Starting phenix.real_space_refine on Mon Aug 25 15:47:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gxz_34366/08_2025/8gxz_34366.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gxz_34366/08_2025/8gxz_34366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gxz_34366/08_2025/8gxz_34366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gxz_34366/08_2025/8gxz_34366.map" model { file = "/net/cci-nas-00/data/ceres_data/8gxz_34366/08_2025/8gxz_34366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gxz_34366/08_2025/8gxz_34366.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 104 5.16 5 C 18715 2.51 5 N 5121 2.21 5 O 5555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 29499 Number of models: 1 Model: "" Number of chains: 14 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: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.82, per 1000 atoms: 0.27 Number of scatterers: 29499 At special positions: 0 Unit cell: (147.42, 148.23, 171.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 104 16.00 P 3 15.00 Mg 1 11.99 O 5555 8.00 N 5121 7.00 C 18715 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: 2.79 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 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: 143 helices and 29 sheets defined 47.9% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 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: 4.427A pdb=" N MET A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 297 through 317 removed outlier: 4.403A pdb=" N ALA A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 342 removed outlier: 3.921A 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 removed outlier: 3.508A pdb=" N GLY A 389 " --> pdb=" O PRO A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 401 removed outlier: 3.716A pdb=" N ARG A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 416 Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 446 through 472 removed outlier: 3.696A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) 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 544 through 551 Processing helix chain 'A' and resid 558 through 577 removed outlier: 3.912A pdb=" N LEU A 577 " --> pdb=" O ALA A 573 " (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 280 through 283 Processing helix chain 'B' and resid 295 through 317 removed outlier: 4.760A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY B 317 " --> pdb=" O PHE B 313 " (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 401 Processing helix chain 'B' and resid 410 through 416 removed outlier: 3.501A pdb=" N ALA B 414 " --> pdb=" O ASP B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 443 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 446 through 464 Processing helix chain 'B' and resid 464 through 471 Processing helix chain 'B' and resid 472 through 476 Processing helix chain 'B' and resid 477 through 494 removed outlier: 3.503A pdb=" N VAL B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 533 Processing helix chain 'B' and resid 535 through 540 Processing helix chain 'B' and resid 543 through 550 Processing helix chain 'B' and resid 558 through 576 removed outlier: 4.261A pdb=" N GLN B 571 " --> pdb=" O MET B 567 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY B 572 " --> pdb=" O LYS B 568 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 98 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: 4.039A pdb=" N MET C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 297 through 316 removed outlier: 4.254A pdb=" N ALA C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 342 removed outlier: 3.986A pdb=" N TRP C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 364 removed outlier: 3.776A pdb=" N ARG C 364 " --> pdb=" O ALA C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 393 through 401 Processing helix chain 'C' and resid 410 through 416 removed outlier: 3.565A pdb=" N ARG C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 443 removed outlier: 3.566A pdb=" N ASP C 436 " --> pdb=" O THR C 432 " (cutoff:3.500A) Proline residue: C 437 - end of helix removed outlier: 3.584A pdb=" N GLU C 441 " --> pdb=" O PRO C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 472 removed outlier: 3.992A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 494 Processing helix chain 'C' and resid 508 through 532 Processing helix chain 'C' and resid 535 through 541 removed outlier: 3.515A pdb=" N ILE C 539 " --> pdb=" O SER C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 549 removed outlier: 3.872A pdb=" N ARG C 547 " --> pdb=" O PRO C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 554 Processing helix chain 'C' and resid 558 through 578 removed outlier: 4.096A pdb=" N GLU C 564 " --> pdb=" O PRO C 560 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS C 575 " --> pdb=" O GLN C 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 159 through 171 Processing helix chain 'D' and resid 175 through 178 Processing helix chain 'D' and resid 197 through 211 removed outlier: 4.161A 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 removed outlier: 3.520A pdb=" N TYR D 263 " --> pdb=" O ASP D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 283 removed outlier: 3.742A pdb=" N GLY D 282 " --> pdb=" O GLY D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 340 through 346 Processing helix chain 'D' and resid 361 through 365 Processing helix chain 'D' and resid 374 through 400 removed outlier: 3.819A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 404 Processing helix chain 'D' and resid 405 through 422 removed outlier: 3.593A pdb=" N ASP D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 446 removed outlier: 3.645A pdb=" N MET D 445 " --> pdb=" O ALA D 441 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU D 446 " --> pdb=" O LEU D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 463 Processing helix chain 'D' and resid 467 through 472 Processing helix chain 'E' and resid 23 through 27 removed outlier: 4.590A pdb=" N ASP E 26 " --> pdb=" O ASN E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 89 removed outlier: 3.623A pdb=" N LEU E 89 " --> pdb=" O LYS E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 124 Processing helix chain 'E' and resid 135 through 142 Processing helix chain 'E' and resid 159 through 171 removed outlier: 3.516A pdb=" N ILE E 163 " --> pdb=" O PRO E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 179 removed outlier: 3.604A pdb=" N GLY E 179 " --> pdb=" O ASP E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 210 Processing helix chain 'E' and resid 212 through 215 Processing helix chain 'E' and resid 227 through 250 removed outlier: 3.815A pdb=" N ARG E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) removed outlier: 3.785A 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: 3.650A pdb=" N TYR E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 Processing helix chain 'E' and resid 317 through 320 Processing helix chain 'E' and resid 323 through 333 removed outlier: 3.557A pdb=" N ILE E 332 " --> pdb=" O LEU E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 346 Processing helix chain 'E' and resid 361 through 366 removed outlier: 3.557A pdb=" N GLY E 365 " --> pdb=" O LEU E 361 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL E 366 " --> pdb=" O MET E 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 361 through 366' Processing helix chain 'E' and resid 374 through 400 removed outlier: 3.569A pdb=" N ALA E 397 " --> pdb=" O ARG E 393 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE E 399 " --> pdb=" O LEU E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 404 removed outlier: 3.791A pdb=" N LEU E 404 " --> pdb=" O GLU E 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 401 through 404' Processing helix chain 'E' and resid 405 through 422 Processing helix chain 'E' and resid 431 through 444 Processing helix chain 'E' and resid 455 through 463 Processing helix chain 'F' and resid 85 through 89 removed outlier: 3.511A pdb=" N MET F 88 " --> pdb=" O SER F 85 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU F 89 " --> pdb=" O LYS F 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 85 through 89' Processing helix chain 'F' and resid 135 through 140 Processing helix chain 'F' and resid 159 through 171 Processing helix chain 'F' and resid 174 through 179 removed outlier: 3.551A pdb=" N SER F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 211 Processing helix chain 'F' and resid 212 through 215 removed outlier: 3.831A pdb=" N SER F 215 " --> pdb=" O GLY F 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 212 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: 3.669A pdb=" N TYR F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.541A 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: 3.596A pdb=" N ALA F 397 " --> pdb=" O ARG F 393 " (cutoff:3.500A) removed outlier: 3.918A 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 removed outlier: 3.577A pdb=" N LEU F 451 " --> pdb=" O GLN F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 463 Processing helix chain 'F' and resid 466 through 471 removed outlier: 3.970A pdb=" N ILE F 470 " --> pdb=" O LYS F 466 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 71 removed outlier: 3.726A pdb=" N GLY G 41 " --> pdb=" O ALA G 37 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 83 Processing helix chain 'G' and resid 109 through 113 removed outlier: 3.595A pdb=" N LEU G 113 " --> pdb=" O ASP G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 167 removed outlier: 3.822A pdb=" N GLU G 125 " --> pdb=" O ALA G 121 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA G 126 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG G 128 " --> pdb=" O LEU G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 209 Processing helix chain 'H' and resid 6 through 16 Processing helix chain 'H' and resid 25 through 39 Processing helix chain 'H' and resid 54 through 59 Processing helix chain 'H' and resid 59 through 66 Processing helix chain 'H' and resid 78 through 83 Processing helix chain 'H' and resid 85 through 98 Processing helix chain 'I' and resid 82 through 106 removed outlier: 3.568A pdb=" N ALA I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG I 106 " --> pdb=" O LYS I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 119 Processing helix chain 'J' and resid 62 through 94 Processing helix chain 'J' and resid 95 through 97 No H-bonds generated for 'chain 'J' and resid 95 through 97' Processing helix chain 'J' and resid 99 through 115 removed outlier: 3.807A pdb=" N VAL J 103 " --> pdb=" O GLU J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 139 removed outlier: 4.282A pdb=" N ALA J 133 " --> pdb=" O PRO J 129 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU J 134 " --> pdb=" O HIS J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 187 removed outlier: 3.741A pdb=" N LEU J 171 " --> pdb=" O LEU J 167 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASP J 172 " --> pdb=" O LEU J 168 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG J 173 " --> pdb=" O ALA J 169 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 83 No H-bonds generated for 'chain 'K' and resid 81 through 83' Processing helix chain 'K' and resid 84 through 119 removed outlier: 3.791A pdb=" N TYR K 88 " --> pdb=" O LEU K 84 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG K 100 " --> pdb=" O ALA K 96 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ARG K 106 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ASP K 108 " --> pdb=" O MET K 104 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N GLU K 109 " --> pdb=" O ALA K 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 93 removed outlier: 3.871A pdb=" N LEU L 66 " --> pdb=" O SER L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 97 Processing helix chain 'L' and resid 99 through 115 Processing helix chain 'L' and resid 128 through 130 No H-bonds generated for 'chain 'L' and resid 128 through 130' Processing helix chain 'L' and resid 131 through 139 Processing helix chain 'L' and resid 166 through 187 removed outlier: 3.799A pdb=" N ASP L 172 " --> pdb=" O LEU L 168 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG L 173 " --> pdb=" O ALA L 169 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LYS L 181 " --> pdb=" O ALA L 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 10 removed outlier: 6.574A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.050A 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: 5.659A pdb=" N ILE A 39 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLN A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.784A 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: 6.144A pdb=" N ILE B 39 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLN B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 4.122A 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: 6.467A pdb=" N PHE C 48 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LEU C 42 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N THR C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 46 through 51 current: chain 'D' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 18 through 22 current: chain 'D' and resid 42 through 51 removed outlier: 5.590A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU D 49 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR D 54 " --> pdb=" O SER D 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 54 through 59 current: chain 'E' and resid 18 through 21 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 21 current: chain 'E' and resid 42 through 51 removed outlier: 6.087A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU E 49 " --> pdb=" O VAL E 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 55 through 59 current: chain 'F' and resid 18 through 21 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 18 through 21 current: chain 'F' and resid 42 through 51 removed outlier: 5.969A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 55 through 59 current: chain 'J' and resid 141 through 144 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 141 through 144 current: chain 'J' and resid 161 through 164 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 161 through 164 current: chain 'L' and resid 141 through 142 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 141 through 142 current: chain 'L' and resid 161 through 164 Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 75 Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 83 through 84 current: chain 'A' and resid 285 through 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: 3.667A pdb=" N GLY A 136 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 5.677A 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: 6.924A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 72 through 75 Processing sheet with id=AA7, first strand: chain 'B' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 83 through 84 current: chain 'B' and resid 285 through 288 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 285 through 288 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: 3.827A pdb=" N GLY B 136 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 5.839A 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: 3.510A pdb=" N VAL B 173 " --> pdb=" O LEU B 181 " (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 382 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 117 through 119 Processing sheet with id=AB4, first strand: chain 'C' and resid 128 through 129 removed outlier: 6.682A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL C 160 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N VAL C 172 " --> pdb=" O VAL C 160 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 134 through 139 removed outlier: 6.658A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 405 through 406 Processing sheet with id=AB7, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.564A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 92 through 93 removed outlier: 5.795A pdb=" N PHE D 93 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N LYS D 223 " --> pdb=" O PHE D 93 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL D 253 " --> pdb=" O THR D 309 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 144 through 145 removed outlier: 4.533A pdb=" N LEU D 144 " --> pdb=" O ILE D 131 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 152 through 154 removed outlier: 3.515A pdb=" N LEU D 314 " --> pdb=" O ILE D 152 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 81 through 84 Processing sheet with id=AC3, first strand: chain 'E' and resid 92 through 93 removed outlier: 3.583A pdb=" N MET E 194 " --> pdb=" O THR E 258 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.560A pdb=" N LEU E 144 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 313 through 315 Processing sheet with id=AC6, first strand: chain 'F' and resid 81 through 82 Processing sheet with id=AC7, first strand: chain 'F' and resid 91 through 94 removed outlier: 6.587A pdb=" N ARG F 91 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU F 221 " --> pdb=" O ARG F 91 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N PHE F 93 " --> pdb=" O LEU F 221 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA F 188 " --> pdb=" O LEU F 254 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE F 256 " --> pdb=" O ALA F 188 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL F 190 " --> pdb=" O ILE F 256 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 144 through 145 removed outlier: 4.598A pdb=" N LEU F 144 " --> pdb=" O ILE F 131 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR F 172 " --> pdb=" O GLN F 132 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 313 through 315 removed outlier: 6.480A pdb=" N ILE F 337 " --> pdb=" O PHE F 153 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 91 through 96 removed outlier: 3.508A pdb=" N SER G 99 " --> pdb=" O VAL G 96 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 19 through 22 removed outlier: 6.800A pdb=" N VAL H 3 " --> pdb=" O TYR H 21 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL H 45 " --> pdb=" O LEU H 72 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ILE H 74 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL H 47 " --> pdb=" O ILE H 74 " (cutoff:3.500A) 1303 hydrogen bonds defined for protein. 3738 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.06 Time building geometry restraints manager: 3.71 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: 9960 1.34 - 1.46: 4580 1.46 - 1.57: 15313 1.57 - 1.69: 5 1.69 - 1.81: 194 Bond restraints: 30052 Sorted by residual: bond pdb=" CB ARG C 95 " pdb=" CG ARG C 95 " ideal model delta sigma weight residual 1.520 1.399 0.121 3.00e-02 1.11e+03 1.62e+01 bond pdb=" CG ARG C 95 " pdb=" CD ARG C 95 " ideal model delta sigma weight residual 1.520 1.405 0.115 3.00e-02 1.11e+03 1.47e+01 bond pdb=" O4 SO4 A 600 " pdb=" S SO4 A 600 " ideal model delta sigma weight residual 1.499 1.455 0.044 2.00e-02 2.50e+03 4.90e+00 bond pdb=" O3 SO4 A 600 " pdb=" S SO4 A 600 " ideal model delta sigma weight residual 1.499 1.455 0.044 2.00e-02 2.50e+03 4.82e+00 bond pdb=" CA ARG C 95 " pdb=" CB ARG C 95 " ideal model delta sigma weight residual 1.531 1.498 0.034 1.57e-02 4.06e+03 4.60e+00 ... (remaining 30047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 39887 1.50 - 3.00: 628 3.00 - 4.50: 185 4.50 - 6.00: 13 6.00 - 7.50: 3 Bond angle restraints: 40716 Sorted by residual: angle pdb=" CG ARG C 95 " pdb=" CD ARG C 95 " pdb=" NE ARG C 95 " ideal model delta sigma weight residual 112.00 104.50 7.50 2.20e+00 2.07e-01 1.16e+01 angle pdb=" N HIS E 375 " pdb=" CA HIS E 375 " pdb=" C HIS E 375 " ideal model delta sigma weight residual 111.07 114.08 -3.01 1.07e+00 8.73e-01 7.89e+00 angle pdb=" N ILE F 100 " pdb=" CA ILE F 100 " pdb=" C ILE F 100 " ideal model delta sigma weight residual 113.20 110.56 2.64 9.60e-01 1.09e+00 7.54e+00 angle pdb=" C2' ATP C 601 " pdb=" C3' ATP C 601 " pdb=" O3' ATP C 601 " ideal model delta sigma weight residual 111.83 104.97 6.86 2.67e+00 1.40e-01 6.61e+00 angle pdb=" C GLU B 347 " pdb=" CA GLU B 347 " pdb=" CB GLU B 347 " ideal model delta sigma weight residual 110.42 115.22 -4.80 1.99e+00 2.53e-01 5.81e+00 ... (remaining 40711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 16690 17.91 - 35.82: 1335 35.82 - 53.73: 217 53.73 - 71.63: 57 71.63 - 89.54: 39 Dihedral angle restraints: 18338 sinusoidal: 7516 harmonic: 10822 Sorted by residual: dihedral pdb=" CA LEU F 257 " pdb=" C LEU F 257 " pdb=" N THR F 258 " pdb=" CA THR F 258 " ideal model delta harmonic sigma weight residual 180.00 -157.61 -22.39 0 5.00e+00 4.00e-02 2.00e+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 -159.58 -20.42 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA LEU L 128 " pdb=" C LEU L 128 " pdb=" N PRO L 129 " pdb=" CA PRO L 129 " ideal model delta harmonic sigma weight residual -180.00 -160.85 -19.15 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 18335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3899 0.058 - 0.116: 593 0.116 - 0.174: 69 0.174 - 0.232: 0 0.232 - 0.290: 3 Chirality restraints: 4564 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 2.10e+00 chirality pdb=" C3' ATP C 601 " pdb=" C2' ATP C 601 " pdb=" C4' ATP C 601 " pdb=" O3' ATP C 601 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" C4' ATP C 601 " pdb=" C3' ATP C 601 " pdb=" C5' ATP C 601 " pdb=" O4' ATP C 601 " both_signs ideal model delta sigma weight residual False -2.49 -2.73 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 4561 not shown) Planarity restraints: 5331 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 393 " -0.029 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO A 394 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 394 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 394 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 355 " 0.028 5.00e-02 4.00e+02 4.24e-02 2.87e+00 pdb=" N PRO D 356 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 356 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 356 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 228 " 0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO B 229 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 229 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 229 " 0.022 5.00e-02 4.00e+02 ... (remaining 5328 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 117 2.44 - 3.06: 20498 3.06 - 3.67: 42898 3.67 - 4.29: 64431 4.29 - 4.90: 111267 Nonbonded interactions: 239211 Sorted by model distance: nonbonded pdb=" O1G ATP C 601 " pdb="MG MG C 602 " model vdw 1.826 2.170 nonbonded pdb=" O1B ATP C 601 " pdb="MG MG C 602 " model vdw 1.888 2.170 nonbonded pdb=" O3B ATP C 601 " pdb="MG MG C 602 " model vdw 1.893 2.170 nonbonded pdb=" OG SER H 24 " pdb=" OE1 GLU H 28 " model vdw 1.939 3.040 nonbonded pdb=" O LYS D 370 " pdb=" OG1 THR D 371 " model vdw 1.953 3.040 ... (remaining 239206 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' selection = (chain 'C' and resid 1 through 578) } ncs_group { reference = (chain 'D' and resid 5 through 470) selection = (chain 'E' and resid 5 through 470) selection = (chain 'F' and resid 5 through 470) } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = (chain 'L' and resid 61 through 187) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 31.520 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 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 0.121 30052 Z= 0.239 Angle : 0.536 7.501 40716 Z= 0.283 Chirality : 0.043 0.290 4564 Planarity : 0.004 0.058 5331 Dihedral : 13.924 89.543 11420 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.17 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % 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: 0.46 (0.14), residues: 3764 helix: 1.46 (0.13), residues: 1571 sheet: -1.06 (0.21), residues: 594 loop : -0.19 (0.16), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 174 TYR 0.021 0.001 TYR D 331 PHE 0.018 0.001 PHE A 269 TRP 0.012 0.001 TRP L 175 HIS 0.004 0.001 HIS B 145 Details of bonding type rmsd covalent geometry : bond 0.00555 (30052) covalent geometry : angle 0.53582 (40716) hydrogen bonds : bond 0.15271 ( 1303) hydrogen bonds : angle 6.30966 ( 3738) *********************** 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 823 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 823 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7517 (mt-10) REVERT: A 95 ARG cc_start: 0.6391 (tpt-90) cc_final: 0.6012 (tpt-90) REVERT: A 96 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6398 (pt0) REVERT: A 129 VAL cc_start: 0.7083 (t) cc_final: 0.6662 (m) REVERT: A 143 PHE cc_start: 0.7299 (m-80) cc_final: 0.6979 (m-80) REVERT: A 156 ARG cc_start: 0.5953 (mtp-110) cc_final: 0.5209 (ttp-170) REVERT: A 174 VAL cc_start: 0.7585 (t) cc_final: 0.7216 (p) REVERT: A 182 LYS cc_start: 0.6738 (mtmm) cc_final: 0.6368 (mptt) REVERT: A 323 MET cc_start: 0.8377 (mmt) cc_final: 0.8068 (mmm) REVERT: A 337 ILE cc_start: 0.7042 (mm) cc_final: 0.6587 (mt) REVERT: A 340 ARG cc_start: 0.6537 (tpp-160) cc_final: 0.5995 (mpt180) REVERT: A 348 GLU cc_start: 0.7167 (mt-10) cc_final: 0.5920 (tt0) REVERT: A 374 GLU cc_start: 0.7015 (mt-10) cc_final: 0.6043 (tt0) REVERT: A 375 GLU cc_start: 0.6368 (tt0) cc_final: 0.6057 (tt0) REVERT: A 416 ARG cc_start: 0.7283 (mtm-85) cc_final: 0.6309 (mtp85) REVERT: A 481 ARG cc_start: 0.7125 (mtm-85) cc_final: 0.6650 (mtp-110) REVERT: A 492 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6996 (tt0) REVERT: A 517 LYS cc_start: 0.6952 (mmtp) cc_final: 0.6710 (mtpt) REVERT: A 518 MET cc_start: 0.8303 (mtp) cc_final: 0.8051 (mtm) REVERT: A 541 GLN cc_start: 0.6311 (mt0) cc_final: 0.5858 (pt0) REVERT: A 546 GLU cc_start: 0.6922 (mt-10) cc_final: 0.6170 (mm-30) REVERT: A 550 ARG cc_start: 0.6935 (mtm-85) cc_final: 0.6555 (tpp-160) REVERT: A 557 GLU cc_start: 0.7214 (pm20) cc_final: 0.6413 (tp30) REVERT: A 558 GLU cc_start: 0.7353 (mt-10) cc_final: 0.7085 (mt-10) REVERT: A 565 GLU cc_start: 0.7347 (tp30) cc_final: 0.6834 (mt-10) REVERT: A 567 MET cc_start: 0.6993 (mmm) cc_final: 0.6690 (mmm) REVERT: B 3 GLN cc_start: 0.7514 (tt0) cc_final: 0.6932 (mt0) REVERT: B 29 LYS cc_start: 0.7039 (mtpt) cc_final: 0.6664 (mttt) REVERT: B 59 LYS cc_start: 0.7602 (mtpp) cc_final: 0.7089 (mttp) REVERT: B 93 ARG cc_start: 0.6342 (mtm-85) cc_final: 0.6125 (mtm180) REVERT: B 130 ARG cc_start: 0.5639 (ttm-80) cc_final: 0.5288 (tpt170) REVERT: B 133 MET cc_start: 0.6094 (mmm) cc_final: 0.5823 (mmt) REVERT: B 134 VAL cc_start: 0.7311 (m) cc_final: 0.7072 (t) REVERT: B 159 GLU cc_start: 0.7268 (tt0) cc_final: 0.6060 (tp30) REVERT: B 166 TYR cc_start: 0.7004 (m-10) cc_final: 0.5893 (m-80) REVERT: B 197 ARG cc_start: 0.6468 (ttp80) cc_final: 0.6115 (ttp-110) REVERT: B 200 ASP cc_start: 0.6602 (m-30) cc_final: 0.6366 (m-30) REVERT: B 220 MET cc_start: 0.7641 (tpp) cc_final: 0.7379 (ttm) REVERT: B 236 VAL cc_start: 0.7230 (t) cc_final: 0.7006 (p) REVERT: B 243 LYS cc_start: 0.7176 (mtpp) cc_final: 0.6917 (mtpp) REVERT: B 264 ASP cc_start: 0.6515 (m-30) cc_final: 0.6230 (m-30) REVERT: B 340 ARG cc_start: 0.6820 (tpp-160) cc_final: 0.6513 (tpt-90) REVERT: B 374 GLU cc_start: 0.6185 (mt-10) cc_final: 0.5722 (mm-30) REVERT: B 480 GLU cc_start: 0.6331 (mp0) cc_final: 0.5936 (mt-10) REVERT: B 481 ARG cc_start: 0.6785 (mmm-85) cc_final: 0.5968 (mmm160) REVERT: B 553 TYR cc_start: 0.7670 (m-10) cc_final: 0.7419 (m-10) REVERT: C 5 VAL cc_start: 0.8148 (t) cc_final: 0.7911 (m) REVERT: C 24 MET cc_start: 0.8053 (mtp) cc_final: 0.7730 (mmm) REVERT: C 69 LEU cc_start: 0.7718 (mt) cc_final: 0.7448 (mp) REVERT: C 84 TYR cc_start: 0.8652 (m-80) cc_final: 0.8437 (m-80) REVERT: C 124 LYS cc_start: 0.7262 (mttt) cc_final: 0.6930 (mtmm) REVERT: C 125 PRO cc_start: 0.7245 (Cg_exo) cc_final: 0.6763 (Cg_endo) REVERT: C 183 MET cc_start: 0.8416 (mtp) cc_final: 0.8203 (mtm) REVERT: C 191 ARG cc_start: 0.7840 (mtp180) cc_final: 0.7503 (ttp80) REVERT: C 197 ARG cc_start: 0.7495 (mtm110) cc_final: 0.7275 (ptm-80) REVERT: C 198 LYS cc_start: 0.7288 (mmtp) cc_final: 0.7047 (mmmt) REVERT: C 268 GLU cc_start: 0.6702 (mt-10) cc_final: 0.5867 (tp30) REVERT: C 272 LEU cc_start: 0.7520 (mt) cc_final: 0.7316 (mt) REVERT: C 338 SER cc_start: 0.7704 (t) cc_final: 0.7232 (p) REVERT: C 344 MET cc_start: 0.7786 (mmm) cc_final: 0.7529 (mmt) REVERT: C 367 LYS cc_start: 0.7633 (ttpp) cc_final: 0.7269 (ttpp) REVERT: C 374 GLU cc_start: 0.7318 (mt-10) cc_final: 0.6663 (mm-30) REVERT: C 393 GLU cc_start: 0.6565 (tm-30) cc_final: 0.6317 (tm-30) REVERT: C 416 ARG cc_start: 0.7325 (mtm110) cc_final: 0.6653 (mtm180) REVERT: C 442 ASN cc_start: 0.8212 (m-40) cc_final: 0.7812 (m-40) REVERT: C 452 ASP cc_start: 0.7241 (m-30) cc_final: 0.6879 (m-30) REVERT: C 460 ARG cc_start: 0.7080 (mtm180) cc_final: 0.6850 (mtm-85) REVERT: C 513 TYR cc_start: 0.7369 (t80) cc_final: 0.6959 (t80) REVERT: C 518 MET cc_start: 0.7998 (mtp) cc_final: 0.7693 (mtm) REVERT: C 524 LYS cc_start: 0.6951 (mtpp) cc_final: 0.6547 (ttpp) REVERT: C 525 GLU cc_start: 0.6628 (mm-30) cc_final: 0.6234 (mt-10) REVERT: C 547 ARG cc_start: 0.6217 (mtp85) cc_final: 0.5803 (mtp85) REVERT: C 550 ARG cc_start: 0.6744 (ttm-80) cc_final: 0.6400 (mtm110) REVERT: D 22 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6928 (mt-10) REVERT: D 51 SER cc_start: 0.7670 (t) cc_final: 0.7406 (p) REVERT: D 52 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7075 (mt-10) REVERT: D 92 ARG cc_start: 0.7576 (mtm110) cc_final: 0.6990 (mtm-85) REVERT: D 111 ARG cc_start: 0.7359 (mtp-110) cc_final: 0.7026 (mmm-85) REVERT: D 199 ARG cc_start: 0.6475 (ttp80) cc_final: 0.6116 (ttp80) REVERT: D 231 ARG cc_start: 0.7450 (ttm170) cc_final: 0.7236 (ttm170) REVERT: D 232 ILE cc_start: 0.7456 (mm) cc_final: 0.7174 (mt) REVERT: D 250 ASP cc_start: 0.7756 (m-30) cc_final: 0.7547 (m-30) REVERT: D 269 GLU cc_start: 0.6088 (tt0) cc_final: 0.5757 (mt-10) REVERT: D 280 ARG cc_start: 0.7016 (mtp85) cc_final: 0.6387 (mtp-110) REVERT: D 302 GLU cc_start: 0.6876 (mt-10) cc_final: 0.6552 (mm-30) REVERT: D 305 LYS cc_start: 0.6868 (mtmm) cc_final: 0.6115 (mtpp) REVERT: D 337 ILE cc_start: 0.8288 (mt) cc_final: 0.8076 (mm) REVERT: D 338 GLN cc_start: 0.8540 (tt0) cc_final: 0.8031 (tp40) REVERT: D 376 LYS cc_start: 0.6549 (tppt) cc_final: 0.5787 (tttm) REVERT: D 406 GLU cc_start: 0.6061 (tp30) cc_final: 0.5379 (pm20) REVERT: D 409 ARG cc_start: 0.6647 (ttm-80) cc_final: 0.6269 (mtt90) REVERT: D 416 ASP cc_start: 0.7040 (t0) cc_final: 0.6240 (m-30) REVERT: D 461 LYS cc_start: 0.6961 (tttt) cc_final: 0.6754 (ttmt) REVERT: D 463 TYR cc_start: 0.7646 (t80) cc_final: 0.7394 (t80) REVERT: D 465 GLN cc_start: 0.6690 (mm-40) cc_final: 0.6374 (mp10) REVERT: E 25 LYS cc_start: 0.7336 (ttmm) cc_final: 0.7055 (mtpp) REVERT: E 128 GLU cc_start: 0.7079 (pt0) cc_final: 0.6701 (pt0) REVERT: E 228 THR cc_start: 0.8009 (t) cc_final: 0.7392 (m) REVERT: E 251 TYR cc_start: 0.7793 (m-80) cc_final: 0.7274 (m-80) REVERT: E 252 HIS cc_start: 0.8169 (m-70) cc_final: 0.7881 (m170) REVERT: E 302 GLU cc_start: 0.6980 (tt0) cc_final: 0.5904 (tp30) REVERT: E 345 ARG cc_start: 0.6305 (mtm110) cc_final: 0.6068 (mtm-85) REVERT: E 394 LYS cc_start: 0.6768 (tptp) cc_final: 0.6283 (tttm) REVERT: E 410 ARG cc_start: 0.4761 (mtm180) cc_final: 0.4097 (mmp80) REVERT: E 420 ARG cc_start: 0.7440 (mtm110) cc_final: 0.7236 (mtm-85) REVERT: E 445 MET cc_start: 0.7298 (mtp) cc_final: 0.7016 (mtt) REVERT: E 450 GLU cc_start: 0.5914 (mm-30) cc_final: 0.5698 (mt-10) REVERT: F 6 LYS cc_start: 0.6096 (tptm) cc_final: 0.5689 (mtpp) REVERT: F 7 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6813 (mt-10) REVERT: F 13 TYR cc_start: 0.8585 (t80) cc_final: 0.8252 (t80) REVERT: F 53 GLU cc_start: 0.6863 (mt-10) cc_final: 0.6390 (mm-30) REVERT: F 77 GLU cc_start: 0.7454 (mt-10) cc_final: 0.6940 (pt0) REVERT: F 81 ARG cc_start: 0.7387 (mtt-85) cc_final: 0.6880 (mtm-85) REVERT: F 98 LYS cc_start: 0.7429 (mttt) cc_final: 0.7055 (mmtm) REVERT: F 207 GLU cc_start: 0.6592 (mm-30) cc_final: 0.5996 (tm-30) REVERT: F 209 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6725 (mt-10) REVERT: F 210 ARG cc_start: 0.6282 (ttp80) cc_final: 0.5322 (ttm110) REVERT: F 230 GLU cc_start: 0.7137 (mt-10) cc_final: 0.6928 (mt-10) REVERT: F 280 ARG cc_start: 0.7680 (mtp85) cc_final: 0.7365 (mtt180) REVERT: F 302 GLU cc_start: 0.7292 (tt0) cc_final: 0.6717 (mm-30) REVERT: F 305 LYS cc_start: 0.7994 (mttt) cc_final: 0.7787 (mttm) REVERT: F 362 MET cc_start: 0.8007 (ttp) cc_final: 0.7771 (ttt) REVERT: F 409 ARG cc_start: 0.6795 (ttm110) cc_final: 0.6117 (mtt90) REVERT: F 412 LEU cc_start: 0.7402 (tp) cc_final: 0.7183 (tp) REVERT: F 453 ARG cc_start: 0.6971 (mmt90) cc_final: 0.6716 (mmm-85) REVERT: G 17 GLN cc_start: 0.6886 (mm-40) cc_final: 0.6570 (mm-40) REVERT: G 38 GLU cc_start: 0.6675 (mt-10) cc_final: 0.6467 (tp30) REVERT: G 47 MET cc_start: 0.5255 (mmm) cc_final: 0.4213 (ttm) REVERT: G 177 ARG cc_start: 0.6645 (mtp85) cc_final: 0.6267 (mtm-85) REVERT: G 180 GLN cc_start: 0.7189 (mt0) cc_final: 0.6964 (mt0) REVERT: G 198 LYS cc_start: 0.6461 (tttm) cc_final: 0.6256 (ttmm) REVERT: H 63 MET cc_start: 0.3761 (mmm) cc_final: 0.2141 (ttp) REVERT: J 65 GLU cc_start: 0.4107 (mt-10) cc_final: 0.3655 (mm-30) REVERT: J 86 ARG cc_start: 0.4035 (mmp80) cc_final: 0.3396 (ttm-80) REVERT: J 105 ARG cc_start: 0.3493 (mtt-85) cc_final: 0.3235 (mtt-85) REVERT: J 112 LEU cc_start: 0.4601 (mp) cc_final: 0.4061 (tt) REVERT: J 158 GLU cc_start: 0.5277 (mp0) cc_final: 0.4537 (mt-10) REVERT: J 182 VAL cc_start: 0.3334 (t) cc_final: 0.3066 (p) REVERT: L 86 ARG cc_start: 0.5163 (mtt180) cc_final: 0.4852 (mtp180) REVERT: L 102 GLU cc_start: 0.5661 (mp0) cc_final: 0.4687 (tp30) REVERT: L 153 ARG cc_start: 0.3855 (ttm170) cc_final: 0.3545 (ttp-170) outliers start: 0 outliers final: 0 residues processed: 823 average time/residue: 0.2168 time to fit residues: 262.6206 Evaluate side-chains 506 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 506 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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: 3.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.0980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 0.4980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN A 442 ASN A 571 GLN B 145 HIS B 185 HIS B 571 GLN C 81 ASN C 145 HIS C 283 HIS C 316 GLN C 397 GLN C 418 HIS C 459 GLN C 496 GLN D 252 HIS ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 HIS D 448 GLN E 58 GLN E 148 GLN E 249 HIS ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 ASN F 206 GLN F 388 ASN F 413 GLN F 427 GLN G 180 GLN L 130 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.152418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.119343 restraints weight = 34472.805| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.33 r_work: 0.3053 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.137 30052 Z= 0.158 Angle : 0.575 10.360 40716 Z= 0.298 Chirality : 0.045 0.216 4564 Planarity : 0.005 0.043 5331 Dihedral : 5.140 83.532 4214 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.44 % Favored : 97.50 % Rotamer: Outliers : 1.52 % Allowed : 9.93 % Favored : 88.55 % 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: 0.84 (0.14), residues: 3764 helix: 1.64 (0.13), residues: 1597 sheet: -0.72 (0.22), residues: 570 loop : 0.05 (0.16), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 111 TYR 0.017 0.002 TYR H 89 PHE 0.016 0.002 PHE F 130 TRP 0.012 0.001 TRP L 175 HIS 0.005 0.001 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00371 (30052) covalent geometry : angle 0.57494 (40716) hydrogen bonds : bond 0.04434 ( 1303) hydrogen bonds : angle 4.84965 ( 3738) *********************** 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 577 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 530 time to evaluate : 0.771 Fit side-chains REVERT: A 95 ARG cc_start: 0.7195 (tpt-90) cc_final: 0.6723 (tpt-90) REVERT: A 154 ARG cc_start: 0.7147 (mtp85) cc_final: 0.6847 (mtp180) REVERT: A 156 ARG cc_start: 0.6248 (mtp-110) cc_final: 0.5713 (ttp-170) REVERT: A 169 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7291 (mm-30) REVERT: A 174 VAL cc_start: 0.8065 (t) cc_final: 0.7725 (p) REVERT: A 200 ASP cc_start: 0.7223 (m-30) cc_final: 0.6815 (m-30) REVERT: A 243 LYS cc_start: 0.8793 (mtmt) cc_final: 0.8557 (mtpt) REVERT: A 262 MET cc_start: 0.8691 (mmp) cc_final: 0.8012 (mmt) REVERT: A 340 ARG cc_start: 0.7478 (tpp-160) cc_final: 0.7024 (mmp80) REVERT: A 348 GLU cc_start: 0.6883 (mt-10) cc_final: 0.6271 (tt0) REVERT: A 374 GLU cc_start: 0.7491 (mt-10) cc_final: 0.6934 (tt0) REVERT: A 416 ARG cc_start: 0.7794 (mtm-85) cc_final: 0.7246 (mtp85) REVERT: A 481 ARG cc_start: 0.7716 (mtm-85) cc_final: 0.7236 (mtp-110) REVERT: A 492 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7381 (pt0) REVERT: A 518 MET cc_start: 0.8844 (mtp) cc_final: 0.8605 (mtm) REVERT: A 541 GLN cc_start: 0.6612 (mt0) cc_final: 0.6140 (pt0) REVERT: A 546 GLU cc_start: 0.7700 (mt-10) cc_final: 0.6875 (mm-30) REVERT: A 557 GLU cc_start: 0.7291 (pm20) cc_final: 0.6787 (tp30) REVERT: A 567 MET cc_start: 0.7587 (mmm) cc_final: 0.7381 (mmm) REVERT: B 156 ARG cc_start: 0.7122 (ttp-170) cc_final: 0.6189 (mpt-90) REVERT: B 159 GLU cc_start: 0.7385 (tt0) cc_final: 0.6617 (tp30) REVERT: B 166 TYR cc_start: 0.7186 (m-10) cc_final: 0.6336 (m-80) REVERT: B 197 ARG cc_start: 0.7273 (ttp80) cc_final: 0.7025 (ttp-110) REVERT: B 220 MET cc_start: 0.8253 (tpp) cc_final: 0.7988 (ttm) REVERT: B 241 LEU cc_start: 0.8424 (mp) cc_final: 0.7940 (tt) REVERT: B 243 LYS cc_start: 0.7755 (mtpp) cc_final: 0.7470 (mtpt) REVERT: B 449 GLU cc_start: 0.6348 (mm-30) cc_final: 0.5964 (mp0) REVERT: B 452 ASP cc_start: 0.7872 (m-30) cc_final: 0.7618 (m-30) REVERT: B 480 GLU cc_start: 0.6598 (mp0) cc_final: 0.5909 (mt-10) REVERT: B 481 ARG cc_start: 0.7139 (mmm-85) cc_final: 0.6554 (ttt-90) REVERT: B 570 ILE cc_start: 0.5969 (tt) cc_final: 0.5697 (mt) REVERT: C 101 TYR cc_start: 0.8012 (m-80) cc_final: 0.7567 (m-80) REVERT: C 130 ARG cc_start: 0.7156 (ttp-110) cc_final: 0.6594 (tpp-160) REVERT: C 183 MET cc_start: 0.8785 (mtp) cc_final: 0.8481 (mtm) REVERT: C 374 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7712 (mm-30) REVERT: C 416 ARG cc_start: 0.7942 (mtm110) cc_final: 0.7403 (mtm180) REVERT: C 442 ASN cc_start: 0.8740 (m-40) cc_final: 0.8378 (m-40) REVERT: C 452 ASP cc_start: 0.7685 (m-30) cc_final: 0.7379 (m-30) REVERT: C 460 ARG cc_start: 0.7665 (mtm180) cc_final: 0.7452 (mtp180) REVERT: C 518 MET cc_start: 0.8507 (mtp) cc_final: 0.8273 (mtm) REVERT: C 524 LYS cc_start: 0.7303 (mtpp) cc_final: 0.7086 (ttpp) REVERT: C 547 ARG cc_start: 0.6482 (mtp85) cc_final: 0.6010 (mtp85) REVERT: C 550 ARG cc_start: 0.7103 (ttm-80) cc_final: 0.6794 (mtm110) REVERT: D 22 GLU cc_start: 0.7230 (mt-10) cc_final: 0.7027 (mt-10) REVERT: D 34 ASP cc_start: 0.7323 (m-30) cc_final: 0.6884 (t0) REVERT: D 52 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7143 (mt-10) REVERT: D 231 ARG cc_start: 0.8560 (ttm170) cc_final: 0.8339 (ttp-170) REVERT: D 305 LYS cc_start: 0.7395 (mtmm) cc_final: 0.6494 (tttt) REVERT: D 322 THR cc_start: 0.8107 (p) cc_final: 0.7895 (p) REVERT: D 338 GLN cc_start: 0.8649 (tt0) cc_final: 0.8447 (tp40) REVERT: D 406 GLU cc_start: 0.5837 (tp30) cc_final: 0.5598 (pm20) REVERT: D 409 ARG cc_start: 0.6940 (ttm-80) cc_final: 0.6593 (mtt90) REVERT: D 437 GLN cc_start: 0.8272 (tt0) cc_final: 0.8070 (tt0) REVERT: D 461 LYS cc_start: 0.7482 (tttt) cc_final: 0.7245 (tttp) REVERT: D 463 TYR cc_start: 0.7845 (t80) cc_final: 0.7438 (t80) REVERT: E 110 LYS cc_start: 0.7447 (ttmm) cc_final: 0.6745 (mtpp) REVERT: E 128 GLU cc_start: 0.7040 (pt0) cc_final: 0.6716 (pt0) REVERT: E 194 MET cc_start: 0.8800 (mtm) cc_final: 0.8541 (mtm) REVERT: E 209 GLU cc_start: 0.6369 (mt-10) cc_final: 0.6074 (mm-30) REVERT: E 259 ASP cc_start: 0.7044 (m-30) cc_final: 0.6659 (m-30) REVERT: E 278 PRO cc_start: 0.8629 (Cg_endo) cc_final: 0.8230 (Cg_exo) REVERT: E 302 GLU cc_start: 0.6945 (tt0) cc_final: 0.6447 (tp30) REVERT: E 360 ARG cc_start: 0.8033 (mtm-85) cc_final: 0.7798 (mtt90) REVERT: E 445 MET cc_start: 0.7323 (mtp) cc_final: 0.7024 (mtt) REVERT: F 6 LYS cc_start: 0.6423 (tptm) cc_final: 0.5785 (mtpp) REVERT: F 7 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7042 (mt-10) REVERT: F 74 SER cc_start: 0.8622 (p) cc_final: 0.8069 (t) REVERT: F 109 GLU cc_start: 0.6813 (mt-10) cc_final: 0.6447 (mm-30) REVERT: F 207 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7435 (tm-30) REVERT: F 210 ARG cc_start: 0.6973 (ttp80) cc_final: 0.6174 (ttm110) REVERT: F 302 GLU cc_start: 0.8108 (tt0) cc_final: 0.7794 (mm-30) REVERT: F 399 ILE cc_start: 0.6557 (mm) cc_final: 0.6007 (mt) REVERT: G 47 MET cc_start: 0.5234 (mmm) cc_final: 0.4674 (ttm) REVERT: G 59 GLU cc_start: 0.5421 (pp20) cc_final: 0.4321 (tp30) REVERT: G 180 GLN cc_start: 0.8109 (mt0) cc_final: 0.7866 (mt0) REVERT: G 197 ILE cc_start: 0.6403 (pt) cc_final: 0.5896 (mm) REVERT: H 63 MET cc_start: 0.4052 (mmm) cc_final: 0.2335 (ttp) REVERT: J 65 GLU cc_start: 0.4185 (mt-10) cc_final: 0.3764 (tt0) REVERT: J 81 GLU cc_start: 0.4505 (tt0) cc_final: 0.4138 (tp30) REVERT: J 86 ARG cc_start: 0.4318 (mmp80) cc_final: 0.3588 (ttm-80) REVERT: J 112 LEU cc_start: 0.4590 (mp) cc_final: 0.4011 (tt) REVERT: J 162 GLN cc_start: 0.6310 (tt0) cc_final: 0.5987 (tt0) REVERT: J 164 GLU cc_start: 0.5384 (tp30) cc_final: 0.4804 (mt-10) REVERT: K 102 LYS cc_start: 0.5990 (tptp) cc_final: 0.4302 (mmtt) REVERT: L 86 ARG cc_start: 0.5538 (mtt180) cc_final: 0.5104 (mtp180) REVERT: L 102 GLU cc_start: 0.5539 (mp0) cc_final: 0.4676 (tp30) REVERT: L 141 GLU cc_start: 0.5119 (tt0) cc_final: 0.4182 (mm-30) REVERT: L 153 ARG cc_start: 0.4201 (ttm170) cc_final: 0.3635 (ttm-80) outliers start: 47 outliers final: 28 residues processed: 556 average time/residue: 0.2132 time to fit residues: 175.0199 Evaluate side-chains 475 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 447 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 143 THR Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 410 ARG Chi-restraints excluded: chain F residue 413 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 78 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 288 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 96 optimal weight: 8.9990 chunk 295 optimal weight: 4.9990 chunk 129 optimal weight: 10.0000 chunk 353 optimal weight: 20.0000 chunk 133 optimal weight: 6.9990 chunk 169 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 GLN A 498 ASN D 170 GLN D 310 GLN D 323 HIS D 364 ASN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 364 ASN ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 458 HIS F 249 HIS F 381 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.151878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.121171 restraints weight = 34637.193| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.22 r_work: 0.3016 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.149 30052 Z= 0.241 Angle : 0.654 12.727 40716 Z= 0.339 Chirality : 0.049 0.235 4564 Planarity : 0.006 0.071 5331 Dihedral : 5.523 78.790 4214 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.87 % Favored : 97.10 % Rotamer: Outliers : 2.50 % Allowed : 11.35 % Favored : 86.15 % 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: 0.39 (0.14), residues: 3764 helix: 1.28 (0.13), residues: 1574 sheet: -0.89 (0.21), residues: 570 loop : -0.20 (0.16), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 95 TYR 0.019 0.002 TYR C 562 PHE 0.023 0.002 PHE F 20 TRP 0.015 0.002 TRP A 119 HIS 0.020 0.002 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00589 (30052) covalent geometry : angle 0.65425 (40716) hydrogen bonds : bond 0.05177 ( 1303) hydrogen bonds : angle 4.95190 ( 3738) *********************** 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 523 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 446 time to evaluate : 0.786 Fit side-chains REVERT: A 93 ARG cc_start: 0.7793 (mmm160) cc_final: 0.7508 (mpt180) REVERT: A 95 ARG cc_start: 0.7240 (tpt-90) cc_final: 0.6631 (tpt-90) REVERT: A 154 ARG cc_start: 0.7194 (mtp85) cc_final: 0.6906 (mtp180) REVERT: A 156 ARG cc_start: 0.6170 (mtp-110) cc_final: 0.5626 (ttp-170) REVERT: A 174 VAL cc_start: 0.8003 (t) cc_final: 0.7625 (p) REVERT: A 340 ARG cc_start: 0.7537 (tpp-160) cc_final: 0.6770 (mpt180) REVERT: A 374 GLU cc_start: 0.7520 (mt-10) cc_final: 0.6920 (tt0) REVERT: A 416 ARG cc_start: 0.7880 (mtm-85) cc_final: 0.7233 (mtp85) REVERT: A 481 ARG cc_start: 0.7678 (mtm-85) cc_final: 0.7257 (mtp-110) REVERT: A 491 ARG cc_start: 0.7618 (mtm-85) cc_final: 0.7395 (mtm180) REVERT: A 541 GLN cc_start: 0.6590 (mt0) cc_final: 0.6131 (pt0) REVERT: A 546 GLU cc_start: 0.7631 (mt-10) cc_final: 0.6809 (mm-30) REVERT: A 557 GLU cc_start: 0.7234 (pm20) cc_final: 0.6783 (tp30) REVERT: B 119 TRP cc_start: 0.7050 (t60) cc_final: 0.6835 (t60) REVERT: B 166 TYR cc_start: 0.7307 (m-80) cc_final: 0.6423 (m-80) REVERT: B 197 ARG cc_start: 0.7389 (ttp80) cc_final: 0.6988 (ttp-110) REVERT: B 340 ARG cc_start: 0.7552 (tpp-160) cc_final: 0.7139 (tpt-90) REVERT: B 449 GLU cc_start: 0.6478 (mm-30) cc_final: 0.6042 (mp0) REVERT: B 477 GLN cc_start: 0.6464 (pm20) cc_final: 0.6235 (mp10) REVERT: B 480 GLU cc_start: 0.6560 (mp0) cc_final: 0.5788 (mt-10) REVERT: B 481 ARG cc_start: 0.7036 (mmm-85) cc_final: 0.6316 (ttt-90) REVERT: C 125 PRO cc_start: 0.7450 (Cg_exo) cc_final: 0.6981 (Cg_endo) REVERT: C 130 ARG cc_start: 0.7035 (ttp-110) cc_final: 0.6226 (ttm110) REVERT: C 183 MET cc_start: 0.8773 (mtp) cc_final: 0.8489 (mtm) REVERT: C 416 ARG cc_start: 0.7823 (mtm110) cc_final: 0.7279 (mtm180) REVERT: C 440 ARG cc_start: 0.7608 (mtt-85) cc_final: 0.7393 (mtt-85) REVERT: C 442 ASN cc_start: 0.8768 (m-40) cc_final: 0.8357 (m110) REVERT: C 518 MET cc_start: 0.8675 (mtp) cc_final: 0.8421 (mtm) REVERT: C 547 ARG cc_start: 0.6405 (mtp85) cc_final: 0.6031 (mtp180) REVERT: C 550 ARG cc_start: 0.7365 (ttm-80) cc_final: 0.6609 (mtm110) REVERT: D 34 ASP cc_start: 0.7347 (m-30) cc_final: 0.6852 (t0) REVERT: D 52 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7107 (mt-10) REVERT: D 201 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8143 (tp) REVERT: D 305 LYS cc_start: 0.7554 (OUTLIER) cc_final: 0.6964 (mtpp) REVERT: D 338 GLN cc_start: 0.8714 (tt0) cc_final: 0.8499 (tp40) REVERT: D 380 ASP cc_start: 0.7821 (m-30) cc_final: 0.7555 (m-30) REVERT: D 409 ARG cc_start: 0.6730 (ttm-80) cc_final: 0.6332 (mtt90) REVERT: D 420 ARG cc_start: 0.7444 (mtp-110) cc_final: 0.7057 (mtp-110) REVERT: D 437 GLN cc_start: 0.8282 (tt0) cc_final: 0.7982 (tt0) REVERT: D 461 LYS cc_start: 0.7519 (tttt) cc_final: 0.7260 (tttp) REVERT: D 463 TYR cc_start: 0.7992 (t80) cc_final: 0.7545 (t80) REVERT: E 26 ASP cc_start: 0.7165 (t0) cc_final: 0.6922 (t0) REVERT: E 259 ASP cc_start: 0.7156 (m-30) cc_final: 0.6750 (m-30) REVERT: E 278 PRO cc_start: 0.8682 (Cg_endo) cc_final: 0.8265 (Cg_exo) REVERT: E 302 GLU cc_start: 0.7233 (tt0) cc_final: 0.6512 (tp30) REVERT: E 380 ASP cc_start: 0.6643 (t0) cc_final: 0.6410 (t0) REVERT: E 445 MET cc_start: 0.7462 (mtp) cc_final: 0.6910 (mtt) REVERT: E 448 GLN cc_start: 0.5637 (OUTLIER) cc_final: 0.4949 (mm110) REVERT: F 6 LYS cc_start: 0.6407 (tptm) cc_final: 0.6145 (mtpp) REVERT: F 7 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7195 (mt-10) REVERT: F 109 GLU cc_start: 0.6824 (mt-10) cc_final: 0.6364 (mm-30) REVERT: F 207 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7234 (tm-30) REVERT: F 210 ARG cc_start: 0.7003 (ttp80) cc_final: 0.6641 (ttp80) REVERT: F 405 THR cc_start: 0.6996 (OUTLIER) cc_final: 0.6737 (t) REVERT: G 47 MET cc_start: 0.5460 (mmm) cc_final: 0.4908 (ttm) REVERT: G 59 GLU cc_start: 0.5575 (pp20) cc_final: 0.4573 (tp30) REVERT: G 139 ARG cc_start: 0.5301 (ttp80) cc_final: 0.4524 (ptm160) REVERT: H 63 MET cc_start: 0.3983 (mmm) cc_final: 0.2511 (ttp) REVERT: H 77 LEU cc_start: 0.3929 (mm) cc_final: 0.3686 (mp) REVERT: J 65 GLU cc_start: 0.4534 (mt-10) cc_final: 0.4231 (mt-10) REVERT: J 86 ARG cc_start: 0.4397 (mmp80) cc_final: 0.3490 (ttm-80) REVERT: J 112 LEU cc_start: 0.4596 (OUTLIER) cc_final: 0.4032 (tt) REVERT: J 162 GLN cc_start: 0.6038 (tt0) cc_final: 0.5712 (tt0) REVERT: J 173 ARG cc_start: 0.3524 (ttt-90) cc_final: 0.3233 (mtp85) REVERT: K 102 LYS cc_start: 0.5649 (tptp) cc_final: 0.4009 (mmtt) REVERT: L 86 ARG cc_start: 0.5681 (mtt180) cc_final: 0.5187 (mtp180) REVERT: L 102 GLU cc_start: 0.5518 (mp0) cc_final: 0.4613 (tp30) REVERT: L 113 GLU cc_start: 0.5700 (mm-30) cc_final: 0.5366 (mp0) REVERT: L 153 ARG cc_start: 0.4141 (ttm170) cc_final: 0.3630 (ttm-80) outliers start: 77 outliers final: 51 residues processed: 498 average time/residue: 0.2206 time to fit residues: 162.9153 Evaluate side-chains 457 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 401 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 399 ILE Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 362 MET Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 410 ARG Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain L residue 134 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 350 optimal weight: 1.9990 chunk 245 optimal weight: 0.0770 chunk 241 optimal weight: 0.7980 chunk 153 optimal weight: 4.9990 chunk 275 optimal weight: 7.9990 chunk 165 optimal weight: 2.9990 chunk 342 optimal weight: 9.9990 chunk 325 optimal weight: 10.0000 chunk 360 optimal weight: 9.9990 chunk 5 optimal weight: 0.7980 chunk 311 optimal weight: 6.9990 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 290 ASN E 161 ASN ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 249 HIS G 180 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.154448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.122872 restraints weight = 34398.382| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.78 r_work: 0.3016 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 30052 Z= 0.125 Angle : 0.507 9.660 40716 Z= 0.263 Chirality : 0.043 0.195 4564 Planarity : 0.004 0.061 5331 Dihedral : 5.125 80.482 4214 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.91 % Favored : 98.06 % Rotamer: Outliers : 2.04 % Allowed : 12.94 % Favored : 85.01 % 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: 0.71 (0.14), residues: 3764 helix: 1.61 (0.13), residues: 1589 sheet: -0.83 (0.20), residues: 581 loop : -0.06 (0.16), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 95 TYR 0.010 0.001 TYR C 562 PHE 0.017 0.001 PHE E 130 TRP 0.017 0.001 TRP A 119 HIS 0.008 0.001 HIS F 249 Details of bonding type rmsd covalent geometry : bond 0.00295 (30052) covalent geometry : angle 0.50709 (40716) hydrogen bonds : bond 0.03961 ( 1303) hydrogen bonds : angle 4.60386 ( 3738) *********************** 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 488 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 425 time to evaluate : 0.980 Fit side-chains REVERT: A 95 ARG cc_start: 0.7344 (tpt-90) cc_final: 0.6758 (tpt-90) REVERT: A 156 ARG cc_start: 0.6265 (mtp-110) cc_final: 0.5602 (ttp-170) REVERT: A 374 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7010 (tt0) REVERT: A 416 ARG cc_start: 0.7843 (mtm-85) cc_final: 0.7264 (mtp85) REVERT: A 478 ASP cc_start: 0.6548 (m-30) cc_final: 0.6272 (m-30) REVERT: A 481 ARG cc_start: 0.7849 (mtm-85) cc_final: 0.7331 (mtp-110) REVERT: A 518 MET cc_start: 0.8832 (mtp) cc_final: 0.8558 (mtm) REVERT: A 541 GLN cc_start: 0.6680 (mt0) cc_final: 0.6149 (pt0) REVERT: A 546 GLU cc_start: 0.7773 (mt-10) cc_final: 0.6936 (mm-30) REVERT: A 547 ARG cc_start: 0.7340 (ttm110) cc_final: 0.6870 (ttm110) REVERT: A 557 GLU cc_start: 0.7269 (pm20) cc_final: 0.6802 (tp30) REVERT: B 166 TYR cc_start: 0.7265 (m-80) cc_final: 0.6424 (m-80) REVERT: B 197 ARG cc_start: 0.7445 (ttp80) cc_final: 0.7065 (ttp-110) REVERT: B 241 LEU cc_start: 0.8401 (mp) cc_final: 0.8067 (tt) REVERT: B 340 ARG cc_start: 0.7618 (tpp-160) cc_final: 0.7208 (tpt-90) REVERT: B 449 GLU cc_start: 0.6517 (mm-30) cc_final: 0.6170 (mp0) REVERT: B 477 GLN cc_start: 0.6595 (pm20) cc_final: 0.6284 (mp10) REVERT: B 480 GLU cc_start: 0.6724 (mp0) cc_final: 0.5939 (mt-10) REVERT: B 481 ARG cc_start: 0.7097 (mmm-85) cc_final: 0.6578 (ttt-90) REVERT: B 547 ARG cc_start: 0.5841 (mmm-85) cc_final: 0.5537 (mmm160) REVERT: B 567 MET cc_start: 0.6914 (mmt) cc_final: 0.6683 (mmt) REVERT: C 106 VAL cc_start: 0.8442 (OUTLIER) cc_final: 0.8200 (t) REVERT: C 115 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.8018 (tttp) REVERT: C 130 ARG cc_start: 0.7226 (ttp-110) cc_final: 0.6426 (ttm110) REVERT: C 183 MET cc_start: 0.8733 (mtp) cc_final: 0.8487 (mtt) REVERT: C 344 MET cc_start: 0.8170 (mmt) cc_final: 0.7469 (mmm) REVERT: C 416 ARG cc_start: 0.7972 (mtm110) cc_final: 0.7417 (mtm180) REVERT: C 442 ASN cc_start: 0.8762 (m-40) cc_final: 0.8322 (m110) REVERT: C 460 ARG cc_start: 0.7698 (mtm180) cc_final: 0.7469 (mtp180) REVERT: C 547 ARG cc_start: 0.6434 (mtp85) cc_final: 0.5943 (mtp85) REVERT: C 550 ARG cc_start: 0.7340 (ttm-80) cc_final: 0.6631 (mtm110) REVERT: D 34 ASP cc_start: 0.7472 (m-30) cc_final: 0.7010 (t0) REVERT: D 42 VAL cc_start: 0.7754 (t) cc_final: 0.7541 (m) REVERT: D 52 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7214 (mt-10) REVERT: D 201 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8183 (tp) REVERT: D 231 ARG cc_start: 0.8599 (ttm170) cc_final: 0.8382 (ttp-110) REVERT: D 305 LYS cc_start: 0.7614 (mtmm) cc_final: 0.7321 (mtpt) REVERT: D 321 ARG cc_start: 0.7851 (tpp80) cc_final: 0.7630 (tpp80) REVERT: D 338 GLN cc_start: 0.8694 (tt0) cc_final: 0.8385 (tp40) REVERT: D 380 ASP cc_start: 0.7758 (m-30) cc_final: 0.7554 (m-30) REVERT: D 409 ARG cc_start: 0.6825 (ttm-80) cc_final: 0.6527 (mtt90) REVERT: D 420 ARG cc_start: 0.7566 (mtp-110) cc_final: 0.7226 (mtp-110) REVERT: D 461 LYS cc_start: 0.7563 (tttt) cc_final: 0.7325 (tttp) REVERT: D 463 TYR cc_start: 0.7946 (t80) cc_final: 0.7438 (t80) REVERT: E 26 ASP cc_start: 0.7100 (t0) cc_final: 0.6735 (t0) REVERT: E 259 ASP cc_start: 0.7125 (m-30) cc_final: 0.6715 (m-30) REVERT: E 278 PRO cc_start: 0.8650 (Cg_endo) cc_final: 0.8263 (Cg_exo) REVERT: E 302 GLU cc_start: 0.7213 (tt0) cc_final: 0.6477 (tp30) REVERT: E 445 MET cc_start: 0.7426 (mtp) cc_final: 0.7038 (mtt) REVERT: F 6 LYS cc_start: 0.6389 (tptm) cc_final: 0.6139 (mtpp) REVERT: F 7 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7218 (mt-10) REVERT: F 109 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6422 (mm-30) REVERT: F 207 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7432 (tm-30) REVERT: F 210 ARG cc_start: 0.6988 (ttp80) cc_final: 0.6196 (ttm110) REVERT: F 405 THR cc_start: 0.6915 (p) cc_final: 0.6710 (t) REVERT: F 406 GLU cc_start: 0.6143 (tm-30) cc_final: 0.5894 (pm20) REVERT: F 410 ARG cc_start: 0.7042 (OUTLIER) cc_final: 0.6664 (mtm-85) REVERT: G 47 MET cc_start: 0.5616 (mmm) cc_final: 0.5117 (ttm) REVERT: G 59 GLU cc_start: 0.5603 (OUTLIER) cc_final: 0.4617 (tp30) REVERT: G 200 LYS cc_start: 0.5670 (OUTLIER) cc_final: 0.5001 (mttt) REVERT: H 63 MET cc_start: 0.3951 (mmm) cc_final: 0.2387 (ttp) REVERT: H 77 LEU cc_start: 0.4115 (mm) cc_final: 0.3729 (mt) REVERT: J 65 GLU cc_start: 0.4510 (mt-10) cc_final: 0.4218 (mt-10) REVERT: J 86 ARG cc_start: 0.4491 (mmp80) cc_final: 0.3558 (ttm-80) REVERT: J 112 LEU cc_start: 0.4656 (OUTLIER) cc_final: 0.4365 (mp) REVERT: K 102 LYS cc_start: 0.5941 (tptp) cc_final: 0.4195 (mmtt) REVERT: L 86 ARG cc_start: 0.5786 (mtt180) cc_final: 0.5314 (mtp180) REVERT: L 102 GLU cc_start: 0.5638 (mp0) cc_final: 0.4737 (tp30) REVERT: L 113 GLU cc_start: 0.5675 (mm-30) cc_final: 0.5245 (mp0) REVERT: L 153 ARG cc_start: 0.4055 (ttm170) cc_final: 0.3582 (ttm-80) outliers start: 63 outliers final: 39 residues processed: 465 average time/residue: 0.2250 time to fit residues: 153.6125 Evaluate side-chains 452 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 406 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 410 ARG Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain L residue 134 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 320 optimal weight: 3.9990 chunk 234 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 271 optimal weight: 0.5980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 133 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 274 optimal weight: 0.5980 chunk 108 optimal weight: 6.9990 chunk 167 optimal weight: 5.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 GLN G 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.156207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.135169 restraints weight = 34540.785| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 0.79 r_work: 0.3131 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 30052 Z= 0.131 Angle : 0.507 7.281 40716 Z= 0.261 Chirality : 0.043 0.198 4564 Planarity : 0.004 0.046 5331 Dihedral : 4.962 78.875 4214 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.39 % Favored : 97.58 % Rotamer: Outliers : 2.40 % Allowed : 13.69 % Favored : 83.91 % 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: 0.80 (0.14), residues: 3764 helix: 1.67 (0.13), residues: 1590 sheet: -0.77 (0.20), residues: 581 loop : -0.02 (0.16), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 159 TYR 0.011 0.001 TYR C 562 PHE 0.017 0.001 PHE E 130 TRP 0.015 0.001 TRP A 119 HIS 0.004 0.001 HIS D 375 Details of bonding type rmsd covalent geometry : bond 0.00315 (30052) covalent geometry : angle 0.50704 (40716) hydrogen bonds : bond 0.03873 ( 1303) hydrogen bonds : angle 4.48692 ( 3738) *********************** 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 500 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 426 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: A 95 ARG cc_start: 0.7255 (tpt-90) cc_final: 0.6641 (tpt-90) REVERT: A 156 ARG cc_start: 0.6286 (mtp-110) cc_final: 0.5771 (ttp-170) REVERT: A 354 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7776 (tp) REVERT: A 374 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7124 (tt0) REVERT: A 416 ARG cc_start: 0.7633 (mtm-85) cc_final: 0.7174 (mtp85) REVERT: A 478 ASP cc_start: 0.6373 (m-30) cc_final: 0.6129 (m-30) REVERT: A 481 ARG cc_start: 0.7694 (mtm-85) cc_final: 0.7360 (mtp-110) REVERT: A 518 MET cc_start: 0.8675 (mtp) cc_final: 0.8417 (mtm) REVERT: A 541 GLN cc_start: 0.6515 (mt0) cc_final: 0.6140 (pt0) REVERT: A 546 GLU cc_start: 0.7636 (mt-10) cc_final: 0.6897 (mm-30) REVERT: B 54 ASP cc_start: 0.7448 (p0) cc_final: 0.7178 (p0) REVERT: B 166 TYR cc_start: 0.7198 (m-80) cc_final: 0.6453 (m-80) REVERT: B 197 ARG cc_start: 0.7443 (ttp80) cc_final: 0.7097 (ttp-110) REVERT: B 241 LEU cc_start: 0.8477 (mp) cc_final: 0.8140 (tt) REVERT: B 340 ARG cc_start: 0.7437 (tpp-160) cc_final: 0.7022 (tpt-90) REVERT: B 449 GLU cc_start: 0.6399 (mm-30) cc_final: 0.6165 (mp0) REVERT: B 477 GLN cc_start: 0.6731 (pm20) cc_final: 0.6443 (mp10) REVERT: B 480 GLU cc_start: 0.6763 (mp0) cc_final: 0.6029 (mt-10) REVERT: B 481 ARG cc_start: 0.7091 (mmm-85) cc_final: 0.6577 (ttt-90) REVERT: B 567 MET cc_start: 0.6928 (mmt) cc_final: 0.6718 (mmt) REVERT: C 115 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7978 (tttm) REVERT: C 130 ARG cc_start: 0.7070 (ttp-110) cc_final: 0.6404 (ttm110) REVERT: C 183 MET cc_start: 0.8617 (mtp) cc_final: 0.8340 (mtt) REVERT: C 209 MET cc_start: 0.8190 (mtp) cc_final: 0.7900 (ttm) REVERT: C 262 MET cc_start: 0.7753 (mmm) cc_final: 0.7456 (mmm) REVERT: C 344 MET cc_start: 0.7966 (mmt) cc_final: 0.7326 (mmm) REVERT: C 416 ARG cc_start: 0.7790 (mtm110) cc_final: 0.7379 (mtm180) REVERT: C 442 ASN cc_start: 0.8727 (m-40) cc_final: 0.8364 (m110) REVERT: C 460 ARG cc_start: 0.7681 (mtm180) cc_final: 0.7476 (mtp180) REVERT: C 518 MET cc_start: 0.8736 (mtp) cc_final: 0.8510 (mtm) REVERT: C 547 ARG cc_start: 0.6394 (mtp85) cc_final: 0.5965 (mtp85) REVERT: C 550 ARG cc_start: 0.7325 (ttm-80) cc_final: 0.6761 (mtm110) REVERT: D 34 ASP cc_start: 0.7234 (m-30) cc_final: 0.6743 (t0) REVERT: D 42 VAL cc_start: 0.7653 (t) cc_final: 0.7382 (m) REVERT: D 52 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7132 (mt-10) REVERT: D 201 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8170 (tp) REVERT: D 231 ARG cc_start: 0.8585 (ttm170) cc_final: 0.8381 (ttp-110) REVERT: D 305 LYS cc_start: 0.7472 (OUTLIER) cc_final: 0.6769 (mtpt) REVERT: D 338 GLN cc_start: 0.8551 (tt0) cc_final: 0.8277 (tp40) REVERT: D 362 MET cc_start: 0.8338 (ttp) cc_final: 0.8120 (ttt) REVERT: D 420 ARG cc_start: 0.7409 (mtp-110) cc_final: 0.7046 (mtp-110) REVERT: D 461 LYS cc_start: 0.7464 (tttt) cc_final: 0.7237 (tttp) REVERT: D 463 TYR cc_start: 0.7953 (t80) cc_final: 0.7480 (t80) REVERT: E 88 MET cc_start: 0.7813 (OUTLIER) cc_final: 0.7573 (mtt) REVERT: E 259 ASP cc_start: 0.6857 (m-30) cc_final: 0.6476 (m-30) REVERT: E 278 PRO cc_start: 0.8576 (Cg_endo) cc_final: 0.8158 (Cg_exo) REVERT: E 302 GLU cc_start: 0.7054 (tt0) cc_final: 0.6600 (tp30) REVERT: E 360 ARG cc_start: 0.8045 (mtt90) cc_final: 0.7787 (mtt90) REVERT: E 380 ASP cc_start: 0.6375 (t0) cc_final: 0.6123 (t0) REVERT: E 445 MET cc_start: 0.7422 (mtp) cc_final: 0.7021 (mtt) REVERT: E 448 GLN cc_start: 0.5617 (OUTLIER) cc_final: 0.4931 (mm110) REVERT: F 6 LYS cc_start: 0.6417 (tptm) cc_final: 0.6160 (mtpp) REVERT: F 7 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7045 (mt-10) REVERT: F 109 GLU cc_start: 0.6743 (mt-10) cc_final: 0.6352 (mm-30) REVERT: F 210 ARG cc_start: 0.6940 (ttp80) cc_final: 0.6185 (ttm110) REVERT: G 47 MET cc_start: 0.5607 (mmm) cc_final: 0.5101 (ttm) REVERT: G 59 GLU cc_start: 0.5701 (OUTLIER) cc_final: 0.4693 (tp30) REVERT: G 200 LYS cc_start: 0.5836 (OUTLIER) cc_final: 0.5167 (mttt) REVERT: H 63 MET cc_start: 0.4076 (mmm) cc_final: 0.2351 (ttp) REVERT: H 77 LEU cc_start: 0.4197 (mm) cc_final: 0.3631 (mt) REVERT: J 65 GLU cc_start: 0.4611 (mt-10) cc_final: 0.4328 (mt-10) REVERT: J 86 ARG cc_start: 0.4559 (mmp80) cc_final: 0.3555 (ttm-80) REVERT: J 112 LEU cc_start: 0.4612 (mp) cc_final: 0.4409 (mp) REVERT: K 102 LYS cc_start: 0.6044 (tptp) cc_final: 0.4326 (mmtt) REVERT: L 86 ARG cc_start: 0.5844 (mtt180) cc_final: 0.5400 (mtp180) REVERT: L 102 GLU cc_start: 0.5594 (mp0) cc_final: 0.4690 (tp30) REVERT: L 113 GLU cc_start: 0.5655 (mm-30) cc_final: 0.5309 (mp0) REVERT: L 153 ARG cc_start: 0.4197 (ttm170) cc_final: 0.3762 (ttm-80) outliers start: 74 outliers final: 46 residues processed: 476 average time/residue: 0.2168 time to fit residues: 152.9196 Evaluate side-chains 456 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 402 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 200 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 205 optimal weight: 3.9990 chunk 278 optimal weight: 6.9990 chunk 117 optimal weight: 0.7980 chunk 358 optimal weight: 6.9990 chunk 159 optimal weight: 0.5980 chunk 361 optimal weight: 20.0000 chunk 97 optimal weight: 4.9990 chunk 297 optimal weight: 3.9990 chunk 356 optimal weight: 10.0000 chunk 219 optimal weight: 8.9990 chunk 288 optimal weight: 0.8980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 GLN ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN G 180 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.151742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.119740 restraints weight = 34699.483| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.35 r_work: 0.3018 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 30052 Z= 0.146 Angle : 0.522 6.954 40716 Z= 0.269 Chirality : 0.044 0.203 4564 Planarity : 0.005 0.047 5331 Dihedral : 5.005 80.109 4214 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.69 % Allowed : 14.01 % Favored : 83.30 % 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: 0.71 (0.14), residues: 3764 helix: 1.58 (0.13), residues: 1600 sheet: -0.77 (0.20), residues: 591 loop : -0.08 (0.16), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 159 TYR 0.011 0.001 TYR C 562 PHE 0.018 0.002 PHE E 130 TRP 0.020 0.001 TRP G 97 HIS 0.005 0.001 HIS D 375 Details of bonding type rmsd covalent geometry : bond 0.00355 (30052) covalent geometry : angle 0.52193 (40716) hydrogen bonds : bond 0.03961 ( 1303) hydrogen bonds : angle 4.49115 ( 3738) *********************** 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 495 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 412 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: A 95 ARG cc_start: 0.7289 (tpt-90) cc_final: 0.6574 (tpt-90) REVERT: A 354 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7810 (tp) REVERT: A 374 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7065 (tt0) REVERT: A 416 ARG cc_start: 0.7818 (mtm-85) cc_final: 0.7127 (mtp85) REVERT: A 478 ASP cc_start: 0.6501 (m-30) cc_final: 0.6234 (m-30) REVERT: A 481 ARG cc_start: 0.7805 (mtm-85) cc_final: 0.7307 (mtp-110) REVERT: A 518 MET cc_start: 0.8755 (mtp) cc_final: 0.8480 (mtm) REVERT: A 541 GLN cc_start: 0.6562 (mt0) cc_final: 0.6109 (pt0) REVERT: A 546 GLU cc_start: 0.7602 (mt-10) cc_final: 0.6815 (mm-30) REVERT: A 547 ARG cc_start: 0.7377 (ttm110) cc_final: 0.6785 (ttm110) REVERT: B 54 ASP cc_start: 0.7541 (p0) cc_final: 0.6340 (t70) REVERT: B 166 TYR cc_start: 0.7303 (m-80) cc_final: 0.6500 (m-80) REVERT: B 197 ARG cc_start: 0.7452 (ttp80) cc_final: 0.7071 (ttp-110) REVERT: B 340 ARG cc_start: 0.7546 (tpp-160) cc_final: 0.7145 (tpt-90) REVERT: B 449 GLU cc_start: 0.6425 (mm-30) cc_final: 0.6127 (mp0) REVERT: B 477 GLN cc_start: 0.6672 (pm20) cc_final: 0.6458 (mp10) REVERT: B 480 GLU cc_start: 0.6762 (mp0) cc_final: 0.5971 (mt-10) REVERT: B 481 ARG cc_start: 0.6991 (mmm-85) cc_final: 0.6396 (ttt-90) REVERT: C 1 MET cc_start: 0.5994 (mmm) cc_final: 0.5342 (mmp) REVERT: C 115 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.8011 (tttm) REVERT: C 125 PRO cc_start: 0.7474 (Cg_exo) cc_final: 0.7036 (Cg_endo) REVERT: C 130 ARG cc_start: 0.7116 (ttp-110) cc_final: 0.6308 (ttm110) REVERT: C 183 MET cc_start: 0.8680 (mtp) cc_final: 0.8427 (mtt) REVERT: C 262 MET cc_start: 0.7870 (mmm) cc_final: 0.7578 (mmm) REVERT: C 344 MET cc_start: 0.8030 (mmt) cc_final: 0.7382 (mmm) REVERT: C 416 ARG cc_start: 0.7871 (mtm110) cc_final: 0.7361 (mtm180) REVERT: C 442 ASN cc_start: 0.8761 (m-40) cc_final: 0.8334 (m110) REVERT: C 460 ARG cc_start: 0.7669 (mtm180) cc_final: 0.7468 (mtp180) REVERT: C 518 MET cc_start: 0.8715 (mtp) cc_final: 0.8476 (mtm) REVERT: C 547 ARG cc_start: 0.6450 (mtp85) cc_final: 0.5954 (mtp85) REVERT: C 550 ARG cc_start: 0.7333 (ttm-80) cc_final: 0.6768 (mtm110) REVERT: D 34 ASP cc_start: 0.7377 (m-30) cc_final: 0.6894 (t0) REVERT: D 42 VAL cc_start: 0.7657 (t) cc_final: 0.7407 (m) REVERT: D 52 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7233 (mt-10) REVERT: D 201 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8157 (tp) REVERT: D 206 GLN cc_start: 0.6903 (tp40) cc_final: 0.6627 (mm-40) REVERT: D 231 ARG cc_start: 0.8608 (ttm170) cc_final: 0.8393 (ttp-110) REVERT: D 305 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.6748 (mtpt) REVERT: D 338 GLN cc_start: 0.8719 (tt0) cc_final: 0.8514 (tp40) REVERT: D 420 ARG cc_start: 0.7498 (mtp-110) cc_final: 0.7141 (mtp-110) REVERT: D 461 LYS cc_start: 0.7516 (tttt) cc_final: 0.7312 (ttmt) REVERT: D 463 TYR cc_start: 0.8002 (t80) cc_final: 0.7444 (t80) REVERT: E 88 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7586 (mtt) REVERT: E 259 ASP cc_start: 0.7040 (m-30) cc_final: 0.6639 (m-30) REVERT: E 278 PRO cc_start: 0.8530 (Cg_endo) cc_final: 0.8151 (Cg_exo) REVERT: E 302 GLU cc_start: 0.7354 (tt0) cc_final: 0.6657 (tp30) REVERT: E 410 ARG cc_start: 0.5832 (mtm-85) cc_final: 0.4534 (mmp80) REVERT: E 445 MET cc_start: 0.7519 (mtp) cc_final: 0.7026 (mtt) REVERT: E 448 GLN cc_start: 0.5520 (OUTLIER) cc_final: 0.5079 (mm110) REVERT: F 6 LYS cc_start: 0.6491 (tptm) cc_final: 0.6215 (mtpp) REVERT: F 7 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7173 (mt-10) REVERT: F 109 GLU cc_start: 0.6850 (mt-10) cc_final: 0.6386 (mm-30) REVERT: G 9 MET cc_start: 0.7617 (ttp) cc_final: 0.7185 (ptm) REVERT: G 47 MET cc_start: 0.5519 (mmm) cc_final: 0.4983 (ttm) REVERT: G 59 GLU cc_start: 0.5590 (OUTLIER) cc_final: 0.4584 (tp30) REVERT: G 200 LYS cc_start: 0.5752 (OUTLIER) cc_final: 0.5119 (mttt) REVERT: H 63 MET cc_start: 0.3989 (mmm) cc_final: 0.2382 (ttp) REVERT: H 77 LEU cc_start: 0.4159 (mm) cc_final: 0.3627 (mt) REVERT: J 65 GLU cc_start: 0.4605 (mt-10) cc_final: 0.4353 (mt-10) REVERT: J 86 ARG cc_start: 0.4628 (mmp80) cc_final: 0.3580 (ttm-80) REVERT: J 112 LEU cc_start: 0.4605 (OUTLIER) cc_final: 0.4389 (mp) REVERT: K 102 LYS cc_start: 0.5945 (tptp) cc_final: 0.4240 (mmtt) REVERT: L 86 ARG cc_start: 0.5752 (mtt180) cc_final: 0.5362 (mtp180) REVERT: L 102 GLU cc_start: 0.5612 (mp0) cc_final: 0.4681 (tp30) REVERT: L 141 GLU cc_start: 0.5057 (OUTLIER) cc_final: 0.4267 (mm-30) REVERT: L 153 ARG cc_start: 0.4167 (ttm170) cc_final: 0.3584 (ttm-80) outliers start: 83 outliers final: 56 residues processed: 466 average time/residue: 0.2130 time to fit residues: 147.3096 Evaluate side-chains 468 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 402 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 413 GLN Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 112 LEU Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 168 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 13 optimal weight: 4.9990 chunk 301 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 309 optimal weight: 9.9990 chunk 173 optimal weight: 10.0000 chunk 300 optimal weight: 2.9990 chunk 295 optimal weight: 3.9990 chunk 291 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 284 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 HIS A 498 ASN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN G 180 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.151759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.117306 restraints weight = 34588.943| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.44 r_work: 0.3068 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 30052 Z= 0.178 Angle : 0.554 7.555 40716 Z= 0.286 Chirality : 0.045 0.292 4564 Planarity : 0.005 0.047 5331 Dihedral : 5.152 79.554 4214 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.85 % Allowed : 14.69 % Favored : 82.45 % 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: 0.56 (0.14), residues: 3764 helix: 1.43 (0.13), residues: 1583 sheet: -0.77 (0.20), residues: 596 loop : -0.14 (0.16), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 159 TYR 0.013 0.002 TYR C 562 PHE 0.019 0.002 PHE F 414 TRP 0.014 0.002 TRP A 119 HIS 0.005 0.001 HIS D 375 Details of bonding type rmsd covalent geometry : bond 0.00437 (30052) covalent geometry : angle 0.55357 (40716) hydrogen bonds : bond 0.04237 ( 1303) hydrogen bonds : angle 4.55599 ( 3738) *********************** 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 493 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 405 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7558 (mt-10) REVERT: A 95 ARG cc_start: 0.7271 (tpt-90) cc_final: 0.6562 (tpt-90) REVERT: A 156 ARG cc_start: 0.6379 (mtp-110) cc_final: 0.5869 (ttp-170) REVERT: A 354 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7871 (tp) REVERT: A 374 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7096 (tt0) REVERT: A 416 ARG cc_start: 0.7918 (mtm-85) cc_final: 0.7210 (mtp85) REVERT: A 478 ASP cc_start: 0.6575 (m-30) cc_final: 0.6304 (m-30) REVERT: A 481 ARG cc_start: 0.7860 (mtm-85) cc_final: 0.7392 (mtp-110) REVERT: A 541 GLN cc_start: 0.6588 (mt0) cc_final: 0.6067 (pt0) REVERT: A 546 GLU cc_start: 0.7655 (mt-10) cc_final: 0.6859 (mm-30) REVERT: A 547 ARG cc_start: 0.7451 (ttm110) cc_final: 0.6923 (ttm110) REVERT: B 54 ASP cc_start: 0.7574 (p0) cc_final: 0.6356 (t70) REVERT: B 166 TYR cc_start: 0.7308 (m-80) cc_final: 0.6502 (m-80) REVERT: B 197 ARG cc_start: 0.7466 (ttp80) cc_final: 0.7074 (ttp-110) REVERT: B 340 ARG cc_start: 0.7564 (tpp-160) cc_final: 0.7165 (tpt-90) REVERT: B 449 GLU cc_start: 0.6486 (mm-30) cc_final: 0.6192 (mp0) REVERT: B 480 GLU cc_start: 0.6850 (mp0) cc_final: 0.6061 (mt-10) REVERT: B 481 ARG cc_start: 0.7071 (mmm-85) cc_final: 0.6481 (ttt-90) REVERT: B 547 ARG cc_start: 0.6441 (ttm-80) cc_final: 0.5517 (mmm160) REVERT: C 95 ARG cc_start: 0.7417 (mtp180) cc_final: 0.7142 (ttp-170) REVERT: C 115 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.8000 (tttm) REVERT: C 125 PRO cc_start: 0.7584 (Cg_exo) cc_final: 0.7093 (Cg_endo) REVERT: C 130 ARG cc_start: 0.7139 (ttp-110) cc_final: 0.6325 (ttm110) REVERT: C 183 MET cc_start: 0.8683 (mtp) cc_final: 0.8422 (mtt) REVERT: C 209 MET cc_start: 0.8424 (mtp) cc_final: 0.8147 (ttm) REVERT: C 262 MET cc_start: 0.7872 (mmm) cc_final: 0.7661 (mmm) REVERT: C 344 MET cc_start: 0.8013 (mmt) cc_final: 0.7371 (mmm) REVERT: C 416 ARG cc_start: 0.7899 (mtm110) cc_final: 0.7379 (mtm180) REVERT: C 442 ASN cc_start: 0.8780 (m-40) cc_final: 0.8344 (m110) REVERT: C 547 ARG cc_start: 0.6580 (mtp85) cc_final: 0.6046 (mtp85) REVERT: C 550 ARG cc_start: 0.7455 (ttm-80) cc_final: 0.6827 (mtm110) REVERT: D 34 ASP cc_start: 0.7515 (m-30) cc_final: 0.7030 (t0) REVERT: D 42 VAL cc_start: 0.7703 (t) cc_final: 0.7482 (m) REVERT: D 52 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7319 (mt-10) REVERT: D 201 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8190 (tp) REVERT: D 305 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.6879 (mtpt) REVERT: D 338 GLN cc_start: 0.8785 (tt0) cc_final: 0.8556 (tp40) REVERT: D 420 ARG cc_start: 0.7577 (mtp-110) cc_final: 0.7234 (mtp-110) REVERT: D 461 LYS cc_start: 0.7576 (tttt) cc_final: 0.7375 (ttmt) REVERT: D 463 TYR cc_start: 0.8031 (t80) cc_final: 0.7444 (t80) REVERT: E 88 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.7646 (mtt) REVERT: E 259 ASP cc_start: 0.7178 (m-30) cc_final: 0.6757 (m-30) REVERT: E 278 PRO cc_start: 0.8564 (Cg_endo) cc_final: 0.8207 (Cg_exo) REVERT: E 302 GLU cc_start: 0.7501 (tt0) cc_final: 0.6744 (tp30) REVERT: E 410 ARG cc_start: 0.5945 (mtm-85) cc_final: 0.4662 (mmp80) REVERT: E 445 MET cc_start: 0.7498 (mtp) cc_final: 0.6983 (mtt) REVERT: F 6 LYS cc_start: 0.6566 (tptm) cc_final: 0.6277 (mtpp) REVERT: F 7 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7037 (mt-10) REVERT: F 109 GLU cc_start: 0.6968 (mt-10) cc_final: 0.6492 (mm-30) REVERT: F 177 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7883 (mp) REVERT: G 47 MET cc_start: 0.5687 (mmm) cc_final: 0.5032 (ttm) REVERT: G 59 GLU cc_start: 0.5587 (OUTLIER) cc_final: 0.4559 (tp30) REVERT: G 150 ILE cc_start: 0.7579 (mt) cc_final: 0.7285 (tt) REVERT: G 200 LYS cc_start: 0.5799 (OUTLIER) cc_final: 0.5184 (mttt) REVERT: H 63 MET cc_start: 0.3879 (mmm) cc_final: 0.2402 (ttp) REVERT: H 77 LEU cc_start: 0.4297 (mm) cc_final: 0.3774 (mt) REVERT: J 65 GLU cc_start: 0.4536 (mt-10) cc_final: 0.4250 (mt-10) REVERT: J 162 GLN cc_start: 0.6162 (tt0) cc_final: 0.5921 (tt0) REVERT: J 184 GLN cc_start: 0.3711 (OUTLIER) cc_final: 0.2821 (tm-30) REVERT: K 102 LYS cc_start: 0.5750 (tptp) cc_final: 0.4080 (mmtt) REVERT: L 86 ARG cc_start: 0.5754 (mtt180) cc_final: 0.5357 (mtp180) REVERT: L 102 GLU cc_start: 0.5574 (mp0) cc_final: 0.4623 (tp30) REVERT: L 141 GLU cc_start: 0.5157 (OUTLIER) cc_final: 0.4378 (mm-30) REVERT: L 164 GLU cc_start: 0.5945 (tp30) cc_final: 0.5301 (mt-10) outliers start: 88 outliers final: 64 residues processed: 467 average time/residue: 0.2036 time to fit residues: 142.2231 Evaluate side-chains 467 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 392 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 538 GLU Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 368 LYS Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain J residue 184 GLN Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 168 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 255 optimal weight: 10.0000 chunk 223 optimal weight: 7.9990 chunk 54 optimal weight: 0.0980 chunk 85 optimal weight: 4.9990 chunk 171 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 266 optimal weight: 8.9990 chunk 329 optimal weight: 0.9990 chunk 206 optimal weight: 4.9990 chunk 325 optimal weight: 0.9990 chunk 254 optimal weight: 8.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 448 GLN G 180 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.153956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.121343 restraints weight = 34613.194| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.38 r_work: 0.3045 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 30052 Z= 0.120 Angle : 0.499 7.422 40716 Z= 0.257 Chirality : 0.043 0.255 4564 Planarity : 0.004 0.048 5331 Dihedral : 4.927 79.940 4214 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.56 % Allowed : 15.24 % Favored : 82.19 % 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: 0.71 (0.14), residues: 3764 helix: 1.61 (0.13), residues: 1581 sheet: -0.80 (0.20), residues: 611 loop : -0.06 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 159 TYR 0.010 0.001 TYR B 439 PHE 0.018 0.001 PHE F 414 TRP 0.013 0.001 TRP A 119 HIS 0.003 0.001 HIS D 375 Details of bonding type rmsd covalent geometry : bond 0.00284 (30052) covalent geometry : angle 0.49881 (40716) hydrogen bonds : bond 0.03718 ( 1303) hydrogen bonds : angle 4.40559 ( 3738) *********************** 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 481 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 402 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7421 (mt-10) REVERT: A 95 ARG cc_start: 0.7240 (tpt-90) cc_final: 0.6525 (tpt-90) REVERT: A 156 ARG cc_start: 0.6340 (mtp-110) cc_final: 0.5847 (ttp-170) REVERT: A 354 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7779 (tp) REVERT: A 374 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7078 (tt0) REVERT: A 416 ARG cc_start: 0.7859 (mtm-85) cc_final: 0.7147 (mtp85) REVERT: A 478 ASP cc_start: 0.6405 (m-30) cc_final: 0.6094 (m-30) REVERT: A 481 ARG cc_start: 0.7725 (mtm-85) cc_final: 0.7277 (mtp-110) REVERT: A 518 MET cc_start: 0.8715 (mtp) cc_final: 0.8486 (mtm) REVERT: A 541 GLN cc_start: 0.6587 (mt0) cc_final: 0.6030 (pt0) REVERT: A 542 LEU cc_start: 0.7587 (mm) cc_final: 0.7362 (mp) REVERT: A 547 ARG cc_start: 0.7353 (ttm110) cc_final: 0.6828 (ttm110) REVERT: B 54 ASP cc_start: 0.7524 (p0) cc_final: 0.6322 (t70) REVERT: B 166 TYR cc_start: 0.7284 (m-80) cc_final: 0.6466 (m-80) REVERT: B 197 ARG cc_start: 0.7414 (ttp80) cc_final: 0.7044 (ttp-110) REVERT: B 340 ARG cc_start: 0.7558 (tpp-160) cc_final: 0.7159 (tpt-90) REVERT: B 449 GLU cc_start: 0.6427 (mm-30) cc_final: 0.6151 (mp0) REVERT: B 480 GLU cc_start: 0.6776 (mp0) cc_final: 0.5923 (mt-10) REVERT: B 481 ARG cc_start: 0.7018 (mmm-85) cc_final: 0.6444 (ttt-90) REVERT: B 547 ARG cc_start: 0.6422 (ttm-80) cc_final: 0.5437 (mmm160) REVERT: C 1 MET cc_start: 0.6021 (mmm) cc_final: 0.5227 (mmp) REVERT: C 3 GLN cc_start: 0.7570 (mt0) cc_final: 0.7251 (mm-40) REVERT: C 95 ARG cc_start: 0.7280 (mtp180) cc_final: 0.7071 (ttp-170) REVERT: C 106 VAL cc_start: 0.8429 (OUTLIER) cc_final: 0.8197 (t) REVERT: C 125 PRO cc_start: 0.7489 (Cg_exo) cc_final: 0.7037 (Cg_endo) REVERT: C 130 ARG cc_start: 0.7070 (ttp-110) cc_final: 0.6284 (ttm110) REVERT: C 183 MET cc_start: 0.8647 (mtp) cc_final: 0.8321 (mtt) REVERT: C 262 MET cc_start: 0.7864 (mmm) cc_final: 0.7654 (mmm) REVERT: C 344 MET cc_start: 0.7945 (mmt) cc_final: 0.7419 (mmm) REVERT: C 416 ARG cc_start: 0.7837 (mtm110) cc_final: 0.7338 (mtm180) REVERT: C 442 ASN cc_start: 0.8747 (m-40) cc_final: 0.8279 (m110) REVERT: C 547 ARG cc_start: 0.6520 (mtp85) cc_final: 0.5964 (mtp85) REVERT: C 550 ARG cc_start: 0.7415 (ttm-80) cc_final: 0.6800 (mtm110) REVERT: C 562 TYR cc_start: 0.8033 (t80) cc_final: 0.7483 (t80) REVERT: D 34 ASP cc_start: 0.7419 (m-30) cc_final: 0.6940 (t0) REVERT: D 42 VAL cc_start: 0.7680 (t) cc_final: 0.7396 (m) REVERT: D 52 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7235 (mt-10) REVERT: D 201 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8137 (tp) REVERT: D 231 ARG cc_start: 0.8573 (ttm170) cc_final: 0.8371 (ttp-110) REVERT: D 305 LYS cc_start: 0.7570 (OUTLIER) cc_final: 0.6811 (mtpt) REVERT: D 338 GLN cc_start: 0.8827 (tt0) cc_final: 0.8555 (tp40) REVERT: D 420 ARG cc_start: 0.7491 (mtp-110) cc_final: 0.7130 (mtp-110) REVERT: D 461 LYS cc_start: 0.7532 (tttt) cc_final: 0.7321 (ttmt) REVERT: D 463 TYR cc_start: 0.7976 (t80) cc_final: 0.7395 (t80) REVERT: E 88 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7650 (mtt) REVERT: E 259 ASP cc_start: 0.6966 (m-30) cc_final: 0.6563 (m-30) REVERT: E 278 PRO cc_start: 0.8503 (Cg_endo) cc_final: 0.8170 (Cg_exo) REVERT: E 302 GLU cc_start: 0.7467 (tt0) cc_final: 0.6720 (tp30) REVERT: E 410 ARG cc_start: 0.5897 (mtm-85) cc_final: 0.4610 (mmp80) REVERT: E 433 GLU cc_start: 0.7292 (mp0) cc_final: 0.6994 (mp0) REVERT: E 445 MET cc_start: 0.7489 (mtp) cc_final: 0.7032 (mtt) REVERT: F 6 LYS cc_start: 0.6492 (tptm) cc_final: 0.6215 (mtpp) REVERT: F 7 GLU cc_start: 0.7705 (mt-10) cc_final: 0.6880 (mt-10) REVERT: F 109 GLU cc_start: 0.6873 (mt-10) cc_final: 0.6393 (mm-30) REVERT: F 177 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7850 (mp) REVERT: F 210 ARG cc_start: 0.6735 (ttp80) cc_final: 0.5846 (mtm110) REVERT: G 9 MET cc_start: 0.7590 (ttp) cc_final: 0.7213 (ptm) REVERT: G 47 MET cc_start: 0.5586 (mmm) cc_final: 0.4957 (ttm) REVERT: G 59 GLU cc_start: 0.5596 (OUTLIER) cc_final: 0.4601 (tp30) REVERT: G 200 LYS cc_start: 0.5712 (OUTLIER) cc_final: 0.5078 (mttt) REVERT: H 63 MET cc_start: 0.3897 (mmm) cc_final: 0.2422 (ttp) REVERT: H 77 LEU cc_start: 0.4102 (mm) cc_final: 0.3603 (mt) REVERT: J 65 GLU cc_start: 0.4541 (mt-10) cc_final: 0.4291 (mt-10) REVERT: K 102 LYS cc_start: 0.5762 (tptp) cc_final: 0.4052 (mmtt) REVERT: L 86 ARG cc_start: 0.5765 (mtt180) cc_final: 0.5392 (mtp180) REVERT: L 102 GLU cc_start: 0.5540 (mp0) cc_final: 0.4628 (tp30) REVERT: L 141 GLU cc_start: 0.5038 (OUTLIER) cc_final: 0.4348 (mm-30) REVERT: L 153 ARG cc_start: 0.5871 (mtp-110) cc_final: 0.3839 (mtt180) REVERT: L 164 GLU cc_start: 0.5801 (tp30) cc_final: 0.4874 (mt-10) outliers start: 79 outliers final: 58 residues processed: 457 average time/residue: 0.2047 time to fit residues: 139.5006 Evaluate side-chains 461 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 393 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 368 LYS Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 459 ILE Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 168 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 134 optimal weight: 7.9990 chunk 294 optimal weight: 8.9990 chunk 272 optimal weight: 0.9990 chunk 235 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 278 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 chunk 308 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 298 optimal weight: 0.0050 chunk 67 optimal weight: 0.0570 overall best weight: 1.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 GLN ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN G 180 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.153288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.119245 restraints weight = 34502.662| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.41 r_work: 0.3093 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30052 Z= 0.128 Angle : 0.504 7.280 40716 Z= 0.260 Chirality : 0.043 0.243 4564 Planarity : 0.004 0.048 5331 Dihedral : 4.906 81.225 4214 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.37 % Allowed : 15.21 % Favored : 82.42 % 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: 0.72 (0.14), residues: 3764 helix: 1.62 (0.13), residues: 1581 sheet: -0.77 (0.20), residues: 612 loop : -0.07 (0.16), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 159 TYR 0.010 0.001 TYR C 562 PHE 0.017 0.001 PHE E 130 TRP 0.012 0.001 TRP A 119 HIS 0.004 0.001 HIS D 375 Details of bonding type rmsd covalent geometry : bond 0.00305 (30052) covalent geometry : angle 0.50409 (40716) hydrogen bonds : bond 0.03732 ( 1303) hydrogen bonds : angle 4.39182 ( 3738) *********************** 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 469 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 396 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7397 (mt-10) REVERT: A 95 ARG cc_start: 0.7239 (tpt-90) cc_final: 0.6514 (tpt-90) REVERT: A 156 ARG cc_start: 0.6352 (mtp-110) cc_final: 0.5848 (ttp-170) REVERT: A 354 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7796 (tp) REVERT: A 374 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7084 (tt0) REVERT: A 416 ARG cc_start: 0.7870 (mtm-85) cc_final: 0.7153 (mtp85) REVERT: A 478 ASP cc_start: 0.6449 (m-30) cc_final: 0.6198 (m-30) REVERT: A 481 ARG cc_start: 0.7774 (mtm-85) cc_final: 0.7298 (mtp-110) REVERT: A 541 GLN cc_start: 0.6557 (mt0) cc_final: 0.6005 (pt0) REVERT: A 547 ARG cc_start: 0.7325 (ttm110) cc_final: 0.6832 (ttm110) REVERT: B 54 ASP cc_start: 0.7503 (p0) cc_final: 0.6337 (t70) REVERT: B 166 TYR cc_start: 0.7298 (m-80) cc_final: 0.6466 (m-80) REVERT: B 197 ARG cc_start: 0.7416 (ttp80) cc_final: 0.7046 (ttp-110) REVERT: B 340 ARG cc_start: 0.7549 (tpp-160) cc_final: 0.7147 (tpt-90) REVERT: B 449 GLU cc_start: 0.6459 (mm-30) cc_final: 0.6180 (mp0) REVERT: B 480 GLU cc_start: 0.6762 (mp0) cc_final: 0.5904 (mt-10) REVERT: B 481 ARG cc_start: 0.7014 (mmm-85) cc_final: 0.6539 (ttt-90) REVERT: B 547 ARG cc_start: 0.6438 (ttm-80) cc_final: 0.5425 (mmm160) REVERT: C 1 MET cc_start: 0.6147 (mmm) cc_final: 0.5334 (mmp) REVERT: C 3 GLN cc_start: 0.7605 (mt0) cc_final: 0.7278 (mm-40) REVERT: C 95 ARG cc_start: 0.7314 (mtp180) cc_final: 0.7083 (ttp-170) REVERT: C 125 PRO cc_start: 0.7523 (Cg_exo) cc_final: 0.7081 (Cg_endo) REVERT: C 130 ARG cc_start: 0.7123 (ttp-110) cc_final: 0.6296 (ttm110) REVERT: C 183 MET cc_start: 0.8633 (mtp) cc_final: 0.8296 (mtt) REVERT: C 344 MET cc_start: 0.8079 (mmt) cc_final: 0.7550 (mmm) REVERT: C 416 ARG cc_start: 0.7825 (mtm110) cc_final: 0.7351 (mtm180) REVERT: C 442 ASN cc_start: 0.8742 (m-40) cc_final: 0.8275 (m110) REVERT: C 547 ARG cc_start: 0.6545 (mtp85) cc_final: 0.6204 (mtp180) REVERT: C 550 ARG cc_start: 0.7391 (ttm-80) cc_final: 0.6757 (mtm110) REVERT: C 562 TYR cc_start: 0.8041 (t80) cc_final: 0.7536 (t80) REVERT: D 34 ASP cc_start: 0.7469 (m-30) cc_final: 0.6991 (t0) REVERT: D 42 VAL cc_start: 0.7645 (t) cc_final: 0.7402 (m) REVERT: D 52 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7229 (mt-10) REVERT: D 201 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8147 (tp) REVERT: D 231 ARG cc_start: 0.8592 (ttm170) cc_final: 0.8374 (ttp-110) REVERT: D 305 LYS cc_start: 0.7584 (OUTLIER) cc_final: 0.6826 (mtpt) REVERT: D 338 GLN cc_start: 0.8833 (tt0) cc_final: 0.8555 (tp40) REVERT: D 420 ARG cc_start: 0.7493 (mtp-110) cc_final: 0.7150 (mtp-110) REVERT: D 461 LYS cc_start: 0.7543 (tttt) cc_final: 0.7332 (ttmt) REVERT: D 463 TYR cc_start: 0.7971 (t80) cc_final: 0.7376 (t80) REVERT: E 88 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7638 (mtt) REVERT: E 259 ASP cc_start: 0.7033 (m-30) cc_final: 0.6626 (m-30) REVERT: E 278 PRO cc_start: 0.8514 (Cg_endo) cc_final: 0.8201 (Cg_exo) REVERT: E 302 GLU cc_start: 0.7495 (tt0) cc_final: 0.6736 (tp30) REVERT: E 410 ARG cc_start: 0.5897 (mtm-85) cc_final: 0.4687 (mmp80) REVERT: E 433 GLU cc_start: 0.7285 (mp0) cc_final: 0.6834 (mp0) REVERT: E 445 MET cc_start: 0.7497 (mtp) cc_final: 0.7024 (mtt) REVERT: F 6 LYS cc_start: 0.6486 (tptm) cc_final: 0.6208 (mtpp) REVERT: F 7 GLU cc_start: 0.7735 (mt-10) cc_final: 0.6918 (mt-10) REVERT: F 109 GLU cc_start: 0.6860 (mt-10) cc_final: 0.6383 (mm-30) REVERT: F 210 ARG cc_start: 0.6646 (ttp80) cc_final: 0.5716 (mtm110) REVERT: G 9 MET cc_start: 0.7615 (ttp) cc_final: 0.7228 (ptm) REVERT: G 47 MET cc_start: 0.5473 (mmm) cc_final: 0.4934 (ttm) REVERT: G 59 GLU cc_start: 0.5483 (OUTLIER) cc_final: 0.4503 (tp30) REVERT: G 149 LYS cc_start: 0.7393 (tptt) cc_final: 0.7103 (tptt) REVERT: G 150 ILE cc_start: 0.7485 (mt) cc_final: 0.7213 (tt) REVERT: G 200 LYS cc_start: 0.5753 (OUTLIER) cc_final: 0.5127 (mttt) REVERT: H 63 MET cc_start: 0.3990 (mmm) cc_final: 0.2424 (ttp) REVERT: H 77 LEU cc_start: 0.4095 (mm) cc_final: 0.3626 (mt) REVERT: J 65 GLU cc_start: 0.4466 (mt-10) cc_final: 0.4255 (mt-10) REVERT: K 102 LYS cc_start: 0.5727 (tptp) cc_final: 0.4023 (mmtt) REVERT: L 86 ARG cc_start: 0.5764 (mtt180) cc_final: 0.5371 (mtp180) REVERT: L 102 GLU cc_start: 0.5549 (mp0) cc_final: 0.4646 (tp30) REVERT: L 138 ARG cc_start: 0.4507 (mtt180) cc_final: 0.3790 (mtt90) REVERT: L 141 GLU cc_start: 0.5028 (OUTLIER) cc_final: 0.4408 (mm-30) REVERT: L 153 ARG cc_start: 0.6016 (mtp-110) cc_final: 0.3908 (mtt180) REVERT: L 164 GLU cc_start: 0.5741 (tp30) cc_final: 0.4884 (mt-10) outliers start: 73 outliers final: 60 residues processed: 447 average time/residue: 0.2039 time to fit residues: 135.9503 Evaluate side-chains 453 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 385 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 413 GLN Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 168 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 272 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 198 optimal weight: 4.9990 chunk 234 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 346 optimal weight: 8.9990 chunk 168 optimal weight: 0.7980 chunk 146 optimal weight: 8.9990 chunk 185 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 GLN ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 GLN G 180 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.153192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.118699 restraints weight = 34458.711| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.43 r_work: 0.3093 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30052 Z= 0.124 Angle : 0.498 7.084 40716 Z= 0.257 Chirality : 0.043 0.239 4564 Planarity : 0.004 0.048 5331 Dihedral : 4.871 82.036 4214 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.37 % Allowed : 15.24 % Favored : 82.39 % 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: 0.75 (0.14), residues: 3764 helix: 1.65 (0.13), residues: 1582 sheet: -0.74 (0.20), residues: 612 loop : -0.06 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 159 TYR 0.012 0.001 TYR B 439 PHE 0.018 0.001 PHE F 414 TRP 0.012 0.001 TRP A 119 HIS 0.004 0.001 HIS D 375 Details of bonding type rmsd covalent geometry : bond 0.00297 (30052) covalent geometry : angle 0.49797 (40716) hydrogen bonds : bond 0.03671 ( 1303) hydrogen bonds : angle 4.36480 ( 3738) ********************** 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 466 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 393 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7394 (mt-10) REVERT: A 95 ARG cc_start: 0.7260 (tpt-90) cc_final: 0.6539 (tpt-90) REVERT: A 156 ARG cc_start: 0.6343 (mtp-110) cc_final: 0.5837 (ttp-170) REVERT: A 354 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7824 (tp) REVERT: A 374 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7093 (tt0) REVERT: A 416 ARG cc_start: 0.7872 (mtm-85) cc_final: 0.7160 (mtp85) REVERT: A 478 ASP cc_start: 0.6447 (m-30) cc_final: 0.6201 (m-30) REVERT: A 481 ARG cc_start: 0.7788 (mtm-85) cc_final: 0.7320 (mtp-110) REVERT: A 518 MET cc_start: 0.8701 (mtp) cc_final: 0.8463 (mtm) REVERT: A 541 GLN cc_start: 0.6582 (mt0) cc_final: 0.6036 (pt0) REVERT: A 547 ARG cc_start: 0.7318 (ttm110) cc_final: 0.6824 (ttm110) REVERT: B 54 ASP cc_start: 0.7501 (p0) cc_final: 0.6371 (t70) REVERT: B 161 LYS cc_start: 0.6988 (OUTLIER) cc_final: 0.6588 (mmtm) REVERT: B 166 TYR cc_start: 0.7310 (m-80) cc_final: 0.6414 (m-80) REVERT: B 197 ARG cc_start: 0.7425 (ttp80) cc_final: 0.7058 (ttp-110) REVERT: B 340 ARG cc_start: 0.7606 (tpp-160) cc_final: 0.7205 (tpt-90) REVERT: B 449 GLU cc_start: 0.6452 (mm-30) cc_final: 0.6185 (mp0) REVERT: B 480 GLU cc_start: 0.6830 (mp0) cc_final: 0.5919 (mt-10) REVERT: B 481 ARG cc_start: 0.7030 (mmm-85) cc_final: 0.6554 (ttt-90) REVERT: B 547 ARG cc_start: 0.6415 (ttm-80) cc_final: 0.5306 (mmm160) REVERT: C 1 MET cc_start: 0.6130 (mmm) cc_final: 0.5314 (mmp) REVERT: C 3 GLN cc_start: 0.7620 (mt0) cc_final: 0.7302 (mm-40) REVERT: C 95 ARG cc_start: 0.7320 (mtp180) cc_final: 0.7108 (ttp-170) REVERT: C 125 PRO cc_start: 0.7520 (Cg_exo) cc_final: 0.7082 (Cg_endo) REVERT: C 130 ARG cc_start: 0.7141 (ttp-110) cc_final: 0.6326 (ttm110) REVERT: C 183 MET cc_start: 0.8624 (mtp) cc_final: 0.8272 (mtt) REVERT: C 312 TYR cc_start: 0.8861 (t80) cc_final: 0.8596 (t80) REVERT: C 344 MET cc_start: 0.8066 (mmt) cc_final: 0.7527 (mmm) REVERT: C 416 ARG cc_start: 0.7824 (mtm110) cc_final: 0.7369 (mtm180) REVERT: C 442 ASN cc_start: 0.8734 (m-40) cc_final: 0.8299 (m110) REVERT: C 547 ARG cc_start: 0.6535 (mtp85) cc_final: 0.6193 (mtp180) REVERT: C 550 ARG cc_start: 0.7391 (ttm-80) cc_final: 0.6756 (mtm110) REVERT: C 562 TYR cc_start: 0.8039 (t80) cc_final: 0.7550 (t80) REVERT: C 574 PHE cc_start: 0.6217 (m-80) cc_final: 0.5840 (m-80) REVERT: D 34 ASP cc_start: 0.7497 (m-30) cc_final: 0.7017 (t0) REVERT: D 42 VAL cc_start: 0.7648 (t) cc_final: 0.7417 (m) REVERT: D 52 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7227 (mt-10) REVERT: D 201 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8152 (tp) REVERT: D 231 ARG cc_start: 0.8595 (ttm170) cc_final: 0.8384 (ttp-110) REVERT: D 305 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.6844 (mtpt) REVERT: D 338 GLN cc_start: 0.8818 (tt0) cc_final: 0.8545 (tp40) REVERT: D 420 ARG cc_start: 0.7496 (mtp-110) cc_final: 0.7157 (mtp-110) REVERT: D 461 LYS cc_start: 0.7556 (tttt) cc_final: 0.7343 (ttmt) REVERT: D 463 TYR cc_start: 0.7957 (t80) cc_final: 0.7375 (t80) REVERT: E 88 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7645 (mtt) REVERT: E 259 ASP cc_start: 0.6965 (m-30) cc_final: 0.6560 (m-30) REVERT: E 278 PRO cc_start: 0.8530 (Cg_endo) cc_final: 0.8229 (Cg_exo) REVERT: E 302 GLU cc_start: 0.7520 (tt0) cc_final: 0.6770 (tp30) REVERT: E 410 ARG cc_start: 0.5896 (mtm-85) cc_final: 0.4548 (mmp80) REVERT: E 433 GLU cc_start: 0.7286 (mp0) cc_final: 0.6857 (mp0) REVERT: E 445 MET cc_start: 0.7511 (mtp) cc_final: 0.7081 (mtt) REVERT: F 6 LYS cc_start: 0.6497 (tptm) cc_final: 0.6218 (mtpp) REVERT: F 7 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7117 (mt-10) REVERT: F 109 GLU cc_start: 0.6840 (mt-10) cc_final: 0.6347 (mm-30) REVERT: F 210 ARG cc_start: 0.6658 (ttp80) cc_final: 0.5742 (mtm110) REVERT: G 9 MET cc_start: 0.7610 (ttp) cc_final: 0.7239 (ptm) REVERT: G 47 MET cc_start: 0.5510 (mmm) cc_final: 0.4966 (ttm) REVERT: G 59 GLU cc_start: 0.5498 (OUTLIER) cc_final: 0.4519 (tp30) REVERT: G 149 LYS cc_start: 0.7478 (tptt) cc_final: 0.7189 (tptt) REVERT: G 200 LYS cc_start: 0.5704 (OUTLIER) cc_final: 0.5083 (mttt) REVERT: H 63 MET cc_start: 0.4007 (mmm) cc_final: 0.2445 (ttp) REVERT: H 77 LEU cc_start: 0.4142 (mm) cc_final: 0.3670 (mt) REVERT: K 102 LYS cc_start: 0.5725 (tptp) cc_final: 0.4036 (mmtt) REVERT: L 86 ARG cc_start: 0.5774 (mtt180) cc_final: 0.5388 (mtp180) REVERT: L 102 GLU cc_start: 0.5546 (mp0) cc_final: 0.4642 (tp30) REVERT: L 138 ARG cc_start: 0.4521 (mtt180) cc_final: 0.3819 (mtt90) REVERT: L 141 GLU cc_start: 0.5049 (OUTLIER) cc_final: 0.4434 (mm-30) REVERT: L 164 GLU cc_start: 0.5739 (tp30) cc_final: 0.4998 (mt-10) outliers start: 73 outliers final: 61 residues processed: 446 average time/residue: 0.2132 time to fit residues: 142.3563 Evaluate side-chains 457 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 387 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 209 MET Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 433 SER Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 259 ASP Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 130 PHE Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 237 MET Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 413 GLN Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 137 LEU Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 200 LYS Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 168 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 251 optimal weight: 7.9990 chunk 135 optimal weight: 9.9990 chunk 318 optimal weight: 6.9990 chunk 305 optimal weight: 0.9980 chunk 254 optimal weight: 6.9990 chunk 358 optimal weight: 8.9990 chunk 161 optimal weight: 9.9990 chunk 281 optimal weight: 7.9990 chunk 354 optimal weight: 20.0000 chunk 178 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN B 145 HIS B 316 GLN C 260 ASN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 GLN G 166 GLN G 180 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.148886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.114387 restraints weight = 35046.231| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.45 r_work: 0.3009 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.090 30052 Z= 0.339 Angle : 0.751 10.533 40716 Z= 0.390 Chirality : 0.053 0.290 4564 Planarity : 0.007 0.054 5331 Dihedral : 5.806 83.445 4214 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.63 % Allowed : 15.31 % Favored : 82.06 % 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: -0.17 (0.13), residues: 3764 helix: 0.71 (0.13), residues: 1580 sheet: -0.90 (0.20), residues: 590 loop : -0.50 (0.16), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 153 TYR 0.020 0.003 TYR B 304 PHE 0.031 0.003 PHE F 414 TRP 0.023 0.003 TRP J 175 HIS 0.012 0.002 HIS D 375 Details of bonding type rmsd covalent geometry : bond 0.00838 (30052) covalent geometry : angle 0.75128 (40716) hydrogen bonds : bond 0.05597 ( 1303) hydrogen bonds : angle 5.01945 ( 3738) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8117.75 seconds wall clock time: 138 minutes 56.93 seconds (8336.93 seconds total)