42 residues processed: 458 average time/residue: 0.9351 time to fit residues: 485.9358 Evaluate side-chains 428 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 370 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 481 ARG Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 459 GLN Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain C residue 548 ILE Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain D residue 388 ASN Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 126 LYS Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 181 GLN Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain L residue 92 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 310 optimal weight: 6.9990 chunk 184 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 186 optimal weight: 0.7980 chunk 372 optimal weight: 10.0000 chunk 159 optimal weight: 5.9990 chunk 111 optimal weight: 0.0770 chunk 315 optimal weight: 1.9990 chunk 305 optimal weight: 0.8980 chunk 181 optimal weight: 0.0270 chunk 55 optimal weight: 2.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN A 316 GLN B 397 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 338 GLN ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 ASN F 413 GLN G 10 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.162479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.127757 restraints weight = 35170.525| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.30 r_work: 0.3237 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 30085 Z= 0.108 Angle : 0.506 10.428 40768 Z= 0.257 Chirality : 0.042 0.161 4568 Planarity : 0.004 0.052 5332 Dihedral : 5.693 89.657 4248 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.05 % Favored : 97.93 % Rotamer: Outliers : 3.24 % Allowed : 17.35 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.14), residues: 3764 helix: 1.84 (0.13), residues: 1588 sheet: -0.11 (0.21), residues: 574 loop : 0.31 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 547 TYR 0.016 0.001 TYR A 166 PHE 0.015 0.001 PHE A 559 TRP 0.010 0.001 TRP A 119 HIS 0.004 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00246 (30085) covalent geometry : angle 0.50586 (40768) hydrogen bonds : bond 0.03697 ( 1327) hydrogen bonds : angle 4.52436 ( 3771) *********************** 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 493 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 393 time to evaluate : 1.376 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8651 (tttp) cc_final: 0.8353 (tmmt) REVERT: A 133 MET cc_start: 0.7979 (mtp) cc_final: 0.7762 (mtt) REVERT: A 156 ARG cc_start: 0.7199 (ttp80) cc_final: 0.6886 (ttm110) REVERT: A 323 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8139 (mpt) REVERT: A 374 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7620 (mm-30) REVERT: A 393 GLU cc_start: 0.6490 (tt0) cc_final: 0.6148 (tp30) REVERT: A 397 GLN cc_start: 0.8515 (mm110) cc_final: 0.8204 (mm110) REVERT: A 445 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.7055 (mm-30) REVERT: A 491 ARG cc_start: 0.7464 (mmt180) cc_final: 0.6894 (ttp-110) REVERT: A 524 LYS cc_start: 0.7729 (mmmt) cc_final: 0.7496 (ttmm) REVERT: B 282 MET cc_start: 0.8522 (mmm) cc_final: 0.7973 (tpt) REVERT: B 342 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7475 (pt0) REVERT: B 391 MET cc_start: 0.7017 (mmt) cc_final: 0.6366 (mmp) REVERT: B 412 SER cc_start: 0.7601 (OUTLIER) cc_final: 0.7334 (p) REVERT: B 449 GLU cc_start: 0.5490 (mp0) cc_final: 0.4589 (mt-10) REVERT: B 452 ASP cc_start: 0.6676 (m-30) cc_final: 0.5855 (t70) REVERT: B 471 VAL cc_start: 0.6763 (OUTLIER) cc_final: 0.6404 (m) REVERT: B 477 GLN cc_start: 0.4741 (mt0) cc_final: 0.4198 (mt0) REVERT: B 481 ARG cc_start: 0.7388 (mmm-85) cc_final: 0.6961 (mmm-85) REVERT: B 524 LYS cc_start: 0.5953 (OUTLIER) cc_final: 0.5395 (ttmt) REVERT: B 548 ILE cc_start: 0.6926 (tt) cc_final: 0.6507 (tp) REVERT: C 53 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7819 (mt-10) REVERT: C 133 MET cc_start: 0.8314 (mtp) cc_final: 0.8052 (mtp) REVERT: C 424 TRP cc_start: 0.8012 (p90) cc_final: 0.7676 (p-90) REVERT: C 425 ASN cc_start: 0.8212 (m-40) cc_final: 0.7974 (t0) REVERT: C 488 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7340 (ttt-90) REVERT: C 567 MET cc_start: 0.7104 (mmm) cc_final: 0.6768 (mmm) REVERT: D 26 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7725 (m-30) REVERT: D 96 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7318 (tt) REVERT: D 275 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6681 (mp0) REVERT: D 316 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.7085 (mpp) REVERT: D 364 ASN cc_start: 0.8195 (OUTLIER) cc_final: 0.7455 (t0) REVERT: D 402 ASP cc_start: 0.6664 (m-30) cc_final: 0.6432 (m-30) REVERT: E 5 LYS cc_start: 0.5726 (mttt) cc_final: 0.5210 (pttt) REVERT: E 49 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8064 (tm-30) REVERT: E 248 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7526 (mm-30) REVERT: E 265 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7548 (mt-10) REVERT: E 380 ASP cc_start: 0.7585 (m-30) cc_final: 0.7348 (m-30) REVERT: E 410 ARG cc_start: 0.7164 (mtm180) cc_final: 0.6750 (ttt180) REVERT: E 428 GLN cc_start: 0.8018 (mt0) cc_final: 0.7791 (mt0) REVERT: E 445 MET cc_start: 0.7404 (mtt) cc_final: 0.6917 (mtt) REVERT: E 456 LYS cc_start: 0.5910 (mmmm) cc_final: 0.5651 (mmtm) REVERT: E 457 ASP cc_start: 0.5910 (t70) cc_final: 0.5458 (t0) REVERT: F 5 LYS cc_start: 0.7901 (tttt) cc_final: 0.7473 (ttmt) REVERT: F 206 GLN cc_start: 0.7940 (mm-40) cc_final: 0.7639 (mt0) REVERT: G 5 SER cc_start: 0.7105 (p) cc_final: 0.6456 (t) REVERT: G 44 ARG cc_start: 0.6170 (mtm180) cc_final: 0.5518 (mmp80) REVERT: G 48 GLU cc_start: 0.6162 (OUTLIER) cc_final: 0.5833 (mp0) REVERT: H 63 MET cc_start: 0.2081 (OUTLIER) cc_final: 0.1743 (mpt) REVERT: J 145 GLU cc_start: 0.2503 (pm20) cc_final: 0.1228 (tm-30) REVERT: J 160 LYS cc_start: 0.7258 (mmtm) cc_final: 0.6753 (mmpt) REVERT: L 78 GLU cc_start: 0.6039 (mt-10) cc_final: 0.5351 (mp0) REVERT: L 102 GLU cc_start: 0.3707 (tp30) cc_final: 0.3367 (tm-30) REVERT: L 128 LEU cc_start: 0.3714 (pt) cc_final: 0.3473 (mp) REVERT: L 132 GLU cc_start: 0.3474 (mm-30) cc_final: 0.2462 (tt0) outliers start: 100 outliers final: 36 residues processed: 453 average time/residue: 0.8771 time to fit residues: 453.8251 Evaluate side-chains 424 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 372 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 181 GLN Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 122 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 306 optimal weight: 4.9990 chunk 76 optimal weight: 0.0970 chunk 98 optimal weight: 0.6980 chunk 238 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 158 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 349 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 320 optimal weight: 6.9990 chunk 288 optimal weight: 3.9990 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN A 316 GLN B 283 HIS B 397 GLN C 260 ASN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 338 GLN E 377 GLN E 427 GLN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN G 10 ASN L 130 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.159818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.125744 restraints weight = 35334.319| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.48 r_work: 0.3175 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 30085 Z= 0.188 Angle : 0.604 13.591 40768 Z= 0.307 Chirality : 0.046 0.186 4568 Planarity : 0.005 0.055 5332 Dihedral : 6.020 82.964 4248 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.10 % Favored : 97.87 % Rotamer: Outliers : 3.41 % Allowed : 17.52 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.14), residues: 3764 helix: 1.57 (0.13), residues: 1586 sheet: -0.16 (0.21), residues: 576 loop : 0.21 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 488 TYR 0.016 0.002 TYR A 304 PHE 0.022 0.002 PHE A 559 TRP 0.011 0.002 TRP B 330 HIS 0.007 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00449 (30085) covalent geometry : angle 0.60407 (40768) hydrogen bonds : bond 0.04634 ( 1327) hydrogen bonds : angle 4.79102 ( 3771) *********************** 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 474 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 369 time to evaluate : 1.252 Fit side-chains REVERT: A 8 LYS cc_start: 0.8853 (tttp) cc_final: 0.8472 (tmmt) REVERT: A 93 ARG cc_start: 0.8007 (mmp80) cc_final: 0.7746 (mmp80) REVERT: A 133 MET cc_start: 0.8060 (mtp) cc_final: 0.7822 (mtt) REVERT: A 156 ARG cc_start: 0.7212 (ttp80) cc_final: 0.6901 (ttm110) REVERT: A 323 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8242 (mpt) REVERT: A 374 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7662 (mm-30) REVERT: A 397 GLN cc_start: 0.8648 (mm110) cc_final: 0.8404 (mm110) REVERT: A 491 ARG cc_start: 0.7548 (mmt180) cc_final: 0.6963 (ttp-110) REVERT: A 520 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8131 (mt) REVERT: A 524 LYS cc_start: 0.7765 (mmmt) cc_final: 0.7531 (ttmm) REVERT: B 282 MET cc_start: 0.8603 (mmm) cc_final: 0.8379 (mmm) REVERT: B 449 GLU cc_start: 0.5545 (mp0) cc_final: 0.4693 (mt-10) REVERT: B 452 ASP cc_start: 0.6820 (m-30) cc_final: 0.5910 (t70) REVERT: B 471 VAL cc_start: 0.6767 (OUTLIER) cc_final: 0.6444 (m) REVERT: B 477 GLN cc_start: 0.4844 (mt0) cc_final: 0.4213 (mt0) REVERT: B 481 ARG cc_start: 0.7413 (mmm-85) cc_final: 0.6961 (mmm-85) REVERT: B 524 LYS cc_start: 0.6011 (OUTLIER) cc_final: 0.5440 (ttmt) REVERT: B 548 ILE cc_start: 0.7118 (tt) cc_final: 0.6737 (tp) REVERT: C 53 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7949 (mt-10) REVERT: C 133 MET cc_start: 0.8336 (mtp) cc_final: 0.8074 (mtp) REVERT: C 424 TRP cc_start: 0.8086 (p90) cc_final: 0.7696 (p-90) REVERT: C 425 ASN cc_start: 0.8257 (m-40) cc_final: 0.7987 (t0) REVERT: C 488 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7382 (ttt-90) REVERT: C 557 GLU cc_start: 0.7153 (mp0) cc_final: 0.6828 (mp0) REVERT: C 567 MET cc_start: 0.7100 (mmm) cc_final: 0.6742 (mmm) REVERT: D 26 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7804 (m-30) REVERT: D 109 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7042 (mp0) REVERT: D 275 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6776 (mp0) REVERT: D 316 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7415 (mpp) REVERT: D 364 ASN cc_start: 0.8213 (OUTLIER) cc_final: 0.7467 (t0) REVERT: D 402 ASP cc_start: 0.6732 (m-30) cc_final: 0.6512 (m-30) REVERT: E 5 LYS cc_start: 0.5796 (mttt) cc_final: 0.5258 (ptmt) REVERT: E 49 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8196 (tm-30) REVERT: E 81 ARG cc_start: 0.7575 (mtt-85) cc_final: 0.7186 (mtt180) REVERT: E 236 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.6696 (mtt90) REVERT: E 248 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7563 (mm-30) REVERT: E 265 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7656 (mt-10) REVERT: E 380 ASP cc_start: 0.7687 (m-30) cc_final: 0.7476 (m-30) REVERT: E 410 ARG cc_start: 0.7203 (mtm180) cc_final: 0.6758 (ttt180) REVERT: E 433 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7811 (mp0) REVERT: E 445 MET cc_start: 0.7321 (mtt) cc_final: 0.7070 (mtp) REVERT: F 5 LYS cc_start: 0.8076 (tttt) cc_final: 0.7591 (ttmt) REVERT: F 49 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8095 (tm-30) REVERT: G 5 SER cc_start: 0.7272 (p) cc_final: 0.6578 (t) REVERT: G 48 GLU cc_start: 0.6136 (OUTLIER) cc_final: 0.5666 (mp0) REVERT: H 63 MET cc_start: 0.2199 (OUTLIER) cc_final: 0.1725 (mpt) REVERT: H 104 LEU cc_start: 0.4106 (pp) cc_final: 0.3846 (mt) REVERT: J 160 LYS cc_start: 0.7321 (mmtm) cc_final: 0.6814 (mmpt) REVERT: L 78 GLU cc_start: 0.6102 (mt-10) cc_final: 0.5370 (mp0) REVERT: L 92 GLU cc_start: 0.4883 (tt0) cc_final: 0.4616 (tt0) REVERT: L 150 LEU cc_start: 0.4893 (OUTLIER) cc_final: 0.4674 (pt) outliers start: 105 outliers final: 52 residues processed: 435 average time/residue: 0.9226 time to fit residues: 455.9776 Evaluate side-chains 423 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 352 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 481 ARG Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 535 SER Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain C residue 568 LYS Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain D residue 388 ASN Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 236 ARG Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 433 GLU Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 181 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain L residue 150 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 170 optimal weight: 0.8980 chunk 189 optimal weight: 6.9990 chunk 271 optimal weight: 0.4980 chunk 359 optimal weight: 8.9990 chunk 200 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 292 optimal weight: 0.9990 chunk 354 optimal weight: 10.0000 chunk 361 optimal weight: 8.9990 chunk 158 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN B 397 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 338 GLN ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN G 10 ASN H 30 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.161390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.127347 restraints weight = 35331.606| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.48 r_work: 0.3191 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30085 Z= 0.125 Angle : 0.535 12.018 40768 Z= 0.272 Chirality : 0.043 0.171 4568 Planarity : 0.004 0.052 5332 Dihedral : 5.796 83.362 4248 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.86 % Favored : 98.11 % Rotamer: Outliers : 2.72 % Allowed : 18.78 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.14), residues: 3764 helix: 1.72 (0.13), residues: 1585 sheet: -0.13 (0.21), residues: 568 loop : 0.26 (0.16), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 547 TYR 0.015 0.001 TYR A 166 PHE 0.015 0.001 PHE A 559 TRP 0.010 0.001 TRP A 119 HIS 0.002 0.001 HIS E 344 Details of bonding type rmsd covalent geometry : bond 0.00289 (30085) covalent geometry : angle 0.53527 (40768) hydrogen bonds : bond 0.03951 ( 1327) hydrogen bonds : angle 4.60484 ( 3771) *********************** 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 455 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 371 time to evaluate : 1.179 Fit side-chains revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8794 (tttp) cc_final: 0.8411 (tmmt) REVERT: A 93 ARG cc_start: 0.7996 (mmp80) cc_final: 0.7744 (mmp80) REVERT: A 133 MET cc_start: 0.8100 (mtp) cc_final: 0.7852 (mtt) REVERT: A 156 ARG cc_start: 0.7257 (ttp80) cc_final: 0.6955 (ttm110) REVERT: A 323 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8221 (mpt) REVERT: A 374 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7648 (mm-30) REVERT: A 393 GLU cc_start: 0.6629 (tt0) cc_final: 0.6114 (tp30) REVERT: A 397 GLN cc_start: 0.8597 (mm110) cc_final: 0.8263 (mm110) REVERT: A 491 ARG cc_start: 0.7574 (mmt180) cc_final: 0.6980 (ttp-110) REVERT: A 524 LYS cc_start: 0.7797 (mmmt) cc_final: 0.7549 (ttmm) REVERT: B 282 MET cc_start: 0.8582 (mmm) cc_final: 0.8035 (tpt) REVERT: B 342 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7521 (pt0) REVERT: B 412 SER cc_start: 0.7679 (OUTLIER) cc_final: 0.7363 (p) REVERT: B 449 GLU cc_start: 0.5574 (mp0) cc_final: 0.4662 (mt-10) REVERT: B 452 ASP cc_start: 0.6807 (m-30) cc_final: 0.5941 (t70) REVERT: B 471 VAL cc_start: 0.6747 (OUTLIER) cc_final: 0.6386 (m) REVERT: B 477 GLN cc_start: 0.4829 (mt0) cc_final: 0.4210 (mt0) REVERT: B 481 ARG cc_start: 0.7411 (mmm-85) cc_final: 0.6973 (mmm-85) REVERT: B 524 LYS cc_start: 0.5997 (OUTLIER) cc_final: 0.5396 (ttmt) REVERT: B 548 ILE cc_start: 0.7116 (tt) cc_final: 0.6722 (tp) REVERT: C 53 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7906 (mt-10) REVERT: C 133 MET cc_start: 0.8341 (mtp) cc_final: 0.8083 (mtp) REVERT: C 424 TRP cc_start: 0.8096 (p90) cc_final: 0.7703 (p-90) REVERT: C 425 ASN cc_start: 0.8261 (m-40) cc_final: 0.7992 (t0) REVERT: C 488 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7393 (ttt-90) REVERT: C 567 MET cc_start: 0.7074 (mmm) cc_final: 0.6727 (mmm) REVERT: D 26 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7794 (m-30) REVERT: D 96 ILE cc_start: 0.7917 (OUTLIER) cc_final: 0.7142 (tt) REVERT: D 275 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6768 (mp0) REVERT: D 316 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.7158 (mpp) REVERT: D 364 ASN cc_start: 0.8235 (OUTLIER) cc_final: 0.7475 (t0) REVERT: D 402 ASP cc_start: 0.6717 (m-30) cc_final: 0.6503 (m-30) REVERT: E 5 LYS cc_start: 0.5893 (mttt) cc_final: 0.5293 (pttt) REVERT: E 49 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8196 (tm-30) REVERT: E 81 ARG cc_start: 0.7595 (mtt-85) cc_final: 0.7207 (mtt180) REVERT: E 128 GLU cc_start: 0.7430 (pt0) cc_final: 0.7110 (pt0) REVERT: E 236 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.6632 (mtt90) REVERT: E 248 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7572 (mm-30) REVERT: E 265 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7683 (mt-10) REVERT: E 380 ASP cc_start: 0.7715 (m-30) cc_final: 0.7501 (m-30) REVERT: E 410 ARG cc_start: 0.7187 (mtm180) cc_final: 0.6784 (ttt180) REVERT: F 5 LYS cc_start: 0.8115 (tttt) cc_final: 0.7626 (ttmt) REVERT: F 206 GLN cc_start: 0.7984 (mm-40) cc_final: 0.7674 (mt0) REVERT: G 5 SER cc_start: 0.7070 (p) cc_final: 0.6419 (t) REVERT: G 48 GLU cc_start: 0.6126 (OUTLIER) cc_final: 0.5838 (mp0) REVERT: H 63 MET cc_start: 0.2389 (OUTLIER) cc_final: 0.1834 (mpt) REVERT: H 104 LEU cc_start: 0.4001 (pp) cc_final: 0.3781 (mt) REVERT: J 145 GLU cc_start: 0.2305 (pm20) cc_final: 0.1652 (pm20) REVERT: J 160 LYS cc_start: 0.7286 (mmtm) cc_final: 0.6809 (mmpt) REVERT: L 78 GLU cc_start: 0.6115 (mt-10) cc_final: 0.5365 (mp0) REVERT: L 92 GLU cc_start: 0.4837 (tt0) cc_final: 0.4580 (tt0) REVERT: L 102 GLU cc_start: 0.3814 (tp30) cc_final: 0.3142 (tm-30) REVERT: L 132 GLU cc_start: 0.3439 (mm-30) cc_final: 0.2558 (tt0) REVERT: L 143 GLN cc_start: 0.4867 (OUTLIER) cc_final: 0.4666 (mp10) outliers start: 84 outliers final: 38 residues processed: 422 average time/residue: 0.9045 time to fit residues: 434.1942 Evaluate side-chains 418 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 363 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain C residue 568 LYS Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain D residue 388 ASN Chi-restraints excluded: chain E residue 49 GLU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 236 ARG Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 181 GLN Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain L residue 143 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 296 optimal weight: 3.9990 chunk 271 optimal weight: 0.9990 chunk 236 optimal weight: 5.9990 chunk 355 optimal weight: 9.9990 chunk 263 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 215 optimal weight: 0.0770 chunk 203 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 301 optimal weight: 5.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 338 GLN ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN G 10 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.162337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.128081 restraints weight = 35332.789| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.36 r_work: 0.3237 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30085 Z= 0.114 Angle : 0.516 11.255 40768 Z= 0.261 Chirality : 0.043 0.165 4568 Planarity : 0.004 0.052 5332 Dihedral : 5.646 84.198 4248 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.07 % Favored : 97.90 % Rotamer: Outliers : 2.30 % Allowed : 19.20 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.14), residues: 3764 helix: 1.83 (0.13), residues: 1592 sheet: -0.16 (0.21), residues: 574 loop : 0.30 (0.16), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 547 TYR 0.015 0.001 TYR A 166 PHE 0.016 0.001 PHE A 559 TRP 0.010 0.001 TRP A 119 HIS 0.002 0.001 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00262 (30085) covalent geometry : angle 0.51577 (40768) hydrogen bonds : bond 0.03682 ( 1327) hydrogen bonds : angle 4.50138 ( 3771) *********************** 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 450 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 379 time to evaluate : 1.215 Fit side-chains REVERT: A 8 LYS cc_start: 0.8695 (tttp) cc_final: 0.8357 (tmmt) REVERT: A 93 ARG cc_start: 0.7941 (mmp80) cc_final: 0.7699 (mmp80) REVERT: A 133 MET cc_start: 0.8015 (mtp) cc_final: 0.7765 (mtt) REVERT: A 156 ARG cc_start: 0.7231 (ttp80) cc_final: 0.6953 (ttm110) REVERT: A 323 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8047 (mpt) REVERT: A 374 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7559 (mm-30) REVERT: A 393 GLU cc_start: 0.6537 (tt0) cc_final: 0.6067 (tp30) REVERT: A 397 GLN cc_start: 0.8558 (mm110) cc_final: 0.8242 (mm110) REVERT: A 491 ARG cc_start: 0.7511 (mmt180) cc_final: 0.6932 (ttp-110) REVERT: B 92 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7415 (mp0) REVERT: B 282 MET cc_start: 0.8537 (mmm) cc_final: 0.7997 (tpt) REVERT: B 342 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7469 (pt0) REVERT: B 412 SER cc_start: 0.7609 (OUTLIER) cc_final: 0.7363 (p) REVERT: B 449 GLU cc_start: 0.5543 (mp0) cc_final: 0.4643 (mt-10) REVERT: B 452 ASP cc_start: 0.6651 (m-30) cc_final: 0.5872 (t70) REVERT: B 471 VAL cc_start: 0.6697 (OUTLIER) cc_final: 0.6309 (m) REVERT: B 477 GLN cc_start: 0.4683 (mt0) cc_final: 0.4111 (mt0) REVERT: B 481 ARG cc_start: 0.7381 (mmm-85) cc_final: 0.6960 (mmm-85) REVERT: B 524 LYS cc_start: 0.5929 (OUTLIER) cc_final: 0.5354 (ttmt) REVERT: B 548 ILE cc_start: 0.7047 (tt) cc_final: 0.6684 (tp) REVERT: C 53 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7840 (mt-10) REVERT: C 424 TRP cc_start: 0.8033 (p90) cc_final: 0.7612 (p-90) REVERT: C 488 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7333 (ttt-90) REVERT: C 567 MET cc_start: 0.7017 (mmm) cc_final: 0.6697 (mmm) REVERT: D 26 ASP cc_start: 0.8106 (OUTLIER) cc_final: 0.7687 (m-30) REVERT: D 96 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7080 (tt) REVERT: D 275 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6693 (mp0) REVERT: D 316 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.7134 (mpp) REVERT: D 364 ASN cc_start: 0.8267 (OUTLIER) cc_final: 0.7459 (t0) REVERT: D 402 ASP cc_start: 0.6620 (m-30) cc_final: 0.6393 (m-30) REVERT: E 5 LYS cc_start: 0.5780 (mttt) cc_final: 0.5265 (ptmt) REVERT: E 81 ARG cc_start: 0.7494 (mtt-85) cc_final: 0.7118 (mtt180) REVERT: E 128 GLU cc_start: 0.7297 (pt0) cc_final: 0.6972 (pt0) REVERT: E 236 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7793 (mpt180) REVERT: E 248 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7482 (mm-30) REVERT: E 265 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7560 (mt-10) REVERT: E 380 ASP cc_start: 0.7604 (m-30) cc_final: 0.7387 (m-30) REVERT: E 410 ARG cc_start: 0.7208 (mtm180) cc_final: 0.6771 (ttt180) REVERT: E 445 MET cc_start: 0.7313 (mtt) cc_final: 0.6900 (mtt) REVERT: F 5 LYS cc_start: 0.8061 (tttt) cc_final: 0.7570 (ttmt) REVERT: G 5 SER cc_start: 0.7088 (p) cc_final: 0.6408 (t) REVERT: G 48 GLU cc_start: 0.6028 (OUTLIER) cc_final: 0.5712 (mp0) REVERT: H 63 MET cc_start: 0.2533 (OUTLIER) cc_final: 0.1712 (mtp) REVERT: H 71 LEU cc_start: 0.4262 (mt) cc_final: 0.4041 (mp) REVERT: J 145 GLU cc_start: 0.2117 (pm20) cc_final: 0.1620 (pm20) REVERT: J 160 LYS cc_start: 0.7297 (mmtm) cc_final: 0.6814 (mmpt) REVERT: L 78 GLU cc_start: 0.6088 (mt-10) cc_final: 0.5322 (mp0) REVERT: L 102 GLU cc_start: 0.3625 (tp30) cc_final: 0.3059 (tm-30) REVERT: L 132 GLU cc_start: 0.3270 (mm-30) cc_final: 0.2487 (tt0) outliers start: 71 outliers final: 38 residues processed: 423 average time/residue: 0.9254 time to fit residues: 444.5737 Evaluate side-chains 413 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 359 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain C residue 568 LYS Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain D residue 388 ASN Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 236 ARG Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 398 ILE Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 181 GLN Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain J residue 122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 184 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 324 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 314 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN A 465 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 170 GLN E 338 GLN E 427 GLN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN G 10 ASN G 17 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.158755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.124620 restraints weight = 35090.630| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.48 r_work: 0.3172 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 30085 Z= 0.253 Angle : 0.683 12.898 40768 Z= 0.350 Chirality : 0.049 0.197 4568 Planarity : 0.006 0.062 5332 Dihedral : 6.245 84.226 4248 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.47 % Favored : 97.50 % Rotamer: Outliers : 2.37 % Allowed : 19.62 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.14), residues: 3764 helix: 1.29 (0.13), residues: 1578 sheet: -0.31 (0.21), residues: 593 loop : 0.15 (0.16), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 280 TYR 0.021 0.003 TYR A 304 PHE 0.023 0.002 PHE C 559 TRP 0.013 0.002 TRP C 187 HIS 0.007 0.002 HIS B 283 Details of bonding type rmsd covalent geometry : bond 0.00609 (30085) covalent geometry : angle 0.68339 (40768) hydrogen bonds : bond 0.05187 ( 1327) hydrogen bonds : angle 4.99135 ( 3771) ********************** 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 423 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 350 time to evaluate : 1.198 Fit side-chains REVERT: A 8 LYS cc_start: 0.8887 (tttp) cc_final: 0.8446 (tmmt) REVERT: A 93 ARG cc_start: 0.7976 (mmp80) cc_final: 0.7722 (mmp80) REVERT: A 95 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.6243 (tpt-90) REVERT: A 128 GLU cc_start: 0.7747 (mm-30) cc_final: 0.6605 (tp30) REVERT: A 133 MET cc_start: 0.8002 (mtp) cc_final: 0.7755 (mtt) REVERT: A 323 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8239 (mpt) REVERT: A 374 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7648 (mm-30) REVERT: A 397 GLN cc_start: 0.8663 (mm110) cc_final: 0.8412 (mm110) REVERT: A 488 ARG cc_start: 0.8295 (ttp80) cc_final: 0.8040 (ttp-110) REVERT: A 491 ARG cc_start: 0.7507 (mmt180) cc_final: 0.6923 (ttp-110) REVERT: A 520 LEU cc_start: 0.8427 (mm) cc_final: 0.8110 (mt) REVERT: A 532 ARG cc_start: 0.6156 (ttp-110) cc_final: 0.5848 (ttm-80) REVERT: B 92 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7520 (mp0) REVERT: B 282 MET cc_start: 0.8542 (mmm) cc_final: 0.8337 (mmm) REVERT: B 449 GLU cc_start: 0.5583 (mp0) cc_final: 0.5261 (mp0) REVERT: B 452 ASP cc_start: 0.6823 (m-30) cc_final: 0.5928 (t70) REVERT: B 471 VAL cc_start: 0.6731 (OUTLIER) cc_final: 0.6426 (m) REVERT: B 477 GLN cc_start: 0.4803 (mt0) cc_final: 0.4205 (mt0) REVERT: B 481 ARG cc_start: 0.7468 (mmm-85) cc_final: 0.6983 (mmm-85) REVERT: B 524 LYS cc_start: 0.5991 (OUTLIER) cc_final: 0.5411 (ttmt) REVERT: C 53 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7902 (mt-10) REVERT: C 424 TRP cc_start: 0.8090 (p90) cc_final: 0.7684 (p-90) REVERT: C 425 ASN cc_start: 0.8235 (m-40) cc_final: 0.7963 (t0) REVERT: C 480 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6546 (mp0) REVERT: C 488 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7343 (ttt-90) REVERT: C 557 GLU cc_start: 0.7231 (mp0) cc_final: 0.7014 (mp0) REVERT: C 567 MET cc_start: 0.7151 (mmm) cc_final: 0.6866 (mmm) REVERT: D 26 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7789 (m-30) REVERT: D 96 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7337 (tt) REVERT: D 275 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6749 (mp0) REVERT: D 316 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7371 (mpp) REVERT: D 364 ASN cc_start: 0.8160 (OUTLIER) cc_final: 0.7344 (t0) REVERT: D 402 ASP cc_start: 0.6875 (m-30) cc_final: 0.6597 (m-30) REVERT: E 81 ARG cc_start: 0.7574 (mtt-85) cc_final: 0.7219 (mtp180) REVERT: E 128 GLU cc_start: 0.7408 (pt0) cc_final: 0.7103 (pt0) REVERT: E 248 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7565 (mm-30) REVERT: E 380 ASP cc_start: 0.7717 (m-30) cc_final: 0.7496 (m-30) REVERT: E 382 LEU cc_start: 0.8635 (mt) cc_final: 0.8368 (mt) REVERT: E 410 ARG cc_start: 0.7209 (mtm180) cc_final: 0.6736 (ttt180) REVERT: F 5 LYS cc_start: 0.8044 (tttt) cc_final: 0.7618 (ttmt) REVERT: F 49 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8084 (tm-30) REVERT: F 413 GLN cc_start: 0.8090 (mt0) cc_final: 0.7852 (mt0) REVERT: G 5 SER cc_start: 0.7209 (p) cc_final: 0.6488 (t) REVERT: G 48 GLU cc_start: 0.6026 (OUTLIER) cc_final: 0.5729 (mp0) REVERT: H 63 MET cc_start: 0.2396 (mpt) cc_final: 0.1553 (mtp) REVERT: J 121 LEU cc_start: 0.4772 (OUTLIER) cc_final: 0.4280 (mm) REVERT: J 145 GLU cc_start: 0.2251 (pm20) cc_final: 0.1096 (tm-30) REVERT: L 78 GLU cc_start: 0.6069 (mt-10) cc_final: 0.5360 (mp0) REVERT: L 102 GLU cc_start: 0.3800 (tp30) cc_final: 0.3193 (tm-30) outliers start: 73 outliers final: 39 residues processed: 400 average time/residue: 0.9124 time to fit residues: 414.3186 Evaluate side-chains 394 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 339 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 481 ARG Chi-restraints excluded: chain B residue 92 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 550 ARG Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 480 GLU Chi-restraints excluded: chain C residue 488 ARG Chi-restraints excluded: chain C residue 568 LYS Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain F residue 49 GLU Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 181 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 291 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 328 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 344 optimal weight: 0.7980 chunk 233 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 346 optimal weight: 4.9990 chunk 294 optimal weight: 1.9990 chunk 305 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 GLN E 338 GLN ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 GLN ** F 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 ASN G 17 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.161281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.127021 restraints weight = 35330.414| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.43 r_work: 0.3215 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30085 Z= 0.127 Angle : 0.545 11.450 40768 Z= 0.277 Chirality : 0.044 0.197 4568 Planarity : 0.004 0.051 5332 Dihedral : 5.821 81.016 4248 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.78 % Favored : 98.19 % Rotamer: Outliers : 2.11 % Allowed : 19.88 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.14), residues: 3764 helix: 1.60 (0.13), residues: 1596 sheet: -0.23 (0.21), residues: 573 loop : 0.22 (0.16), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 547 TYR 0.015 0.001 TYR A 166 PHE 0.014 0.001 PHE A 559 TRP 0.011 0.001 TRP B 424 HIS 0.003 0.001 HIS C 145 Details of bonding type rmsd covalent geometry : bond 0.00295 (30085) covalent geometry : angle 0.54486 (40768) hydrogen bonds : bond 0.03968 ( 1327) hydrogen bonds : angle 4.64777 ( 3771) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13258.41 seconds wall clock time: 226 minutes 7.04 seconds (13567.04 seconds total)